From 115c411cf264f6883c564e43110ff6b5d397c77b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 7 Sep 2022 13:19:29 +0200
Subject: [PATCH] lDDT: allow custom compounds which are not in default
compound lib
---
modules/mol/alg/doc/molalg.rst | 3 ++
modules/mol/alg/pymod/lddt.py | 65 +++++++++++++++++++++++++++-------
2 files changed, 55 insertions(+), 13 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 23d670854..89b170b95 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -34,6 +34,9 @@ Local Distance Test scores (lDDT, DRMSD)
.. autofunction:: ost.mol.alg.lddt.GetDefaultSymmetrySettings
+.. autoclass:: ost.mol.alg.lddt.CustomCompound
+ :members:
+
.. function:: CheckStructure(ent, \
bond_table, \
angle_table, \
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 4f8565bc7..f905cf416 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -4,6 +4,34 @@ from ost import mol
from ost import conop
+class CustomCompound:
+ """ Defines atoms for custom compounds
+
+ lDDT requires the reference atoms of a compound which are typically
+ extracted from a :class:`ost.conop.CompoundLib`. This lightweight
+ container allows to handle arbitrary compounds which are not
+ necessarily in the compound library.
+
+ :param atom_names: Names of atoms of custom compound
+ :type atom_names: :class:`list` of :class:`str`
+ """
+ def __init__(self, atom_names):
+ self.atom_names = atom_names
+
+ @staticmethod
+ def FromResidue(res):
+ """ Construct custom compound from residue
+
+ :param res: Residue from which reference atom names are extracted
+ :type res: :class:`ost.mol.ResidueView`/:class:`ost.mol.ResidueHandle`
+ :returns: :class:`CustomCompound`
+ """
+ atom_names = [a.GetName() for a in res.atoms]
+ if len(atom_names) != len(set(atom_names)):
+ raise RuntimeError("Duplicate atoms detected in CustomCompound")
+ compound = CustomCompound(atom_names)
+ return compound
+
class SymmetrySettings:
"""Container for symmetric compounds
@@ -99,6 +127,11 @@ class lDDTScorer:
["A", "B"] but the compound has ["A", "B", "C"], "C" is
considered missing and does not influence scoring, even
if present in the model.
+ :param custom_compounds: Custom compounds defining reference atoms. If
+ given, *custom_compounds* take precedent over
+ *compound_lib*.
+ :type custom_compounds: :class:`dict` with residue names (:class:`str`) as
+ key and :class:`CustomCompound` as value.
:type compound_lib: :class:`ost.conop.CompoundLib`
:param inclusion_radius: All pairwise distances < *inclusion_radius* are
considered for scoring
@@ -151,6 +184,7 @@ class lDDTScorer:
self,
target,
compound_lib=None,
+ custom_compounds=None,
inclusion_radius=15,
sequence_separation=0,
symmetry_settings=None,
@@ -167,6 +201,7 @@ class lDDTScorer:
raise RuntimeError("No compound_lib given and conop.GetDefaultLib "
"returns no valid compound library")
self.compound_lib = compound_lib
+ self.custom_compounds = custom_compounds
if symmetry_settings is None:
self.symmetry_settings = GetDefaultSymmetrySettings()
else:
@@ -225,8 +260,8 @@ class lDDTScorer:
self.symmetric_atoms = set()
# setup members defined above
- self._SetupEnv(self.compound_lib, self.symmetry_settings,
- seqres_mapping, self.bb_only)
+ self._SetupEnv(self.compound_lib, self.custom_compounds,
+ self.symmetry_settings, seqres_mapping, self.bb_only)
# distance related members are lazily computed as they're affected
# by different flavours of lDDT (e.g. lDDT including inter-chain
@@ -709,8 +744,8 @@ class lDDTScorer:
return rnums
- def _SetupEnv(self, compound_lib, symmetry_settings, seqres_mapping,
- bb_only):
+ def _SetupEnv(self, compound_lib, custom_compounds, symmetry_settings,
+ seqres_mapping, bb_only):
"""Sets target related lDDTScorer members defined in constructor
No distance related members - see _SetupDistances
@@ -727,8 +762,8 @@ class lDDTScorer:
if r.name not in self.compound_anames:
# sets compound info in self.compound_anames and
# self.compound_symmetric_atoms
- self._SetupCompound(r, compound_lib, symmetry_settings,
- bb_only)
+ self._SetupCompound(r, compound_lib, custom_compounds,
+ symmetry_settings, bb_only)
self.res_start_indices.append(current_idx)
self.res_mapper[(ch_name, rnum)] = len(self.compound_names)
@@ -807,7 +842,8 @@ class lDDTScorer:
residue_numbers[ch_name] = rnums
return residue_numbers
- def _SetupCompound(self, r, compound_lib, symmetry_settings, bb_only):
+ def _SetupCompound(self, r, compound_lib, custom_compounds,
+ symmetry_settings, bb_only):
"""fill self.compound_anames/self.compound_symmetric_atoms
"""
if bb_only:
@@ -823,12 +859,15 @@ class lDDTScorer:
else:
atom_names = list()
symmetric_atoms = list()
- compound = compound_lib.FindCompound(r.name)
- if compound is None:
- raise RuntimeError(f"no entry for {r} in compound_lib")
- for atom_spec in compound.GetAtomSpecs():
- if atom_spec.element not in ["H", "D"]:
- atom_names.append(atom_spec.name)
+ if custom_compounds is not None and r.GetName() in custom_compounds:
+ atom_names = list(custom_compounds[r.GetName()].atom_names)
+ else:
+ compound = compound_lib.FindCompound(r.name)
+ if compound is None:
+ raise RuntimeError(f"no entry for {r} in compound_lib")
+ for atom_spec in compound.GetAtomSpecs():
+ if atom_spec.element not in ["H", "D"]:
+ atom_names.append(atom_spec.name)
if r.name in symmetry_settings.symmetric_compounds:
for pair in symmetry_settings.symmetric_compounds[r.name]:
try:
--
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