diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index ac23b70c3bd51d49509b710ab096fce7266829df..2ec26dc0ee6fef295ef194dba1d795681478d920 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -24,21 +24,21 @@ Dependencies
--------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-|ost_version|. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to
-use |openmm|_. To create the build system, |cmake|_ is required. The same
-versions of |python|_ and |boost|_ are needed as used in |ost_s|. For |eigen3|_
-we need at least version 3.3.0. To build the documentation, |sphinx|_ is
-required.
+|ost_version|. A C++11 compatible compiler is required. |ost_s| must be
+configured and compiled with ``ENABLE_MM=1`` to use |openmm|_. To create the
+build system, |cmake|_ is required. The same versions of |python|_ and |boost|_
+are needed as used in |ost_s|. For |eigen3|_ we need at least version 3.3.0. To
+build the documentation, |sphinx|_ is required.
The currently preferred versions are:
* |ost_s|_ |ost_version|
* |openmm|_ 7.1.1
* |cmake|_ 2.8.12
-* |python|_ 2.7.5
+* |python|_ 2.7.11
* |boost|_ 1.53.0
-* |eigen3|_ 3.3.0
-* |sphinx|_ 1.3.1
+* |eigen3|_ 3.3.1
+* |sphinx|_ 1.4.1
--------------------------------------------------------------------------------
Using |cmake|
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index 67c6449a8c77ba6a9eae9b7aa2af68ec4d2c97c6..0e9ceb554298f192f7dea1e1b082a380fff4a766 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -5,6 +5,19 @@
Changelog
================================================================================
+Release 2.1.0
+--------------------------------------------------------------------------------
+
+* This is expected to be the last release supporting Python 2.
+* This project now requires a C++11 compatible compiler.
+* Introduced VINA scoring function in the sidechain module. A scoring function
+ specific RotamerConstructor is provided that comes with extensive heuristics
+ to parametrize arbitrary compounds.
+* Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+ The algorithm is based on principles of geometric hashing.
+* Several minor bug fixes, improvements, and speed-ups
+
+
Release 2.0.0
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
index 3acc2f8e1a2b74a97e559c050e71eb97c777802e..e5e2d9964cfb6cd7cce133bd1cd5869c3bd19d19 100644
--- a/doc/html/_sources/loop/backbone.txt
+++ b/doc/html/_sources/loop/backbone.txt
@@ -79,6 +79,22 @@ The BackboneList class
code which is not one of the 20 default amino acids or if
*sequence* and *dihedral_angles* are inconsistent in size.
+ .. method:: BackboneList(residues)
+
+ Creates a BackboneList with positions and sequence extracted from
+ *residues*.
+
+ :param residues: List of :class:`ost.mol.ResidueHandle` objects from
+ which the backbone positions and one letter codes
+ are extracted.
+
+ :type residues: :class:`list`
+
+ :raises: :exc:`~exceptions.RuntimeError` if a residue in *residues*
+ contains a one letter code which is not one of the 20 default
+ amino acids or when there is a residue not providing all
+ required positions.
+
.. method:: BackboneList(sequence, residues)
Creates a BackboneList from given *sequence* and positions extracted from
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
index b3089c7248bc40d5f4bd292125795b2edde82204..756afe78cd46954025953926e787eb618c2f5f58 100644
--- a/doc/html/_sources/loop/structure_db.txt
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -141,6 +141,7 @@ database, you might want to consider two things:
The StructureDBDataType enum has to be passed at initialization of a
StructureDB in order to define what data you want to store additionally
to backbone coordinates and sequence.
+ For the bare minimum (only backbone coordinates and sequence), use Minimal.
If you want to store all data possible, use All. If you only want a subset,
you can combine some of the datatypes with a bitwise or operation
(see example script for :class:`StructureDB`). One important note:
@@ -148,8 +149,8 @@ database, you might want to consider two things:
assigned. Only the according memory is allocated and set to zero, the actual
information must be assigned manually (see example script again...).
- All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP, AAFrequencies,
- AAFrequenciesStruct
+ Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
+ AAFrequencies, AAFrequenciesStruct
.. class:: StructureDB(data_to_store)
@@ -249,7 +250,8 @@ database, you might want to consider two things:
:type id: :class:`str`
:type chain_name: :class:`str`
- :type ent: :class:`ost.mol.EntityView`
+ :type ent: :class:`ost.mol.EntityHandle` /
+ :class:`ost.mol.EntityView`
:type seqres: :class:`ost.seq.SequenceHandle`
:type prof: :class:`ost.seq.ProfileHandle`
:type only_longest_strech: :class:`bool`
@@ -314,14 +316,22 @@ database, you might want to consider two things:
.. method:: GetBackboneList(fragment, sequence)
- GetBackboneList(n_stem, c_stem, fragment, sequence)
+ GetBackboneList(n_stem, c_stem, fragment, sequence="")
+ GetBackboneList(coord_idx, sequence="")
+ GetBackboneList(n_stem, c_stem, coord_idx, sequence="")
- :returns: Backbone list with positions extracted from *fragment*.
+
+ :returns: Backbone list with positions extracted from *fragment* or
+ full entry at *coord_idx*
:rtype: :class:`BackboneList`
:param fragment: Fragment definition from which to extract positions.
:type fragment: :class:`FragmentInfo`
- :param sequence: Sequence to set for the returned backbone list.
+ :param coord_idx: Idx of entry from which to extract positions.
+ :type coord_idx: :class:`int`
+ :param sequence: Sequence of the returned backbone list. If not
+ set, the original sequence at specified location in the
+ database is used.
:type sequence: :class:`str`
:param n_stem: Positions on which the backbone list's N-terminus should be
superposed onto.
@@ -330,89 +340,116 @@ database, you might want to consider two things:
superposed onto.
:type c_stem: :class:`ost.mol.ResidueHandle`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid (happens
- if the fragment does not fully fit into one of the connected
- stretches in the database) or if *sequence* contains a one letter
- code which is not one of the 20 default amino acids.
-
+ :raises: :exc:`~exceptions.RuntimeError` if the length of *sequence* does
+ not match with the desired backbone list, if *sequence* contains
+ a character which does not belong to the 20 proteinogenic amino
+ acids or if *fragment* or *coord_idx* is invalid. Fragment can
+ be invalid when it does not fully fit into one of the connected
+ stretches of residues in the database.
.. method:: GetSequence(fragment)
+ GetSequence(coord_idx)
- :returns: The sequence of *fragment*
+ :returns: The sequence of *fragment* or full entry at *coord_idx*
:rtype: :class:`str`
:param fragment: Fragment definition from which to extract the sequence.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
- connected stretches of residues in the database.
+ :param coord_idx: Idx of entry from which to extract the sequence
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if fragment or coord_idx is
+ invalid. Fragment can be invalid when it does not fully fit into
+ one of the connected stretches of residues in the database.
.. method:: GetDSSPStates(fragment)
+ GetDSSPStates(coord_idx)
- :returns: The dssp states of *fragment*
+ :returns: The dssp states of *fragment* or full entry at *coord_idx*
:rtype: :class:`str`
:param fragment: Fragment definition from which to extract the states.
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the dssp states
+ :type coord_idx: :class:`int`
+
:raises: :exc:`~exceptions.RuntimeError` if database does not contain dssp
- data or if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
- connected stretches of residues in the database.
+ data or if fragment/ coord_idx is invalid. Fragment can be invalid
+ when it does not fully fit into one of the connected stretches of
+ residues in the database.
.. method:: GetDihedralAngles(fragment)
+ GetDihedralAngles(coord_idx)
:returns: The phi and psi dihedral angles of every residue of *fragment*
+ or full entry at *coord_idx*
:rtype: :class:`list` of pairs (:class:`tuple`)
:param fragment: Fragment definition from which to extract the dihedrals.
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the dihedral angles
+ :type coord_idx: :class:`int`
+
:raises: :exc:`~exceptions.RuntimeError` if database does not contain
- dihedral angle data or if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
+ dihedral angle data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetResidueDepths(fragment)
+ GetResidueDepths(coord_idx)
- :returns: Residue depth for each residue of *fragment*.
+ :returns: Residue depth for each residue of *fragment* or full entry
+ at *coord_idx*
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the residue
depths
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the residue depths
+ :type coord_idx: :class:`int`
+
:raises: :exc:`~exceptions.RuntimeError` if database does not contain
- residue depth data or if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
+ residue depth data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetSolventAccessibilitites(fragment)
+ GetSolventAccessibilitites(coord_idx)
- :returns: Solvent accessibility for each residue of *fragment* in square A
- as calculated by :meth:`~ost.mol.alg.Accessibility` when adding
- the structure to the database.
+ :returns: Solvent accessibility for each residue of *fragment* or full entry
+ at *coord_idx* in square A as calculated by
+ :meth:`~ost.mol.alg.Accessibility` when adding the structure to
+ the database.
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the solvent
accessibilities
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the solvent
+ accessibilities
+ :type coord_idx: :class:`int`
+
:raises: :exc:`~exceptions.RuntimeError` if database does not contain
- solvent accessibility data or if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
+ solvent accessibility data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetSequenceProfile(fragment)
+ GetSequenceProfile(coord_idx)
- :returns: The sequence profile for the residues defined by *fragment* with
- the BLOSUM62 probabilities as NULL model.
+ :returns: The sequence profile for the residues defined by *fragment* or
+ full entry at *coord_idx* with the BLOSUM62 probabilities as NULL
+ model.
:rtype: :class:`ost.seq.ProfileHandle`
:param fragment: Fragment definition from which to extract the sequence
@@ -420,16 +457,21 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if database does not cotain
- aa frequency data or if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
+ :param coord_idx: Idx of entry from which to extract the sequence profile
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ sequence profile data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetStructureProfile(fragment)
+ GetStructureProfile(coord_idx)
- :returns: The structure profile for the residues defined by *fragment* with
- the BLOSUM62 probabilities as NULL model.
+ :returns: The structure profile for the residues defined by *fragment* or
+ full entry at *coord_idx* with the BLOSUM62 probabilities as NULL
+ model.
:rtype: :class:`ost.seq.ProfileHandle`
:param fragment: Fragment definition from which to extract the structure
@@ -437,9 +479,12 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if database does not contain
- aa frequencies struct data or if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
+ :param coord_idx: Idx of entry from which to extract the structure profile
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ structure profile data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
@@ -461,7 +506,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* and
*residue_depths* differ in size, when their size is 0
- or when database does not contain aa frequencies struct data.
+ or when database does not contain residue depth data.
.. method:: SetStructureProfile(coord_idx, prof)
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.txt
index 51357bc0615a49e58f2ef12f3efad67eeb3b003d..7c775b0a1ba537244c4f7e22bdff9a38cb5ef582 100644
--- a/doc/html/_sources/modelling/algorithms.txt
+++ b/doc/html/_sources/modelling/algorithms.txt
@@ -164,3 +164,165 @@ example pipeline.
.. autofunction:: GenerateDeNovoTrajectories
+Motif Finder
+--------------------------------------------------------------------------------
+
+Distinct spatial arrangements of atoms or functional groups are key for protein
+function. For their detection, ProMod3 implements the MotifFinder algorithm
+which is based on geometric hashing as described by Nussinov and Wolfson
+[nussinov1991]_. The algorithm consists of a learning stage, a detection stage
+and a refinement stage.
+
+Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
+(p1, p2, p3) of coordinates are selected that define triangles. For each
+triangle one can define an orthogonal vector basis
+(in our case v1 = norm(p2-p1), v3 = norm(cross(v1,p3-p1),
+v2 = norm(cross(v1,v3)))). For each coordinate not in [p1,p2,p3], we add the
+identity of the query/triangle as value to a hash map.
+The corresponding key consists of discretized values describing the edge lengths
+of the triangle, as well as the coordinate transformed into the triangle
+specific orthogonal vector basis. That's 6 numbers in total.
+
+Detection Stage: The goal is to identify one or several subsets of target
+coordinates that resemble an input query.
+We first setup an accumulator containing a counter for each triangle observed
+in the input query. We then iterate over each possible triangle with vertices
+p1, p2 and p3 in the target coordinates. At the beginning of each iteration,
+all counters in the accumulator are set to zero. Again, we build a vector basis
+given that triangle and transform all coordinates not in [p1,p2,p3] into that
+vector space. For each transformed coordinate we obtain a key for the query hash
+map. If there is one or several values at that location in the hash map,
+we increment the corresponding locations in the accumulator.
+Once all coordinates are processed, we search for high counts in the
+accumulator. Given *N* query coordinates, we keep a solution for further
+refinement if count/(*N*-3) >= *hash_tresh*. This is repeated until all
+triangles in the target are processed. One key problem with this approach is
+the discretization of floating point numbers that give raise to the hash map
+keys. Two extremely close values might end up in different bins just because
+they are close to the bin boundaries. For each of the 6 relevant numbers
+we estimate the actual bin as well as the closest neighbouring bin. Processing
+all possible combinations results in 64 hash map lookups instead of only one.
+
+Refinement Stage: Every potential solution identified in the detection stage is
+further refined based on the *distance_thresh* and *refine_thresh* parameters.
+A potential solution found in the detection stage is a pair of triangles, one
+in the query and one in the target, for which we find many matching coordinates
+in their respective vector space. We start with a coordinate mapping based on
+the triangle vertices from the query and the target (3 pairs).
+This coordinate mapping is iteratively updated by estimating the minimum RMSD
+superposition of the mapped query coordinates onto the target, apply that
+superposition on the query, find the closest target coordinate for each
+coordinate in the query and redo the mapping by including all pairs with
+minimum distance < *distance_thresh*. Iteration stops if nothing changes
+anymore. The solution is returned to the user if the final fraction of mapped
+query coordinates is larger or equal *refine_thresh*.
+The larger the mapping, the more accurate the superposition. As we start with
+only the three triangle vertices, *distance_thresh* is doubled for the initial
+iteration.
+
+.. literalinclude:: ../../../tests/doc/scripts/modelling_motif_finder.py
+
+.. class:: MotifQuery(positions, identifier, min_triangle_edge_length, \
+ max_triangle_edge_length, bin_size)
+ MotifQuery(positions, identifier, min_triangle_edge_length, \
+ max_triangle_edge_length, bin_size, flags)
+ MotifQuery(query_list)
+
+ A single query or a container of queries.
+ The constructor performs the learning stage of a single query or combines
+ several queries, so they can be searched at once.
+
+ :param positions: Coordinates of the query
+ :param identifier: Descriptor of the query
+ :param min_triangle_edge_length: To avoid the full O(n^3) hell, triangles
+ with any edge length below *min_triangle_edge_length*
+ are skipped
+ :param max_triangle_edge_length: Same as *min_triangle_edge_length* but
+ upper bound
+ :param bin_size: Bin size in A, relevant to generate hash map keys
+ :param flags: Flag in range [0,63] for every coordinate in *positions*.
+ They're also added to the hash map keys (default: 0).
+ This means that additionally to having a matching
+ relative position, the coordinates must also have a
+ matching flag in the detection/refinement stage.
+ If not provided (in the query and in the search),
+ only coordinates matter.
+ :param query_list: E pluribus unum
+
+ :type positions: :class:`ost.geom.Vec3List`
+ :type identifier: :class:`str`
+ :type min_triangle_edge_length: :class:`float`
+ :type max_triangle_edge_length: :class:`float`
+ :type bin_size: :class:`float`
+ :type flags: :class:`list` of :class:`int`
+ :type query_list: :class:`list` of :class:`MotifQuery`
+
+
+ .. method:: Save(filename)
+
+ Saves the query down to disk
+
+ :param filename: filename
+ :type filename: :class:`str`
+
+ .. staticmethod:: Load(filename)
+
+ Load query from disk
+
+ :param filename: filename
+ :type filename: :class:`str`
+
+ .. method:: GetPositions(query_idx)
+
+ Returns coordinates of specified query
+
+ :param query_idx: Query from which you want the positions
+ :type query_idx: :class:`int`
+
+ .. method:: GetIdentifiers()
+
+ Returns a list of all query identifiers.
+
+ .. method:: GetN()
+
+ Returns the number of queries
+
+
+
+.. class:: MotifMatch
+
+ Object that holds information about a match found in :meth:`FindMotifs`
+
+ .. attribute:: query_idx
+
+ Index of matching query
+
+ .. attribute:: mat
+
+ Transformation matrix to superpose matching query onto target
+
+ .. attribute:: alignment
+
+ List of tuples which define matching pairs of query/target coordinates
+
+
+.. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \
+ distance_thresh=1.0, refine_thresh=0.7, \
+ flags=list())
+
+ Performs the detection and refinement stages of the geometric hashing
+ algorithm.
+
+ :param query: Query to be searched
+ :param target_positions: Coordinates of the target
+ :param hash_thresh: Parameter relevant for detection stage
+ :param distance_thresh: Parameter relevant for refinement stage
+ :param refine_thresh: Parameter relevant for refinement stage
+ :param flags: Equivalent to *flags* in :class:`MotifQuery`
+ constructor. If you didn't provide anything there,
+ this can be ignored. Only the actual coordinates
+ matter in this case.
+
+ :returns: All found matches
+
+ :rtype: :class:`list` of :class:`MotifMatch`
diff --git a/doc/html/_sources/references.txt b/doc/html/_sources/references.txt
index 927de6ddbad6c032f0f760c17384e977d1ed31e9..18a5a3b25ba4779ccd336b9bbfdae278f04735ab 100644
--- a/doc/html/_sources/references.txt
+++ b/doc/html/_sources/references.txt
@@ -62,6 +62,10 @@ References
Exploring the conformational space of protein side chains using
dead-end elimination and the A* algorithm. Proteins.
+.. [nussinov1991] Nussinov R and Wolfson HJ (1991).
+ Efficient detection of three-dimensional structural motifs in
+ biological macromolecules by computer vision techniques. PNAS.
+
.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011).
A smoothed backbone-dependent rotamer library for proteins
derived from adaptive kernel density estimates and
@@ -75,6 +79,10 @@ References
potentials and threading score functions using information
maximization. Proteins.
+.. [trott2010] Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+ accuracy of docking with a new scoring function, efficient
+ optimization and multithreading. J Comput Chem
+
.. [zhou2005] Zhou H, Zhou Y (2005).
Fold Recognition by Combining Sequence Profiles Derived From
Evolution and From Depth-Dependent Structural Alignment of
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.txt
index d8365f4a5316d2efebaaaafb50a87238b1b3ac2d..94a3150d0361fa6fe2b468b35752f0f19d57cebb 100644
--- a/doc/html/_sources/sidechain/frame.txt
+++ b/doc/html/_sources/sidechain/frame.txt
@@ -14,7 +14,7 @@
.. limitations under the License.
-Frame
+Frame - The Rigid Part
================================================================================
.. currentmodule:: promod3.sidechain
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.txt
index aeac7212ce7a9232b81c95d2178cb32d07ff6595..192257b499d3826c3ed5891cadb39ede1f7a7291 100644
--- a/doc/html/_sources/sidechain/index.txt
+++ b/doc/html/_sources/sidechain/index.txt
@@ -42,11 +42,10 @@ Contents:
.. toctree::
:maxdepth: 2
- rotamer_id
rotamer
frame
- rotamer_lib
rotamer_constructor
+ rotamer_lib
graph
disulfid
loading
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
index d3ae44ebe66b3f2139cd7a5ba04e29de80efc9ac..56b95301448e5a955ef38ee0105c9d60b9de291f 100644
--- a/doc/html/_sources/sidechain/rotamer.txt
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -14,22 +14,96 @@
.. limitations under the License.
-Rotamers
+Representing Sidechains - Rotamers & Co.
================================================================================
.. currentmodule:: promod3.sidechain
-A rotamer represents an amino acid sidechain and is basically a set of
-:class:`Particle` objects. There exist two types. The :class:`RRMRotamer` and
-:class:`FRMRotamer`.
-To gather all possible rotamers for one particular sidechain position,
+A rotamer represents an amino acid sidechain identified by a :class:`RotamerID`
+and is a set of :class:`Particle` objects.
+Two types of rotamers exist. The :class:`RRMRotamer` and :class:`FRMRotamer`.
+To gather all possible rotamers for one location,
ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
-Pairwise interactions between particles give raise to pairwise energies between
-rotamers. Nevertheless, the energy calculation itself happens on the level
-of RotamerGroups and is mostly hidden away in the construction of the
-the :class:`RotamerGraph`. If you're too lazy to build up your rotamers
-by hand, you might be interested in the :class:`RotamerConstructor`.
+All parts of the structure that are kept rigid can be represented by
+a :class:`Frame` object.
+
+RotamerID
+--------------------------------------------------------------------------------
+
+The sidechain module has its own definition of amino acids to satisfy custom
+requirements for the implemented sidechain construction algorithms.
+As an example there are histidine in two possible protonation states,
+that affect the hbond term or different versions of proline/cysteine.
+
+.. class:: RotamerID
+
+ Enumerates the amino acids. Possible values:
+
+ .. hlist::
+ :columns: 2
+
+ * ARG - Arginine
+ * ASN - Asparagine
+ * ASP - Aspartate
+ * GLN - Glutamine
+ * GLU - Glutamate
+ * LYS - Lysine
+ * SER - Serine
+ * CYS - Cystein
+ * CYH - "free" Cystein
+ * CYD - disulfid bonded Cystein
+ * MET - Methionine
+ * TRP - Tryptophane
+ * TYR - Tyrosine
+ * THR - Threonine
+ * VAL - Valine
+ * ILE - Isoleucine
+ * LEU - Leucine
+ * PRO - Proline
+ * CPR - cis-Proline
+ * TPR - trans-Proline
+ * HIS - Histidine
+ * HSD - d-protonated Histidine
+ * HSE - e-protonated Histidine
+ * PHE - Phenylalanine
+ * GLY - Glycine
+ * ALA - Alanine
+ * XXX - Invalid
+
+ The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
+ or as ``promod3.sidechain.RotamerID.ARG``.
+
+
+How can I get an ID?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The RotamerID enum can directly be accessed from Python. Two convenient
+functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
+or from amino acid three letter codes.
+
+.. method:: TLCToRotID(tlc)
+
+ Directly translates the three letter code into a RotamerID. Following
+ exactly the naming convention defined above.
+
+ :param tlc: Three letter code of amino acid
+ :type tlc: :class:`str`
+
+ :returns: :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
+
+
+.. method:: AAToRotID(aa)
+
+ Directly translates **aa** into a RotamerID. Note, that it is not possible
+ to generate special IDs this way
+ (e.g. HSD, HSE or the special prolines/cysteins) since they're simply not
+ defined in :class:`ost.conop.AminoAcid`
+
+ :param aa: AA enum of amino acid
+ :type aa: :class:`ost.conop.AminoAcid`
+
+ :returns: :class:`RotamerID`, XXX if **aa** is invalid.
The Smallest Building Block - The Particle
@@ -44,7 +118,9 @@ function.
The available scoring functions between :class:`Particle` objects
- * SCWRL4
+ * SCWRL4 - :ref:`scwrl4-scoring-function`
+ * SCWRL3 - :ref:`scwrl3-scoring-function`
+ * VINA - :ref:`vina-scoring-function`
.. class:: Particle
@@ -93,13 +169,19 @@ function.
+.. _scwrl4-scoring-function:
The SCWRL4 scoring function
---------------------------------------------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL4 scoring function combines a Lennard-Jones style term with
+a hydrogen bond term. Details can be found in the relevant publication
+[krivov2009]_.
.. class:: SCWRL4ParticleType
The SCWRL4 energy function differentiates between following particle types
+ that define the behaviour of the Lennard-Jones style term:
* HParticle - represents hydrogen
* CParticle - default representation of a carbon
@@ -123,9 +205,17 @@ The SCWRL4 scoring function
:param charge: The charge of the particle, relevant for the hydrogen
bond term
:param lone_pairs: Direction of all possible lone pairs of the particle,
- relevant for the hydrogen bond term
+ relevant for the hydrogen bond term. If set, the
+ particle is a potential hydrogen bond acceptor.
+ An example would be the Serine OG atom, where you can
+ represent the two lone pairs with vectors pointing
+ from the OG position towards the lone pair centers.
:param polar_direction: The polar direction of the particle,
- relevant for the hdrogen bond term
+ relevant for the hydrogen bond term. If set, the
+ particle is a potential hydrogen bond donor. An
+ example would be the Serine HG hydrogen. The
+ *polar_direction* would be a vector
+ estimated as follows: hg_pos-og_pos.
:type name: :class:`str`
:type particle_type: :class:`SCWRL4ParticleType`
@@ -135,6 +225,82 @@ The SCWRL4 scoring function
:type polar_direction: :class:`ost.geom.Vec3`
+.. _scwrl3-scoring-function:
+
+The SCWRL3 scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL3 scoring function implements a simple repulsion term that depends on
+the hard-sphere radius of the involved particles.
+Details can be found in the relevant publication [canutescu2003]_.
+
+.. method:: CreateSCWRL3Particle(name, radius, pos)
+
+ Creates and returns a :class:`Particle` that can evaluate the SCWRL3 scoring
+ function
+
+ :param name: The name of the particle
+ :param radius: The hard-sphere radius of the particle, relevant for the
+ repulsion term.
+ :param pos: The position of the particle
+
+ :type name: :class:`str`
+ :type radius: :class:`float`
+ :type pos: :class:`ost.geom.Vec3`
+
+
+.. _vina-scoring-function:
+
+The VINA scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The VINA scoring function is a combination of scores that are named
+gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
+software [trott2010]_. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+evaluated between C_VINAParticle :class:`VINAParticleType` and hbond is
+evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
+are intended to evaluate sidechain-sidechain interactions in proteins,
+VINA is mainly targeted at interactions between sidechains and ligands.
+
+The VINA scoring function differentiates between the following particle types:
+
+.. class:: VINAParticleType
+
+ * O_D_VINAParticle - Oxygen that can be a hydrogen bond donor
+ * N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor
+ * O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor
+ * N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor
+ * O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor
+ * N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor
+ * O_VINAParticle - Oxygen
+ * N_VINAParticle - Nitrogen
+ * S_VINAParticle - Sulfur
+ * P_VINAParticle - Phosphorus
+ * C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom
+ * C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens
+ * F_VINAParticle - Fluorine
+ * Cl_VINAParticle - Chlorine
+ * Br_VINAParticle - Bromine
+ * I_VINAParticle - Iodine
+ * M_VINAParticle - Metals
+ * INVALID_VINAParticle - Invalid particle...
+
+
+.. method:: CreateVINAParticle(name, particle_type, pos)
+
+ Creates and returns a :class:`Particle` that can evaluate the VINA scoring
+ function
+
+ :param name: The name of the particle
+ :param radius: The type of the particle
+ :param pos: The position of the particle
+
+ :type name: :class:`str`
+ :type radius: :class:`VINAParticleType`
+ :type pos: :class:`ost.geom.Vec3`
+
+
Rotamers
--------------------------------------------------------------------------------
@@ -692,3 +858,4 @@ Rotamer Groups
Searches rotamer with lowest self energy *l_e* and deletes all
rotamers with *self_energy* > *l_e* + *thresh*
+
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.txt
index 3a297d5d0846dd0808cad22419dad15add0bf11b..c8cca8deb12f3b56c889c32e9c9bcc954d38599f 100644
--- a/doc/html/_sources/sidechain/rotamer_constructor.txt
+++ b/doc/html/_sources/sidechain/rotamer_constructor.txt
@@ -19,18 +19,18 @@ Rotamer Constructor
.. currentmodule:: promod3.sidechain
-Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by ProMod3.
+Instead of creating rotamers or frame residues by yourself, you can use the
+convenient functionality provided by ProMod3.
-Constructing Rotamers and Frame Residues
+The RotamerConstructor Baseclass
--------------------------------------------------------------------------------
.. class:: RotamerConstructor
Abstract base class that cannot be initialized from Python. It builds
- an interface implemented by energy function specific constructors
+ an interface implemented by scoring function specific constructors
(e.g. :class:`SCWRL4RotamerConstructor`).
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
@@ -213,6 +213,10 @@ Constructing Rotamers and Frame Residues
+Scoring Function Specific RotamerConstructors
+--------------------------------------------------------------------------------
+
+
.. class:: SCWRL4RotamerConstructor(cb_in_sidechain)
This object implements the full interface defined in
@@ -306,3 +310,180 @@ Constructing Rotamers and Frame Residues
:type psi: :class:`float`
:type n_ter: :class:`bool`
:type c_ter: :class:`bool`
+
+
+
+
+.. class:: SCWRL3RotamerConstructor(cb_in_sidechain)
+
+ This object implements the full interface defined in
+ :class:`RotamerConstructor` and constructs rotamers and frame residues that
+ are parametrized according to the SCWRL3 method. They contain only heavy atoms.
+
+ :param cb_in_sidechain: If set to true, all constructed rotamers will contain
+ the cb atom. This flag also affects the construction
+ of frame residues and controls whether the cb atom
+ shows up in the backbone frame residues or sidechain
+ frame residues.
+ This is useful when you want to represent ALA or
+ GLY with actual rotamers, but be aware of increased
+ runtime. This flag can be set to False for most
+ modeling applications and you just don't generate
+ any rotamers for ALA and GLY.
+
+ :type cb_in_sidechain: :class:`bool`
+
+
+ .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
+
+ Overrides the method defined in :class:`RotamerConstructor`.
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by SCWRL3.
+ => -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+ rotamer specific and max_p is the maximum probablity of any of the rotamers
+ in **rot_group**. If you construct a rotamer group by the
+ ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+ is already called at construction and the energies are properly assigned.
+
+ :param rot_group: containing all rotamers for which internal energies have
+ to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
+
+ :type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+
+.. class:: VINARotamerConstructor(cb_in_sidechain)
+
+ This object implements the full interface defined in
+ :class:`RotamerConstructor` and constructs rotamers and frame residues that
+ are parametrized according to the VINA method. They contain only heavy atoms.
+
+ :param cb_in_sidechain: If set to true, all constructed rotamers will contain
+ the cb atom. This flag also affects the construction
+ of frame residues and controls whether the cb atom
+ shows up in the backbone frame residues or sidechain
+ frame residues.
+ This is useful when you want to represent ALA or
+ GLY with actual rotamers, but be aware of increased
+ runtime. This flag can be set to False for most
+ modeling applications and you just don't generate
+ any rotamers for ALA and GLY.
+
+ :type cb_in_sidechain: :class:`bool`
+
+
+ .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
+
+ Overrides the method defined in :class:`RotamerConstructor`.
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by SCWRL3/SCWRL4.
+ => -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+ rotamer specific and max_p is the maximum probablity of any of the rotamers
+ in **rot_group**. If you construct a rotamer group by the
+ ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+ is already called at construction and the energies are properly assigned.
+
+ :param rot_group: containing all rotamers for which internal energies have
+ to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
+
+ :type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+
+ .. method:: ConstructFrameResidueHeuristic(res, res_idx)
+
+ Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle` using
+ a heuristic treatment of the atoms. It is important that the residue has
+ proper bonds assigned, as they influence the atom typing procedure.
+ Furthermore, you need hydrogens to automatically estimate the correct
+ atom type for oxygens and nitrogens (hydrogen bond donor/acceptor).
+ Alternatively you can assign generic properties to oxygens and nitrogens
+ to circumvent the requirement of hydrogens. This is further described for
+ the case of oxygen.
+
+ * Carbon is assigned C_VINAParticle :class:`VINAParticleType` if its only
+ bound to other carbons or hydrogens (and deuterium). All other carbons are
+ assigned C_P_VINAParticle :class:`VINAParticleType`.
+ * In case of oxygen, the heuristic first checks for set generic properties.
+ If the atom has the bool properties "is_hbond_acceptor" AND
+ "is_hbond_donor" set, it decides between the according oxygen types
+ in :class:`VINAParticleType`. If the generic properties are not set,
+ every oxygen is assumed to be an hbond acceptor. But only an hbond donor
+ if its bound to a hydrogen (or deuterium). You can set the generic
+ properties for an :class:`ost.mol.AtomHandle` by calling
+ at.SetBoolProp("is_hbond_donor", False) and
+ at.SetBoolProp("is_hbond_acceptor", True). An oxygen with those
+ generic properties is assigned O_A_VINAParticle :class:`VINAParticleType`.
+ * In case of nitrogen, the heuristic again first checks for set generic
+ properties.
+ If the atom has the bool properties "is_hbond_acceptor" AND
+ "is_hbond_donor" set, it decides between the according nitrogen types
+ in :class:`VINAParticleType`. If not, nitrogen is expected to be an
+ hbond donor if it is bound to a hydrogen (or deuterium) and
+ an hbond acceptor if it is bound to less than 3 other atoms (sounds
+ horrible but works surprisingly well).
+ * Atoms of elements ["MG", "MN", "ZN", "CA", "FE"] are assigned
+ M_VINAParticle :class:`VINAParticleType`.
+ * Atoms of elements ["S", "P", "F", "CL", "BR", "I"] are assigned their
+ corresponding :class:`VINAParticleType`.
+ * All other atoms are neglected and not added to the returned
+ :class:`FrameResidue`.
+
+ :param res: Residue from which to create the
+ :class:`FrameResidue`
+ :param res_idx: Index that is set in :class:`FrameResidue`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :type res_idx: :class:`int`
+ :rtype: :class:`FrameResidue`
+
+
+ .. method:: ConstructRRMRotamerHeuristic(res)
+
+ Construct a :class:`RRMRotamer` with the atom typing heuristic
+ as in the :meth:`ConstructFrameResidueHeuristic` method.
+
+ :param res: Residue from which to create the
+ :class:`RRMRotamer`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :rtype: :class:`RRMRotamer`
+
+
+ .. method:: ConstructFRMRotamerHeuristic(res)
+
+ Construct a :class:`FRMRotamer` with the atom typing heuristic
+ as in the :meth:`ConstructFrameResidueHeuristic` method. The
+ constructed :class:`FRMRotamer` only contains one subrotamer that
+ contains the atoms from *residue*.
+
+ :param res: Residue from which to create the
+ :class:`FRMRotamer`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :rtype: :class:`FRMRotamer`
diff --git a/doc/html/_sources/sidechain/rotamer_id.txt b/doc/html/_sources/sidechain/rotamer_id.txt
deleted file mode 100644
index 746a51641352c7295152567a742eda8befedc803..0000000000000000000000000000000000000000
--- a/doc/html/_sources/sidechain/rotamer_id.txt
+++ /dev/null
@@ -1,108 +0,0 @@
-.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
-.. Biozentrum - University of Basel
-..
-.. Licensed under the Apache License, Version 2.0 (the "License");
-.. you may not use this file except in compliance with the License.
-.. You may obtain a copy of the License at
-..
-.. http://www.apache.org/licenses/LICENSE-2.0
-..
-.. Unless required by applicable law or agreed to in writing, software
-.. distributed under the License is distributed on an "AS IS" BASIS,
-.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-.. See the License for the specific language governing permissions and
-.. limitations under the License.
-
-
-RotamerID
-================================================================================
-
-.. currentmodule:: promod3.sidechain
-
-The sidechain module has its own definition of amino acids to satisfy custom
-requirements for the implemented sidechain construction algorithms.
-As an example there are histidine in two possible protonation states,
-that affect the hbond term or different versions of proline/cysteine.
-
-
-The RotamerID
---------------------------------------------------------------------------------
-
-.. class:: RotamerID
-
- Enumerates the amino acids. Possible values:
-
- .. hlist::
- :columns: 2
-
- * ARG - Arginine
- * ASN - Asparagine
- * ASP - Aspartate
- * GLN - Glutamine
- * GLU - Glutamate
- * LYS - Lysine
- * SER - Serine
- * CYS - Cystein
- * CYH - "free" Cystein
- * CYD - disulfid bonded Cystein
- * MET - Methionine
- * TRP - Tryptophane
- * TYR - Tyrosine
- * THR - Threonine
- * VAL - Valine
- * ILE - Isoleucine
- * LEU - Leucine
- * PRO - Proline
- * CPR - cis-Proline
- * TPR - trans-Proline
- * HIS - Histidine
- * HSD - d-protonated Histidine
- * HSE - e-protonated Histidine
- * PHE - Phenylalanine
- * GLY - Glycine
- * ALA - Alanine
- * XXX - Invalid
-
- The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
- or as ``promod3.sidechain.RotamerID.ARG``.
-
-
-How can I get an ID?
---------------------------------------------------------------------------------
-The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
-or from amino acid three letter codes.
-
-.. method:: TLCToRotID(tlc)
-
- Directly translates the three letter code into a RotamerID. Following
- exactly the naming convention defined above.
-
- :param tlc: Three letter code of amino acid
- :type tlc: :class:`str`
-
- :returns: :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
-
-
-.. method:: AAToRotID(aa)
-
- Directly translates **aa** into a RotamerID. Note, that it is not possible
- to generate special IDs this way
- (e.g. HSD, HSE or the special prolines/cysteins) since they're simply not
- defined in :class:`ost.conop.AminoAcid`
-
- :param aa: AA enum of amino acid
- :type aa: :class:`ost.conop.AminoAcid`
-
- :returns: :class:`RotamerID`, XXX if **aa** is invalid.
-
-
-
-
-
-
-
-
-
-
-
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index b8d6aa5a8c57bcc6cec7e372194809a028e7efde..22ca5ecdc00fdc3793c2328a87a2226bb4617d45 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Actions — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3 Actions — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
<link rel="prev" title="Getting Started" href="../gettingstarted.html" />
@@ -112,7 +112,7 @@ Example:</p>
</li>
</ul>
<p>Structures can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.9.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.10.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>. At least one structure must be
given and you cannot mix file formats. Multiple structures can be given and each
@@ -139,7 +139,7 @@ to the corresponding target sequences. This has an impact on loop scoring with
the database approach.
The profiles can be provided as plain files or gzipped. Following file
extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
-Consider to use <a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+Consider to use <a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
file in a3m format at hand.</p>
<ul class="simple">
<li>The profiles are mapped based on exact matches towards the gapless
@@ -194,7 +194,7 @@ detects and models disulfid bonds and reconstructs all sidechains with the
flexible rotamer model. The result is stored as <code class="file docutils literal"><span class="pre">out.pdb</span></code>.
The output filename can be controlled with the <code class="docutils literal"><span class="pre">-o</span></code> flag.</p>
<p>A structure can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.9.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.10.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>.</p>
<p>Several flags control the modelling behaviour:</p>
@@ -287,7 +287,7 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 38817d23f9ff466370ec6d216532bb39f123df27..4da2b7382d8d688f3df5c57f972f272b8d0c9690 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>test_actions - Testing Actions — ProMod3 2.0.0 documentation</title>
+ <title>test_actions - Testing Actions — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="ProMod3‘s Share Of CMake" href="../cmake/index.html" />
<link rel="prev" title="Contributing" href="../contributing.html" />
@@ -194,7 +194,7 @@ happens if a user throws dirty input data in.</p>
</div>
<div class="section" id="making-the-script-executable">
<h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
@@ -411,7 +411,7 @@ file (also complains if a directory is found instead).</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index fa8c0e469b4a5eb6c7390314fa906edb0abd5421..8a84acd090055744040cee4e433f39edb1fc5fce 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Building ProMod3 — ProMod3 2.0.0 documentation</title>
+ <title>Building ProMod3 — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 and Containers" href="container/index.html" />
<link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
@@ -47,20 +47,20 @@
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-1.10.0. OST must be configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to
-use <a class="reference external" href="http://openmm.org">OpenMM</a>. To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same
-versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a>
-we need at least version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is
-required.</p>
+1.11.0. A C++11 compatible compiler is required. OST must be
+configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to use <a class="reference external" href="http://openmm.org">OpenMM</a>. To create the
+build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a>
+are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> we need at least version 3.3.0. To
+build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is required.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.10.0</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.11.0</li>
<li><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</li>
<li><a class="reference external" href="https://cmake.org/">CMake</a> 2.8.12</li>
-<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7.5</li>
+<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7.11</li>
<li><a class="reference external" href="https://www.boost.org/">Boost</a> 1.53.0</li>
-<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.0</li>
-<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.3.1</li>
+<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.1</li>
+<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.4.1</li>
</ul>
</div>
<div class="section" id="using-cmake">
@@ -204,7 +204,7 @@ safely delete the whole source folder.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 624bccd94e33f53368466218e89ad9391160b0ab..5a5229642a989f2bd592bbaf602a76587601f08f 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Changelog — ProMod3 2.0.0 documentation</title>
+ <title>Changelog — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="prev" title="References" href="references.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -42,6 +42,19 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-2-1-0">
+<h2>Release 2.1.0<a class="headerlink" href="#release-2-1-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>This is expected to be the last release supporting Python 2.</li>
+<li>This project now requires a C++11 compatible compiler.</li>
+<li>Introduced VINA scoring function in the sidechain module. A scoring function
+specific RotamerConstructor is provided that comes with extensive heuristics
+to parametrize arbitrary compounds.</li>
+<li>Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+The algorithm is based on principles of geometric hashing.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
+</ul>
+</div>
<div class="section" id="release-2-0-0">
<h2>Release 2.0.0<a class="headerlink" href="#release-2-0-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
@@ -150,6 +163,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Changelog</a><ul>
+<li><a class="reference internal" href="#release-2-1-0">Release 2.1.0</a></li>
<li><a class="reference internal" href="#release-2-0-0">Release 2.0.0</a></li>
<li><a class="reference internal" href="#release-1-3-0">Release 1.3.0</a></li>
<li><a class="reference internal" href="#release-1-2-0">Release 1.2.0</a></li>
@@ -188,7 +202,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index dbdb850375223b71efa895b6a0829191f86ef661..f1be147fee04b09b4bae608526b985cdff0642b2 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3‘s Share Of CMake — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3‘s Share Of CMake — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
<link rel="prev" title="test_actions - Testing Actions" href="../actions/index_dev.html" />
@@ -373,7 +373,7 @@ target has to be created <strong>before</strong> any action may be attached to i
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index aabd7220fa7648ca54682b5ecbab4d03828b924e..361df7199becb9d60af6d90f347e332504fb75a2 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Docker — ProMod3 2.0.0 documentation</title>
+ <title>Docker — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="ProMod3 and Containers" href="index.html" />
<link rel="next" title="Singularity" href="singularity.html" />
<link rel="prev" title="ProMod3 and Containers" href="index.html" />
@@ -76,7 +76,7 @@ provide the (relative) path to the script and (relative) path to the file eg:</p
</div>
<div class="section" id="the-compound-library">
<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
Compound libraries contain information on chemical compounds, such as their
connectivity, chemical class and one-letter-code. The compound library has
several uses, but the most important one is to provide the connectivy
@@ -175,7 +175,7 @@ output when running a Python script with following code in the container:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index db0c08685d4d1f055c795f795d7b5ce3553746d3..57ed423f9c5cf4397850c3e32fd12918bebb204a 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 and Containers — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3 and Containers — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Docker" href="docker.html" />
<link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
@@ -94,7 +94,7 @@ some sugar on top.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 1940dd077a6abb6bbd4ec67cd9215e20136d11c2..d3581fe64d2b761ef18aa06316c963d1c47571c4 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Singularity — ProMod3 2.0.0 documentation</title>
+ <title>Singularity — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="ProMod3 and Containers" href="index.html" />
<link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
<link rel="prev" title="Docker" href="docker.html" />
@@ -162,7 +162,7 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 6ba9fbd7067c5142f04d98e093072d0ddd560810..4cb717b7e531fa33b942add272bf1df27d613f33 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 2.0.0 documentation</title>
+ <title>Contributing — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
<link rel="prev" title="ProMod3 Setup" href="dev_setup.html" />
@@ -660,7 +660,7 @@ contributions to web pages using ProMod3.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index d19a2ef9b2d9b9add2b2947d20380f58001ba1ad..6d4e9ca68f9e82a8513a6cc33fe50cf513e75cc2 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Geometry functions — ProMod3 2.0.0 documentation</title>
+ <title>Geometry functions — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
<link rel="prev" title="helper - Shared Functionality For the Everything" href="helper.html" />
@@ -56,14 +56,14 @@
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Gromacs rule</li>
<li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</li>
-<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
+<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -79,16 +79,16 @@
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -105,9 +105,9 @@ dihedral (A-B-C-D).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
-<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
-<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Bond length (C-D)</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (B-C-D)</li>
<li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
@@ -117,7 +117,7 @@ dihedral (A-B-C-D).</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -134,16 +134,16 @@ C-alpha and C atoms.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -160,8 +160,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
-<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
</td>
@@ -169,7 +169,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
</td>
</tr>
</tbody>
@@ -186,7 +186,7 @@ going through the origin.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
</td>
@@ -194,7 +194,7 @@ going through the origin.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -211,7 +211,7 @@ going through the origin.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>res</em> does not contain N, CA and C
atoms.</td>
@@ -230,7 +230,7 @@ atoms.</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -347,7 +347,7 @@ angles and one distance and is used in the fragment database for fast lookups.</
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index d68b21c165fc6019713bed993ea39f8cb2f4253b..e95c19333fd51a6f95e8d9086c3be91731f7eefc 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Graph Minimizer — ProMod3 2.0.0 documentation</title>
+ <title>Graph Minimizer — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
<link rel="prev" title="Runtime profiling" href="runtime_profiling.html" />
@@ -373,7 +373,7 @@ The second element is the according energy value.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 87148791bae5e46800b3e711aab3997235ee5fa9..6690837afb52ef67ca60356b4aea1e1696e5f210 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>helper - Shared Functionality For the Everything — ProMod3 2.0.0 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Geometry functions" href="geometry.html" />
<link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
@@ -247,7 +247,7 @@ script will terminate if a gzip file is found.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 8b6e7db3867d73c6e293926c7fe4559efc646622..c99853589643093ceb89fc0dad473b51d1bdb52a 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>core - ProMod3 Core Functionality — ProMod3 2.0.0 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<link rel="prev" title="Loading Precomputed Objects" href="../loop/load_loop_objects.html" />
@@ -105,7 +105,7 @@ modeling per se but cover standard programming issues.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 5a2053814b6e1a22491d37f93af21b4ec0d7e876..b7d2472f0af8cbe3c684eec4d42083337b8b5996 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>pm3argparse - Parsing Command Lines — ProMod3 2.0.0 documentation</title>
+ <title>pm3argparse - Parsing Command Lines — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
<link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
@@ -252,7 +252,7 @@ input is post processed and checked in <a class="reference internal" href="#prom
by the <code class="xref py py-meth docutils literal"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by
file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
.pssm.gz. Consider to use
-<a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
+<a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
in a3m format at hand.</li>
</ul>
<p>Notes:</p>
@@ -266,7 +266,7 @@ target sequences</li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
ordered to match the target sequences.</li>
</ul>
<p>Exit codes related to profile input:</p>
@@ -424,7 +424,7 @@ and with the right constraints.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index b1d223150b95f9bf449b761943880311ae222d14..1e93da67dc60315f1a49e184805ebc77dec5a60a 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Runtime profiling — ProMod3 2.0.0 documentation</title>
+ <title>Runtime profiling — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
<link rel="prev" title="Geometry functions" href="geometry.html" />
@@ -201,7 +201,7 @@ will fail miserably if timers are currently running.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 7fb563f83c914e52745443e88ba9a11993a702eb..0e9ebf7b873cf65e2a459594f701123ab045d1af 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>SetCompoundsChemlib() — ProMod3 2.0.0 documentation</title>
+ <title>SetCompoundsChemlib() — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Contributing" href="../user_contributions.html" />
<link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
@@ -106,7 +106,7 @@ enabled globally.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 81c008ef7ec5ac3abde06e4c93516bdf3c8f12bd..b1f9b94e87b2209d1bac373e274593f0ea7978b0 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Setup — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3 Setup — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="Contributing" href="contributing.html" />
<link rel="prev" title="Documentation For Developers" href="developers.html" />
@@ -293,7 +293,7 @@ modules from there, use the binaries from <code class="file docutils literal"><s
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index df1b45e5ad8a04972c1e0e61aa33e038ea49b9d7..80e54edf05379533716d36261103e34b904250ba 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Developers — ProMod3 2.0.0 documentation</title>
+ <title>Documentation For Developers — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
<link rel="prev" title="Contributing" href="user_contributions.html" />
@@ -125,7 +125,7 @@ new features.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 8de63c6d8cfc5785d9b7876437a0251f12d01a0f..f0bf33a2b4a6e64aa4a8414a5fff8df4e452402b 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -7,7 +7,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Index — ProMod3 2.0.0 documentation</title>
+ <title>Index — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -25,7 +25,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -66,6 +66,7 @@
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
+ | <a href="#V"><strong>V</strong></a>
</div>
<h2 id="Symbols">Symbols</h2>
@@ -244,7 +245,7 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
</dt>
@@ -414,6 +415,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.alignment">alignment (promod3.modelling.MotifMatch attribute)</a>
+ </dt>
+
+
<dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer">all_atom_scorer (promod3.modelling.ModellingHandle attribute)</a>
</dt>
@@ -421,12 +426,12 @@
<dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer_env">all_atom_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_sidechain_env">all_atom_sidechain_env (promod3.modelling.ModellingHandle attribute)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.all_pos">all_pos (promod3.loop.AllAtomEnvPositions attribute)</a>
</dt>
@@ -583,9 +588,17 @@
<dd><dl>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL3RotamerConstructor method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL4RotamerConstructor method)</a>
</dt>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">(promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
</dl></dd>
<dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AStarSolve">AStarSolve() (promod3.core.GraphMinimizer method)</a>
@@ -632,7 +645,7 @@
</dt>
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">BackboneList() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[2]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[3]</a>
+ <dt><a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">BackboneList() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[2]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[3]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[4]</a>
</dt>
@@ -837,8 +850,6 @@
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearPos">ClearPos() (promod3.loop.AllAtomPositions method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearResidue">ClearResidue() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -881,6 +892,8 @@
</dt>
</dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="modelling/pipeline.html#promod3.modelling.CloseGaps">CloseGaps() (in module promod3.modelling)</a>
</dt>
@@ -991,11 +1004,25 @@
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">ConstructFrameResidueHeuristic() (promod3.sidechain.SCWRL4RotamerConstructor method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">(promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">ConstructFRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[3]</a>
</dt>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">ConstructRRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">ConstructSidechainFrameResidue() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">[1]</a>
</dt>
@@ -1083,10 +1110,18 @@
</dt>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL3Particle">CreateSCWRL3Particle() (in module promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL4Particle">CreateSCWRL4Particle() (in module promod3.sidechain)</a>
</dt>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateVINAParticle">CreateVINAParticle() (in module promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser">CTerminalCloser (class in promod3.modelling)</a>
</dt>
@@ -1391,6 +1426,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.FindMotifs">FindMotifs() (in module promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.force_constant">force_constant (promod3.loop.ForcefieldBondInfo attribute)</a>
</dt>
@@ -1811,6 +1850,10 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetIdentifiers">GetIdentifiers() (promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetIndex">GetIndex() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -1890,6 +1933,12 @@
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetN">GetN() (promod3.loop.BackboneList method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetN">(promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+ </dl></dd>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetName">GetName() (promod3.sidechain.Particle method)</a>
</dt>
@@ -2007,6 +2056,10 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetPositions">GetPositions() (promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetPrediction">GetPrediction() (promod3.loop.PsipredPrediction method)</a>
</dt>
@@ -2478,6 +2531,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Load">(promod3.modelling.MotifQuery static method)</a>
+ </dt>
+
+
<dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Load">(promod3.scoring.AllAtomInteractionScorer static method)</a>
</dt>
@@ -2719,6 +2776,10 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.mat">mat (promod3.modelling.MotifMatch attribute)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.MaxFragLength">MaxFragLength() (promod3.loop.FragDB method)</a>
</dt>
@@ -2802,6 +2863,14 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch">MotifMatch (class in promod3.modelling)</a>
+ </dt>
+
+
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery">MotifQuery (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="core/helper.html#promod3.core.helper.MsgErrorAndExit">MsgErrorAndExit() (in module promod3.core.helper)</a>
</dt>
@@ -3037,6 +3106,12 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.query_idx">query_idx (promod3.modelling.MotifMatch attribute)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.QueryLib">QueryLib() (promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
@@ -3157,7 +3232,7 @@
</dt>
- <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
</dt>
@@ -3258,6 +3333,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Save">(promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+
<dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Save">(promod3.scoring.AllAtomInteractionScorer method)</a>
</dt>
@@ -3393,6 +3472,10 @@
</dt>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor">SCWRL3RotamerConstructor (class in promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer.html#promod3.sidechain.SCWRL4ParticleType">SCWRL4ParticleType (class in promod3.sidechain)</a>
</dt>
@@ -3845,7 +3928,7 @@
</dt>
- <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.TLCToRotID">TLCToRotID() (in module promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.TLCToRotID">TLCToRotID() (in module promod3.sidechain)</a>
</dt>
@@ -3920,6 +4003,22 @@
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.urey_bradley_angles">urey_bradley_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
</dt>
+ </dl></td>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.VINAParticleType">VINAParticleType (class in promod3.sidechain)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor">VINARotamerConstructor (class in promod3.sidechain)</a>
+ </dt>
+
</dl></td>
</tr></table>
@@ -3954,7 +4053,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 357e240355a9190825c5917add13b6acea6f2786..4d7ff9696487f382ec6af7b2464ebabc68f0302b 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Getting Started — ProMod3 2.0.0 documentation</title>
+ <title>Getting Started — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 Actions" href="actions/index.html" />
<link rel="prev" title="Documentation For Users" href="users.html" />
@@ -98,7 +98,7 @@ is conserved</li>
<li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> module)</li>
<li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> module)</li>
<li>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
@@ -157,7 +157,7 @@ not set, 1 thread will be used by default.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/index.html b/doc/html/index.html
index 9d19520871229f8900a8a2009e90705197cff8b1..9e798617816b8b47ed902271e0e3a065ae188aff 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3 — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="#" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="#" />
<link rel="next" title="Documentation For Users" href="users.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -122,7 +122,7 @@ algorithms.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/license.html b/doc/html/license.html
index 1841fd40a92b860fdbde8c9c1062f3075492e7c4..6f42206198fb624746da8fa674b391171a756099 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>License — ProMod3 2.0.0 documentation</title>
+ <title>License — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="References" href="references.html" />
<link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
@@ -293,7 +293,7 @@ doc/Copyright_cmake.py.txt
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index d0aee5addf9fffd6386651ec4a1f6c3c229451c8..4b0276cb78dbd9046716cf9f4cd696d99abd22f1 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling All Atom Positions — ProMod3 2.0.0 documentation</title>
+ <title>Handling All Atom Positions — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
<link rel="prev" title="Structural Data" href="structure_db.html" />
@@ -91,8 +91,8 @@ new loop is being added.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -114,7 +114,7 @@ concatenated one after each other (indexing starts at 0)</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -144,7 +144,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
<li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
</td>
@@ -221,7 +221,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -355,7 +355,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
</ul>
</td>
</tr>
@@ -401,7 +401,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Set position at that index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
</ul>
</td>
</tr>
@@ -451,7 +451,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom position index.</td>
</tr>
@@ -555,7 +555,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
</tr>
@@ -834,9 +834,9 @@ atom (N, CA, C, O).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -856,8 +856,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
</ul>
</td>
</tr>
@@ -950,7 +950,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dt id="promod3.loop.AminoAcidLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
+(<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -963,7 +963,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -985,7 +985,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
@@ -1015,7 +1015,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
@@ -1044,7 +1044,7 @@ atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
</td>
@@ -1072,7 +1072,7 @@ and atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
</td>
@@ -1096,7 +1096,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1128,7 +1128,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1161,7 +1161,7 @@ hydrogens of <em>aa</em>.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1255,7 +1255,7 @@ when residue is peptide bound.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. PRO)</td>
</tr>
@@ -1279,7 +1279,7 @@ when residue is N terminal.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. H3 for PRO)</td>
</tr>
@@ -1343,7 +1343,7 @@ when residue is N terminal.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index f44cf2070cf736fde687d7cbeff88cf77e357bb7..5bc7e7738c7a762b3140782249f5ec57f9593d6b 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Representing Loops — ProMod3 2.0.0 documentation</title>
+ <title>Representing Loops — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
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+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
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@@ -47,7 +47,7 @@
<p>The most simple representation of structural information in ProMod3 is the
<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -150,6 +150,28 @@ code which is not one of the 20 default amino acids or if
</table>
</dd></dl>
+<dl class="method">
+<dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span></dt>
+<dd><p>Creates a BackboneList with positions and sequence extracted from
+<em>residues</em>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+which the backbone positions and one letter codes
+are extracted.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if a residue in <em>residues</em>
+contains a one letter code which is not one of the 20 default
+amino acids or when there is a residue not providing all
+required positions.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="method">
<dt>
<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em>, <em>residues</em><span class="sig-paren">)</span></dt>
@@ -161,7 +183,7 @@ code which is not one of the 20 default amino acids or if
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
-<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions are extracted.</li>
</ul>
</td>
@@ -185,7 +207,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -195,7 +217,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
-<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
</ul>
@@ -214,7 +236,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -231,8 +253,8 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
</ul>
</td>
</tr>
@@ -248,7 +270,7 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
</ul>
@@ -267,7 +289,7 @@ be replaced, otherwise they will be added to the entity.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </td>
</tr>
@@ -371,7 +393,7 @@ actual fragment at specified <em>index</em></p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
atom for residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
</tr>
@@ -396,7 +418,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
/ oxygen atom to this.</li>
</ul>
</td>
@@ -448,7 +470,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
</tr>
@@ -465,7 +487,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
</ul>
</td>
</tr>
@@ -491,12 +513,12 @@ and set the amino acid type according to the given one letter code.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -566,12 +588,12 @@ to the given one letter code.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -635,7 +657,7 @@ reconstructed if the residue handle is valid.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
element of this backbone list)</td>
</tr>
</tbody>
@@ -652,7 +674,7 @@ element of this backbone list)</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -672,7 +694,7 @@ element of this backbone list)</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start index.</li>
<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -688,7 +710,7 @@ element of this backbone list)</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
</tr>
</tbody>
</table>
@@ -708,12 +730,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
</ul>
@@ -733,7 +755,7 @@ positions of the N, CA and C atoms.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
list onto CA positions of <em>other</em> backbone list.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
</tr>
@@ -1005,7 +1027,7 @@ backbone list.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 58b98b7aa4ff3f8e0be5b7e561bd02f62d6661b0..b5c82a2904e1141b2be11b0c06de3e1e21e7952a 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>loop - Loop Handling — ProMod3 2.0.0 documentation</title>
+ <title>loop - Loop Handling — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Representing Loops" href="backbone.html" />
<link rel="prev" title="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
@@ -163,7 +163,7 @@ loops. The following example should give you an idea of what can be done:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index ce2e37a473c1447a33f8ba8679fed9dd2ece6047..862906c9a062de9f3447fbff595aaf1f20d50956 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Precomputed Objects — ProMod3 2.0.0 documentation</title>
+ <title>Loading Precomputed Objects — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
<link rel="prev" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
@@ -204,7 +204,7 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 8dfaaaec37aec2fb0da5bfca21607687e1e8147f..a46f522fd8fab7a5f592707b11e5d2d8676db5a8 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generate ost.mol.mm systems — ProMod3 2.0.0 documentation</title>
+ <title>Generate ost.mol.mm systems — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
<link rel="prev" title="Handling All Atom Positions" href="all_atom.html" />
@@ -43,8 +43,8 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a>) and a
specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>).</p>
<p>The example below showcases the creation and use of an MM system:</p>
@@ -289,7 +289,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. Use this to run
MM simulations.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
</tr>
</tbody>
</table>
@@ -436,7 +436,7 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
<dl class="class">
<dt id="promod3.loop.ForcefieldLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
<li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -549,7 +549,7 @@ for details.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
</tr>
@@ -665,7 +665,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -681,7 +681,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -696,7 +696,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -720,7 +720,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -745,7 +745,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -770,7 +770,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -916,7 +916,7 @@ for details.</p>
<dt id="promod3.loop.ForcefieldAminoAcid">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
@@ -933,7 +933,7 @@ types. The full list of values is:</p>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
@@ -1043,7 +1043,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1105,7 +1105,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1182,7 +1182,7 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1287,8 +1287,8 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1392,7 +1392,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1482,7 +1482,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1593,7 +1593,7 @@ False, False)</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 0b6af0659d3cd5399ce7aa1a943d430a83e6bd49..e9187bffffdf6c3282227c9959f929dfb75e07de 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Structural Data — ProMod3 2.0.0 documentation</title>
+ <title>Structural Data — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
<link rel="prev" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
@@ -126,7 +126,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
<dt id="promod3.loop.CoordInfo.shift">
<code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
-structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -243,16 +243,9 @@ and fill it with content.</p>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetNumCoords</span><span class="p">()):</span>
- <span class="c1"># get the CoordInfo for chain with index i </span>
- <span class="n">coord_info</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetCoordInfo</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
-
- <span class="c1"># define a fragment, that covers the full length</span>
- <span class="n">frag_info</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FragmentInfo</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">coord_info</span><span class="o">.</span><span class="n">size</span><span class="p">)</span>
-
<span class="c1"># extract all required information</span>
- <span class="n">sequence</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="n">frag_info</span><span class="p">)</span>
- <span class="n">bb_list</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">frag_info</span><span class="p">,</span> <span class="n">sequence</span><span class="p">)</span>
- <span class="n">res_depths</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetResidueDepths</span><span class="p">(</span><span class="n">frag_info</span><span class="p">)</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="n">res_depths</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetResidueDepths</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="c1"># generate structure profiles based on structure_db_two</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">structure_db_two</span><span class="o">.</span><span class="n">GenerateStructureProfile</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span>
@@ -275,7 +268,7 @@ database, you might want to consider two things:</p>
<ol class="arabic simple">
<li>Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
running in parallel</li>
</ol>
<dl class="class">
@@ -284,14 +277,15 @@ running in parallel</li>
<dd><p>The StructureDBDataType enum has to be passed at initialization of a
StructureDB in order to define what data you want to store additionally
to backbone coordinates and sequence.
+For the bare minimum (only backbone coordinates and sequence), use Minimal.
If you want to store all data possible, use All. If you only want a subset,
you can combine some of the datatypes with a bitwise or operation
(see example script for <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>). One important note:
If you enable AAFrequenciesStruct, the actual information is not automatically
assigned. Only the according memory is allocated and set to zero, the actual
information must be assigned manually (see example script again...).</p>
-<p>All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP, AAFrequencies,
-AAFrequenciesStruct</p>
+<p>Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
+AAFrequencies, AAFrequenciesStruct</p>
</dd></dl>
<dl class="class">
@@ -409,10 +403,11 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</li>
<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
as specified by <em>chain_name</em>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
<li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
@@ -526,12 +521,17 @@ the database.</td>
<dt id="promod3.loop.StructureDB.GetBackboneList">
<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>fragment</em>, <em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>fragment</em>, <em>sequence</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>fragment</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list with positions extracted from <em>fragment</em>.</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list with positions extracted from <em>fragment</em> or
+full entry at <em>coord_idx</em></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></p>
@@ -539,18 +539,23 @@ the database.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</li>
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence to set for the returned backbone list.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract positions.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
+set, the original sequence at specified location in the
+database is used.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
superposed onto.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid (happens
-if the fragment does not fully fit into one of the connected
-stretches in the database) or if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</p>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if the length of <em>sequence</em> does
+not match with the desired backbone list, if <em>sequence</em> contains
+a character which does not belong to the 20 proteinogenic amino
+acids or if <em>fragment</em> or <em>coord_idx</em> is invalid. Fragment can
+be invalid when it does not fully fit into one of the connected
+stretches of residues in the database.</p>
</td>
</tr>
</tbody>
@@ -560,19 +565,28 @@ code which is not one of the 20 default amino acids.</p>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequence">
<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The sequence of <em>fragment</em></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence of <em>fragment</em> or full entry at <em>coord_idx</em></p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment or coord_idx is
+invalid. Fragment can be invalid when it does not fully fit into
+one of the connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -581,20 +595,29 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDSSPStates">
<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDSSPStates" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The dssp states of <em>fragment</em></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The dssp states of <em>fragment</em> or full entry at <em>coord_idx</em></p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dssp states</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain dssp
-data or if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain dssp
+data or if fragment/ coord_idx is invalid. Fragment can be invalid
+when it does not fully fit into one of the connected stretches of
+residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -603,20 +626,30 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDihedralAngles">
<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDihedralAngles" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The phi and psi dihedral angles of every residue of <em>fragment</em></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The phi and psi dihedral angles of every residue of <em>fragment</em>
+or full entry at <em>coord_idx</em></p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of pairs (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>)</td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of pairs (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>)</p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dihedral angles</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
-dihedral angle data or if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+dihedral angle data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -625,21 +658,31 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetResidueDepths">
<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetResidueDepths" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Residue depth for each residue of <em>fragment</em>.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Residue depth for each residue of <em>fragment</em> or full entry
+at <em>coord_idx</em></p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
-depths</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
+depths</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the residue depths</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
-residue depth data or if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+residue depth data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -648,23 +691,34 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSolventAccessibilitites">
<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSolventAccessibilitites" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Solvent accessibility for each residue of <em>fragment</em> in square A
-as calculated by <a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding
-the structure to the database.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Solvent accessibility for each residue of <em>fragment</em> or full entry
+at <em>coord_idx</em> in square A as calculated by
+<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding the structure to
+the database.</p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
-accessibilities</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
+accessibilities</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the solvent
+accessibilities</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
-solvent accessibility data or if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+solvent accessibility data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -673,22 +727,32 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequenceProfile">
<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequenceProfile" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The sequence profile for the residues defined by <em>fragment</em> with
-the BLOSUM62 probabilities as NULL model.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence profile for the residues defined by <em>fragment</em> or
+full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
+model.</p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
-profile</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
+profile</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence profile</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not cotain
-aa frequency data or if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+sequence profile data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -697,22 +761,32 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetStructureProfile">
<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure profile for the residues defined by <em>fragment</em> with
-the BLOSUM62 probabilities as NULL model.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the residues defined by <em>fragment</em> or
+full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
+model.</p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
-profile</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
+profile</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the structure profile</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
-aa frequencies struct data or if fragment is invalid. This is
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+structure profile data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -739,12 +813,12 @@ containing that data.</li>
probabilities as NULL model.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and
<em>residue_depths</em> differ in size, when their size is 0
-or when database does not contain aa frequencies struct data.</p>
+or when database does not contain residue depth data.</p>
</td>
</tr>
</tbody>
@@ -761,7 +835,7 @@ frequencies in entry with <em>coord_idx</em></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
</ul>
@@ -1064,8 +1138,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues of the fragment</li>
<li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
@@ -1289,7 +1363,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1307,7 +1381,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1761,7 +1835,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index 08cab65299b62467bf9c559ccbd086ddf997ad52..c30bb37417d8f8e58ddb80d0d2aea8dcfd0b2bdd 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sampling Dihedral Angles — ProMod3 2.0.0 documentation</title>
+ <title>Sampling Dihedral Angles — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Structural Data" href="structure_db.html" />
<link rel="prev" title="Representing Loops" href="backbone.html" />
@@ -139,7 +139,7 @@ acids not matching any of the group definitions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
</tr>
</tbody>
</table>
@@ -211,9 +211,9 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -253,9 +253,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -291,9 +291,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
</ul>
</td>
@@ -335,9 +335,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
</ul>
</td>
@@ -379,9 +379,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -425,9 +425,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -449,9 +449,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -590,7 +590,7 @@ standard amino acid</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 2070e317cc6919e6a68be9f020fbbf14782dab0b..bbcc316494931d4b60b9c3bcbe702bf53fa1972b 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Algorithms — ProMod3 2.0.0 documentation</title>
+ <title>Modelling Algorithms — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
<link rel="prev" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
@@ -95,7 +95,7 @@ of the solutions</li>
indices of the common subsets (rigid blocks) relative
to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
</td>
@@ -113,7 +113,7 @@ onto <strong>bb_list_two</strong></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
objects from which the positions are extracted</li>
<li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
positions will be extracted</li>
@@ -134,9 +134,9 @@ of the solutions</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> with the first element being a
<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code> defining the
column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
</td>
@@ -173,7 +173,7 @@ of the solutions</li>
indices of the common subsets (rigid blocks) relative
to the input <code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code> objects
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
</td>
@@ -236,8 +236,8 @@ Weird things are happening otherwise.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
<li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</li>
<li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
@@ -329,7 +329,7 @@ want to generate</li>
<li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
fragment search performance.</li>
<li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
increases the fragment search performance</li>
@@ -360,6 +360,267 @@ with the keys of the scores in <strong>scorer</strong></li>
</table>
</dd></dl>
+</div>
+<div class="section" id="motif-finder">
+<h2>Motif Finder<a class="headerlink" href="#motif-finder" title="Permalink to this headline">¶</a></h2>
+<p>Distinct spatial arrangements of atoms or functional groups are key for protein
+function. For their detection, ProMod3 implements the MotifFinder algorithm
+which is based on geometric hashing as described by Nussinov and Wolfson
+<a class="reference internal" href="../references.html#nussinov1991" id="id1">[nussinov1991]</a>. The algorithm consists of a learning stage, a detection stage
+and a refinement stage.</p>
+<p>Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
+(p1, p2, p3) of coordinates are selected that define triangles. For each
+triangle one can define an orthogonal vector basis
+(in our case v1 = norm(p2-p1), v3 = norm(cross(v1,p3-p1),
+v2 = norm(cross(v1,v3)))). For each coordinate not in [p1,p2,p3], we add the
+identity of the query/triangle as value to a hash map.
+The corresponding key consists of discretized values describing the edge lengths
+of the triangle, as well as the coordinate transformed into the triangle
+specific orthogonal vector basis. That’s 6 numbers in total.</p>
+<p>Detection Stage: The goal is to identify one or several subsets of target
+coordinates that resemble an input query.
+We first setup an accumulator containing a counter for each triangle observed
+in the input query. We then iterate over each possible triangle with vertices
+p1, p2 and p3 in the target coordinates. At the beginning of each iteration,
+all counters in the accumulator are set to zero. Again, we build a vector basis
+given that triangle and transform all coordinates not in [p1,p2,p3] into that
+vector space. For each transformed coordinate we obtain a key for the query hash
+map. If there is one or several values at that location in the hash map,
+we increment the corresponding locations in the accumulator.
+Once all coordinates are processed, we search for high counts in the
+accumulator. Given <em>N</em> query coordinates, we keep a solution for further
+refinement if count/(<em>N</em>-3) >= <em>hash_tresh</em>. This is repeated until all
+triangles in the target are processed. One key problem with this approach is
+the discretization of floating point numbers that give raise to the hash map
+keys. Two extremely close values might end up in different bins just because
+they are close to the bin boundaries. For each of the 6 relevant numbers
+we estimate the actual bin as well as the closest neighbouring bin. Processing
+all possible combinations results in 64 hash map lookups instead of only one.</p>
+<p>Refinement Stage: Every potential solution identified in the detection stage is
+further refined based on the <em>distance_thresh</em> and <em>refine_thresh</em> parameters.
+A potential solution found in the detection stage is a pair of triangles, one
+in the query and one in the target, for which we find many matching coordinates
+in their respective vector space. We start with a coordinate mapping based on
+the triangle vertices from the query and the target (3 pairs).
+This coordinate mapping is iteratively updated by estimating the minimum RMSD
+superposition of the mapped query coordinates onto the target, apply that
+superposition on the query, find the closest target coordinate for each
+coordinate in the query and redo the mapping by including all pairs with
+minimum distance < <em>distance_thresh</em>. Iteration stops if nothing changes
+anymore. The solution is returned to the user if the final fraction of mapped
+query coordinates is larger or equal <em>refine_thresh</em>.
+The larger the mapping, the more accurate the superposition. As we start with
+only the three triangle vertices, <em>distance_thresh</em> is doubled for the initial
+iteration.</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example script that loads protein structures that contain ATP and</span>
+<span class="c1"># generates motif queries describing their binding pockets.</span>
+<span class="c1"># In a second step, those pockets are matched against a protein </span>
+<span class="c1"># structure that only contains an ATP analog. The ATP from every </span>
+<span class="c1"># match is transformed and stored to disk for further processing.</span>
+
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+
+<span class="n">files</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'data/1E2Q.pdb'</span><span class="p">,</span> <span class="s1">'data/1KO5.pdb'</span><span class="p">,</span> <span class="s1">'data/2IYW.pdb'</span><span class="p">]</span>
+
+<span class="n">atp_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+<span class="n">query_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+
+<span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
+
+ <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">peptide_sel</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=true"</span><span class="p">)</span>
+ <span class="n">atp_sel</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"rname=ATP"</span><span class="p">)</span>
+
+ <span class="c1"># generate a single query for each ATP pocket</span>
+ <span class="k">for</span> <span class="n">atp_idx</span><span class="p">,</span> <span class="n">atp_r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">atp_sel</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
+ <span class="n">pocket_view</span> <span class="o">=</span> <span class="n">peptide_sel</span><span class="o">.</span><span class="n">CreateEmptyView</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">atp_at</span> <span class="ow">in</span> <span class="n">atp_r</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
+ <span class="n">close_at</span> <span class="o">=</span> <span class="n">peptide_sel</span><span class="o">.</span><span class="n">FindWithin</span><span class="p">(</span><span class="n">atp_at</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span> <span class="mf">4.5</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">at</span> <span class="ow">in</span> <span class="n">close_at</span><span class="p">:</span>
+ <span class="n">r</span> <span class="o">=</span> <span class="n">at</span><span class="o">.</span><span class="n">handle</span><span class="o">.</span><span class="n">GetResidue</span><span class="p">()</span>
+ <span class="n">add_flag</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">INCLUDE_ATOMS</span> <span class="o">|</span> <span class="n">mol</span><span class="o">.</span><span class="n">CHECK_DUPLICATES</span>
+ <span class="n">pocket_view</span><span class="o">.</span><span class="n">AddResidue</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">add_flag</span><span class="p">)</span>
+
+ <span class="n">ca_positions</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Vec3List</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">pocket_view</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
+ <span class="n">ca_positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
+ <span class="n">i</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">_</span><span class="si">%i</span><span class="s2">"</span><span class="o">%</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">atp_idx</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">MotifQuery</span><span class="p">(</span><span class="n">ca_positions</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="mf">4.0</span><span class="p">,</span> <span class="mf">9.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)</span>
+ <span class="n">query_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+
+ <span class="c1"># create an entity from atp for later use</span>
+ <span class="n">atp_view</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">CreateEmptyView</span><span class="p">()</span>
+ <span class="n">atp_view</span><span class="o">.</span><span class="n">AddResidue</span><span class="p">(</span><span class="n">atp_r</span><span class="p">,</span> <span class="n">mol</span><span class="o">.</span><span class="n">INCLUDE_ATOMS</span><span class="p">)</span>
+ <span class="n">atp_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">atp_view</span><span class="p">,</span> <span class="kc">True</span><span class="p">))</span>
+
+<span class="c1"># That's it, let's combine the single queries</span>
+<span class="n">full_query</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">MotifQuery</span><span class="p">(</span><span class="n">query_list</span><span class="p">)</span>
+
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">"data/1AKE.pdb"</span><span class="p">)</span>
+<span class="n">peptide_sel</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=true"</span><span class="p">)</span>
+<span class="n">ca_positions</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Vec3List</span><span class="p">()</span>
+<span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">peptide_sel</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
+ <span class="n">ca_positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
+
+<span class="c1"># search all matches, fetch the corresponding atps,</span>
+<span class="c1"># transform them onto the 1ake binding site and dump them to disk</span>
+<span class="n">matches</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">FindMotifs</span><span class="p">(</span><span class="n">full_query</span><span class="p">,</span> <span class="n">ca_positions</span><span class="p">)</span>
+<span class="k">for</span> <span class="n">m_idx</span><span class="p">,</span> <span class="n">m</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">matches</span><span class="p">):</span>
+ <span class="n">atp</span> <span class="o">=</span> <span class="n">atp_list</span><span class="p">[</span><span class="n">m</span><span class="o">.</span><span class="n">query_idx</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">atp</span><span class="o">.</span><span class="n">EditXCS</span><span class="p">()</span><span class="o">.</span><span class="n">ApplyTransform</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">mat</span><span class="p">)</span>
+ <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">atp</span><span class="p">,</span> <span class="s2">"m_</span><span class="si">%i</span><span class="s2">.pdb"</span><span class="o">%</span><span class="p">(</span><span class="n">m_idx</span><span class="p">))</span>
+
+</pre></div>
+</div>
+<dl class="class">
+<dt id="promod3.modelling.MotifQuery">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery" title="Permalink to this definition">¶</a></dt>
+<dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em>, <em>flags</em><span class="sig-paren">)</span></dt>
+<dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>query_list</em><span class="sig-paren">)</span></dt>
+<dd><p>A single query or a container of queries.
+The constructor performs the learning stage of a single query or combines
+several queries, so they can be searched at once.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Coordinates of the query</li>
+<li><strong>identifier</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Descriptor of the query</li>
+<li><strong>min_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – To avoid the full O(n^3) hell, triangles
+with any edge length below <em>min_triangle_edge_length</em>
+are skipped</li>
+<li><strong>max_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Same as <em>min_triangle_edge_length</em> but
+upper bound</li>
+<li><strong>bin_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Bin size in A, relevant to generate hash map keys</li>
+<li><strong>flags</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Flag in range [0,63] for every coordinate in <em>positions</em>.
+They’re also added to the hash map keys (default: 0).
+This means that additionally to having a matching
+relative position, the coordinates must also have a
+matching flag in the detection/refinement stage.
+If not provided (in the query and in the search),
+only coordinates matter.</li>
+<li><strong>query_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal"><span class="pre">MotifQuery</span></code></a>) – E pluribus unum</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.Save">
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Saves the query down to disk</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – filename</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="promod3.modelling.MotifQuery.Load">
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Load" title="Permalink to this definition">¶</a></dt>
+<dd><p>Load query from disk</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – filename</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.GetPositions">
+<code class="descname">GetPositions</code><span class="sig-paren">(</span><em>query_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetPositions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns coordinates of specified query</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>query_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Query from which you want the positions</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.GetIdentifiers">
+<code class="descname">GetIdentifiers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetIdentifiers" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a list of all query identifiers.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.GetN">
+<code class="descname">GetN</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetN" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the number of queries</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.MotifMatch">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifMatch</code><a class="headerlink" href="#promod3.modelling.MotifMatch" title="Permalink to this definition">¶</a></dt>
+<dd><p>Object that holds information about a match found in <a class="reference internal" href="#promod3.modelling.FindMotifs" title="promod3.modelling.FindMotifs"><code class="xref py py-meth docutils literal"><span class="pre">FindMotifs()</span></code></a></p>
+<dl class="attribute">
+<dt id="promod3.modelling.MotifMatch.query_idx">
+<code class="descname">query_idx</code><a class="headerlink" href="#promod3.modelling.MotifMatch.query_idx" title="Permalink to this definition">¶</a></dt>
+<dd><p>Index of matching query</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.MotifMatch.mat">
+<code class="descname">mat</code><a class="headerlink" href="#promod3.modelling.MotifMatch.mat" title="Permalink to this definition">¶</a></dt>
+<dd><p>Transformation matrix to superpose matching query onto target</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.MotifMatch.alignment">
+<code class="descname">alignment</code><a class="headerlink" href="#promod3.modelling.MotifMatch.alignment" title="Permalink to this definition">¶</a></dt>
+<dd><p>List of tuples which define matching pairs of query/target coordinates</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.FindMotifs">
+<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
+<dd><p>Performs the detection and refinement stages of the geometric hashing
+algorithm.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>query</strong> – Query to be searched</li>
+<li><strong>target_positions</strong> – Coordinates of the target</li>
+<li><strong>hash_thresh</strong> – Parameter relevant for detection stage</li>
+<li><strong>distance_thresh</strong> – Parameter relevant for refinement stage</li>
+<li><strong>refine_thresh</strong> – Parameter relevant for refinement stage</li>
+<li><strong>flags</strong> – Equivalent to <em>flags</em> in <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal"><span class="pre">MotifQuery</span></code></a>
+constructor. If you didn’t provide anything there,
+this can be ignored. Only the actual coordinates
+matter in this case.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All found matches</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference internal" href="#promod3.modelling.MotifMatch" title="promod3.modelling.MotifMatch"><code class="xref py py-class docutils literal"><span class="pre">MotifMatch</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</div>
</div>
@@ -374,6 +635,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<li><a class="reference internal" href="#">Modelling Algorithms</a><ul>
<li><a class="reference internal" href="#rigid-blocks">Rigid Blocks</a></li>
<li><a class="reference internal" href="#de-novo-modelling">De Novo Modelling</a></li>
+<li><a class="reference internal" href="#motif-finder">Motif Finder</a></li>
</ul>
</li>
</ul>
@@ -412,7 +674,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 5d52d66e2f53f35fe5e372accb51963bceef9d14..856ed3a388cb7915ae2d01dab313469d5e6c2824 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Gaps — ProMod3 2.0.0 documentation</title>
+ <title>Handling Gaps — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
<link rel="prev" title="Model Checking" href="model_checking.html" />
@@ -61,8 +61,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal"><span class="pre">seq</span></code></a></li>
</ul>
</td>
@@ -117,7 +117,7 @@ are valid and:</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -268,13 +268,13 @@ extend the gap past another gap.</p>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
<code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
<code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -319,7 +319,7 @@ False if no new extension possible.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
</ul>
</td>
</tr>
@@ -360,7 +360,7 @@ valid termini.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
<li>If -1, all possible non-terminal gaps are returned.</li>
<li>If >= 0, this restricts the max. gap-length
@@ -413,7 +413,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
<li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for length of gap.</li>
<li><strong>penalties</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
<li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a>
(i.e. it stops at gaps and termini).</li>
@@ -653,7 +653,7 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index d23c5cba75446f74ed5ef10605a6c07b8e44f214..4d1d100b5b554a0b27e792d8f223784866bc4aac 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>modelling - Protein Modelling — ProMod3 2.0.0 documentation</title>
+ <title>modelling - Protein Modelling — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Modelling Pipeline" href="pipeline.html" />
<link rel="prev" title="Singularity" href="../container/singularity.html" />
@@ -114,6 +114,7 @@ a model fully automatically as follows:</p>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html">Modelling Algorithms</a><ul>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#rigid-blocks">Rigid Blocks</a></li>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#de-novo-modelling">De Novo Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="algorithms.html#motif-finder">Motif Finder</a></li>
</ul>
</li>
</ul>
@@ -158,7 +159,7 @@ a model fully automatically as follows:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 2c2ed901ea6407d3f0c1662efa8e1052550ff6e1..82e51fce4011104f6a35012c2e1d73417da3b4b4 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Loop Candidates — ProMod3 2.0.0 documentation</title>
+ <title>Handling Loop Candidates — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
<link rel="prev" title="Handling Gaps" href="gap_handling.html" />
@@ -133,8 +133,8 @@ a fragment database.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
<em>n_stem</em> and <em>c_stem</em></li>
<li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
@@ -245,9 +245,9 @@ not depending on a metropolis criterium.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
@@ -289,9 +289,9 @@ candidate. This leads to an increase in number of loops.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match</li>
<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First pivot residue</li>
<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Second pivot residue</li>
@@ -365,7 +365,7 @@ anything is raised when calculating the scores.</p>
<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
details, <em>prof.null_model</em> is used for weighting).</p>
<p>Note that for profile scores a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
@@ -381,7 +381,7 @@ with this DB).</p>
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
</ul>
</td>
@@ -413,8 +413,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
</ul>
</td>
</tr>
@@ -1140,7 +1140,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index b80eab62447dcba8e7a6a7fce292eb359a5eb063..7c104e3051826856a67092851e155c422174f8a3 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Fitting Loops Into Gaps — ProMod3 2.0.0 documentation</title>
+ <title>Fitting Loops Into Gaps — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
<link rel="prev" title="Handling Loop Candidates" href="loop_candidates.html" />
@@ -84,11 +84,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
psi angle (-0.7854) to evaluate the last angle.</li>
@@ -125,8 +125,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
be closed has RMSD below the given <em>c_stem</em></li>
@@ -327,7 +327,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -349,7 +349,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -372,7 +372,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -394,7 +394,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -416,7 +416,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -643,7 +643,7 @@ the one given in the constructor.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 7c4a7a84be245178429a9b27b181b29da09d76a2..b944116fa0366bf0023ddaa88572d819f5cd94f3 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Model Checking — ProMod3 2.0.0 documentation</title>
+ <title>Model Checking — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Gaps" href="gap_handling.html" />
<link rel="prev" title="Modelling Pipeline" href="pipeline.html" />
@@ -58,14 +58,14 @@ three of the atoms exist (center and radii are estimated then).</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of rings to perform ring checks. Each ring is a named
tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
radius (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
</tr>
</tbody>
</table>
@@ -81,11 +81,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</td>
</tr>
@@ -104,7 +104,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
@@ -129,7 +129,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>candidates</strong> (<code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
Offending candidates are removed from this list.</li>
-<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
<li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
<li><strong>orig_indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – Mapping to old indexing of candidates. If given, it
must have as many elements as <em>candidates</em>.</li>
@@ -194,7 +194,7 @@ with <code class="docutils literal"><span class="pre">MolProbity</span> <span cl
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a></p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
</td>
</tr>
@@ -211,7 +211,7 @@ executable is not found.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
</tr>
</tbody>
</table>
@@ -283,7 +283,7 @@ executable is not found.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 36c37e6adae99ef01fc1e36b383ca6cc525e14b3..e10a1bfadccc3282e33e6e99a11a4ba2272e5154 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generating Loops De Novo — ProMod3 2.0.0 documentation</title>
+ <title>Generating Loops De Novo — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
<link rel="prev" title="Fitting Loops Into Gaps" href="loop_closing.html" />
@@ -506,9 +506,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
@@ -556,9 +556,9 @@ dihedral angles as it is the case for the <a class="reference internal" href="#p
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
</ul>
</td>
@@ -598,9 +598,9 @@ solutions. The KICCloser simply picks the first one.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
</ul>
@@ -639,7 +639,7 @@ superposing the c_stem with the desired positions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
</tbody>
@@ -677,7 +677,7 @@ superposing the n_stem with the desired positions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
</tbody>
@@ -940,7 +940,7 @@ internal counter to 0</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 70a70284b31c5fa1fe17ea2b1acd9290dfda5763..33215e8bfb81487a015e272515314a80690fa0ee 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Pipeline — ProMod3 2.0.0 documentation</title>
+ <title>Modelling Pipeline — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Model Checking" href="model_checking.html" />
<link rel="prev" title="modelling - Protein Modelling" href="index.html" />
@@ -118,7 +118,7 @@ chain follows afterwards.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -144,13 +144,13 @@ Gaps of different chains are appended one after another.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
<code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -159,7 +159,7 @@ of the target protein.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
<code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>). Please note, that this
attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
@@ -168,7 +168,7 @@ to fill it manually or even better by the convenient function
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -355,7 +355,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
<p>Each alignment handle must contain exactly two sequences and the second
sequence is considered the template sequence, which must have a
-<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
<p>This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
side chain coordinates are also copied. Gaps are ignored. Hydrogen an
@@ -383,7 +383,7 @@ as information about insertions and deletions in the gaps list.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
list of alignment handles for raw model with multiple chains.</li>
<li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
@@ -409,7 +409,7 @@ in SMTL). All ligands are added to a new chain named
<li>the second sequence does not have an attached structure</li>
<li>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
template sequence (but not for the target))</li>
<li>the target sequence has a non-zero offset (cannot be honored as
the resulting model will always start its residue numbering at 1)</li>
@@ -453,12 +453,12 @@ return an incomplete model.</p>
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
alignment.</li>
<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.9.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.9.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
@@ -479,7 +479,7 @@ limited. Termini of length 1 won’t be modelled.</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -654,7 +654,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
<li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</li>
<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First residue of the copied stretch</li>
<li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
they’re copied over</li>
</ul>
</td>
@@ -685,7 +685,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
+<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
</ul>
</td>
</tr>
@@ -842,7 +842,7 @@ For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a> is
called (e.g. with
-<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
@@ -913,7 +913,7 @@ both in this resnum range.</li>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByDatabase">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragment_db</em>, <em>structure_db</em>, <em>torsion_sampler</em>, <em>max_loops_to_search=40</em>, <em>min_loops_required=4</em>, <em>max_res_extension=-1</em>, <em>extended_search=True</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>max_num_all_atom=0</em>, <em>clash_thresh=-1</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragment_db</em>, <em>structure_db</em>, <em>torsion_sampler=None</em>, <em>max_loops_to_search=40</em>, <em>min_loops_required=4</em>, <em>max_res_extension=-1</em>, <em>extended_search=True</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>max_num_all_atom=0</em>, <em>clash_thresh=-1</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops from a structural database.</p>
<p>Usually this will extend the gaps a bit to match candidates from the
database. Do not expect a gap being filled in between its actual stem
@@ -946,7 +946,8 @@ This function cannot fill gaps at C- or N-terminal.</p>
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – A fragment database coupled to the <em>structure_db</em>.</li>
<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Backbone/profile data.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
+loaded if None.</li>
<li><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
evaluated per loop. The actual found candidates
may be more (if we found ‘enough’) or less (if
@@ -1015,7 +1016,7 @@ loops.</li>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByMonteCarlo">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler</em>, <em>max_loops_to_search=6</em>, <em>max_extension=30</em>, <em>mc_num_loops=2</em>, <em>mc_steps=5000</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler=None</em>, <em>max_loops_to_search=6</em>, <em>max_extension=30</em>, <em>mc_num_loops=2</em>, <em>mc_steps=5000</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops with Monte Carlo sampling.</p>
<p>This is meant as a “last-resort” approach when it is not possible to fill
the loops from the database with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>.
@@ -1049,7 +1050,8 @@ is only used if the gap length is >= the length of fragments stored.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
+loaded if None.</li>
<li><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
evaluated per loop.</li>
<li><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
@@ -1211,7 +1213,7 @@ one is loaded if None.</li>
<dt id="promod3.modelling.MinimizeModelEnergy">
<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
<li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
@@ -1239,7 +1241,7 @@ minimization is aborted. This issue is logged and added as a major issue to
<li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</li>
<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
</ul>
</td>
@@ -1247,7 +1249,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -1335,8 +1337,8 @@ set to True, if the problem affects backbone atoms.</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueView</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueView</span></code></a></td>
</tr>
</tbody>
</table>
@@ -1453,7 +1455,7 @@ attribute yet, it is added.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 58ac0f35df0c576c780fb241eb008d389dba9dcc..0a2b09ea8c269e3a61396bf576b543c5f59cf734 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sidechain Reconstruction — ProMod3 2.0.0 documentation</title>
+ <title>Sidechain Reconstruction — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Modelling Algorithms" href="algorithms.html" />
<link rel="prev" title="Generating Loops De Novo" href="monte_carlo.html" />
@@ -47,7 +47,7 @@
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
<li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
<li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
and used to reconstruct sidechains of single loops</li>
</ul>
@@ -102,7 +102,7 @@ and used to reconstruct sidechains of single loops</li>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
reconstruction gets directly applied on the structure itself.</li>
<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
@@ -214,7 +214,7 @@ environment before calling this!</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</li>
<li><strong>start_resnum_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Starts of loops.</li>
@@ -441,7 +441,7 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 01a546df33de2546098bf5872f811a54f33353fe..02ecc00e655c54dada0b5e1e709b33f23e845db2 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index b1fbc6e8a0374ebe94ecc2eaa2d0ee2f8623c101..807daaeef51b0813f61a4e40407916889de0aa02 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Using Binary Files In ProMod3 — ProMod3 2.0.0 documentation</title>
+ <title>Using Binary Files In ProMod3 — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="License" href="license.html" />
<link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
@@ -478,7 +478,7 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 47841194a7a87d9425151bf3bb96d3332b3d75cb..8382e9e26c6f32c6bdb0bac184c676e330cf50fd 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Python Module Index — ProMod3 2.0.0 documentation</title>
+ <title>Python Module Index — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -132,7 +132,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/references.html b/doc/html/references.html
index d0836ee0a3ecb34c9bc50de14cb86f68f3ce9c47..cee6d5434a8074eff00e925c919d771815a4f10d 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>References — ProMod3 2.0.0 documentation</title>
+ <title>References — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="Changelog" href="changelog.html" />
<link rel="prev" title="License" href="license.html" />
@@ -132,6 +132,14 @@ Exploring the conformational space of protein side chains using
dead-end elimination and the A* algorithm. Proteins.</td></tr>
</tbody>
</table>
+<table class="docutils citation" frame="void" id="nussinov1991" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[nussinov1991]</td><td>Nussinov R and Wolfson HJ (1991).
+Efficient detection of three-dimensional structural motifs in
+biological macromolecules by computer vision techniques. PNAS.</td></tr>
+</tbody>
+</table>
<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
@@ -157,6 +165,14 @@ potentials and threading score functions using information
maximization. Proteins.</td></tr>
</tbody>
</table>
+<table class="docutils citation" frame="void" id="trott2010" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[trott2010]</td><td>Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+accuracy of docking with a new scoring function, efficient
+optimization and multithreading. J Comput Chem</td></tr>
+</tbody>
+</table>
<table class="docutils citation" frame="void" id="zhou2005" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
@@ -204,7 +220,7 @@ Fragments. Proteins.</td></tr>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 9c9f58223d159cc67c8941f0301d9412442629be..2c1ceae1ca06c0417fd24bbe814e340ccb68e694 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>All Atom Scorers — ProMod3 2.0.0 documentation</title>
+ <title>All Atom Scorers — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
<link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
@@ -672,7 +672,7 @@ of residues in the input loop. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 6235608ccb7f65b630125f4963999b8efe227e07..4102971fd221d81757841b4e3daa61f0d0a36a4b 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Score Environment — ProMod3 2.0.0 documentation</title>
+ <title>Backbone Score Environment — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
<link rel="prev" title="scoring - Loop Scoring" href="index.html" />
@@ -69,8 +69,8 @@ task.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -107,7 +107,7 @@ structural data was already set, all the existing data gets cleared first.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -131,7 +131,7 @@ positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
</td>
@@ -280,7 +280,7 @@ providing lists of integers.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -387,7 +387,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
or CB atoms</li>
</ul>
@@ -402,7 +402,7 @@ or CB atoms</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</td>
</tr>
@@ -508,7 +508,7 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 7b8ad9e7b4e2f9a759ccd41078a13c8d9cb4cf1a..5787bc4c9307fa8d0716f96a6d7593a821b593ea 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Scorers — ProMod3 2.0.0 documentation</title>
+ <title>Backbone Scorers — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
<link rel="prev" title="Backbone Score Environment" href="backbone_score_env.html" />
@@ -381,7 +381,7 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</li>
<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
@@ -515,8 +515,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
@@ -695,8 +695,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</li>
<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</li>
@@ -1388,7 +1388,7 @@ of residues to be scored. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index f56b23ba357753d48b79c1708a60c2c588312afe..c4a6177e14b51adb45f06bd050d16a21184d1994 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>scoring - Loop Scoring — ProMod3 2.0.0 documentation</title>
+ <title>scoring - Loop Scoring — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
<link rel="prev" title="Subrotamer Optimization" href="../sidechain/subrotamer_optimizer.html" />
@@ -152,7 +152,7 @@ scorers to it and finally score some loops:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 57c6c16db63043d18557fa5de92e3348e1fc74b0..b639d4f79929726ca22d0eb2ff8a075318326e28 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Other Scoring Functions — ProMod3 2.0.0 documentation</title>
+ <title>Other Scoring Functions — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
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FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
<link rel="prev" title="All Atom Scorers" href="all_atom_scorers.html" />
@@ -159,7 +159,7 @@ construction algorithm <a class="reference internal" href="../references.html#ca
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/search.html b/doc/html/search.html
index 4eb4082b859a1ecc68b3dd78a53e83b6061b6eb1..874ca440df26a4aac33d1d09769355e081d5c63a 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Search — ProMod3 2.0.0 documentation</title>
+ <title>Search — ProMod3 2.1.0 documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
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FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -25,7 +25,7 @@
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<script type="text/javascript" src="_static/searchtools.js"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<script type="text/javascript">
jQuery(function() { Search.loadIndex("searchindex.js"); });
</script>
@@ -87,7 +87,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
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index 7b6f6337667fa0eb0c3269740f31f593b2cd9106..e1c5ff506a9a7a8823d27608488d58c7dd5905d5 100644
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+++ b/doc/html/searchindex.js
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urs:8,coutsia:38,coutsias2005:[32,38],cover:[0,1,8,12,13,14,21,25,26,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[51,52],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,createalign:[31,35],createentityfromview:[36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl4particl:49,createsequ:[26,31,35],creation:[25,32,49],creator:[25,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:20,crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,53],custom:[8,26,34,35,36,37,48,51],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[51,52],cyh:[51,52],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,51],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25],data_:37,data_gener:[3,37,48],data_to_stor:26,data_typ:26,databas:[0,9,23,24],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,46],decreas:34,dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25],definem:8,degre:[22,26,27],delet:[0,2,8,22,35,49],deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:0,dependency1:4,dependency2:4,depends_on:4,depth:[26,38],deriv:[1,20,26,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,29,30,32,33,37,39,41,44,47,48,49,52,55],descript:[0,5,13,16,20,34,35,52],descriptor:26,descsrib:10,design:[1,3,19,20],desir:[9,18,25,31,32,34,35,39,40,41],despit:3,detail:[0,9,13,16,20,25,26,27,31,33,34,35,39,41,48,52],detect:[0,11,28,30],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:35,develop:[1,3,8,16],deviat:[22,33,34,52],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:7,didnt:5,differ:[1,2,4,8,10,15,16,20,21,26,28,29,31,35,39,41,47,51,52],differenti:49,dihedr:[9,18,22,23,25,26],dihedral_angl:22,dihedral_bin:41,dihedral_idx:52,dihedral_pair:27,dihedralconfigur:52,dill:38,dimens:27,dir:[4,8,18],direct:[8,20,22,24,26,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,52,54],directori:[1,2,4,5,7,8],dirti:1,dirtyccdclos:34,disabl:[1,16],disable_doctest:2,disable_document:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[39,41],discuss:[20,26],disk:[8,25,28,39,41,52],displai:[11,13,14,20],dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[9,22,26,28,31,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,36,52],distinguish:3,distribut:[1,8,20,25,26,27,34,37,39,41,48,52],disulfid:[0,25,32,36,43],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],dng:18,do_it:[39,41],doc:[2,4,8,16,20],docker:3,dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,52],doesnt:52,doexternalscor:[39,41],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,31,34,35,37],donor:41,donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubt:13,down:[13,22,26,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:8,dssp:[3,26,41],dssp_state:41,due:[0,26,31,32,35,44],dump:52,dunbrack:[3,38,48],duplic:6,dure:[1,21,32,35,37,45,52],dynam:52,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:10,edge_idx:10,editor:1,editori:20,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,8,13,16,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51,52],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,53],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,33,35,42,47],entityhandl:[13,21,22,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,47,50],enumer:[8,10,21,25,26,31,35,40,47,50,51,52],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39],epsilon:[10,25,36,5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,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,47,50],enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equival:[28,35,39,41],error:[0,11,13,14,26,32,35,37],especi:28,estim:[10,28,33,34,38,41,44,49,50,51],etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,39,40,41],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],exec:7,execut:0,exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:34,expect:[1,3,7,21,25,26,35,36,40,44,50,52],expens:26,experiment:35,explain:[1,8],explan:8,explicit:2,explicitli:20,explor:38,exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,29,35],extension_penalti:29,extent:26,extern:[3,4,5,8,34],external_script:[3,8],extra:[2,3,8,16,22,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[22,28],f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,37,39,40,41,51],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,fed:[4,16],fedora:8,fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:[13,16,18,28],few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cy:25,ff_cys2:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_ly:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,8],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,51],filenotfound:33,fill:[4,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[3,4,7,8,10,16,21,23],findatom:28,findchain:42,findeigen3:20,findmotif:28,findwithin:[8,28],fine:8,finish:52,fire:[1,7],first:[0,1,8,10,13,16,18,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31],fix:[3,8,11,16,25,32,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,4,8,10,11,13,22,26,28,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,52],flip:51,flood:26,fluorin:49,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:23,forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,51],formal:[31,32,49,51],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,3,4,8,11,13,16,19,21,23,26,28,31,32,33,34,35,36,44,46,49,51],foundat:1,four:[9,34],fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[13,23,26,28,34,35],fragger_handl:[13,35],fragger_map:26,fraggerhandl:[0,13,26,28,35],fraggermap:[26,28],fragment:[0,3,9,13,22,23,24],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49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6,40,42],updatedistribut:27,updateposit:[25,32],upon:[26,32,34],upper:28,urei:25,urey_bradley_angl:25,usabl:16,usag:[0,3,10,13,24,26,31,32,36],use_amber_ff:35,use_bbdep_lib:36,use_frm:36,use_full_extend:35,use_scoring_extend:35,user:[1,5,8,19,28,53],userlevel:1,usr:[2,5,7,8],usual:[1,2,4,8,13,14,16,22,31,35,39],utilis:[8,16],v_size:37,val:[27,49],valid:[0,10,16,22,26,29,34,35,36,48,51],valin:49,valu:[2,10,11,13,21,22,25,26,28,31,34,35,37,39,40,41,44,47,49,50,51,52],valueerror:[28,35],vanish:40,varadarajan:38,vari:[4,37],variabl:[1,2,8,14,18,25,33,35,37],variant:[25,31],variou:[1,2,4,16,30],vec3:[9,21,22,26,32,33,43,44,49],vec3list:[28,49],vector:[25,27,28,31,37,49],verbal:20,verbos:1,veri:[1,8,11,16,25,28,35,37],verif:13,verifi:[1,11,16],version:[2,3,5,8,16,20,26,35,37,48,49],vertic:28,via:[1,5,8,13,15,25],view:[13,16,27,35,40],vina:[3,38],vinaparticletyp:[49,50],vinarotamerconstructor:50,virtual:8,visibl:36,vision:38,visual:18,volum:5,wai:[1,2,4,5,8,16,22,23,25,31,41,47,49],wait:8,walk:[1,8],want:[1,2,3,8,15,16,22,26,28,31,32,35,40,49,50,51,52,53],warn:[8,16,35],warranti:20,watch:8,web:[2,8],weight:[3,26,28,31,34,35,39,41],weird:[28,32,47],well:[0,4,16,21,27,28,29,31,35,37,41,47,50,51],went:[0,8],were:[16,26,31,35],wester:38,wether:10,what:[1,8,11,13,16,23,26,36,40],when:[1,3,4,5,8,10,13,14,21,22,25,26,27,28,29,31,34,35,36,37,38,40,41,44,47,48,49,50,51],whenev:[8,21,31,40],where:[0,1,3,4,5,8,10,11,13,14,16,20,21,22,25,26,27,31,35,37,39,40,41,48,49,50,51],wherea:26,wherev:20,whether:[3,5,8,10,11,13,20,22,25,26,31,32,34,36,39,40,41,49,50,51],which:[0,1,4,8,9,11,12,13,16,18,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,50,51],whistl:8,whitespac:0,who:[10,47],whole:[1,2,8,16,20,22,26,35,49],whom:20,why:[1,16],width:[10,37,47],wild:4,window:28,window_length:28,wise:4,wish:[2,17,27,35],with_aa:31,with_db:31,within:[2,3,4,8,14,16,20,21,25,28,29,33,35,36,39,41,51],without:[0,1,3,4,8,11,13,20,25,29,32,35,40,51],wolfson:[28,38],won:[0,35,36,50],word:4,work:[1,2,4,5,7,8,14,16,18,20,25,29,35,37,50],worldwid:20,worst:16,worth:53,would:[1,2,8,11,22,26,27,44,49],wrap:26,wrapper:[1,4,8,15,35],write:0,writebasetyp:37,writemagicnumb:37,writetypes:37,writeversionnumb:37,written:[8,20,37],wrong:[2,13],wwpdb:5,www:20,xlabel:27,xlim:27,xml:8,xxx:[22,49],xxx_num_atom:21,xxx_num_hydrogen:21,year:1,yet:[26,31,35],ylabel:27,ylim:27,you:[0,1,2,3,4,5,7,8,10,11,13,14,15,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,39,40,41,47,48,49,50,51,52,53],your:[1,2,4,5,7],your_modul:[8,16],yourself:[2,8,10,16,35,50],yyyi:20,zero:[0,26,28,35,51],zhou2005:[26,38],zhou:38,zip:[26,47]},titles:["ProMod3 Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],acid:[21,25,27],action:[0,1,4,5,7,8],actiontestcas:1,algorithm:28,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,argument:13,atom:[21,32,39],backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,7,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:1,exisit:37,extend:29,featur:[8,26],file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:[5,7],instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:51,novo:[28,34],object:[24,34,45],optim:52,ost:[5,7,25],other:43,output:1,own:8,pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,7,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,7,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 9e47ea4c753400b53429b567c94e62517f6bbdd1..934027fea20063d03c090c1936b0fd653d078932 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Disulfid Bond Evaluation — ProMod3 2.0.0 documentation</title>
+ <title>Disulfid Bond Evaluation — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
<link rel="prev" title="Rotamer Graph" href="graph.html" />
@@ -77,10 +77,10 @@ rotamers to the result of the geometric expression.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
</ul>
</td>
</tr>
@@ -113,8 +113,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_groups</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</li>
-<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
-<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
+<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
as a disulfid bond</li>
<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
@@ -180,7 +180,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index a40d117535fa22c6b4ee6610509f3ec34afffdde..b754527088d1cbe230c678d2500463cb3ffa54dd 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Frame — ProMod3 2.0.0 documentation</title>
+ <title>Frame - The Rigid Part — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
- <link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
- <link rel="prev" title="Rotamers" href="rotamer.html" />
+ <link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
+ <link rel="prev" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -42,8 +42,8 @@
<div class="bodywrapper">
<div class="body" role="main">
- <div class="section" id="frame">
-<h1>Frame<a class="headerlink" href="#frame" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="frame-the-rigid-part">
+<h1>Frame - The Rigid Part<a class="headerlink" href="#frame-the-rigid-part" title="Permalink to this headline">¶</a></h1>
<p>In contrast to the rotamers, the frame is a rigid object. It either
represents the protein backbone or sidechains kept rigid during the
sidechain modelling process. Regions, that should not be occupied by
@@ -129,7 +129,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Frame</a><ul>
+<li><a class="reference internal" href="#">Frame - The Rigid Part</a><ul>
<li><a class="reference internal" href="#the-frame-objects">The Frame Objects</a></li>
</ul>
</li>
@@ -140,8 +140,8 @@ can be passed to rotamer groups for calculating frame energies.</p>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer.html" title="previous chapter">Rotamers</a></li>
- <li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
+ <li>Previous: <a href="rotamer.html" title="previous chapter">Representing Sidechains - Rotamers & Co.</a></li>
+ <li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -169,7 +169,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index e843e0a687a79b945b82600f3087b3f90451be9a..03f601c9b5ab3462fc42aafdac4f90b0e57546c1 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Graph — ProMod3 2.0.0 documentation</title>
+ <title>Rotamer Graph — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
- <link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
+ <link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -91,7 +91,7 @@ conformations for every amino acid position.</td>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer_constructor.html" title="previous chapter">Rotamer Constructor</a></li>
+ <li>Previous: <a href="rotamer_lib.html" title="previous chapter">Rotamer Library</a></li>
<li>Next: <a href="disulfid.html" title="next chapter">Disulfid Bond Evaluation</a></li>
</ul></li>
</ul></li>
@@ -120,7 +120,7 @@ conformations for every amino acid position.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 1f48d7131a1c4e1b7064a8ebd8f819e8300316f5..57f8e3d4ae42ec76cedc4fab30b4402a7e32d8a3 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>sidechain - Sidechain Modelling — ProMod3 2.0.0 documentation</title>
+ <title>sidechain - Sidechain Modelling — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,9 +24,9 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
- <link rel="next" title="RotamerID" href="rotamer_id.html" />
+ <link rel="next" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
<link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -145,22 +145,22 @@ pipelines available in the modelling module.</p>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
-<li class="toctree-l1"><a class="reference internal" href="rotamer_id.html">RotamerID</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rotamer_id.html#the-rotamerid">The RotamerID</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer_id.html#how-can-i-get-an-id">How can I get an ID?</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="rotamer.html">Rotamers</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="rotamer.html">Representing Sidechains - Rotamers & Co.</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamerid">RotamerID</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer.html#the-scwrl4-scoring-function">The SCWRL4 scoring function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer.html#id1">Rotamers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamers">Rotamers</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamer-groups">Rotamer Groups</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="frame.html">Frame</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="frame.html">Frame - The Rigid Part</a><ul>
<li class="toctree-l2"><a class="reference internal" href="frame.html#the-frame-objects">The Frame Objects</a></li>
</ul>
</li>
+<li class="toctree-l1"><a class="reference internal" href="rotamer_constructor.html">Rotamer Constructor</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_constructor.html#the-rotamerconstructor-baseclass">The RotamerConstructor Baseclass</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_constructor.html#scoring-function-specific-rotamerconstructors">Scoring Function Specific RotamerConstructors</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="rotamer_lib.html">Rotamer Library</a><ul>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
@@ -168,10 +168,6 @@ pipelines available in the modelling module.</p>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#rotamer-configurations">Rotamer Configurations</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="rotamer_constructor.html">Rotamer Constructor</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rotamer_constructor.html#constructing-rotamers-and-frame-residues">Constructing Rotamers and Frame Residues</a></li>
-</ul>
-</li>
<li class="toctree-l1"><a class="reference internal" href="graph.html">Rotamer Graph</a></li>
<li class="toctree-l1"><a class="reference internal" href="disulfid.html">Disulfid Bond Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="loading.html">Loading Rotamer Libraries</a></li>
@@ -191,7 +187,7 @@ pipelines available in the modelling module.</p>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li>Previous: <a href="../modelling/algorithms.html" title="previous chapter">Modelling Algorithms</a></li>
- <li>Next: <a href="rotamer_id.html" title="next chapter">RotamerID</a></li>
+ <li>Next: <a href="rotamer.html" title="next chapter">Representing Sidechains - Rotamers & Co.</a></li>
</ul></li>
</ul></li>
</ul>
@@ -218,7 +214,7 @@ pipelines available in the modelling module.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 1e7bc1857b82f08787f9391ab628bbf4b25680de..1cd38b191475013d7c8f3f9386a78dc28747c80d 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Rotamer Libraries — ProMod3 2.0.0 documentation</title>
+ <title>Loading Rotamer Libraries — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
<link rel="prev" title="Disulfid Bond Evaluation" href="disulfid.html" />
@@ -159,7 +159,7 @@ incomplete if the last problem gets triggered.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index e91619bdea34caade0bbe9f581575b1ef222ce51..74427adf1f6b560313d9863e8ee20eb13ec118e4 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamers — ProMod3 2.0.0 documentation</title>
+ <title>Representing Sidechains - Rotamers & Co. — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
- <link rel="next" title="Frame" href="frame.html" />
- <link rel="prev" title="RotamerID" href="rotamer_id.html" />
+ <link rel="next" title="Frame - The Rigid Part" href="frame.html" />
+ <link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -42,18 +42,104 @@
<div class="bodywrapper">
<div class="body" role="main">
- <div class="section" id="rotamers">
-<h1>Rotamers<a class="headerlink" href="#rotamers" title="Permalink to this headline">¶</a></h1>
-<p>A rotamer represents an amino acid sidechain and is basically a set of
-<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects. There exist two types. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and
-<a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
-To gather all possible rotamers for one particular sidechain position,
+ <div class="section" id="representing-sidechains-rotamers-co">
+<h1>Representing Sidechains - Rotamers & Co.<a class="headerlink" href="#representing-sidechains-rotamers-co" title="Permalink to this headline">¶</a></h1>
+<p>A rotamer represents an amino acid sidechain identified by a <a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>
+and is a set of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects.
+Two types of rotamers exist. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
+To gather all possible rotamers for one location,
ProMod3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
-Pairwise interactions between particles give raise to pairwise energies between
-rotamers. Nevertheless, the energy calculation itself happens on the level
-of RotamerGroups and is mostly hidden away in the construction of the
-the <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal"><span class="pre">RotamerGraph</span></code></a>. If you’re too lazy to build up your rotamers
-by hand, you might be interested in the <a class="reference internal" href="rotamer_constructor.html#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.</p>
+All parts of the structure that are kept rigid can be represented by
+a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> object.</p>
+<div class="section" id="rotamerid">
+<h2>RotamerID<a class="headerlink" href="#rotamerid" title="Permalink to this headline">¶</a></h2>
+<p>The sidechain module has its own definition of amino acids to satisfy custom
+requirements for the implemented sidechain construction algorithms.
+As an example there are histidine in two possible protonation states,
+that affect the hbond term or different versions of proline/cysteine.</p>
+<dl class="class">
+<dt id="promod3.sidechain.RotamerID">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
+<dd><p>Enumerates the amino acids. Possible values:</p>
+<table class="hlist"><tr><td><ul class="simple">
+<li>ARG - Arginine</li>
+<li>ASN - Asparagine</li>
+<li>ASP - Aspartate</li>
+<li>GLN - Glutamine</li>
+<li>GLU - Glutamate</li>
+<li>LYS - Lysine</li>
+<li>SER - Serine</li>
+<li>CYS - Cystein</li>
+<li>CYH - “free” Cystein</li>
+<li>CYD - disulfid bonded Cystein</li>
+<li>MET - Methionine</li>
+<li>TRP - Tryptophane</li>
+<li>TYR - Tyrosine</li>
+<li>THR - Threonine</li>
+</ul>
+</td><td><ul class="simple">
+<li>VAL - Valine</li>
+<li>ILE - Isoleucine</li>
+<li>LEU - Leucine</li>
+<li>PRO - Proline</li>
+<li>CPR - cis-Proline</li>
+<li>TPR - trans-Proline</li>
+<li>HIS - Histidine</li>
+<li>HSD - d-protonated Histidine</li>
+<li>HSE - e-protonated Histidine</li>
+<li>PHE - Phenylalanine</li>
+<li>GLY - Glycine</li>
+<li>ALA - Alanine</li>
+<li>XXX - Invalid</li>
+</ul>
+</td></tr></table>
+<p>The RotamerID enum can be accessed either directly as <code class="docutils literal"><span class="pre">promod3.sidechain.ARG</span></code>
+or as <code class="docutils literal"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
+</dd></dl>
+
+<div class="section" id="how-can-i-get-an-id">
+<h3>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h3>
+<p>The RotamerID enum can directly be accessed from Python. Two convenient
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+or from amino acid three letter codes.</p>
+<dl class="method">
+<dt id="promod3.sidechain.TLCToRotID">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">TLCToRotID</code><span class="sig-paren">(</span><em>tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
+<dd><p>Directly translates the three letter code into a RotamerID. Following
+exactly the naming convention defined above.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>tlc</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Three letter code of amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.AAToRotID">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">AAToRotID</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
+<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
+to generate special IDs this way
+(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
+defined in <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+</div>
<div class="section" id="the-smallest-building-block-the-particle">
<h2>The Smallest Building Block - The Particle<a class="headerlink" href="#the-smallest-building-block-the-particle" title="Permalink to this headline">¶</a></h2>
<p>Particles give raise to more complex objects such as rotamers and frame
@@ -65,7 +151,9 @@ function.</p>
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">PScoringFunction</code><a class="headerlink" href="#promod3.sidechain.PScoringFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>The available scoring functions between <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects</p>
<ul class="simple">
-<li>SCWRL4</li>
+<li>SCWRL4 - <a class="reference internal" href="#scwrl4-scoring-function"><span class="std std-ref">The SCWRL4 scoring function</span></a></li>
+<li>SCWRL3 - <a class="reference internal" href="#scwrl3-scoring-function"><span class="std std-ref">The SCWRL3 scoring function</span></a></li>
+<li>VINA - <a class="reference internal" href="#vina-scoring-function"><span class="std std-ref">The VINA scoring function</span></a></li>
</ul>
</dd></dl>
@@ -140,7 +228,7 @@ evaluated by the underlying scoring function.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The position of the particle</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -163,13 +251,16 @@ evaluated by the underlying scoring function.</td>
</dd></dl>
-</div>
<div class="section" id="the-scwrl4-scoring-function">
-<h2>The SCWRL4 scoring function<a class="headerlink" href="#the-scwrl4-scoring-function" title="Permalink to this headline">¶</a></h2>
+<span id="scwrl4-scoring-function"></span><h3>The SCWRL4 scoring function<a class="headerlink" href="#the-scwrl4-scoring-function" title="Permalink to this headline">¶</a></h3>
+<p>The SCWRL4 scoring function combines a Lennard-Jones style term with
+a hydrogen bond term. Details can be found in the relevant publication
+<a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a>.</p>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4ParticleType">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4ParticleType</code><a class="headerlink" href="#promod3.sidechain.SCWRL4ParticleType" title="Permalink to this definition">¶</a></dt>
-<dd><p>The SCWRL4 energy function differentiates between following particle types</p>
+<dd><p>The SCWRL4 energy function differentiates between following particle types
+that define the behaviour of the Lennard-Jones style term:</p>
<ul class="simple">
<li>HParticle - represents hydrogen</li>
<li>CParticle - default representation of a carbon</li>
@@ -195,13 +286,21 @@ function</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The name of the particle</li>
<li><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
bond term</li>
<li><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
-relevant for the hydrogen bond term</li>
-<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
-relevant for the hdrogen bond term</li>
+relevant for the hydrogen bond term. If set, the
+particle is a potential hydrogen bond acceptor.
+An example would be the Serine OG atom, where you can
+represent the two lone pairs with vectors pointing
+from the OG position towards the lone pair centers.</li>
+<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+relevant for the hydrogen bond term. If set, the
+particle is a potential hydrogen bond donor. An
+example would be the Serine HG hydrogen. The
+<em>polar_direction</em> would be a vector
+estimated as follows: hg_pos-og_pos.</li>
</ul>
</td>
</tr>
@@ -210,8 +309,93 @@ relevant for the hdrogen bond term</li>
</dd></dl>
</div>
-<div class="section" id="id1">
-<h2>Rotamers<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="the-scwrl3-scoring-function">
+<span id="scwrl3-scoring-function"></span><h3>The SCWRL3 scoring function<a class="headerlink" href="#the-scwrl3-scoring-function" title="Permalink to this headline">¶</a></h3>
+<p>The SCWRL3 scoring function implements a simple repulsion term that depends on
+the hard-sphere radius of the involved particles.
+Details can be found in the relevant publication <a class="reference internal" href="../references.html#canutescu2003" id="id2">[canutescu2003]</a>.</p>
+<dl class="method">
+<dt id="promod3.sidechain.CreateSCWRL3Particle">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateSCWRL3Particle</code><span class="sig-paren">(</span><em>name</em>, <em>radius</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL3Particle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL3 scoring
+function</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The name of the particle</li>
+<li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
+repulsion term.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+<div class="section" id="the-vina-scoring-function">
+<span id="vina-scoring-function"></span><h3>The VINA scoring function<a class="headerlink" href="#the-vina-scoring-function" title="Permalink to this headline">¶</a></h3>
+<p>The VINA scoring function is a combination of scores that are named
+gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
+software <a class="reference internal" href="../references.html#trott2010" id="id3">[trott2010]</a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+evaluated between C_VINAParticle <a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a> and hbond is
+evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
+are intended to evaluate sidechain-sidechain interactions in proteins,
+VINA is mainly targeted at interactions between sidechains and ligands.</p>
+<p>The VINA scoring function differentiates between the following particle types:</p>
+<dl class="class">
+<dt id="promod3.sidechain.VINAParticleType">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINAParticleType</code><a class="headerlink" href="#promod3.sidechain.VINAParticleType" title="Permalink to this definition">¶</a></dt>
+<dd><ul class="simple">
+<li>O_D_VINAParticle - Oxygen that can be a hydrogen bond donor</li>
+<li>N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor</li>
+<li>O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor</li>
+<li>N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor</li>
+<li>O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor</li>
+<li>N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor</li>
+<li>O_VINAParticle - Oxygen</li>
+<li>N_VINAParticle - Nitrogen</li>
+<li>S_VINAParticle - Sulfur</li>
+<li>P_VINAParticle - Phosphorus</li>
+<li>C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom</li>
+<li>C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens</li>
+<li>F_VINAParticle - Fluorine</li>
+<li>Cl_VINAParticle - Chlorine</li>
+<li>Br_VINAParticle - Bromine</li>
+<li>I_VINAParticle - Iodine</li>
+<li>M_VINAParticle - Metals</li>
+<li>INVALID_VINAParticle - Invalid particle...</li>
+</ul>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.CreateVINAParticle">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateVINAParticle</code><span class="sig-paren">(</span><em>name</em>, <em>particle_type</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateVINAParticle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the VINA scoring
+function</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The name of the particle</li>
+<li><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+</div>
+<div class="section" id="rotamers">
+<h2>Rotamers<a class="headerlink" href="#rotamers" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RRMRotamer">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer" title="Permalink to this definition">¶</a></dt>
@@ -278,7 +462,7 @@ in this process.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
<strong>res</strong></li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
@@ -554,7 +738,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -954,7 +1138,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1088,7 +1272,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1170,10 +1354,18 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Rotamers</a><ul>
-<li><a class="reference internal" href="#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a></li>
+<li><a class="reference internal" href="#">Representing Sidechains - Rotamers & Co.</a><ul>
+<li><a class="reference internal" href="#rotamerid">RotamerID</a><ul>
+<li><a class="reference internal" href="#how-can-i-get-an-id">How can I get an ID?</a></li>
+</ul>
+</li>
+<li><a class="reference internal" href="#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a><ul>
<li><a class="reference internal" href="#the-scwrl4-scoring-function">The SCWRL4 scoring function</a></li>
-<li><a class="reference internal" href="#id1">Rotamers</a></li>
+<li><a class="reference internal" href="#the-scwrl3-scoring-function">The SCWRL3 scoring function</a></li>
+<li><a class="reference internal" href="#the-vina-scoring-function">The VINA scoring function</a></li>
+</ul>
+</li>
+<li><a class="reference internal" href="#rotamers">Rotamers</a></li>
<li><a class="reference internal" href="#rotamer-groups">Rotamer Groups</a></li>
</ul>
</li>
@@ -1184,8 +1376,8 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer_id.html" title="previous chapter">RotamerID</a></li>
- <li>Next: <a href="frame.html" title="next chapter">Frame</a></li>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li>Next: <a href="frame.html" title="next chapter">Frame - The Rigid Part</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -1213,7 +1405,7 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 992881a63c466cf6e9dad28c2276f87bd8837b6b..cc1e1e8a80f21e51d9942ba7a60803771bfd5835 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Constructor — ProMod3 2.0.0 documentation</title>
+ <title>Rotamer Constructor — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
- <link rel="next" title="Rotamer Graph" href="graph.html" />
- <link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
+ <link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
+ <link rel="prev" title="Frame - The Rigid Part" href="frame.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -44,15 +44,15 @@
<div class="section" id="rotamer-constructor">
<h1>Rotamer Constructor<a class="headerlink" href="#rotamer-constructor" title="Permalink to this headline">¶</a></h1>
-<p>Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by ProMod3.</p>
-<div class="section" id="constructing-rotamers-and-frame-residues">
-<h2>Constructing Rotamers and Frame Residues<a class="headerlink" href="#constructing-rotamers-and-frame-residues" title="Permalink to this headline">¶</a></h2>
+<p>Instead of creating rotamers or frame residues by yourself, you can use the
+convenient functionality provided by ProMod3.</p>
+<div class="section" id="the-rotamerconstructor-baseclass">
+<h2>The RotamerConstructor Baseclass<a class="headerlink" href="#the-rotamerconstructor-baseclass" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RotamerConstructor">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class that cannot be initialized from Python. It builds
-an interface implemented by energy function specific constructors
+an interface implemented by scoring function specific constructors
(e.g. <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="promod3.sidechain.SCWRL4RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">SCWRL4RotamerConstructor</span></code></a>).</p>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">
@@ -79,11 +79,11 @@ an interface implemented by energy function specific constructors
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the required backbone atoms</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
@@ -134,11 +134,11 @@ don’t show up in a rotamer).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
@@ -177,11 +177,11 @@ you observe in a rotamer).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
@@ -219,7 +219,7 @@ to the energy function specific constructors to override that behaviour.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
to be assigned</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
<em>rot_group</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
@@ -235,6 +235,9 @@ to be assigned</li>
</dd></dl>
+</div>
+<div class="section" id="scoring-function-specific-rotamerconstructors">
+<h2>Scoring Function Specific RotamerConstructors<a class="headerlink" href="#scoring-function-specific-rotamerconstructors" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="Permalink to this definition">¶</a></dt>
@@ -262,7 +265,7 @@ any rotamers for ALA and GLY.</td>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
<code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
there won’t be any parametrization of hbonds in this function. All heavy
atoms of the residue will be represented as carbons and hydrogens are
@@ -272,7 +275,7 @@ skipped.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
</ul>
@@ -288,7 +291,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal"><span class="pre">ConstructFrameResidue()</span></code></a>,
which will be called by this function if the residue is not known by the given
@@ -306,10 +309,10 @@ as in the <code class="xref py py-class docutils literal"><span class="pre">Side
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
</ul>
</td>
</tr>
@@ -338,7 +341,121 @@ is already called at construction and the energies are properly assigned.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
to be assigned</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.sidechain.SCWRL3RotamerConstructor">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL3RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<dd><p>This object implements the full interface defined in
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+are parametrized according to the SCWRL3 method. They contain only heavy atoms.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+the cb atom. This flag also affects the construction
+of frame residues and controls whether the cb atom
+shows up in the backbone frame residues or sidechain
+frame residues.
+This is useful when you want to represent ALA or
+GLY with actual rotamers, but be aware of increased
+runtime. This flag can be set to False for most
+modeling applications and you just don’t generate
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+Takes the rotamer group and assigns every single rotamer its internal
+energy based on the probabilistic approach used by SCWRL3.
+=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+rotamer specific and max_p is the maximum probablity of any of the rotamers
+in <strong>rot_group</strong>. If you construct a rotamer group by the
+ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+is already called at construction and the energies are properly assigned.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.sidechain.VINARotamerConstructor">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINARotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<dd><p>This object implements the full interface defined in
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+are parametrized according to the VINA method. They contain only heavy atoms.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+the cb atom. This flag also affects the construction
+of frame residues and controls whether the cb atom
+shows up in the backbone frame residues or sidechain
+frame residues.
+This is useful when you want to represent ALA or
+GLY with actual rotamers, but be aware of increased
+runtime. This flag can be set to False for most
+modeling applications and you just don’t generate
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+Takes the rotamer group and assigns every single rotamer its internal
+energy based on the probabilistic approach used by SCWRL3/SCWRL4.
+=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+rotamer specific and max_p is the maximum probablity of any of the rotamers
+in <strong>rot_group</strong>. If you construct a rotamer group by the
+ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+is already called at construction and the energies are properly assigned.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
<em>rot_group</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
@@ -352,6 +469,102 @@ to be assigned</li>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
+<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>res</em>, <em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+a heuristic treatment of the atoms. It is important that the residue has
+proper bonds assigned, as they influence the atom typing procedure.
+Furthermore, you need hydrogens to automatically estimate the correct
+atom type for oxygens and nitrogens (hydrogen bond donor/acceptor).
+Alternatively you can assign generic properties to oxygens and nitrogens
+to circumvent the requirement of hydrogens. This is further described for
+the case of oxygen.</p>
+<ul class="simple">
+<li>Carbon is assigned C_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a> if its only
+bound to other carbons or hydrogens (and deuterium). All other carbons are
+assigned C_P_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>In case of oxygen, the heuristic first checks for set generic properties.
+If the atom has the bool properties “is_hbond_acceptor” AND
+“is_hbond_donor” set, it decides between the according oxygen types
+in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
+every oxygen is assumed to be an hbond acceptor. But only an hbond donor
+if its bound to a hydrogen (or deuterium). You can set the generic
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+at.SetBoolProp(“is_hbond_donor”, False) and
+at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
+generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>In case of nitrogen, the heuristic again first checks for set generic
+properties.
+If the atom has the bool properties “is_hbond_acceptor” AND
+“is_hbond_donor” set, it decides between the according nitrogen types
+in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>. If not, nitrogen is expected to be an
+hbond donor if it is bound to a hydrogen (or deuterium) and
+an hbond acceptor if it is bound to less than 3 other atoms (sounds
+horrible but works surprisingly well).</li>
+<li>Atoms of elements [“MG”, “MN”, “ZN”, “CA”, “FE”] are assigned
+M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>Atoms of elements [“S”, “P”, “F”, “CL”, “BR”, “I”] are assigned their
+corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>All other atoms are neglected and not added to the returned
+<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
+</ul>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
+<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">
+<code class="descname">ConstructRRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> with the atom typing heuristic
+as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">
+<code class="descname">ConstructFRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> with the atom typing heuristic
+as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method. The
+constructed <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> only contains one subrotamer that
+contains the atoms from <em>residue</em>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
</div>
@@ -366,7 +579,8 @@ to be assigned</li>
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Rotamer Constructor</a><ul>
-<li><a class="reference internal" href="#constructing-rotamers-and-frame-residues">Constructing Rotamers and Frame Residues</a></li>
+<li><a class="reference internal" href="#the-rotamerconstructor-baseclass">The RotamerConstructor Baseclass</a></li>
+<li><a class="reference internal" href="#scoring-function-specific-rotamerconstructors">Scoring Function Specific RotamerConstructors</a></li>
</ul>
</li>
</ul>
@@ -376,8 +590,8 @@ to be assigned</li>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer_lib.html" title="previous chapter">Rotamer Library</a></li>
- <li>Next: <a href="graph.html" title="next chapter">Rotamer Graph</a></li>
+ <li>Previous: <a href="frame.html" title="previous chapter">Frame - The Rigid Part</a></li>
+ <li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -405,7 +619,7 @@ to be assigned</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
deleted file mode 100644
index 80e2b6832047a2ac820f8d5dd21d16cc6b4e7e57..0000000000000000000000000000000000000000
--- a/doc/html/sidechain/rotamer_id.html
+++ /dev/null
@@ -1,202 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-
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- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>RotamerID — ProMod3 2.0.0 documentation</title>
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- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
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-
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- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body" role="main">
-
- <div class="section" id="rotamerid">
-<h1>RotamerID<a class="headerlink" href="#rotamerid" title="Permalink to this headline">¶</a></h1>
-<p>The sidechain module has its own definition of amino acids to satisfy custom
-requirements for the implemented sidechain construction algorithms.
-As an example there are histidine in two possible protonation states,
-that affect the hbond term or different versions of proline/cysteine.</p>
-<div class="section" id="the-rotamerid">
-<h2>The RotamerID<a class="headerlink" href="#the-rotamerid" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="promod3.sidechain.RotamerID">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
-<dd><p>Enumerates the amino acids. Possible values:</p>
-<table class="hlist"><tr><td><ul class="simple">
-<li>ARG - Arginine</li>
-<li>ASN - Asparagine</li>
-<li>ASP - Aspartate</li>
-<li>GLN - Glutamine</li>
-<li>GLU - Glutamate</li>
-<li>LYS - Lysine</li>
-<li>SER - Serine</li>
-<li>CYS - Cystein</li>
-<li>CYH - “free” Cystein</li>
-<li>CYD - disulfid bonded Cystein</li>
-<li>MET - Methionine</li>
-<li>TRP - Tryptophane</li>
-<li>TYR - Tyrosine</li>
-<li>THR - Threonine</li>
-</ul>
-</td><td><ul class="simple">
-<li>VAL - Valine</li>
-<li>ILE - Isoleucine</li>
-<li>LEU - Leucine</li>
-<li>PRO - Proline</li>
-<li>CPR - cis-Proline</li>
-<li>TPR - trans-Proline</li>
-<li>HIS - Histidine</li>
-<li>HSD - d-protonated Histidine</li>
-<li>HSE - e-protonated Histidine</li>
-<li>PHE - Phenylalanine</li>
-<li>GLY - Glycine</li>
-<li>ALA - Alanine</li>
-<li>XXX - Invalid</li>
-</ul>
-</td></tr></table>
-<p>The RotamerID enum can be accessed either directly as <code class="docutils literal"><span class="pre">promod3.sidechain.ARG</span></code>
-or as <code class="docutils literal"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
-</dd></dl>
-
-</div>
-<div class="section" id="how-can-i-get-an-id">
-<h2>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h2>
-<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
-or from amino acid three letter codes.</p>
-<dl class="method">
-<dt id="promod3.sidechain.TLCToRotID">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">TLCToRotID</code><span class="sig-paren">(</span><em>tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
-<dd><p>Directly translates the three letter code into a RotamerID. Following
-exactly the naming convention defined above.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>tlc</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Three letter code of amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.AAToRotID">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">AAToRotID</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
-<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
-to generate special IDs this way
-(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-</div>
-
-
- </div>
- </div>
- </div>
- <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">RotamerID</a><ul>
-<li><a class="reference internal" href="#the-rotamerid">The RotamerID</a></li>
-<li><a class="reference internal" href="#how-can-i-get-an-id">How can I get an ID?</a></li>
-</ul>
-</li>
-</ul>
-<div class="relations">
-<h3>Related Topics</h3>
-<ul>
- <li><a href="../index.html">Documentation overview</a><ul>
- <li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
- <li>Next: <a href="rotamer.html" title="next chapter">Rotamers</a></li>
- </ul></li>
- </ul></li>
- </ul></li>
-</ul>
-</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/rotamer_id.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
-<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
- <form class="search" action="../search.html" method="get">
- <input type="text" name="q" />
- <input type="submit" value="Go" />
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
- </form>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
- </div>
- </div>
- <div class="clearer"></div>
- </div>
- <div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
-
- |
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
-
- |
- <a href="../_sources/sidechain/rotamer_id.txt"
- rel="nofollow">Page source</a>
- </div>
-
-
-
-
- </body>
-</html>
\ No newline at end of file
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index ea9eb17d345a9d27780d4c12a5e80198cfbc9698..9d52fdcf96927e184234973507f62579c7bdc3b2 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Library — ProMod3 2.0.0 documentation</title>
+ <title>Rotamer Library — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
- <link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
- <link rel="prev" title="Frame" href="frame.html" />
+ <link rel="next" title="Rotamer Graph" href="graph.html" />
+ <link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -115,7 +115,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
<li><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</li>
</ul>
</td>
@@ -144,7 +144,7 @@ special <em>id</em> requests.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
probability sorted by their probability</td>
@@ -237,7 +237,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
<li><strong>r1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi1</li>
<li><strong>r2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi2</li>
<li><strong>r3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi3</li>
@@ -284,7 +284,7 @@ special <em>id</em> requests.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle in range [-pi,pi[</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle in range [-pi,pi[</li>
</ul>
@@ -308,11 +308,11 @@ found</p>
<dd><p>Once all rotamers are added, the library can be made static to become readable
and ready for io. Several things get checked during this process</p>
<ul class="simple">
-<li>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>,
+<li>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>,
the same number of rotamers must have been added</li>
<li>All configuration combinations of the added rotamers in one phi/psi bin
-of a particular <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must be unique</li>
-<li>The configuration combinations of a particular <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must
+of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must be unique</li>
+<li>The configuration combinations of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must
be consistent across all phi/psi bins</li>
</ul>
<table class="docutils field-list" frame="void" rules="none">
@@ -436,7 +436,7 @@ functionalities.</p>
<dt id="promod3.sidechain.RotamerLibEntry.FromResidue">
<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
-The function tries to automatically identify the <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> based
+The function tries to automatically identify the <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> based
on the residue name. The probability and standard deviations are set to 0.0,
all not required chi angles with their corresponding standard deviations to
NaN.</p>
@@ -444,12 +444,12 @@ NaN.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if residue name cannot be
-translated to <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> or when not all required atoms
+translated to <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> or when not all required atoms
are present in <em>res</em>.</td>
</tr>
</tbody>
@@ -468,8 +468,8 @@ are NaN.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></li>
</ul>
</td>
</tr>
@@ -528,7 +528,7 @@ the chi2 is checked for its actual value, but also for its flipped state.</p>
<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
considered similar</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
</ul>
</td>
</tr>
@@ -586,7 +586,7 @@ for its actual value, but also for its flipped state.</p>
(0 for chi1, 3 for chi4)</li>
<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
considered similar</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
</ul>
</td>
</tr>
@@ -652,7 +652,7 @@ to also return NON_ROTAMERIC (e.g. chi2 for ASN).</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – Sidechain dihedral angle comes from here</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</li>
<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies angle (0 => chi1, ..., 3 => chi4)</li>
</ul>
</td>
@@ -691,8 +691,8 @@ valid and non rotameric, INVALID otherwise.</p>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="frame.html" title="previous chapter">Frame</a></li>
- <li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
+ <li>Previous: <a href="rotamer_constructor.html" title="previous chapter">Rotamer Constructor</a></li>
+ <li>Next: <a href="graph.html" title="next chapter">Rotamer Graph</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -720,7 +720,7 @@ valid and non rotameric, INVALID otherwise.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 866eab60f7473aaddc35597e20ac9bcd3a9a08ab..4919ec5cd562a672a8c5dd640d7c6a18e2ad2140 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Subrotamer Optimization — ProMod3 2.0.0 documentation</title>
+ <title>Subrotamer Optimization — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
<link rel="prev" title="Loading Rotamer Libraries" href="loading.html" />
@@ -126,7 +126,7 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index ee0f7551b808e93fd74f67b2d31d813b6809ce8c..df6d3a8e13a6c45f1862db56f6eaeda2cddfa4ce 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 2.0.0 documentation</title>
+ <title>Contributing — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="Documentation For Developers" href="developers.html" />
<link rel="prev" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
@@ -92,7 +92,7 @@ information on that matter in the developer section of the documentation
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/users.html b/doc/html/users.html
index e576c73592ed54aaec6a4e2db6c99ad4bbd635ea..dc1a92438ecea83e3e810dbb99cfc865e9503e94 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Users — ProMod3 2.0.0 documentation</title>
+ <title>Documentation For Users — ProMod3 2.1.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />
<link rel="prev" title="ProMod3" href="index.html" />
@@ -82,11 +82,10 @@ scripts using the functionality of this library.</p>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_id.html">RotamerID</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Rotamers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_lib.html">Rotamer Library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Representing Sidechains - Rotamers & Co.</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame - The Rigid Part</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_constructor.html">Rotamer Constructor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_lib.html">Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/graph.html">Rotamer Graph</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/disulfid.html">Disulfid Bond Evaluation</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/loading.html">Loading Rotamer Libraries</a></li>
@@ -159,7 +158,7 @@ scripts using the functionality of this library.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>