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Unverified Commit e8146aea authored by Xavier Robin's avatar Xavier Robin
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feat: SCHWED-5783 accept ligands as input

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modules/mol/alg/pymod/ligand_scoring.py
+ 98
− 18
View file @ e8146aea
......@@ -20,15 +20,19 @@ class LigandScorer:
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
:param model_ligands: Model ligands, as a list of
:class:`ost.mol.ResidueHandle`s belonging to the model
entity. Can be instantiated with 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).
or of :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`.
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
:param target_ligands: Target ligands, as a list of
:class:`ost.mol.ResidueHandle`s belonging to the target
entity. Can be instanciated 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
......@@ -46,38 +50,35 @@ class LigandScorer:
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)
self.model = mol.CreateEntityFromView(model, False)
elif isinstance(model, mol.EntityHandle):
self._model = model.Copy()
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)
self.target = mol.CreateEntityFromView(target, False)
elif isinstance(target, mol.EntityHandle):
self._target = target.Copy()
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)
self.target_ligands = self._extract_ligands(self.target)
else:
# TODO: sanitize given ligands
self.target_ligands = target_ligands
self.target_ligands = self._prepare_ligands(self.target, target, target_ligands)
# Extract ligands from model
if model_ligands is None:
self.model_ligands = self._extract_ligands(self._model)
self.model_ligands = self._extract_ligands(self.model)
else:
# TODO: sanitize given ligands
self.model_ligands = target_ligands
self.model_ligands = self._prepare_ligands(self.model, model, model_ligands)
self._chain_mapper = chain_mapper
self.resnum_alignments = resnum_alignments
......@@ -134,3 +135,82 @@ class LigandScorer:
extracted_ligands.append(residue)
return extracted_ligands
@staticmethod
def _prepare_ligands(new_entity, old_entity, ligands):
"""Prepare the ligands given into a list of ResidueHandles which are
part of the copied entity, suitable for the model_ligands and
target_ligands properties.
This function takes a list of ligands as (Entity|Residue)(Handle|View).
Entities can contain multiple ligands, which will be considered as
separate ligands.
Ligands which are part of the entity are simply fetched in the new
copied entity. Otherwise, they are copied over to the copied entity.
If
Copy ligands into the new copied entity, if needed.
and prepares the list of ligands to be returned as a list of
ResidueHandles which are part of the copied entity, and suitable for
model_ligands and target_ligands.
Multiple ligands can be supplied at once in an entity.
"""
extracted_ligands = []
next_chain_num = 1
new_editor = None
def _copy_residue(handle):
""" Copy the residue handle into the new chain.
Return the new residue handle."""
nonlocal next_chain_num, new_editor
# Instanciate the editor
if new_editor is None:
new_editor = new_entity.EditXCS()
# Add a new chain
new_chain = None
while new_chain is None:
try:
new_chain = new_editor.InsertChain(str(next_chain_num))
next_chain_num += 1
break
except Exception:
next_chain_num += 1
# Add the residue with residue number 1
new_res = new_editor.AppendResidue(new_chain, handle, deep=True)
new_res.SetIsLigand(True)
new_editor.SetResidueNumber(new_res, mol.ResNum(1))
return new_res
def _process_ligand_residue(res):
"""Copy or fetch the residue. Return the residue handle."""
if res.entity.handle == old_entity.handle:
# Residue is already in copied entity. We only need to grab it
new_res = new_entity.FindResidue(res.chain.name, res.number)
else:
# Residue is not part of the entity, need to copy it first
new_res = _copy_residue(res.handle)
return new_res
for ligand in ligands:
if isinstance(ligand, mol.EntityHandle) or isinstance(ligand, mol.EntityView):
for residue in ligand.residues:
new_residue = _process_ligand_residue(residue)
extracted_ligands.append(new_residue)
elif isinstance(ligand, mol.ResidueHandle) or isinstance(ligand, mol.ResidueView):
new_residue = _process_ligand_residue(ligand)
extracted_ligands.append(new_residue)
else:
raise RuntimeError("Ligands should be given as Entity or Residue")
new_editor.UpdateICS()
return extracted_ligands
__all__ = ["LigandScorer"]
modules/mol/alg/tests/test_ligand_scoring.py
+ 73
− 4
View file @ e8146aea
......@@ -12,18 +12,87 @@ except ImportError:
class TestLigandScoring(unittest.TestCase):
def test_extract_ligands(self):
def test_extract_ligands_mmCIF(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"))
trg, trg_seqres = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True)
mdl, mdl_seqres = io.LoadMMCIF(os.path.join('testfiles', "P84080_model_02.cif.gz"), seqres=True)
sc = LigandScorer(mdl, trg, None, None)
assert len(sc.target_ligands) == 7
assert len(sc.model_ligands) == 1
def test_init_given_ligands(self):
"""Test that we can instantiate the scorer with ligands contained in
the target and model entity and given in a list.
"""
trg, trg_seqres = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True)
mdl, mdl_seqres = io.LoadMMCIF(os.path.join('testfiles', "P84080_model_02.cif.gz"), seqres=True)
# Pass entity views
trg_lig = [trg.Select("rname=MG"), trg.Select("rname=G3D")]
mdl_lig = [mdl.Select("rname=G3D")]
sc = LigandScorer(mdl, trg, mdl_lig, trg_lig)
assert len(sc.target_ligands) == 4
assert len(sc.model_ligands) == 1
# Ensure the residues are not copied
assert len(sc._target.Select("rname=MG").residues) == 2
assert len(sc._target.Select("rname=G3D").residues) == 2
assert len(sc._model.Select("rname=G3D").residues) == 1
# Pass residue handles
trg_lig = [trg.FindResidue("F", 1), trg.FindResidue("H", 1)]
mdl_lig = [mdl.FindResidue("L_2", 1)]
sc = LigandScorer(mdl, trg, mdl_lig, trg_lig)
assert len(sc.target_ligands) == 2
assert len(sc.model_ligands) == 1
# Ensure the residues are not copied
assert len(sc._target.Select("rname=ZN").residues) == 1
assert len(sc._target.Select("rname=G3D").residues) == 2
assert len(sc._model.Select("rname=G3D").residues) == 1
def test_init_sdf_ligands(self):
"""Test that we can instantiate the scorer with ligands from separate SDF files.
In order to setup the ligand SDF files, the following code was used:
for prefix in [os.path.join('testfiles', x) for x in ["1r8q", "P84080_model_02"]]:
trg = io.LoadMMCIF("%s.cif.gz" % prefix)
trg_prot = trg.Select("protein=True")
io.SavePDB(trg_prot, "%s_protein.pdb.gz" % prefix)
lig_num = 0
for chain in trg.chains:
if chain.chain_type == mol.ChainType.CHAINTYPE_NON_POLY:
lig_sel = trg.Select("cname=%s" % chain.name)
lig_ent = mol.CreateEntityFromView(lig_sel, False)
io.SaveEntity(lig_ent, "%s_ligand_%d.sdf" % (prefix, lig_num))
lig_num += 1
"""
mdl = io.LoadPDB(os.path.join('testfiles', "P84080_model_02_nolig.pdb"))
mdl_ligs = [io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))]
trg = io.LoadPDB(os.path.join('testfiles', "1r8q_protein.pdb.gz"))
trg_ligs = [io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_%d.sdf" % i)) for i in range(7)]
# Pass entities
sc = LigandScorer(mdl, trg, mdl_ligs, trg_ligs)
assert len(sc.target_ligands) == 7
assert len(sc.model_ligands) == 1
# Pass residues
mdl_ligs_res = [mdl_ligs[0].residues[0]]
trg_ligs_res = [res for ent in trg_ligs for res in ent.residues]
sc = LigandScorer(mdl, trg, mdl_ligs_res, trg_ligs_res)
assert len(sc.target_ligands) == 7
assert len(sc.model_ligands) == 1
if __name__ == "__main__":
from ost import testutils
......
modules/mol/alg/tests/testfiles/1r8q.pdb.gz 0 → 100644
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modules/mol/alg/tests/testfiles/1r8q_ligand_0.sdf 0 → 100644
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E
1 0 0 0 0 0 999 V2000
4.5270 11.5730 44.1300 Mg 0 0 0 0 0 0
M END
$$$$
modules/mol/alg/tests/testfiles/1r8q_ligand_1.sdf 0 → 100644
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6.3360 15.3620 49.2550 C 0 0 0 0 0 0
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M END
$$$$
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M END
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H
1 0 0 0 0 0 999 V2000
26.8150 -11.4220 38.7710 Zn 0 0 0 0 0 0
M END
$$$$
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I
1 0 0 0 0 0 999 V2000
-21.5950 -13.5060 15.1510 Mg 0 0 0 0 0 0
M END
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$$$$
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$$$$
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1 4 1 0 0 0
1 6 1 0 0 0
5 6 1 0 0 0
5 7 2 0 0 0
5 8 1 0 0 0
5 9 1 0 0 0
9 10 1 0 0 0
10 11 1 0 0 0
11 12 1 0 0 0
11 13 1 0 0 0
12 17 1 0 0 0
13 14 1 0 0 0
13 15 1 0 0 0
14 29 1 0 0 0
15 16 1 0 0 0
15 17 1 0 0 0
17 18 1 0 0 0
18 19 1 0 0 0
18 28 1 0 0 0
19 20 2 0 0 0
20 21 1 0 0 0
21 22 1 0 0 0
21 28 2 0 0 0
22 23 2 0 0 0
22 24 1 0 0 0
24 25 1 0 0 0
25 26 1 0 0 0
25 27 2 0 0 0
27 28 1 0 0 0
29 30 1 0 0 0
29 31 1 0 0 0
29 32 2 0 0 0
M END
$$$$
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