diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 3e0f907ae284424631f868c9d145bae6586f67b9..135c5a6936cfef202bc3a9ffbded2d6d26e91bd5 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -5,9 +5,23 @@ Changes in Release 2.4.0
based, natively supports complexes and is able to score DNA/RNA. The
deprecated lDDT implementation remains for consistency.
* Add algorithms to establish one to one mappings between chains in a reference
- structure and a model.
+ structure and a model. Chain mappings can be derived by optimizing oligomeric
+ lDDT, RMSD or QS-score.
* Substitution matrixes for RNA/DNA to compute alignments: seq.alg.IDENTITY and
- seq.alg.NUC44
+ seq.alg.NUC44.
+ * Add binding to DockQ (https://github.com/bjornwallner/DockQ) as well as an
+ OpenStructure specific implementation of it. Also allows to extract CAPRI
+ specific oligo scores (fnat, fnonnat, irmsd, lrmsd etc.)
+ * Reimplentation of QS-score in mol.alg.qsscore. Implements speedups and
+ heavy caching which benefits heavy enumeration approaches in chain mapping.
+ * Stereochemistry related algorithms in mol.alg.stereochemistry. Identifies
+ clashes and non-sensible bond lengths/angles based on parameterizations from
+ CCP4 MON_LIB.
+ * Better compression in OMF structure format.
+ * One central scoring object: mol.alg.scoring.Scorer. Access to all
+ OpenStructure specific scoring capabilities including required
+ pre-processing of model/reference (cleanup, stereochemistry checks,
+ chain mapping etc.).
* Several minor bug fixes and improvements.
Changes in Release 2.3.1
diff --git a/modules/conop/tests/test_heuristic_builder.cc b/modules/conop/tests/test_heuristic_builder.cc
deleted file mode 100644
index 8ec8b697c5db071f340b3b0e8a28d62a8ba19468..0000000000000000000000000000000000000000
--- a/modules/conop/tests/test_heuristic_builder.cc
+++ /dev/null
@@ -1,224 +0,0 @@
-// ------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-
-// Copyright (C) 2008-2020 by the OpenStructure authors
-
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-// ------------------------------------------------------------------------------
-
-#include <ost/mol/mol.hh>
-#include <ost/conop/heuristic_builder.hh>
-
-#define BOOST_TEST_DYN_LINK
-#include <boost/test/unit_test.hpp>
-
-#include <ost/log.hh>
-using boost::unit_test_framework::test_suite;
-using namespace ost;
-using namespace ost::conop;
-using namespace ost::mol;
-namespace {
-} // anon ns
-
-ResidueHandle make_arg(ChainHandle chain)
-{
- XCSEditor e=chain.GetEntity().EditXCS();
- ResidueHandle res = e.AppendResidue(chain, "ARG");
- e.InsertAtom(res, "N",geom::Vec3(20.202,33.112,58.011));
- e.InsertAtom(res, "CA",geom::Vec3(19.396,31.903,58.033));
- e.InsertAtom(res, "C",geom::Vec3(18.608,31.739,59.328));
- e.InsertAtom(res, "O",geom::Vec3(17.651,30.965,59.381));
- e.InsertAtom(res, "CB",geom::Vec3(20.284,30.681,57.801));
- e.InsertAtom(res, "CG",geom::Vec3(20.665,30.488,56.342));
- e.InsertAtom(res, "CD",geom::Vec3(21.557,29.281,56.154));
- e.InsertAtom(res, "NE",geom::Vec3(22.931,29.557,56.551));
- e.InsertAtom(res, "CZ",geom::Vec3(23.901,28.653,56.528));
- e.InsertAtom(res, "NH1",geom::Vec3(23.640,27.417,56.130));
- e.InsertAtom(res, "NH2",geom::Vec3(25.132,28.980,56.893));
- return res;
-}
-
-ResidueHandle make_leu(ChainHandle chain)
-{
- XCSEditor e=chain.GetEntity().EditXCS();
- ResidueHandle res=e.AppendResidue(chain, "LEU");
-
- e.InsertAtom(res, "N", geom::Vec3(19.003,32.473,60.366));
- e.InsertAtom(res, "CA", geom::Vec3(18.330,32.402,61.664));
- e.InsertAtom(res, "C", geom::Vec3(17.884,33.787,62.117));
- e.InsertAtom(res, "O", geom::Vec3(17.853,34.091,63.308));
- e.InsertAtom(res, "CB", geom::Vec3(19.269,31.793,62.710));
- e.InsertAtom(res, "CG", geom::Vec3(19.695,30.340,62.501));
- e.InsertAtom(res, "CD1", geom::Vec3(20.585,29.897,63.648));
- e.InsertAtom(res, "CD2", geom::Vec3(18.461,29.459,62.420));
- return res;
-}
-
-ResidueHandle make_defective_leu(ChainHandle chain)
-{
- XCSEditor e=chain.GetEntity().EditXCS();
- ResidueHandle res=e.AppendResidue(chain, "LEU");
-
- e.InsertAtom(res, "N", geom::Vec3(19.003,32.473,60.366));
- e.InsertAtom(res, "CA", geom::Vec3(18.330,32.402,61.664));
- e.InsertAtom(res, "C", geom::Vec3(17.884,33.787,62.117));
- e.InsertAtom(res, "O", geom::Vec3(17.853,34.091,63.308));
- e.InsertAtom(res, "CB", geom::Vec3(19.269,31.793,102.710));
- e.InsertAtom(res, "CG", geom::Vec3(19.695,30.340,62.501));
- e.InsertAtom(res, "CD1", geom::Vec3(20.585,29.897,63.648));
- e.InsertAtom(res, "CD2", geom::Vec3(18.461,29.459,62.420));
- return res;
-}
-
-void verify_connectivity_x(const ResidueHandle& res)
-{
- BOOST_CHECK(BondExists(res.FindAtom("XN"),
- res.FindAtom("XCA")));
- BOOST_CHECK(BondExists(res.FindAtom("XCA"),
- res.FindAtom("XC")));
- BOOST_CHECK(BondExists(res.FindAtom("XC"),
- res.FindAtom("XO")));
- BOOST_CHECK(BondExists(res.FindAtom("XCA"),
- res.FindAtom("XCB")));
- BOOST_CHECK(BondExists(res.FindAtom("XCB"),
- res.FindAtom("XCG")));
- if (res.GetKey()=="ARG") {
-
- BOOST_CHECK(BondExists(res.FindAtom("XCB"),
- res.FindAtom("XCG")));
- BOOST_CHECK(BondExists(res.FindAtom("XCG"),
- res.FindAtom("XCD")));
- BOOST_CHECK(BondExists(res.FindAtom("XCD"),
- res.FindAtom("XNE")));
- BOOST_CHECK(BondExists(res.FindAtom("XNE"),
- res.FindAtom("XCZ")));
- BOOST_CHECK(BondExists(res.FindAtom("XCZ"),
- res.FindAtom("XNH1")));
- BOOST_CHECK(BondExists(res.FindAtom("XCZ"),
- res.FindAtom("XNH2")));
- // TODO: Check that no other atoms are connected!
- }
- if (res.GetKey()=="ILE") {
- BOOST_CHECK(BondExists(res.FindAtom("XCG"),
- res.FindAtom("XCD1")));
- BOOST_CHECK(BondExists(res.FindAtom("XCG"),
- res.FindAtom("XCD2")));
- // TODO: Check that no other atoms are connected!
- }
-}
-
-void verify_connectivity(const ResidueHandle& res)
-{
- BOOST_CHECK(BondExists(res.FindAtom("N"),
- res.FindAtom("CA")));
- BOOST_CHECK(BondExists(res.FindAtom("CA"),
- res.FindAtom("C")));
- BOOST_CHECK(BondExists(res.FindAtom("C"),
- res.FindAtom("O")));
- BOOST_CHECK(BondExists(res.FindAtom("CA"),
- res.FindAtom("CB")));
- BOOST_CHECK(BondExists(res.FindAtom("CB"),
- res.FindAtom("CG")));
- if (res.GetKey()=="ARG") {
-
- BOOST_CHECK(BondExists(res.FindAtom("CB"),
- res.FindAtom("CG")));
- BOOST_CHECK(BondExists(res.FindAtom("CG"),
- res.FindAtom("CD")));
- BOOST_CHECK(BondExists(res.FindAtom("CD"),
- res.FindAtom("NE")));
- BOOST_CHECK(BondExists(res.FindAtom("NE"),
- res.FindAtom("CZ")));
- BOOST_CHECK(BondExists(res.FindAtom("CZ"),
- res.FindAtom("NH1")));
- BOOST_CHECK(BondExists(res.FindAtom("CZ"),
- res.FindAtom("NH2")));
- // TODO: Check that no other atoms are connected!
- }
- if (res.GetKey()=="ILE") {
- BOOST_CHECK(BondExists(res.FindAtom("CG"),
- res.FindAtom("CD1")));
- BOOST_CHECK(BondExists(res.FindAtom("CG"),
- res.FindAtom("CD2")));
- // TODO: Check that no other atoms are connected!
- }
-}
-
-BOOST_AUTO_TEST_SUITE( conop );
-
-
-BOOST_AUTO_TEST_CASE(name_based_connect)
-{
- EntityHandle e=CreateEntity();
- ChainHandle c=e.EditXCS().InsertChain("A");
- ResidueHandle ile=make_leu(c);
- ResidueHandle arg=make_arg(c);
- HeuristicBuilder heuristic_builder;
- AtomHandleList atoms =e .GetAtomList();
- for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i!=e; ++i ){
- heuristic_builder.FillAtomProps(*i);
- }
-
- EntityHandle de=CreateEntity();
- ChainHandle dc=de.EditXCS().InsertChain("A");
- ResidueHandle dile=make_defective_leu(dc);
- HeuristicBuilder dheuristic_builder;
- dheuristic_builder.SetBondFeasibilityCheck(false);
- atoms = de.GetAtomList();
- for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i!=e; ++i ){
- dheuristic_builder.FillAtomProps(*i);
- }
-
- BOOST_TEST_MESSAGE("running distance based checks on arginine");
- heuristic_builder.ConnectAtomsOfResidue(arg);
- verify_connectivity(arg);
- BOOST_TEST_MESSAGE("running distance based checks on leu");
- heuristic_builder.ConnectAtomsOfResidue(ile);
- verify_connectivity(ile);
-
- BOOST_TEST_MESSAGE("running distance based checks on defective leu");
- dheuristic_builder.ConnectAtomsOfResidue(dile);
- verify_connectivity(dile);
-}
-
-BOOST_AUTO_TEST_CASE(test_assign_torsions){
- EntityHandle e=CreateEntity();
- ChainHandle c=e.EditXCS().InsertChain("A");
- ResidueHandle l1=make_leu(c);
- ResidueHandle a2=make_arg(c);
- ResidueHandle l3=make_leu(c);
- l1.SetChemClass(ChemClass(ChemClass::L_PEPTIDE_LINKING));
- a2.SetChemClass(ChemClass(ChemClass::L_PEPTIDE_LINKING));
- l3.SetChemClass(ChemClass(ChemClass::L_PEPTIDE_LINKING));
- HeuristicBuilder heuristic_builder;
- AtomHandleList atoms = e.GetAtomList();
- for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i!=e; ++i ){
- heuristic_builder.FillAtomProps(*i);
- }
- heuristic_builder.ConnectAtomsOfResidue(l1);
- heuristic_builder.ConnectAtomsOfResidue(a2);
- heuristic_builder.ConnectAtomsOfResidue(l3);
- XCSEditor edi=e.EditXCS();
- edi.Connect(l1.FindAtom("C"), a2.FindAtom("N"));
- edi.Connect(a2.FindAtom("C"), l3.FindAtom("N"));
- heuristic_builder.AssignTorsions(c);
-
- BOOST_CHECK(a2.GetPhiTorsion().IsValid());
- BOOST_CHECK(l3.GetPhiTorsion().IsValid());
-
- BOOST_CHECK(l1.GetPsiTorsion().IsValid());
- BOOST_CHECK(a2.GetPsiTorsion().IsValid());
-}
-
-BOOST_AUTO_TEST_SUITE_END( );
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 41a6ed5f2e59c0c13e915d1bc527d2de5469b498..63bfd882298c4ef22dae31c1ef2d29919296863f 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -96,7 +96,8 @@ of the annotation available.
.. attribute:: method
- Stores the experimental method used to create the structure.
+ Stores the experimental method used to create the structure
+ (|exptl.method|_).
Also available as :meth:`GetMethod`. May also be modified by
:meth:`SetMethod`.
@@ -1308,6 +1309,9 @@ of the annotation available.
See :attr:`bond_order`
+.. |exptl.method| replace:: ``exptl.method``
+.. _exptl.method: https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_exptl.method.html
+
.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
.. LocalWords: biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index c9e9aec85a40f46929024d8510058a194b1197fd..c8bfa7c7789ca7440cdb84c55ce5ea6bf03709cb 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -723,7 +723,8 @@ class ChainMapper:
def GetlDDTMapping(self, model, inclusion_radius=15.0,
thresholds=[0.5, 1.0, 2.0, 4.0], strategy="naive",
steep_opt_rate = None, full_n_mdl_chains = None,
- block_seed_size = 5, block_blocks_per_chem_group = 5):
+ block_seed_size = 5, block_blocks_per_chem_group = 5,
+ chem_mapping_result = None):
""" Identify chain mapping by optimizing lDDT score
Maps *model* chain sequences to :attr:`~chem_groups` and find mapping
@@ -789,6 +790,11 @@ class ChainMapper:
are extended in an initial search
for high scoring local solutions.
:type block_blocks_per_chem_group: :class:`int`
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: A :class:`MappingResult`
"""
@@ -796,7 +802,10 @@ class ChainMapper:
if strategy not in strategies:
raise RuntimeError(f"Strategy must be in {strategies}")
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
@@ -854,7 +863,7 @@ class ChainMapper:
def GetQSScoreMapping(self, model, contact_d = 12.0, strategy = "naive",
full_n_mdl_chains = None, block_seed_size = 5,
block_blocks_per_chem_group = 5,
- steep_opt_rate = None):
+ steep_opt_rate = None, chem_mapping_result = None):
""" Identify chain mapping based on QSScore
Scoring is based on CA/C3' positions which are present in all chains of
@@ -892,6 +901,11 @@ class ChainMapper:
:type contact_d: :class:`float`
:param strategy: Strategy for sampling, must be in ["naive"]
:type strategy: :class:`str`
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: A :class:`MappingResult`
"""
@@ -899,7 +913,10 @@ class ChainMapper:
if strategy not in strategies:
raise RuntimeError(f"strategy must be {strategies}")
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
chem_mapping,
@@ -952,7 +969,8 @@ class ChainMapper:
def GetRigidMapping(self, model, strategy = "greedy_single_gdtts",
single_chain_gdtts_thresh=0.4, subsampling=None,
- first_complete=False, iterative_superposition=False):
+ first_complete=False, iterative_superposition=False,
+ chem_mapping_result = None):
"""Identify chain mapping based on rigid superposition
Superposition and scoring is based on CA/C3' positions which are present
@@ -1007,6 +1025,11 @@ class ChainMapper:
as oposed to
:func:`ost.mol.alg.SuperposeSVD`
:type iterative_superposition: :class:`bool`
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: A :class:`MappingResult`
"""
@@ -1015,7 +1038,10 @@ class ChainMapper:
if strategy not in strategies:
raise RuntimeError(f"strategy must be {strategies}")
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
chem_mapping,
@@ -1111,7 +1137,7 @@ class ChainMapper:
def GetRepr(self, substructure, model, topn=1, inclusion_radius=15.0,
thresholds=[0.5, 1.0, 2.0, 4.0], bb_only=False,
- only_interchain=False):
+ only_interchain=False, chem_mapping_result = None):
""" Identify *topn* representations of *substructure* in *model*
*substructure* defines a subset of :attr:`~target` for which one
@@ -1142,7 +1168,11 @@ class ChainMapper:
:param only_interchain: Only score interchain contacts in lDDT. Useful
if you want to identify interface patches.
:type only_interchain: :class:`bool`
-
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: :class:`list` of :class:`ReprResult`
"""
@@ -1186,7 +1216,10 @@ class ChainMapper:
"a backbone atom named CA or C3\'")
# perform mapping and alignments on full structures
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
chem_mapping,
diff --git a/modules/mol/alg/pymod/qsscore.py b/modules/mol/alg/pymod/qsscore.py
index 3d28456532e7eb94ee80a9ba5a2d88cf6d7bf485..db5079ef9fd8a3b4ddeb70bf3b0fa77d60db9182 100644
--- a/modules/mol/alg/pymod/qsscore.py
+++ b/modules/mol/alg/pymod/qsscore.py
@@ -396,6 +396,41 @@ class QSScorer:
return self.FromFlatMapping(flat_mapping)
+ def ScoreInterface(self, trg_ch1, trg_ch2, mdl_ch1, mdl_ch2):
+ """ Computes QS-score only considering one interface
+
+ This only works for interfaces that are computed in :func:`Score`, i.e.
+ interfaces for which the alignments are set up correctly.
+
+ :param trg_ch1: Name of first interface chain in target
+ :type trg_ch1: :class:`str`
+ :param trg_ch2: Name of second interface chain in target
+ :type trg_ch2: :class:`str`
+ :param mdl_ch1: Name of first interface chain in model
+ :type mdl_ch1: :class:`str`
+ :param mdl_ch2: Name of second interface chain in model
+ :type mdl_ch2: :class:`str`
+ :returns: Result object of type :class:`QSScorerResult`
+ :raises: :class:`RuntimeError` if no aln for trg_ch1/mdl_ch1 or
+ trg_ch2/mdl_ch2 is available.
+ """
+ if (trg_ch1, mdl_ch1) not in self.alns:
+ raise RuntimeError(f"No aln between trg_ch1 ({trg_ch1}) and "
+ f"mdl_ch1 ({mdl_ch1}) available. Did you "
+ f"construct the QSScorer object from a "
+ f"MappingResult and are trg_ch1 and mdl_ch1 "
+ f"mapped to each other?")
+ if (trg_ch2, mdl_ch2) not in self.alns:
+ raise RuntimeError(f"No aln between trg_ch1 ({trg_ch1}) and "
+ f"mdl_ch1 ({mdl_ch1}) available. Did you "
+ f"construct the QSScorer object from a "
+ f"MappingResult and are trg_ch1 and mdl_ch1 "
+ f"mapped to each other?")
+ trg_int = (trg_ch1, trg_ch2)
+ mdl_int = (mdl_ch1, mdl_ch2)
+ a, b, c, d = self._MappedInterfaceScores(trg_int, mdl_int)
+ return QSScorerResult(a, b, c, d)
+
def FromFlatMapping(self, flat_mapping):
""" Same as :func:`Score` but with flat mapping
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 6d5b345ec9bb012c6b262c43bb0b587ff096641d..70f2dd5b2560df259ae3ba5d0fd02b678bc47dc0 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -109,10 +109,11 @@ class Scorer:
colored to True in
:class:`ost.mol.alg.MolckSettings` constructor.
:type molck_settings: :class:`ost.mol.alg.MolckSettings`
- :param naive_chain_mapping_thresh: Chain mappings for targets up to that
- number of chains will be fully enumerated
- to optimize for QS-score. Everything
- above is treated with a heuristic.
+ :param naive_chain_mapping_thresh: Chain mappings for targets/models up to
+ that number of chains will be fully
+ enumerated to optimize for QS-score.
+ Everything above is treated with a
+ heuristic.
:type naive_chain_mapping_thresh: :class:`int`
:param cad_score_exec: Explicit path to voronota-cadscore executable from
voronota installation from
@@ -204,12 +205,19 @@ class Scorer:
self._qs_global = None
self._qs_best = None
-
- self._dockq_interfaces = None
- self._dockq_native_contacts = None
+ self._interface_qs_global = None
+ self._interface_qs_best = None
+
+ self._interfaces = None
+ self._native_contacts = None
+ self._model_contacts = None
+ self._fnat = None
+ self._fnonnat = None
+ self._irmsd = None
+ self._lrmsd = None
+ self._nonmapped_interfaces = None
+ self._nonmapped_interfaces_contacts = None
self._dockq_scores = None
- self._dockq_nonmapped_interfaces = None
- self._dockq_nonmapped_interfaces_counts = None
self._dockq_ave = None
self._dockq_wave = None
self._dockq_ave_full = None
@@ -356,15 +364,20 @@ class Scorer:
"""
if self._mapping is None:
n_trg_chains = len(self.chain_mapper.target.chains)
- if n_trg_chains <= self.naive_chain_mapping_thresh:
+ res = self.chain_mapper.GetChemMapping(self.model)
+ n_mdl_chains = len(res[2].chains)
+ thresh = self.naive_chain_mapping_thresh
+ if n_trg_chains <= thresh and n_mdl_chains <= thresh:
m = self.chain_mapper.GetQSScoreMapping(self.model,
- strategy="naive")
+ strategy="naive",
+ chem_mapping_result=res)
else:
m = self.chain_mapper.GetQSScoreMapping(self.model,
strategy="greedy_block",
steep_opt_rate=3,
block_seed_size=5,
- block_blocks_per_chem_group=6)
+ block_blocks_per_chem_group=6,
+ chem_mapping_result=res)
self._mapping = m
return self._mapping
@@ -476,40 +489,130 @@ class Scorer:
return self._qs_best
@property
- def dockq_interfaces(self):
- """ Interfaces considered in DockQ (i.e. nonzero native contacts)
-
- DockQ is computed on interfaces as defined by :attr:`~mapping`.
+ def interfaces(self):
+ """ Interfaces with nonzero :attr:`native_contacts`
:type: :class:`list` of :class:`tuple` with 4 elements each:
(trg_ch1, trg_ch2, mdl_ch1, mdl_ch2)
"""
- if self._dockq_interfaces is None:
- self._compute_dockq()
- return self._dockq_interfaces
+ if self._interfaces is None:
+ self._compute_per_interface_scores()
+ return self._interfaces
+
+ @property
+ def interface_qs_global(self):
+ """ QS-score for each interface in :attr:`interfaces`
+
+ :type: :class:`list` of :class:`float`
+ """
+ if self._interface_qs_global is None:
+ self._compute_per_interface_scores()
+ return self._interface_qs_global
@property
- def dockq_native_contacts(self):
- """ N native contacts for interfaces in :attr:`~dockq_interfaces`
+ def interface_qs_best(self):
+ """ QS-score for each interface in :attr:`interfaces`
+
+ Only computed on aligned residues
+
+ :type: :class:`list` of :class:`float`
+ """
+ if self._interface_qs_best is None:
+ self._compute_per_interface_scores()
+ return self._interface_qs_best
+
+ @property
+ def native_contacts(self):
+ """ N native contacts for interfaces in :attr:`~interfaces`
+
+ A contact is a pair or residues from distinct chains that have
+ a minimal heavy atom distance < 5A
+
+ :type: :class:`list` of :class:`int`
+ """
+ if self._native_contacts is None:
+ self._compute_per_interface_scores()
+ return self._native_contacts
+
+ @property
+ def model_contacts(self):
+ """ N model contacts for interfaces in :attr:`~interfaces`
+
+ A contact is a pair or residues from distinct chains that have
+ a minimal heavy atom distance < 5A
:type: :class:`list` of :class:`int`
"""
- if self._dockq_native_contacts is None:
- self._compute_dockq()
- return self._dockq_native_contacts
+ if self._model_contacts is None:
+ self._compute_per_interface_scores()
+ return self._model_contacts
@property
def dockq_scores(self):
- """ DockQ scores for interfaces in :attr:`~dockq_interfaces`
+ """ DockQ scores for interfaces in :attr:`~interfaces`
:class:`list` of :class:`float`
"""
if self._dockq_scores is None:
- self._compute_dockq()
+ self._compute_per_interface_scores()
return self._dockq_scores
@property
- def dockq_nonmapped_interfaces(self):
+ def fnat(self):
+ """ fnat scores for interfaces in :attr:`~interfaces`
+
+ fnat: Fraction of native contacts that are also present in model
+
+ :class:`list` of :class:`float`
+ """
+ if self._fnat is None:
+ self._compute_per_interface_scores()
+ return self._fnat
+
+ @property
+ def fnonnat(self):
+ """ fnonnat scores for interfaces in :attr:`~interfaces`
+
+ fnat: Fraction of model contacts that are not present in target
+
+ :class:`list` of :class:`float`
+ """
+ if self._fnonnat is None:
+ self._compute_per_interface_scores()
+ return self._fnonnat
+
+ @property
+ def irmsd(self):
+ """ irmsd scores for interfaces in :attr:`~interfaces`
+
+ irmsd: RMSD of interface (RMSD computed on N, CA, C, O atoms) which
+ consists of each residue that has at least one heavy atom within 10A of
+ other chain.
+
+ :class:`list` of :class:`float`
+ """
+ if self._irmsd is None:
+ self._compute_per_interface_scores()
+ return self._irmsd
+
+ @property
+ def lrmsd(self):
+ """ lrmsd scores for interfaces in :attr:`~interfaces`
+
+ lrmsd: The interfaces are superposed based on the receptor (rigid
+ min RMSD superposition) and RMSD for the ligand is reported.
+ Superposition and RMSD are based on N, CA, C and O positions,
+ receptor is the chain contributing to the interface with more
+ residues in total.
+
+ :class:`list` of :class:`float`
+ """
+ if self._lrmsd is None:
+ self._compute_per_interface_scores()
+ return self._lrmsd
+
+ @property
+ def nonmapped_interfaces(self):
""" Interfaces present in target that are not mapped
At least one of the chains is not present in target
@@ -517,19 +620,19 @@ class Scorer:
:type: :class:`list` of :class:`tuple` with two elements each:
(trg_ch1, trg_ch2)
"""
- if self._dockq_nonmapped_interfaces is None:
- self._compute_dockq()
- return self._dockq_nonmapped_interfaces
+ if self._nonmapped_interfaces is None:
+ self._compute_per_interface_scores()
+ return self._nonmapped_interfaces
@property
- def dockq_nonmapped_interfaces_counts(self):
- """ Number of native contacts in :attr:`~dockq_nonmapped_interfaces`
+ def nonmapped_interfaces_contacts(self):
+ """ Number of native contacts in :attr:`~nonmapped_interfaces`
:type: :class:`list` of :class:`int`
"""
- if self._dockq_nonmapped_interfaces_counts is None:
- self._compute_dockq()
- return self._dockq_nonmapped_interfaces_counts
+ if self._nonmapped_interfaces_contacts is None:
+ self._compute_per_interface_scores()
+ return self._nonmapped_interfaces_contacts
@property
def dockq_ave(self):
@@ -542,42 +645,42 @@ class Scorer:
:type: :class:`float`
"""
if self._dockq_ave is None:
- self._compute_dockq()
+ self._compute_per_interface_scores()
return self._dockq_ave
@property
def dockq_wave(self):
- """ Same as :attr:`dockq_ave`, weighted by :attr:`dockq_native_contacts`
+ """ Same as :attr:`dockq_ave`, weighted by :attr:`native_contacts`
:type: :class:`float`
"""
if self._dockq_wave is None:
- self._compute_dockq()
+ self._compute_per_interface_scores()
return self._dockq_wave
@property
def dockq_ave_full(self):
""" Same as :attr:`~dockq_ave` but penalizing for missing interfaces
- Interfaces in :attr:`dockq_nonmapped_interfaces` are added as 0.0
+ Interfaces in :attr:`nonmapped_interfaces` are added as 0.0
in average computation.
:type: :class:`float`
"""
if self._dockq_ave_full is None:
- self._compute_dockq()
+ self._compute_per_interface_scores()
return self._dockq_ave_full
@property
def dockq_wave_full(self):
""" Same as :attr:`~dockq_ave_full`, but weighted
- Interfaces in :attr:`dockq_nonmapped_interfaces` are added as 0.0 in
+ Interfaces in :attr:`nonmapped_interfaces` are added as 0.0 in
average computations and the respective weights are derived from
- :attr:`~dockq_nonmapped_interfaces_counts`
+ :attr:`~nonmapped_interfaces_contacts`
"""
if self._dockq_wave_full is None:
- self._compute_dockq()
+ self._compute_per_interface_scores()
return self._dockq_wave_full
@property
@@ -856,24 +959,25 @@ class Scorer:
self._qs_global = qs_score_result.QS_global
self._qs_best = qs_score_result.QS_best
- def _compute_dockq(self):
- if not self.resnum_alignments:
- raise RuntimeError("DockQ computations rely on residue numbers "
- "that are consistent between target and model "
- "chains, i.e. only work if resnum_alignments "
- "is True at Scorer construction.")
-
+ def _compute_per_interface_scores(self):
flat_mapping = self.mapping.GetFlatMapping()
# list of [trg_ch1, trg_ch2, mdl_ch1, mdl_ch2]
- self._dockq_interfaces = list()
+ self._interfaces = list()
# lists with respective values for these interfaces
- self._dockq_native_contacts = list()
+ self._native_contacts = list()
+ self._model_contacts = list()
+ self._interface_qs_global = list()
+ self._interface_qs_best = list()
self._dockq_scores = list()
+ self._fnat = list()
+ self._fnonnat = list()
+ self._irmsd = list()
+ self._lrmsd = list()
# list of interfaces which are present in target but not mapped, i.e.
# not present in mdl
- self._dockq_nonmapped_interfaces = list()
- self._dockq_nonmapped_interfaces_counts = list()
+ self._nonmapped_interfaces = list()
+ self._nonmapped_interfaces_contacts = list()
nonmapped_interface_counts = list()
@@ -898,10 +1002,6 @@ class Scorer:
s.AttachView(self.model.Select(f"cname={cname}"))
mdl_seqs[ch.GetName()] = s
- trg_pep_chains = [s.GetName() for s in self.chain_mapper.polypep_seqs]
- trg_nuc_chains = [s.GetName() for s in self.chain_mapper.polynuc_seqs]
- trg_pep_chains = set(trg_pep_chains)
- trg_nuc_chains = set(trg_nuc_chains)
dockq_alns = dict()
for trg_ch, mdl_ch in flat_mapping.items():
if trg_ch in pep_seqs:
@@ -922,10 +1022,19 @@ class Scorer:
trg_ch1, trg_ch2, ch1_aln=aln1,
ch2_aln=aln2)
if res["nnat"] > 0:
- self._dockq_interfaces.append((trg_ch1, trg_ch2,
- mdl_ch1, mdl_ch2))
- self._dockq_native_contacts.append(res["nnat"])
+ self._interfaces.append((trg_ch1, trg_ch2,
+ mdl_ch1, mdl_ch2))
+ self._native_contacts.append(res["nnat"])
+ self._model_contacts.append(res["nmdl"])
+ self._fnat.append(res["fnat"])
+ self._fnonnat.append(res["fnonnat"])
+ self._irmsd.append(res["irmsd"])
+ self._lrmsd.append(res["lrmsd"])
self._dockq_scores.append(res["DockQ"])
+ qs_res = self.qs_scorer.ScoreInterface(trg_ch1, trg_ch2,
+ mdl_ch1, mdl_ch2)
+ self._interface_qs_best.append(qs_res.QS_best)
+ self._interface_qs_global.append(qs_res.QS_global)
else:
# interface which is not covered by mdl... let's run DockQ
# with trg as trg/mdl in order to get the native contacts
@@ -935,20 +1044,19 @@ class Scorer:
trg_ch1, trg_ch2, trg_ch1, trg_ch2)
nnat = res["nnat"]
if nnat > 0:
- self._dockq_nonmapped_interfaces.append((trg_ch1,
- trg_ch2))
- self._dockq_nonmapped_interfaces_counts.append(nnat)
+ self._nonmapped_interfaces.append((trg_ch1, trg_ch2))
+ self._nonmapped_interfaces_contacts.append(nnat)
# there are 4 types of combined scores
# - simple average
# - average weighted by native_contacts
# - the two above including nonmapped_interfaces => set DockQ to 0.0
scores = np.array(self._dockq_scores)
- weights = np.array(self._dockq_native_contacts)
+ weights = np.array(self._native_contacts)
self._dockq_ave = np.mean(scores)
self._dockq_wave = np.sum(np.multiply(weights/np.sum(weights), scores))
- scores = np.append(scores, [0.0]*len(self._dockq_nonmapped_interfaces))
- weights = np.append(weights, self._dockq_nonmapped_interfaces_counts)
+ scores = np.append(scores, [0.0]*len(self._nonmapped_interfaces))
+ weights = np.append(weights, self._nonmapped_interfaces_contacts)
self._dockq_ave_full = np.mean(scores)
self._dockq_wave_full = np.sum(np.multiply(weights/np.sum(weights),
scores))
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 71577df3659a187de0de1d57683cf155a16ceb86..e2218db714d771cd1c8ed66c6659b0148ed0f719 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -69,15 +69,21 @@ The basic functionality of editors is implemented in the EditorBase class.
:returns: :class:`ChainHandle`
.. method:: AppendResidue(chain, residue_name, [res_num])
+ AppendResidue(chain, residue_name, deep=False)
Append residue to the end of the chain. If res_num is not given, the
residue number will be set to the residue number of the last added residue
plus one. The insertion code is the same.
+ By default, atoms and bonds are not added. If deep is `True`, atoms (but
+ not bonds) are added to the new residue, including alternative atoms.
+
:param chain: Must be a valid chain
:type chain: :class:`ChainHandle`
:param residue_name: 3-letter-code of the residue, e.g. ``GLY``.
- :type residue_name: string
+ :type residue_name: :class:`string`
+ :param deep: If set to true, insert atoms as well.
+ :type deep: :class:`bool`
:returns: :class:`ResidueHandle`
.. method:: RenameResidue(residue, new_name)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 5e778d670030a26e19533f4a679c5fbcde9cd2d3..173ea4a9296c87a2f96345d1857aa9edf3b3189a 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -98,19 +98,28 @@ The Handle Classes
:type: float
+ .. attribute:: center_of_atoms
+
+ Center of atoms, that is the average atom position of the entity.
+ Use :attr:`center_of_mass` for the the mass-weighted center of the entity.
+ Also available as :meth:`GetCenterOfAtoms`.
+
+ :type: :class:`~ost.geom.Vec3`
+
.. attribute:: center_of_mass
- Center of mass. Also available as :meth:`GetCenterOfMass`
-
- :type: :class:`~ost.geom.Vec3`
-
- .. attribute:: center_of_atoms
-
- Center of atoms (not mass-weighted). Also available as
- :meth:`GetCenterOfAtoms`.
+ Center of mass of the entity.
+ Also available as :meth:`GetCenterOfMass`
:type: :class:`~ost.geom.Vec3`
+ .. attribute:: geometric_center
+
+ Mid-point of the axis aligned bounding box of the entity.
+ Also available as :meth:`GetGeometricCenter`
+
+ :type: Vec3
+
.. attribute:: positions
Equivalent to calling :meth:`GetPositions` with *sort_by_index = True*. This
@@ -286,29 +295,21 @@ The Handle Classes
alternative atom positions are not handled yet.
+ .. method:: GetMass()
+
+ See :attr:`mass`
+
.. method:: GetCenterOfAtoms()
-
- Get center of atoms, that is the average atom position of the entity. Use
- :meth:`GetCenterOfMass` to calculate the mass-weighted center of the entity.
-
- :returns: :class:`~ost.geom.Vec3`
-
+
+ See :attr:`center_of_atoms`
+
.. method:: GetCenterOfMass()
-
- Calculates the center of mass of the entity. Use :meth:`GetCenterOfAtoms`
- to calculate the non-mass-weighted center of the entity.
-
- :returns: :class:`~ost.geom.Vec3`
-
+
+ See :attr:`center_of_mass`
+
.. method:: GetGeometricCenter()
-
- Calculates the mid-point of the axis aligned bounding box of the entity.
-
- :returns: :class:`~ost.geom.Vec3`
-
- .. method:: GetMass()
-
- See :attr:`mass`
+
+ See :attr:`geometric_center`
.. method:: GetPositions(sort_by_index=True)
@@ -367,10 +368,17 @@ The Handle Classes
.. attribute:: center_of_mass
- Center of mass. Also available as :meth:`GetCenterOfMass`
+ Center of mass. Also available as :meth:`GetCenterOfMass`.
:type: :class:`~ost.geom.Vec3`
+ .. attribute:: geometric_center
+
+ Mid-point of the axis aligned bounding box of the chain.
+ Also available as :meth:`GetGeometricCenter`
+
+ :type: Vec3
+
.. attribute:: description
Details about the chain. Not categorised, just text.
@@ -567,9 +575,20 @@ The Handle Classes
The residue name is usually a str of 3 characters, e.g. `GLY` for
glycine or `ALA` for alanine, but may be shorter, e.g. `G` for guanosine,
or longer for structures loaded from formats other than PDB.
+ Also available as :meth:`GetName`.
This property is read-only. To change the name of the residue, use
:meth:`~EditorBase.RenameResidue`.
+
+ :type: str
+
+ .. attribute:: qualified_name
+
+ The qualified name consists of a residue identifier and chain name.
+ For a glycine with residue number 2 of chain A, the qualified name is
+ "A.GLY2". Also available as :meth:`GetQualifiedName`.
+
+ :type: str
.. attribute:: number
@@ -605,6 +624,18 @@ The Handle Classes
:type: :class:`AtomHandleList` (list of :class:`AtomHandle`)
+ .. attribute:: atom_count
+
+ Number of atoms. Read-only. See :meth:`GetAtomCount`.
+
+ :type: :class:`int`
+
+ .. attribute:: bond_count
+
+ Number of bonds. Read-only. See :meth:`GetBondCount`.
+
+ :type: :class:`int`
+
.. attribute:: bounds
Axis-aligned bounding box of the residue. Read-only.
@@ -616,12 +647,6 @@ The Handle Classes
The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
:type: float
-
- .. attribute:: center_of_mass
-
- Center of mass. Also available as :meth:`GetCenterOfMass`
-
- :type: :class:`~ost.geom.Vec3`
.. attribute:: center_of_atoms
@@ -630,6 +655,18 @@ The Handle Classes
:type: :class:`~ost.geom.Vec3`
+ .. attribute:: center_of_mass
+
+ Center of mass. Also available as :meth:`GetCenterOfMass`
+
+ :type: :class:`~ost.geom.Vec3`
+
+ .. attribute:: geometric_center
+
+ Mid-point of the axis aligned bounding box of the residue.
+
+ :type: Vec3
+
.. attribute:: chain
The chain this residue belongs to. Read-only. Also available as
@@ -656,6 +693,15 @@ The Handle Classes
torsion, the PSI torsion is an invalid handle.
Read-only. Also available as :meth:`GetPsiTorsion`
+
+ .. attribute:: omega_torsion
+
+ The OMEGA dihedral angle between this residue and the previous. For residues
+ that are not amino acids, residues that do not have all atoms required or
+ residues that do not have bonds between the four atoms involved in the
+ torsion, the OMEGA torsion is an invalid handle.
+
+ Read-only. Also available as :meth:`GetOmegaTorsion`
:type: :class:`TorsionHandle`
@@ -808,42 +854,98 @@ The Handle Classes
:returns: Whether the switch was successful (e.g. False if no such
group exists)
+ .. method:: GetName()
+
+ See :attr:`name`
+
+ .. method:: GetQualifiedName()
+
+ See :attr:`qualified_name`
+
+ .. method:: GetNumber()
+
+ See :attr:`number`
+
+ .. method:: GetOneLetterCode()
+
+ See :attr:`one_letter_code`
+
.. method:: GetAtomList()
See :attr:`atoms`
- .. method:: IsPeptideLinking()
+ .. method:: GetAtomCount()
- See :attr:`peptide_linking`
+ See :attr:`atom_count`
- .. method:: IsNucleotideLinking()
+ .. method:: GetBondCount()
+
+ See :attr:`bond_count`
+
+ .. method:: GetBounds()
+
+ See :attr:`bounds`
+
+ .. method:: GetMass()
+
+ See :attr:`mass`
- See :attr:`nucleotide_linking`
-
- .. method:: GetChain()
-
- See :attr:`chain`
-
.. method:: GetCenterOfAtoms()
-
+
See :attr:`center_of_atoms`
-
+
.. method:: GetCenterOfMass()
-
+
See :attr:`center_of_mass`
-
+
+ .. method:: GetGeometricCenter()
+
+ See :attr:`geometric_center`
+
+ .. method:: GetChain()
+
+ See :attr:`chain`
+
.. method:: GetPhiTorsion()
-
+
See :attr:`phi_torsion`
-
+
.. method:: GetPsiTorsion()
-
+
See :attr:`psi_torsion`
-
+
+ .. method:: GetOmegaTorsion()
+
+ See :attr:`omega_torsion`
+
+ .. method:: GetChemClass()
+
+ See :attr:`chem_class`
+
.. method:: GetChemType()
-
+
See :attr:`chem_type`
+ .. method:: GetSecStructure()
+
+ See :attr:`sec_structure`
+
+ .. method:: IsLigand()
+
+ See :attr:`is_ligand`
+
+ .. method:: IsProtein()
+
+ See :attr:`is_protein`
+
+ .. method:: IsPeptideLinking()
+
+ See :attr:`peptide_linking`
+
+ .. method:: IsNucleotideLinking()
+
+ See :attr:`nucleotide_linking`
+
.. method:: GetIndex()
See :attr:`index`
@@ -861,10 +963,6 @@ The Handle Classes
See :attr:`valid`
- .. method:: IsLigand()
-
- See :attr:`is_ligand`
-
.. method:: SetIsLigand()
Set the :meth:`IsLigand` flag explicitly.
@@ -872,10 +970,6 @@ The Handle Classes
:param ligand: Whether this residue is a ligand or not
:type ligand: bool
- .. method:: IsProtein()
-
- See :attr:`is_protein`
-
.. method:: SetIsProtein()
Set the :meth:`IsProtein` flag explicitly.
@@ -883,6 +977,14 @@ The Handle Classes
:param protein: Whether this residue is a protein or not
:type protein: bool
+ .. method:: GetNext()
+
+ See :attr:`next`
+
+ .. method:: GetPrev()
+
+ See :attr:`next`
+
.. class:: AtomHandle
@@ -900,7 +1002,7 @@ The Handle Classes
.. attribute:: qualified_name
- The qualified name consists of the atom name as well as a unique residue
+ The qualified name consists of the atom name as well as a residue
identifier and chain name. For CA of a glycine with residue number 2 of
chain A, the qualified name is "A.GLY2.CA".
@@ -1230,6 +1332,13 @@ The View Classes
An entity view represents a structural subset of an :class:`EntityHandle`. For
an introduction ,see :doc:`../../intro-01`.
+
+ .. attribute:: handle
+
+ The underlying :class:`handle <EntityHandle>` of the entity view. Also
+ available as :meth:`GetHandle`.
+
+ :type: :class:`EntityHandle`
.. attribute:: chains
@@ -1291,16 +1400,23 @@ The View Classes
.. attribute:: bounds
- Axis-aligned bounding box of the entity view. Read-only.
-
- :type: :class:`ost.geom.AlignedCuboid`
+ See :attr:`EntityHandle.bounds`
- .. attribute:: handle
-
- The underlying :class:`handle <EntityHandle>` of the entity view. Also
- available as :meth:`GetHandle`.
-
- :type: :class:`EntityHandle`
+ .. attribute:: mass
+
+ See :attr:`EntityHandle.mass`
+
+ .. attribute:: center_of_atoms
+
+ See :attr:`EntityHandle.center_of_atoms`
+
+ .. attribute:: center_of_mass
+
+ See :attr:`EntityHandle.center_of_mass`
+
+ .. attribute:: geometric_center
+
+ See :attr:`EntityHandle.geometric_center`
.. attribute:: valid
@@ -1581,6 +1697,12 @@ The View Classes
A view representation of a :class:`ChainHandle`. Mostly, the same
functionality is provided as for the handle.
+ .. attribute:: handle
+
+ The chain handle this view points to. Also available as :meth:`GetHandle`.
+
+ :type: :class:`ChainHandle`
+
.. attribute:: name
The chain name. The name uniquely identifies the chain in the entity. In
@@ -1629,6 +1751,11 @@ The View Classes
print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
print(chain.in_sequence) # prints false
+ Note that the value of `in_sequence` is independent from the value of
+ :attr:`ChainHandle.in_sequence`.
+
+ :type: bool
+
.. attribute:: atoms
Get list of all atoms of this chain. To access a single atom, use
@@ -1650,38 +1777,17 @@ The View Classes
:type: float
- .. attribute:: center_of_mass
-
- Center of mass. Also available as :meth:`GetCenterOfMass`
-
- :type: :class:`~ost.geom.Vec3`
-
.. attribute:: center_of_atoms
-
- Center of atoms (not mass weighted). Also available as
- :meth:`GetCenterOfAtoms`.
-
- :type: :class:`~ost.geom.Vec3`
- .. attribute:: handle
+ See :attr:`ChainHandle.center_of_atoms`
- The chain handle this view points to. Also available as :meth:`GetHandle`.
-
- :type: :class:`ChainHandle`
-
- .. attribute:: in_sequence
-
- Whether the residue numbers are in ascending order. Note that the value of
- `in_sequence` is independent from the value of
- :attr:`ChainHandle.in_sequence`.
-
- :type: bool
+ .. attribute:: center_of_mass
- .. attribute:: geometric_center
+ See :attr:`ChainHandle.center_of_mass`
- Mid-point of the axis aligned bounding box of the entity.
+ .. attribute:: geometric_center
- :type: Vec3
+ See :attr:`ChainHandle.geometric_center`
.. attribute:: valid
@@ -1822,63 +1928,47 @@ The View Classes
:type: :class:`ResidueHandle`
.. attribute:: name
+ qualified_name
+ number
+ one_letter_code
+ bounds
+ mass
+ center_of_atoms
+ center_of_mass
+ geometric_center
+ phi_torsion
+ psi_torsion
+ omega_torsion
+ chem_class
+ chem_type
+ sec_structure
+ is_ligand
+ is_protein
+ peptide_linking
+ nucleotide_linking
+ central_atom
+ central_normal
+ valid
+ next
+ prev
+
+ See the respective attributes in :class:`ResidueHandle`.
- The residue name is usually a str of 3 characters, e.g. `GLY` for
- glycine or `ALA` for alanine, but may be shorter, e.g. `G` for guanosine,
- or longer for structures loaded from formats other than PDB.
-
- This property is read-only. To change the name of the residue, use
- :meth:`~EditorBase.RenameResidue`.
-
- .. attribute:: number
-
- The number of this residue. The residue number has a numeric part and an
- insertion-code. This property is read-only. Also available as
- :meth:`GetNumber`.
-
- :type: :class:`ResNum`
-
- .. attribute:: one_letter_code
-
- For amino acids, and nucleotides the `one_letter_code` is an alpha-numeric
- character. For unknown or more *exotic* residues, the one letter code is set
- to '?'.
-
- **Example**
-
- This code-snippet shows how to get the sequence string from a list of
- residues.
-
- .. code-block:: python
-
- print(''.join([r.one_letter_code for r in chain.residues]))
-
- :type: str
-
- .. attribute:: bounds
-
- Axis-aligned bounding box of the residue view. Read-only
-
- :type: :class:`ost.geom.AlignedCuboid`
-
- .. attribute:: mass
+ .. attribute:: atoms
- The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
+ Get list of all atoms of this residue included in the view.
+ To access a single atom, use
+ :meth:`FindAtom`.
- :type: float
+ This property is read-only. Also available as :meth:`GetAtomList`
- .. attribute:: center_of_mass
+ :type: :class:`AtomViewList` (list of :class:`AtomView`)
- Center of mass. Also available as :meth:`GetCenterOfMass`
+ .. attribute:: atom_count
- :type: :class:`~ost.geom.Vec3`
+ Number of atoms included in the view. Read-only. See :meth:`GetAtomCount`.
- .. attribute:: center_of_atoms
-
- Center of atoms (not mass weighted). Also available as
- :meth:`GetCenterOfAtoms`.
-
- :type: :class:`~ost.geom.Vec3`
+ :type: :class:`int`
.. attribute:: chain
@@ -1887,21 +1977,6 @@ The View Classes
:type: :class:`ChainView`
- .. attribute:: handle
-
- The residue handle this view points to
-
- :type: :class:`ResidueHandle`
-
- .. attribute:: atoms
-
- Get list of all atoms of this residue. To access a single atom, use
- :meth:`FindAtom`.
-
- This property is read-only. Also available as :meth:`GetAtomList`
-
- :type: :class:`AtomHandleList` (list of :class:`AtomHandle`)
-
.. attribute:: index
Residue index (starting at 0) within chain view.
@@ -1919,9 +1994,34 @@ The View Classes
See :attr:`handle`
- .. method:: GetMass()
-
- See :attr:`mass`
+ .. method:: GetName
+ GetQualifiedName
+ GetNumber
+ GetOneLetterCode
+ GetBounds
+ GetMass
+ GetCenterOfAtoms
+ GetCenterOfMass
+ GetGeometricCenter
+ GetPhiTorsion
+ GetPsiTorsion
+ GetOmegaTorsion
+ GetChemClass
+ GetChemType
+ GetSecStructure
+ IsLigand
+ SetIsLigand
+ IsProtein
+ IsPeptideLinking
+ IsNucleotideLinking
+ GetCentralAtom
+ SetCentralAtom
+ GetCentralNormal
+ IsValid
+ GetNext
+ GetPrev
+
+ See the respective methods in :class:`ResidueHandle`.
.. method:: GetChain()
@@ -1936,14 +2036,6 @@ The View Classes
:type atom_name: str
:rtype: :class:`AtomView`
- .. method:: GetIndex()
-
- See :attr:`index`
-
- .. method:: GetCenterOfMass()
-
- See :attr:`center_of_mass`
-
.. method:: IsAtomIncluded(atom_handle)
Returns true if the given atom is part of the view, false if not.
@@ -1952,10 +2044,6 @@ The View Classes
:type atom_handle: :class:`AtomHandle`
:rtype: bool
- .. method:: GetGeometricCenter()
-
- See :attr:`geometric_center`
-
.. method:: AddAtom(atom_handle[, flags])
Add atom to the view.
@@ -1966,13 +2054,17 @@ The View Classes
:type flags: :class:`int` / :class:`ViewAddFlag`
:rtype: :class:`AtomView`
- .. method:: GetCenterOfAtoms()
-
- See :attr:`center_of_atoms`
-
.. method:: GetAtomList()
See :attr:`atoms`
+
+ .. method:: GetAtomCount()
+
+ See :attr:`atom_count`
+
+ .. method:: GetIndex()
+
+ See :attr:`index`
.. method:: Select(query, flags=0)
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 8a6fbe99ece49ddfc6e5d2a5fb723239d69619e0..9016f9d02f209c2e3ac339be7cec631099af4b96 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -261,6 +261,7 @@ void export_Residue()
.def("GetAtomCount", &ResidueHandle::GetAtomCount)
.def("GetBondCount", &ResidueHandle::GetBondCount)
.add_property("atom_count", &ResidueHandle::GetAtomCount)
+ .add_property("bond_count", &ResidueHandle::GetBondCount)
.add_property("index", &ResidueHandle::GetIndex)
.def("Select", select_string, arg("flags")=0)
.def("Select", select_query, arg("flags")=0)
diff --git a/modules/mol/base/pymod/export_residue_view.cc b/modules/mol/base/pymod/export_residue_view.cc
index a3a7f16eaa232216a97b1091fd9048ff3a7e87c0..9d14320de594bb3220792085258551f9e1d82cbe 100644
--- a/modules/mol/base/pymod/export_residue_view.cc
+++ b/modules/mol/base/pymod/export_residue_view.cc
@@ -64,6 +64,7 @@ void export_ResidueView()
.add_property("atoms",
make_function(&ResidueView::GetAtomList,
return_value_policy<copy_const_reference>()))
+ .add_property("atom_count", &ResidueView::GetAtomCount)
.def("FindAtom", string_find_atom, args("atom_name"))
.def("AddAtom", add_atom_handle, X_add_atom_overloads(args("atom_handle", "flags")))
.def("AddAtom", add_atom_view, X_add_atom_overloads(args("atom_view", "flags")))