diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 829d32eb7bd1bb74204f85c716cfa6872bca42c3..0da8fe4a2c491f49301cd64888dad01412516d0c 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -240,7 +240,7 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Make alignment based on residue number instead of using\n"
- "Clustal."))
+ "a global BLOSUM62-based alignment."))
#
# lDDT options
#
diff --git a/modules/mol/alg/doc/lddt.rst b/modules/mol/alg/doc/lddt.rst
index 48a9493c9fe8e8e3b1d1799da5149c784657ce74..3201243bdaa59551cc73e543e16100c161bfb5f4 100644
--- a/modules/mol/alg/doc/lddt.rst
+++ b/modules/mol/alg/doc/lddt.rst
@@ -136,15 +136,13 @@ for bonds and angles respectively.
For steric clashes, the lddt executable recovers atomic radii and clashing
tolerance distances from the parameter file, depending on the atomic element under
-investigation. When an atomic element cannot be determined, the lddt executable
-uses a default atomic radius of 1.5 Angstrom. This value can be overriden using
-the -m value, passing a new radius (in Ansgstroms) to the program.
+investigation.
For example:
.. code-block:: bash
- lddt -f -p stereo_chemical_params.txt -b 8 -a 8 -m 1.0 mdl1.pdb ref.pdb
+ lddt -f -p stereo_chemical_params.txt -b 8 -a 8 mdl1.pdb ref.pdb
-----------------------------
@@ -227,8 +225,8 @@ One can replicate the binary using simple python script:
# Prepare residue map from references
rdmap = PreparelDDTGlobalRDMap(references,
cutoffs=cutoffs,
- sequence_separation=0,
- radius=15)
+ sequence_separation=settings.sequence_separation,
+ radius=settings.radius)
#
# This part is optional and it depends on our settings parameter
if structural_checks:
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 7a66937a12af17ad74b8859310849b2aee468aa4..81f3e77643c0eae354f789288741fd2d43de2b94 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -359,9 +359,9 @@ Local Distance Test scores (lDDT, DRMSD)
:class:`~ost.io.StereoChemicalParamsReader` or :func:`FillClashingDistances`
:type nonbonded_table: :class:`~ost.mol.alg.ClashingDistances`
:param bond_tolerance: Tolerance in stddev for bonds
- :type bond_tolerance: float
+ :type bond_tolerance: :class:`float`
:param angle_tolerance: Tolerance in stddev for angles
- :type angle_tolerance: float
+ :type angle_tolerance: :class:`float`
.. function:: GetlDDTPerResidueStats(model, distance_list, structural_checks, label)
@@ -372,8 +372,11 @@ Local Distance Test scores (lDDT, DRMSD)
:type model: :class:`~ost.mol.EntityHandle`
:param distance_list: The list of distances to check for conservation
:type distance_list: :class:`~ost.mol.alg.GlobalRDMap`
- :param structural_checks: Where structural checks performed on the model?
- :type structural_checks: bool
+ :param structural_checks: Were structural checks performed on the model?
+ :type structural_checks: :class:`bool`
+ :param label: Label used for ResidueHandle properties that store the local
+ scores.
+ :type label: :class:`str`
:returns: Per-residue local lDDT scores
:rtype: :class:`list` of :class:`~ost.mol.alg.lDDTLocalScore`
@@ -385,9 +388,9 @@ Local Distance Test scores (lDDT, DRMSD)
:param scores: Local lDDT scores
:type scores: :class:`list` of :class:`~ost.mol.alg.lDDTLocalScore`
:param structural_checks: Where structural checks performed on the model?
- :type structural_checks: bool
+ :type structural_checks: :class:`bool`
:param cutoffs_length: Length of the cutoffs list used to calculate lDDT
- :type cutoffs_length: int
+ :type cutoffs_length: :class:`int`
.. class:: lDDTLocalScore(cname, rname, rnum, is_assessed, quality_problems, \
@@ -1658,8 +1661,10 @@ to standard amino acids.
:type src_res: :class:`~ost.mol.ResidueHandle`
:param dst_res: The destination residue
:type dst_res: :class:`~ost.mol.ResidueHandle`
+ :param editor: Editor used to modify *dst_res*.
+ :type editor: :class:`~ost.mol.XCSEditor`
- :returns: true if the residue could be copied, false if not.
+ :returns: True if the residue could be copied, False if not.
.. function:: CopyConserved(src_res, dst_res, editor)
@@ -1679,8 +1684,10 @@ to standard amino acids.
:type src_res: :class:`~ost.mol.ResidueHandle`
:param dst_res: The destination residue
:type dst_res: :class:`~ost.mol.ResidueHandle`
+ :param editor: Editor used to modify *dst_res*.
+ :type editor: :class:`~ost.mol.XCSEditor`
- :returns: a tuple of bools stating whether the residue could be copied and
+ :returns: A tuple of bools stating whether the residue could be copied and
whether the Cbeta atom was inserted into the ``dst_res``.
.. function:: CopyNonConserved(src_res, dst_res, editor)
@@ -1692,8 +1699,10 @@ to standard amino acids.
:type src_res: :class:`~ost.mol.ResidueHandle`
:param dst_res: The destination residue
:type dst_res: :class:`~ost.mol.ResidueHandle`
+ :param editor: Editor used to modify *dst_res*.
+ :type editor: :class:`~ost.mol.XCSEditor`
- :returns: a tuple of bools stating whether the residue could be copied and
+ :returns: A tuple of bools stating whether the residue could be copied and
whether the Cbeta atom was inserted into the ``dst_res``.
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 5936b0584c5b1c3fb8697bb8151859a0a28b017d..1dfaf6addeb0eca91744505ad34d9efb4a0eb6a2 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -18,7 +18,7 @@ To check one PDB file (struc1.pdb) with Molck, use the following command:
molck --complib <PATH TO COMPOUND LIB> struc1.pdb
-The checked and cleaned file will be saved by default ad struc1-molck.pdb.
+The checked and cleaned file will be saved by default ad struc1-molcked.pdb.
Similarly it is possible to check a list of PDB files:
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index b980c48b23706e7bcb5523bc3a8728e1dfd198a2..e58436de55aae1291d55804051c28c0b0576dce1 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -112,6 +112,7 @@ class QSscorer:
:param ent_2: Second structure to be scored.
:type ent_2: :class:`QSscoreEntity`, :class:`~ost.mol.EntityHandle` or
:class:`~ost.mol.EntityView`
+ :param res_num_alignment: Sets :attr:`res_num_alignment`
:raises: :class:`QSscoreError` if input structures are invalid or are monomers
or have issues that make it impossible for a QS score to be computed.
@@ -141,6 +142,13 @@ class QSscorer:
of symmetries and chain mappings. By default it is set to 100.
:type: :class:`int`
+
+ .. attribute:: res_num_alignment
+
+ Forces each alignment in :attr:`alignments` to be based on residue numbers
+ instead of using a global BLOSUM62-based alignment.
+
+ :type: :class:`bool`
"""
def __init__(self, ent_1, ent_2, res_num_alignment=False):
# generate QSscoreEntity objects?
@@ -374,6 +382,11 @@ class QSscorer:
mapped chain names and have views attached into :attr:`QSscoreEntity.ent`
of :attr:`qs_ent_1` and :attr:`qs_ent_2`.
+ If :attr:`res_num_alignment` is False, each alignment is performed using a
+ global BLOSUM62-based alignment. Otherwise, the positions in the alignment
+ sequences are simply given by the residue number so that residues with
+ matching numbers are aligned.
+
:getter: Computed on first use (cached)
:type: :class:`list` of :class:`~ost.seq.AlignmentHandle`
"""
@@ -1386,7 +1399,7 @@ def _AlignAtomSeqs(seq_1, seq_2):
"""
:type seq_1: :class:`ost.seq.SequenceHandle`
:type seq_2: :class:`ost.seq.SequenceHandle`
- :return: Alignment of two sequences using a global aignment. Views attached
+ :return: Alignment of two sequences using a global alignment. Views attached
to the input sequences will remain attached in the aln.
:rtype: :class:`~ost.seq.AlignmentHandle` or None if it failed.
"""
@@ -2588,7 +2601,7 @@ def _AreValidSymmetries(symm_1, symm_2):
return False
return True
-def _GetMappedAlignments(ent_1, ent_2, chain_mapping, res_num_alignment=True):
+def _GetMappedAlignments(ent_1, ent_2, chain_mapping, res_num_alignment):
"""
:return: Alignments of 2 structures given chain mapping
(see :attr:`QSscorer.alignments`).
@@ -2597,6 +2610,7 @@ def _GetMappedAlignments(ent_1, ent_2, chain_mapping, res_num_alignment=True):
:param ent_2: Entity containing all chains in *chain_mapping.values()*.
Views to this entity attached to second sequence of each aln.
:param chain_mapping: See :attr:`QSscorer.chain_mapping`
+ :param res_num_alignment: See :attr:`QSscorer.res_num_alignment`
"""
alns = list()
for ch_1_name in sorted(chain_mapping):