diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 23ad53e3b7042ec636c1ccf535feb0e40cff3e56..e50232556749336687c37a16804da393240066ce 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -27,6 +27,7 @@ set(OST_MOL_ALG_PYMOD_MODULES
scoring.py
chain_mapping.py
stereochemistry.py
+ ligand_scoring.py
)
if (NOT ENABLE_STATIC)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
new file mode 100644
index 0000000000000000000000000000000000000000..fa60fdbb6e4a5fa6f40fe2776b2b9a445714b1c8
--- /dev/null
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -0,0 +1,136 @@
+import os
+from ost import mol
+from ost.mol.alg import chain_mapping
+import numpy as np
+
+
+class LigandScorer:
+ """ Helper class to access the various small molecule ligand (non polymer)
+ scores available from ost.mol.alg.
+
+ Mostly expects cleaned up structures (you can use the
+ `~ost.mol.alg.scoring.Scorer` outputs for that).
+
+ :param model: Model structure - a deep copy is available as :attr:`model`.
+ No additional processing (ie. Molck), checks,
+ stereochemistry checks or sanitization is performed on the
+ input.
+ :type model: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
+ :param target: Target structure - a deep copy is available as :attr:`target`.
+ No additional processing (ie. Molck), checks or sanitization
+ is performed on the input.
+ :type target: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
+ :param model_ligands: Model ligands, either a :class:list of
+ :class:`ost.mol.ResidueHandle`/:class:`ost.mol.ResidueView`
+ or of :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
+ containing a single residue each. If `None`, ligands will be
+ extracted from the `model` entity, from chains with
+ :class:`~ost.mol.ChainType` `CHAINTYPE_NON_POLY` (this is
+ normally set properly in entities loaded from mmCIF).
+ :type model_ligands: :class:`list`
+ :param target_ligands: Target ligands, either a :class:list of
+ :class:`ost.mol.ResidueHandle`/:class:`ost.mol.ResidueView`
+ or of :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
+ containing a single residue each. If `None`, ligands will be
+ extracted from the `target` entity, from chains with
+ :class:`~ost.mol.ChainType` `CHAINTYPE_NON_POLY` (this is
+ normally set properly in entities loaded from mmCIF).
+ :type target_ligands: :class:`list`
+ :param resnum_alignments: Whether alignments between chemically equivalent
+ chains in *model* and *target* can be computed
+ based on residue numbers. This can be assumed in
+ benchmarking setups such as CAMEO/CASP.
+ :type resnum_alignments: :class:`bool`
+ :param chain_mapper: a chain mapper initialized for the target structure.
+ If None (default), a chain mapper will be initialized
+ lazily as required.
+ :type chain_mapper: :class:`ost.mol.alg.chain_mapping.ChainMapper`
+
+
+ """
+ def __init__(self, model, target, model_ligands=None, target_ligands=None,
+ resnum_alignments=False, chain_mapper=None):
+
+ if isinstance(model, mol.EntityView):
+ self._model = mol.CreateEntityFromView(model, False)
+ elif isinstance(model, mol.EntityHandle):
+ self._model = model.Copy()
+ else:
+ raise RuntimeError("model must be of type EntityView/EntityHandle")
+
+ if isinstance(target, mol.EntityView):
+ self._target = mol.CreateEntityFromView(target, False)
+ elif isinstance(target, mol.EntityHandle):
+ self._target = target.Copy()
+ else:
+ raise RuntimeError("model must be of type EntityView/EntityHandle")
+
+ # Extract ligands from target
+ if target_ligands is None:
+ self.target_ligands = self._extract_ligands(self._target)
+ else:
+ # TODO: sanitize given ligands
+ self.target_ligands = target_ligands
+
+ # Extract ligands from model
+ if model_ligands is None:
+ self.model_ligands = self._extract_ligands(self._model)
+ else:
+ # TODO: sanitize given ligands
+ self.model_ligands = target_ligands
+
+ self._chain_mapper = chain_mapper
+ self.resnum_alignments = resnum_alignments
+
+ # lazily computed scores
+ self._lddt_pli = None
+ self._rmsd = None
+ self._lddt_bs = None
+
+ @property
+ def chain_mapper(self):
+ """ Chain mapper object for given :attr:`target`
+
+ :type: :class:`ost.mol.alg.chain_mapping.ChainMapper`
+ """
+ if self._chain_mapper is None:
+ self._chain_mapper = chain_mapping.ChainMapper(self.target,
+ n_max_naive=1e9,
+ resnum_alignments=self.resnum_alignments)
+ return self._chain_mapper
+
+ @staticmethod
+ def _extract_ligands(entity):
+ """Extracts ligands from entity. Returns a list of residues.
+
+ Assumes that ligands are contained in one or more chain with chain type
+ `mol.ChainType.CHAINTYPE_NON_POLY`. This is typically the case
+ for entities loaded from mmCIF (tested with mmCIF files from the PDB
+ and SWISS-MODEL), but it will most likely not work for most entities
+ loaded from PDB files.
+
+ As a deviation from the mmCIF semantics, we allow a chain, set as
+ `CHAINTYPE_NON_POLY`, to contain more than one ligand. This function
+ performs basic checks to ensure that the residues in this chain are
+ not forming polymer bonds (ie peptide/nucleotide ligands) and will
+ raise a RuntimeError if this assumption is broken.
+
+ Note: This will not extract ligands based on the HET record in the old
+ PDB style, as this is not a reliable indicator and depends on how the
+ entity was loaded.
+
+ :param entity: the entity to extract ligands from
+ :type entity: :class:`~ost.mol.EntityHandle`
+ :rtype: :class:`list` of :class:`~ost.mol.ResidueHandle`
+
+ """
+ extracted_ligands = []
+ for chain in entity.chains:
+ if chain.chain_type == mol.ChainType.CHAINTYPE_NON_POLY:
+ for residue in chain.residues:
+ if mol.InSequence(residue, residue.next):
+ raise RuntimeError("Connected residues in non polymer "
+ "chain %s" % (chain.name))
+ extracted_ligands.append(residue)
+ return extracted_ligands
+
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
new file mode 100644
index 0000000000000000000000000000000000000000..7309e270781a601fa0b754c39cb1178906e96525
--- /dev/null
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -0,0 +1,33 @@
+import unittest, os, sys
+
+from ost import io, mol
+# check if we can import: fails if numpy or scipy not available
+try:
+ from ost.mol.alg.ligand_scoring import *
+except ImportError:
+ print("Failed to import ligand_scoring.py. Happens when numpy or scipy " \
+ "missing. Ignoring test_ligand_scoring.py tests.")
+ sys.exit(0)
+
+
+class TestLigandScoring(unittest.TestCase):
+
+ def test_extract_ligands(self):
+ """Test that we can extract ligands from mmCIF files.
+ """
+
+ trg = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"))
+ mdl = io.LoadMMCIF(os.path.join('testfiles', "P84080_model_02.cif.gz"))
+
+ sc = LigandScorer(mdl, trg, None, None)
+
+ assert len(sc.target_ligands) == 7
+ assert len(sc.model_ligands) == 1
+
+
+if __name__ == "__main__":
+ from ost import testutils
+ if testutils.SetDefaultCompoundLib():
+ testutils.RunTests()
+ else:
+ print('No compound lib available. Ignoring test_chain_mapping.py tests.')
diff --git a/modules/mol/alg/tests/testfiles/1r8q.cif.gz b/modules/mol/alg/tests/testfiles/1r8q.cif.gz
new file mode 100644
index 0000000000000000000000000000000000000000..09451cd2eae22d3bfd867ab7f29b70990adf5344
Binary files /dev/null and b/modules/mol/alg/tests/testfiles/1r8q.cif.gz differ
diff --git a/modules/mol/alg/tests/testfiles/P84080_model_02.cif.gz b/modules/mol/alg/tests/testfiles/P84080_model_02.cif.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d382b88bc11043f10df7a30b0cca2525ba204b59
Binary files /dev/null and b/modules/mol/alg/tests/testfiles/P84080_model_02.cif.gz differ