diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index be9f5c7558e9e14d9f90c0507a0766933ed5daaa..bf1a3866356d84db21819df5fa63218a41575b58 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -5,7 +5,8 @@ from promod3 import sidechain
prot = io.LoadPDB('data/1CRN.pdb')
# load rotamer library
library = sidechain.LoadDunbrackLib()
-# we need a rotamer constructor to create any rotamers or frame residues
+# we need a rotamer constructor to create any rotamers or
+# frame residues
rot_constructor = sidechain.SCWRLRotamerConstructor()
# create new entity from protein only containing the amino acids
diff --git a/sidechain/doc/CMakeLists.txt b/sidechain/doc/CMakeLists.txt
index 451e23076d3dd70b2ac3c895636bccc053da930f..b38d2f0a696ad677f23cc4361c77cf83ce9cfe90 100644
--- a/sidechain/doc/CMakeLists.txt
+++ b/sidechain/doc/CMakeLists.txt
@@ -5,7 +5,7 @@ rotamer.rst
rotamer_id.rst
frame.rst
rotamer_lib.rst
-sidechain_settings.rst
+rotamer_constructor.rst
graph.rst
disulfid.rst
loading.rst
diff --git a/sidechain/doc/frame.rst b/sidechain/doc/frame.rst
index d392553cd4cba2ef8dda3e9620cc2f9c0d1be59b..f72d44585d5d0add22d404eae05dcce924eb33aa 100644
--- a/sidechain/doc/frame.rst
+++ b/sidechain/doc/frame.rst
@@ -17,9 +17,6 @@ The Frame Objects
--------------------------------------------------------------------------------
.. class:: FrameResidue(particles, residue_index)
-
- The most simple way of constructing a frame residue is the usage
- of the convenient functions provided by PROMOD3.
:param particles: particles building frame residue
:param residue_index: Interaction energies between the constructed frame
@@ -47,30 +44,12 @@ The Frame Objects
.. class:: Frame(frame_residues)
- The :class:`Frame` object allows to calculate frame energies for rotamers.
- Due to technical reasons, this is only possible if the rotamers are
- part of rotamer groups.
+ The :class:`Frame` object is used as a container for rigid particles, that
+ can be passed to rotamer groups for calculating frame energies.
:param frame_residues: residues building the frame.
:type frame_residues: :class:`list` of :class:`FrameResidue`
- .. method:: SetFrameEnergy(rotamer_group)
-
- Calculates and sets frame energies for all rotamers in the rotamer group.
-
- :param rotamer_group: group of rotamers for energy calculation
-
- :type rotamer_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
-
- .. method:: AddFrameEnergy(rotamer_group)
-
- Calculates and adds frame energies to the already existing frame
- energy values for all rotamers in the rotamer group.
- This is useful if you have several :class:`Frame` objects.
-
- :param rotamer_group: group of rotamers for energy calculation
-
- :type rotamer_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
Convenient functions for constructing frame residues
diff --git a/sidechain/doc/graph.rst b/sidechain/doc/graph.rst
index 965355b4f58358d015dd9b69389ba74de391643b..7e8ae2ef0e7cb029aacc991127a52dccdd0f07c5 100644
--- a/sidechain/doc/graph.rst
+++ b/sidechain/doc/graph.rst
@@ -19,20 +19,13 @@ and finally comes back with a solution.
.. staticmethod:: CreateFromRRMList(rotamer_groups)
- :param rotamer_groups: :class:`RRMRotamerGroup` objects representing the
- possible sidechain conformations for every amino
- acid position.
-
- :type rotamer_groups: :class:`list`
-
-
.. staticmethod:: CreateFromFRMList(rotamer_groups)
- :param rotamer_groups: :class:`FRMRotamerGroup` objects representing the
- possible sidechain conformations for every amino
- acid position.
+ :param rotamer_groups: :class:`RRMRotamerGroup` or :class:`FRMRotamerGroup`
+ objects representing the possible sidechain
+ conformations for every amino acid position.
- :type rotamer_groups: :class:`list`
+ :type rotamer_groups: :class:`list`
.. method:: Prune(epsilon, [e_cut=0.0, consider_all_nodes=False])
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index 62cc9b2d688bafb84e01706bf0ea767cea6bf5a6..a1ba3806d3fff16687944b8a4067be5401680f96 100644
--- a/sidechain/doc/index.rst
+++ b/sidechain/doc/index.rst
@@ -40,7 +40,10 @@ Contents:
rotamer
frame
rotamer_lib
+ rotamer_constructor
graph
- sidechain_settings
disulfid
loading
+
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.
diff --git a/sidechain/doc/loading.rst b/sidechain/doc/loading.rst
index 8f1471906600a90cf1c9fc94bc268c40ee5a600b..b795abc601ad9c617895d86a63316a14623727bf 100644
--- a/sidechain/doc/loading.rst
+++ b/sidechain/doc/loading.rst
@@ -25,8 +25,8 @@ the backbone independent Penultimate library [lovell2000]_ .
Loads the backbone independent Penultimate library. The values for the dihedral
angles are directly extracted from the publication without considering the
- probabilities specifically for helices/sheets. Due to no assigned standard
- deviations, the flexible rotamer model won't work.
+ probabilities specific for helices/sheets. Due to no assigned standard
+ deviations, the flexible rotamer model won't produce meaningful results.
:returns: The requested library
:rtype: :class:`RotamerLib`
@@ -36,7 +36,7 @@ the backbone independent Penultimate library [lovell2000]_ .
Reads a file as it is provided when you get a licence for the 2010 library of
the Dunbrack lab. It can only read the classic version, where all rotamers
- are in a single file. Specific distributions of nonrotameric sidechains also
+ are in a single file. Specific distributions of nonrotameric sidechains
cannot be read.
:param filename: Name of the file
@@ -51,8 +51,6 @@ the backbone independent Penultimate library [lovell2000]_ .
:rtype: :class:`BBDepRotamerLib`
-.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.
-
.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.
.. [lovell2000] Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.
diff --git a/sidechain/doc/rotamer.rst b/sidechain/doc/rotamer.rst
index 3d21bcc74fc1ff859fddbe0110d05c756e904079..2a10c66f1d570c17a7441d0fe891ff26dd279884 100644
--- a/sidechain/doc/rotamer.rst
+++ b/sidechain/doc/rotamer.rst
@@ -3,15 +3,17 @@ Rotamers
.. currentmodule:: promod3.sidechain
-The rotamers in PROMOD3 are heavily based on the definitions from SCWRL4.
-A rotamer is basically a set of :class:`Particle` and exists in two types.
-The :class:`RRMRotamer` and :class:`FRMRotamer`. Pairwise energies between
-rotamer instances get calculated according to the definitions from SCWRL4.
+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,
-PROMOD3 has the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
-Rotamers are not intended to be built from scratch.
-PROMOD3 offers a built-in construction function, directly accessing a
-:class:`BBDepRotamerLib`.
+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:`SCWRLRotamerConstructor`.
+
The Smallest Building Block - The Particle
@@ -114,11 +116,24 @@ Rotamers
--------------------------------------------------------------------------------
-.. class:: RRMRotamer
+.. class:: RRMRotamer(particles, probability, internal_e_prefactor)
The RRMRotamer represents a rotamer of the so called rigid rotamer model.
- The class has no constructor exported to python, the rotamer is expected to
- be constructed with the convenient functions provided by PROMOD3.
+
+ :param particles: List of :class:`Particle` objects
+ :param probability: Probability of rotamers. In case of the SCWRL4
+ energy calculation, this directly controls the
+ internal energy of that rotamer.
+ :param internal_e_prefactor: Factor applied to the internal energy calculated
+ as -log(**probability**/max_probability),
+ where max_probability is the maximum
+ rotamer probability of any rotamer in a
+ particular :class:`RRMRotamerGroup`.
+
+ :type particles: :class:`list`
+ :type probability: :class:`float`
+ :type internal_e_prefactor: :class:`float`
+
.. method:: __getitem__(index)
@@ -139,13 +154,14 @@ Rotamers
.. method:: ApplyOnResidue(res, consider_hydrogens=False, new_res_name="")
- Strips all sidechain atom positions of given residue and reconstructs the
- full sidechain given the positions of the particles in the rotamer.
+ Iterates over every particle and searches for the according atom in
+ **res**. If it's present, the position gets reset to the particle position.
+ If not, a new atom gets added to **res**.
:param res: Residue to be reconstructed
:param consider_hydrogens: Flag, whether polar hydrogens should be added to
- the sidechain
- :param new_res_name: New name of residue. Nothing happens in case of the
+ **res**
+ :param new_res_name: New name of **res**. Nothing happens in case of the
default value ("")
:type res: :class:`ost.mol.ResidueHandle`
@@ -168,26 +184,10 @@ Rotamers
:raises: :exc:`~exceptions.RuntimeError` if *res_idx* is invalid
- .. method:: GetTransformedCopy(transform)
-
- Transforms all particle positions including their lone pair and polar
- directions.
-
- :param transform: Transformation to be applied
-
- :type transform: :class:`ost.geom.Transform`
- :returns: :class:`RRMRotamer` with all particles transformed
-
-
- .. method:: CalculateInternalEnergy(normalization_factor)
-
- Calculates and sets the rotamer internal energy of the form:
- -prefactor*log(probability/normalization_factor)
-
- :param normalization_factor: Normalization factor for internal probability
+ .. method:: GetInternalEnergyPrefactor()
- :type normalization_factor: :class:`float`
+ :returns: Prefactor used in internal energy calculation
.. method:: GetInternalEnergy()
@@ -195,15 +195,11 @@ Rotamers
:returns: Internal Energy if calculated, 0.0 otherwise
- .. method:: GetInternalEnergyPrefactor()
-
- :returns: Prefactor used in internal energy calculation
-
-
.. method:: GetFrameEnergy()
- Returns previously calculated frame energy, this energy has to be calculated
- using a :class:`Frame`.
+ Returns frame energy. This energy can either be manually set or calculated
+ using a :class:`Frame` and the :class:`RRMRotamerGroup` this rotamer
+ belongs to.
:returns: Frame energy if calculated, 0.0 otherwise
@@ -218,16 +214,16 @@ Rotamers
:returns: probability of this rotamer
- .. method:: SetInternalEnergy(energy)
+ .. method:: SetInternalEnergyPrefactor(prefactor)
- :param energy: Internal energy to be set
+ :param energy: Internal energy prefactor to be set
:type energy: :class:`float`
- .. method:: SetInternalEnergyPrefactor(prefactor)
+ .. method:: SetInternalEnergy(energy)
- :param energy: Internal energy prefactor to be set
+ :param energy: Internal energy to be set
:type energy: :class:`float`
@@ -239,6 +235,13 @@ Rotamers
:type energy: :class:`float`
+ .. method:: AddFrameEnergy(energy)
+
+ :param energy: Frame energy to be added
+
+ :type energy: :class:`float`
+
+
.. method:: SetProbability(probability)
:param energy: Internal probability to be set
@@ -247,14 +250,31 @@ Rotamers
-.. class:: FRMRotamer
+.. class:: FRMRotamer(particles, T, probability, internal_e_prefactor)
- The FRMRotamer represents a rotamer of the so called flexible rotamer model.
- The class has no constructor exported to python, the rotamer is expected to
- be constructed with the convenient functions provided by PROMOD3.
- The flexible rotamer contains several so called subrotamers. The internal data
- layout is a list of particles and a list of subrotamer definitions in form
- of particle indices.
+ The FRMRotamer represents a rotamer of the so called flexible rotamer model,
+ where one rotamer gets represented by several subrotamers.
+ The idea is, that all particles of all subrotamers are given at
+ initialization. Subrotamers are then defined by providing lists of indices.
+ One particle can be part of several subrotamers.
+
+ :param particles: List of :class:`Particle` objects
+ :param probability: Probability of rotamers. In case of the SCWRL4
+ energy calculation, this directly controls the
+ internal energy of that rotamer.
+ :param T: Temperature factor, that is used to generate a final
+ energy given the subrotamers according to the formalism
+ described in the SCWRL4 paper.
+ :param internal_e_prefactor: Factor applied to the internal energy calculated
+ as -log(**probability**/max_probability),
+ where max_probability is the maximum
+ rotamer probability of any rotamer in a
+ particular :class:`FRMRotamerGroup`.
+
+ :type particles: :class:`list`
+ :type probability: :class:`float`
+ :type T: :class:`float`
+ :type internal_e_prefactor: :class:`float`
.. method:: __getitem__(index)
@@ -279,35 +299,11 @@ Rotamers
:returns: Number of subrotamers
-
- .. method:: GetSubrotamerDefinition(index)
-
- :param index: Index of subrotamer
-
- :type index: :class:`int`
-
- :returns: :class:`list` of particle indices belonging to this
- particular subrotamer
-
- :raises: :exc:`~exceptions.RuntimeError` if index is invalid
-
-
- .. method:: GetSubrotamerAssociations(index)
-
- :param index: Index of particle
-
- :type index: :class:`int`
-
- :returns: :class:`list` of subrotamer indices this particle is
- associated with
-
- :raises: :exc:`~exceptions.RuntimeError` if index is invalid
-
-
.. method:: ApplyOnResidue(res, consider_hydrogens=False, new_res_name="")
- Strips all sidechain atom positions of given residue and reconstructs the
- full sidechain given the positions of the particles in the rotamer.
+ Iterates over every particle of the first subrotamer and searches for the
+ according atom in **res**. If it's present, the position gets reset to the
+ particle position. If not, a new atom gets added to **res**.
:param res: Residue to be reconstructed
:param consider_hydrogens: Flag, whether polar hydrogens should be added to
@@ -335,51 +331,37 @@ Rotamers
:raises: :exc:`~exceptions.RuntimeError` if *res_idx* is invalid
+ .. method:: GetSubrotamerDefinition(index)
- .. method:: GetTransformedCopy(transform)
-
- Transforms all particle positions including their lone pair and polar
- directions.
-
- :param transform: Transformation to be applied
-
- :type transform: :class:`ost.geom.Transform`
+ :param index: Index of subrotamer
- :returns: :class:`FRMRotamer` with all particles transformed
+ :type index: :class:`int`
+ :returns: :class:`list` of particle indices belonging to this
+ particular subrotamer
- .. method:: CalculateInternalEnergy(normalization_factor)
-
- Calculates and sets the rotamer internal energy of the form:
- -prefactor*log(probability/normalization_factor)
+ :raises: :exc:`~exceptions.RuntimeError` if index is invalid
- :param normalization_factor: Normalization factor for internal probability
- :type normalization_factor: :class:`float`
+ .. method:: GetInternalEnergyPrefactor()
+ :returns: Prefactor used in internal energy calculation
.. method:: GetInternalEnergy()
:returns: Internal Energy if calculated, 0.0 otherwise
-
- .. method:: GetInternalEnergyPrefactor()
-
- :returns: Prefactor used in internal energy calculation
-
-
.. method:: GetFrameEnergy()
- Returns previously calculated frame energy of the full FRMRotamer, this
- energy has to be calculated using a :class:`Frame`.
+ Returns frame energy. This energy can either be manually set or calculated
+ using a :class:`Frame` and the :class:`FRMRotamerGroup` this rotamer
+ belongs to.
:returns: Frame energy if calculated, 0.0 otherwise
-
.. method:: GetFrameEnergy(index)
- Returns previously calculated frame energy of the subrotamer specified by
- *index*, this energy has to be calculated using a :class:`Frame`.
+ Returns frame energy of specified **index**.
:param index: Index of subrotamer you want the frame energy from
@@ -405,35 +387,56 @@ Rotamers
:returns: Probability of this rotamer
- .. method:: SetInternalEnergy(energy)
+ .. method:: SetInternalEnergyPrefactor(prefactor)
- :param energy: Internal energy to be set
+ :param energy: Internal energy prefactor to be set
:type energy: :class:`float`
- .. method:: SetInternalEnergyPrefactor(prefactor)
+ .. method:: SetInternalEnergy(energy)
- :param energy: Internal energy prefactor to be set
+ :param energy: Internal energy to be set
:type energy: :class:`float`
.. method:: SetFrameEnergy(energy)
- :param energy: Frame energy for full rotamer to be set to be set
+ :param energy: Frame energy for full rotamer to be set
:type energy: :class:`float`
.. method:: SetFrameEnergy(energy, index)
- :param energy: Frame energy for single subrotamer to be set to be set
+ :param energy: Frame energy for single subrotamer to be set
+ :param index: Index of subrotamer
+
+ :type energy: :class:`float`
+ :type index: :class:
+
+ .. method:: AddFrameEnergy(energy)
+
+ :param energy: Frame energy for full rotamer to be added
+
+ :type energy: :class:`float`
+
+
+ .. method:: AddFrameEnergy(energy, index)
+
+ :param energy: Frame energy for single subrotamer to be added
:param index: Index of subrotamer
:type energy: :class:`float`
:type index: :class:
+ .. method:: AddSubrotamerDefinition(indices)
+
+ :param indices: List of indices defining a subrotamer
+
+ :type indices: :class:`list`
+
.. method:: SetTemperature(temperature)
@@ -453,15 +456,19 @@ Rotamer Groups
--------------------------------------------------------------------------------
-.. class:: RRMRotamerGroup(rotamers)
+.. class:: RRMRotamerGroup(rotamers, residue_index)
The RRMRotamerGroup groups several :class:`RRMRotamer` objects for the same
- residue position. It can either be constructed by providing a list of
- :class:`RRMRotamer` objects or by convenience functions provided by PROMOD3.
+ residue position.
:param rotamers: A list of :class:`RRMRotamer` objects
+ :param residue_index: Location of residue this :class:`FRMRotamerGroup`
+ represents. This index is important when calculating
+ frame energies to neglect the interactions to frame
+ particles of the same residue.
:type rotamers: :class:`list`
+ :type residue_index: :class:`int`
:raises: :exc:`~exceptions.RuntimeError` if provided *rotamers* is empty
@@ -512,10 +519,21 @@ Rotamer Groups
:type other: :class:`RRMRotamerGroup`
+ .. method:: SetFrameEnergy(frame)
+
+ Calculates sets the energy of all rotamers in the group towards the
+ given **frame**.
+
+ :param frame: Frame containing rigid particles
+ :type frame: :class:`Frame`
- .. method:: CalculateInternalEnergies()
+ .. method:: AddFrameEnergy(frame)
- Calculates internal energies of all rotamers in group
+ Calculates adds the energy of all rotamers in the group towards the
+ given **frame**.
+
+ :param frame: Frame containing rigid particles
+ :type frame: :class:`Frame`
.. method:: ApplySelfEnergyThresh(thresh=30)
@@ -523,15 +541,19 @@ Rotamer Groups
rotamers with *self_energy* > *l_e* + *thresh*
-.. class:: FRMRotamerGroup(rotamers)
+.. class:: FRMRotamerGroup(rotamers, residue_index)
The FRMRotamerGroup groups several :class:`FRMRotamer` objects for the same
- residue position. It can either be constructed by providing a list of
- :class:`FRMRotamer` objects or by convenience functions provided by PROMOD3.
+ residue position.
:param rotamers: A list of :class:`FRMRotamer` objects
+ :param residue_index: Location of residue this :class:`FRMRotamerGroup`
+ represents. This index is important when calculating
+ frame energies to neglect the interactions to frame
+ particles of the same residue.
:type rotamers: :class:`list`
+ :type residue_index: :class:`int`
:raises: :exc:`~exceptions.RuntimeError` if provided *rotamers* is empty
@@ -582,238 +604,23 @@ Rotamer Groups
:type other: :class:`FRMRotamerGroup`
+ .. method:: SetFrameEnergy(frame)
- .. method:: CalculateInternalEnergies()
-
- Calculates internal energies of all rotamers in group
-
- .. method:: ApplySelfEnergyThresh(thresh=30)
-
- Searches rotamer with lowest self energy *l_e* and deletes all
- rotamers with *self_energy* > *l_e* + *thresh*
+ Calculates sets the energy of all rotamers in the group towards the
+ given **frame**.
+ :param frame: Frame containing rigid particles
+ :type frame: :class:`Frame`
+ .. method:: AddFrameEnergy(frame)
+ Calculates adds the energy of all rotamers in the group towards the
+ given **frame**.
+ :param frame: Frame containing rigid particles
+ :type frame: :class:`Frame`
+ .. method:: ApplySelfEnergyThresh(thresh=30)
-
-
-Convenient functions for constructing rotamers
---------------------------------------------------------------------------------
-
-For convenience, |project| offers some functionality to directly build single
-rotamers or groups (see :ref:`below <rotamer_group_construction_label>`).
-
-.. method:: ConstructRRMRotamer(n_pos, ca_pos, cb_pos, rotamer_id, settings, \
- probability, chi1=NaN, chi2=NaN, chi3=NaN, \
- chi4=NaN)
- ConstructRRMRotamer(residue, rotamer_id, settings, probability, \
- chi1=NaN, chi2=NaN, chi3=NaN, chi4=NaN)
-
- :param n_pos: Position of nitrogen used as anchor for the rotamer
- :param ca_pos: Position of alpha carbon used as anchor for the rotamer
- :param cb_pos: Position of beta carbon used as anchor for the rotamer
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of :class:`RRMRotamer`
- :param settings: Settings to control parametrization of the single
- particles.
- :param probability: Probability of occurence of this particular rotamer.
- :param chi1: First sidechain dihedral angle
- :param chi2: Second sidechain dihedral angle
- :param chi3: Third sidechain dihedral angle
- :param chi4: Fourth sidechain dihedral angle
-
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type residue: :class:`ost.mol.ResideHandle`
- :type rotamer_id: :class:`RotamerID`
- :type settings: :class:`RotamerSettings`
- :type probability: :class:`float`
- :type chi1: :class:`float`
- :type chi2: :class:`float`
- :type chi3: :class:`float`
- :type chi4: :class:`float`
-
- :returns: :class:`RRMRotamer`
-
- :raises: :exc:`~exceptions.RuntimeError` if not all required chi angles
- for this particular *id* are given or when not all required
- anchor atoms are present in *residue*.
-
-
-.. method:: ConstructFRMRotamer(n_pos, ca_pos, cb_pos, rotamer_id, settings, \
- probability, chi1=NaN, sig1=NaN, chi2=NaN, \
- sig2=NaN, chi3=NaN, sig3=NaN, chi4=NaN, \
- sig4=NaN)
- ConstructFRMRotamer(residue, rotamer_id, settings, probability, \
- chi1=NaN, sig1=NaN, chi2=NaN, sig2=NaN, \
- chi3=NaN, sig3=NaN, chi4=NaN, sig4=NaN)
-
- :param n_pos: Position of nitrogen used as anchor for the rotamer
- :param ca_pos: Position of alpha carbon used as anchor for the rotamer
- :param cb_pos: Position of beta carbon used as anchor for the rotamer
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of :class:`FRMRotamer`
- :param settings: Settings to control parametrization of the single
- particles.
- :param probability: Probability of occurence of this particular rotamer.
- :param chi1: First sidechain dihedral angle
- :param sig1: Standard deviation of first dihedral angle
- :param chi2: Second sidechain dihedral angle
- :param sig2: Standard deviation of second dihedral angle
- :param chi3: Third sidechain dihedral angle
- :param sig3: Standard deviation of third dihedral angle
- :param chi4: Fourth sidechain dihedral angle
- :param sig4: Standard deviation of fourth dihedral angle
-
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type residue: :class:`ost.mol.ResideHandle`
- :type rotamer_id: :class:`RotamerID`
- :type settings: :class:`RotamerSettings`
- :type probability: :class:`float`
- :type chi1: :class:`float`
- :type sig1: :class:`float`
- :type chi2: :class:`float`
- :type sig2: :class:`float`
- :type chi3: :class:`float`
- :type sig3: :class:`float`
- :type chi4: :class:`float`
- :type sig4: :class:`float`
-
- :returns: :class:`FRMRotamer`
-
- :raises: :exc:`~exceptions.RuntimeError` if not all required chi angles
- or standard deviations for this particular *id* are given or when
- not all required anchor atoms are present in *residue*.
-
-
-Convenient functions for constructing rotamer groups
---------------------------------------------------------------------------------
-
-Instead of building single rotamers, following convenient functions query a
-rotamer library and build all possible rotamers for a particular residue
-position. If hbond scoring is enabled and *sample_polar_hydrogens* is true (in
-*settings*), several rotamers might be constructed and added to the group per
-library instance:
-
-#. SER construct three rotamers with hydrogen chi angles 180, -60 and 60
-#. THR construct three rotamers with hydrogen chi angles 180, -60 and 60
-#. TYR construct two rotamers with hydrogen chi angles 180 and 0
-#. HIS construct both possible protonation states (HSE,HSD)
-
-.. _rotamer_group_construction_label:
-
-.. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, rotamer_id, \
- residue_index, bbdep_rot_lib, settings, \
- phi=-1.0472, psi=-0.7854)
- ConstructRRMRotamerGroup(residue, rotamer_id, residue_index, \
- bbdep_rot_lib, settings, phi=-1.0472, \
- psi=-0.7854)
- ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, rotamer_id, \
- residue_index, rot_lib, settings)
- ConstructRRMRotamerGroup(residue, rotamer_id, residue_index, \
- rot_lib, settings)
-
- Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
- from a rotamer library and adds them to the group until the summed probability
- reaches the probability cutoff defined in *settings*.
-
- :param n_pos: Position of nitrogen used as anchor for the rotamers
- :param ca_pos: Position of alpha carbon used as anchor for the rotamers
- :param cb_pos: Position of beta carbon used as anchor for the rotamers
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of of the constructed rotamers
- :param residue_index: Index of rotamer in constructed rotamer group. This
- matters for calculating the frame energy. Interactions
- to frame residues with same index get neglected.
- :param bbdep_rot_lib: Backbone dependent rotamer library from which the data
- is taken to construct the rotamers.
- :param rot_lib: Non-backbone-dependent rotamer library from which the
- data is taken to construct the rotamers.
- :param settings: Settings to control parametrization of the single
- particles.
- :param phi: Phi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :param psi: Psi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
-
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type residue: :class:`ost.mol.ResideHandle`
- :type rotamer_id: :class:`RotamerID`
- :type residue_index: :class:`int`
- :type bbdep_rot_lib: :class:`BBDepRotamerLib`
- :type rot_lib: :class:`RotamerLib`
- :type settings: :class:`RotamerSettings`
- :type phi: :class:`float`
- :type psi: :class:`float`
-
- :returns: :class:`RRMRotamerGroup`
-
- :raises: :exc:`~exceptions.RuntimeError` if not all required anchor atoms
- are present in *residue*.
-
-
-.. method:: ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos, rotamer_id, \
- residue_index, bbdep_rot_lib, settings, \
- phi=-1.0472, psi=-0.7854)
- ConstructFRMRotamerGroup(residue, rotamer_id, residue_index, \
- bbdep_rot_lib, settings, phi=-1.0472, \
- psi=-0.7854)
- ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos, rotamer_id, \
- residue_index, rot_lib, settings)
- ConstructFRMRotamerGroup(residue, rotamer_id, residue_index, \
- rot_lib, settings)
-
- Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
- from a rotamer library and adds them to the group until the summed probability
- reaches the probability cutoff defined in *settings*.
-
- :param n_pos: Position of nitrogen used as anchor for the rotamers
- :param ca_pos: Position of alpha carbon used as anchor for the rotamers
- :param cb_pos: Position of beta carbon used as anchor for the rotamers
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of of the constructed rotamers
- :param residue_index: Index of rotamer in constructed rotamer group. This
- matters for calculating the frame energy. Interactions
- to frame residues with same index get neglected.
- :param bbdep_rot_lib: Backbone dependent rotamer library from which the data
- is taken to construct the rotamers.
- :param rot_lib: Non-backbone-dependent rotamer library from which the
- data is taken to construct the rotamers.
- :param settings: Settings to control parametrization of the single
- particles.
- :param phi: Phi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :param psi: Psi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
-
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type residue: :class:`ost.mol.ResideHandle`
- :type rotamer_id: :class:`RotamerID`
- :type residue_index: :class:`int`
- :type bbdep_rot_lib: :class:`BBDepRotamerLib`
- :type rot_lib: :class:`RotamerLib`
- :type settings: :class:`RotamerSettings`
- :type phi: :class:`float`
- :type psi: :class:`float`
-
- :returns: :class:`FRMRotamerGroup`
-
- :raises: :exc:`~exceptions.RuntimeError` if not all required anchor atoms
- are present in *residue*.
\ No newline at end of file
+ Searches rotamer with lowest self energy *l_e* and deletes all
+ rotamers with *self_energy* > *l_e* + *thresh*
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
new file mode 100644
index 0000000000000000000000000000000000000000..08032435ae0bf530c1f4695ffb919f6b027c9d19
--- /dev/null
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -0,0 +1,203 @@
+Rotamer Constructor
+================================================================================
+
+.. currentmodule:: promod3.sidechain
+
+Instead of creating rotamers by yourself, you can simply use the convenient
+functionality provided by PROMOD3
+
+
+Constructing Rotamers and Frame Residues
+--------------------------------------------------------------------------------
+
+
+.. class:: SCWRLRotamerConstructor()
+
+ Constructing rotamers and frame residues that are parametrized according to
+ the SCWRL4 method. They contain all heavy atoms, but also the
+ polar hydrogens. The rotamers start after the CB atom (typically CG).
+ In case of the :class:`FrameResidue` construction, the
+ constructor distinguishes between backbone and sidechain frame residues.
+
+ .. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
+ [probability_cutoff = 0.98])
+ .. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
+ residue_index, rot_lib,\
+ [probability_cutoff = 0.98])
+ .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
+ residue_index, rot_lib,\
+ [probability_cutoff = 0.98])
+ .. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
+ [phi = -1.0472, psi = -0.7854,\
+ probability_cutoff = 0.98])
+ .. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
+ residue_index, rot_lib,\
+ [phi = -1.0472, psi = -0.7854,\
+ probability_cutoff = 0.98])
+ .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
+ residue_index, rot_lib,\
+ [phi = -1.0472, psi = -0.7854,\
+ probability_cutoff = 0.98])
+
+ All functions are also avaible for their flexible rotamer model counterpart.
+ =>ConstructFRMRotamerGroup(...) with exactly the same parameters.
+
+ :param res: To extract the N, CA, CB backbone anchor
+ :param all_atom_pos: To extract the N, CA, CB backbone anchor
+ :param aa_res_idx: Index of residue in **all_atom_pos** from which to
+ extract the backbone anchor
+ :param n_pos: To directly feed in the backbone anchor positions
+ :param ca_pos: To directly feed in the backbone anchor positions
+ :param cb_pos: To directly feed in the backbone anchor positions
+ :param id: Identifies the sidechain.
+ :param residue_index: Important for the energy calculations towards the
+ :class:`Frame` you don't want to calculate a pairwise
+ energy of the sidechain particles towards particles
+ representing the own backbone...
+ :param rot_lib: To search for rotamers
+ :param phi: Phi dihedral angle used to search for rotamers if a
+ :class:`BBDepRotamerLib` is given as input
+ :param psi: Psi dihedral angle used to search for rotamers if a
+ :class:`BBDepRotamerLib` is given as input
+ :param probability_cutoff: For some rotamers, there might be many low
+ probability entries in the library.
+ The function adds single rotamers to the group until
+ the cumulative probability of the added rotamers is
+ larger or equal **probability_cutoff**.
+
+ :returns: The rotamer group containing all constructed rotamers
+ with internal energies assigned based on the
+ probabilities extracted from the rotamer library.
+
+ :type res: :class:`ost.mol.ResidueHandle`
+ :type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
+ :type aa_res_idx: :class:`int`
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`RotamerLib` / :class:`BBDepRotamerLib`
+ :type probability_cutoff: :class:`float`
+ :rtype: :class:`RRMRotamerGroup`
+
+ :raises: :exc:`~exceptions.RuntimeError` when not all required backbone
+ atoms are present in **residue**, not all required atom
+ positions are set in **all_atom_pos** or when the rotamer library
+ does not contain any entries for **id**
+
+
+ .. method:: ConstructBackboneFrameResidue(res, id, residue_index, Real phi,\
+ [n_ter = False, c_ter = False])
+
+ .. method:: ConstructBackboneFrameResidue(all_atom_pos, aa_res_idx, id,\
+ residue_index, Real phi,\
+ [n_ter = False, c_ter = False])
+
+ .. method:: ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos, o_pos, cb_pos,\
+ id, residue_index, Real phi,\
+ [n_ter = False, c_ter = False])
+
+ Constructs backbone frame residues for amino acid residues. It extracts
+ the n, ca, c, o and cb positions and constructs a frame residue based on
+ the parametrizations of SCWRL4. In case of **n_ter**, there are additional
+ hydrogens added at the nitrogen to represent a proper n-terminus. The same
+ is true for **c_ter**, an additional oxygen is built instead. In any case,
+ a single hydrogen is added to the nitrogen (except proline), this is
+ why the phi angle of the residue is required as an input.
+
+ :param res: Residue from which to extract the backbone positions
+ :param all_atom_pos: To extract the backbone positions
+ :param aa_res_idx: Index of residue in **all_atom_pos** from which to
+ extract the backbone positions
+ :param n_pos: To directly feed in the backbone positions
+ :param ca_pos: To directly feed in the backbone positions
+ :param c_pos: To directly feed in the backbone positions
+ :param o_pos: To directly feed in the backbone positions
+ :param cb_pos: To directly feed in the backbone positions
+ :param id: Identifies the sidechain
+ :param residue_index: Important for the energy calculations towards the
+ :class:`Frame` you don't want to calculate a pairwise
+ energy of the sidechain particles towards particles
+ representing the own backbone...
+ :param phi: The dihedral angle of the current residue, required to
+ construct the polar nitrogen hydrogen
+ :param n_ter: Whether to add additional hydrogens at the nitrogen
+ to represent a proper n-terminus
+ :param c_ter: Whether to add an additional oxygen at the carbon to
+ represent a proper c-terminus
+
+ :type res: :class:`ost.mol.ResidueHandle`
+ :type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
+ :type aa_res_idx: :class:`int`
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type c_pos: :class:`ost.geom.Vec3`
+ :type o_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+ :rtype: :class:`FrameResidue`
+
+
+ :raises: :exc:`~exceptions.RuntimeError` when not all required backbone
+ atoms are present in **residue**, not all required atom
+ positions are set in **all_atom_pos**.
+
+
+ .. method:: ConstructSidechainFrameResidue(res, id, residue_index)
+
+ .. method:: ConstructSidechainFrameResidue(all_atom, aa_res_idx, id,\
+ residue_index)
+
+ Extracts all required positions from the input and generates a sidechain
+ frame residue. Additionally to the heavy atoms, the function also produces
+ particles for all polar hydrogens.
+
+ :param res: Residue from which to extract the sidechain positions
+ :param all_atom_pos: To extract the sidechain positions
+ :param aa_res_idx: Index of residue in **all_atom_pos** from which to
+ extract the sidechain positions
+ :param id: Identifies the sidechain
+ :param residue_index: idenfifies residue in frame
+
+ :type res: :class:`ost.mol.ResidueHandle`
+ :type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
+ :type aa_res_idx: :class:`int`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+
+ :rtype: :class:`FrameResidue`
+
+
+ :raises: :exc:`~exceptions.RuntimeError` when not all required sidechain
+ atoms are present in **residue** or not all required sidechain
+ atom positions are set in **all_atom_pos**.
+
+
+ .. method:: AssignInternalEnergies(rot_group)
+
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by 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.
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/sidechain/doc/sidechain_settings.rst b/sidechain/doc/sidechain_settings.rst
deleted file mode 100644
index 5652f945b9b321b969605f019e29bfd94bd8159d..0000000000000000000000000000000000000000
--- a/sidechain/doc/sidechain_settings.rst
+++ /dev/null
@@ -1,193 +0,0 @@
-Rotamer Settings
-================================================================================
-
-.. currentmodule:: promod3.sidechain
-
-The rotamer settings control the sidechain modelling algorithms at different
-stages. Most of the parameters that can be set are related to the flexible
-rotamer model (temperature factor and delta factors to control the
-variability of the subrotamers in the flexible rotamer model)
-or the internal energy prefactor used for the different amino
-acids. Other parameters include the radius influencing the pseudo Lennard
-Jones term for the different atom types and the max interaction radius.
-The max interaction radius is more a technical thing and is used by a
-collision detection algorithm to define the collision distance, i.e.
-two particles with max radii a,b collide/interact if the distance between
-them is smaller than a+b. The last three parameters control the buildup of the
-rotamers. It is possible to deactivate the hbond term, resulting in
-no hydrogens being constructed. The sampling of polar hydrogens can also
-be controlled resulting in several rotamers per rotamer lib entry for
-Ser,Thr and Tyr when using the convenient functions for constructing full
-rotamer groups of them (see :ref:`here <rotamer_group_construction_label>`).
-Constructing the rotamer groups can further be controlled by assigning a max
-summed probability resulting in less very unlikely rotamers added to the
-rotamer group (see :ref:`here <rotamer_group_construction_label>`).
-
-.. class:: RotamerSettings
-
- .. attribute:: FRM_T_ARG default: 1.23
-
- .. attribute:: FRM_T_ASN default: 1.41
-
- .. attribute:: FRM_T_ASP default: 1.48
-
- .. attribute:: FRM_T_GLN default: 1.32
-
- .. attribute:: FRM_T_GLU default: 0.94
-
- .. attribute:: FRM_T_LYS default: 1.27
-
- .. attribute:: FRM_T_SER default: 3.53
-
- .. attribute:: FRM_T_CYS default: 1.69
-
- .. attribute:: FRM_T_MET default: 1.77
-
- .. attribute:: FRM_T_TRP default: 0.99
-
- .. attribute:: FRM_T_TYR default: 1.96
-
- .. attribute:: FRM_T_THR default: 1.11
-
- .. attribute:: FRM_T_VAL default: 2.20
-
- .. attribute:: FRM_T_ILE default: 2.03
-
- .. attribute:: FRM_T_LEU default: 2.55
-
- .. attribute:: FRM_T_PRO default: 2.62
-
- .. attribute:: FRM_T_HIS default: 1.35
-
- .. attribute:: FRM_T_PHE default: 1.07
-
- .. attribute:: FRM_delta1_ARG default: 0.87
-
- .. attribute:: FRM_delta2_ARG default: 1.62
-
- .. attribute:: FRM_delta3_ARG default: 1.67
-
- .. attribute:: FRM_delta4_ARG default: 0.78
-
- .. attribute:: FRM_delta1_ASN default: 0.62
-
- .. attribute:: FRM_delta2_ASN default: 1.93
-
- .. attribute:: FRM_delta1_ASP default: 1.59
-
- .. attribute:: FRM_delta2_ASP default: 0.63
-
- .. attribute:: FRM_delta1_GLN default: 1.55
-
- .. attribute:: FRM_delta2_GLN default: 0.68
-
- .. attribute:: FRM_delta3_GLN default: 1.88
-
- .. attribute:: FRM_delta1_GLU default: 0.82
-
- .. attribute:: FRM_delta2_GLU default: 1.57
-
- .. attribute:: FRM_delta3_GLU default: 0.78
-
- .. attribute:: FRM_delta1_LYS default: 1.62
-
- .. attribute:: FRM_delta2_LYS default: 0.99
-
- .. attribute:: FRM_delta3_LYS default: 0.96
-
- .. attribute:: FRM_delta4_LYS default: 1.48
-
- .. attribute:: FRM_delta1_SER default: 0.65
-
- .. attribute:: FRM_delta2_SER default: 2.98
-
- .. attribute:: FRM_delta1_CYS default: 1.69
-
- .. attribute:: FRM_delta1_MET default: 0.97
-
- .. attribute:: FRM_delta2_MET default: 1.54
-
- .. attribute:: FRM_delta3_MET default: 1.21
-
- .. attribute:: FRM_delta1_TRP default: 1.28
-
- .. attribute:: FRM_delta2_TRP default: 1.48
-
- .. attribute:: FRM_delta1_TYR default: 1.48
-
- .. attribute:: FRM_delta2_TYR default: 0.73
-
- .. attribute:: FRM_delta3_TYR default: 0.96
-
- .. attribute:: FRM_delta1_THR default: 0.88
-
- .. attribute:: FRM_delta2_THR default: 0.88
-
- .. attribute:: FRM_delta1_VAL default: 2.08
-
- .. attribute:: FRM_delta1_ILE default: 1.23
-
- .. attribute:: FRM_delta2_ILE default: 0.98
-
- .. attribute:: FRM_delta1_LEU default: 1.15
-
- .. attribute:: FRM_delta2_LEU default: 1.48
-
- .. attribute:: FRM_delta1_PRO default: 0.78
-
- .. attribute:: FRM_delta2_PRO default: 1.27
-
- .. attribute:: FRM_delta1_HIS default: 1.84
-
- .. attribute:: FRM_delta2_HIS default: 0.85
-
- .. attribute:: FRM_delta1_PHE default: 1.45
-
- .. attribute:: FRM_delta2_PHE default: 1.35
-
- .. attribute:: internal_e_prefactor_ARG default: 2.27
-
- .. attribute:: internal_e_prefactor_ASN default: 1.80
-
- .. attribute:: internal_e_prefactor_ASP default: 2.44
-
- .. attribute:: internal_e_prefactor_GLN default: 1.61
-
- .. attribute:: internal_e_prefactor_GLU default: 1.85
-
- .. attribute:: internal_e_prefactor_LYS default: 2.13
-
- .. attribute:: internal_e_prefactor_SER default: 2.78
-
- .. attribute:: internal_e_prefactor_CYS default: 4.07
-
- .. attribute:: internal_e_prefactor_MET default: 1.95
-
- .. attribute:: internal_e_prefactor_TRP default: 3.24
-
- .. attribute:: internal_e_prefactor_TYR default: 2.00
-
- .. attribute:: internal_e_prefactor_THR default: 2.96
-
- .. attribute:: internal_e_prefactor_VAL default: 1.62
-
- .. attribute:: internal_e_prefactor_ILE default: 2.18
-
- .. attribute:: internal_e_prefactor_LEU default: 2.25
-
- .. attribute:: internal_e_prefactor_PRO default: 0.76
-
- .. attribute:: internal_e_prefactor_HIS default: 2.01
-
- .. attribute:: internal_e_prefactor_PHE default: 1.71
-
- .. attribute:: probability_cutoff default: 0.98
-
- .. attribute:: consider_hbonds default: True
-
- .. attribute:: sample_polar_hydrogens default: True
-
-
-
-
-
diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index d402500c1f650893e0c4ce4ed8345a335b7cead4..3afeada1ee3cb3f4b0a3561aee875379cbc66718 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -377,7 +377,7 @@ def _GetDisulfidBridges(frame_residues, cystein_indices, res_list, rotamer_libra
def Reconstruct(ent, keep_sidechains=False, build_disulfids=True,
rotamer_model="frm", consider_ligands=True,
- rotamer_library=None, rotamer_constructor=None):
+ rotamer_library=None):
'''Reconstruct sidechains for the given structure.
:param ent: Structure for sidechain reconstruction. Note, that the
@@ -431,8 +431,8 @@ def Reconstruct(ent, keep_sidechains=False, build_disulfids=True,
bbdep = False
if type(rotamer_library) is sidechain.BBDepRotamerLib:
bbdep = True
- if rotamer_constructor == None:
- rotamer_constructor = sidechain.SCWRLRotamerConstructor()
+
+ rotamer_constructor = sidechain.SCWRLRotamerConstructor()
# take out ligand chain and any non-peptides
prot = ent.Select("peptide=true and cname!='_'")