diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index bb7557d6ffe83550814da5bf93c6efb3ce3d9c2c..fc197d71a20d0d41f14fca019119c952b9292eec 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -316,6 +316,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
target_ligands=reference_ligands,
resnum_alignments=args.residue_number_alignment,
check_resnames=args.enforce_consistency,
+ rename_ligand_chain=True,
substructure_match=args.substructure_match,
radius=args.radius,
lddt_pli_radius=args.lddt_pli_radius,
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 85190fe114adc9096ffc8d30bba01af95dc5a48b..9e3616cb33d816ebcc81dcc01ee44da06f2237a0 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -138,6 +138,16 @@ class LigandScorer:
:param check_resnames: On by default. Enforces residue name matches
between mapped model and target residues.
:type check_resnames: :class:`bool`
+ :param rename_ligand_chain: If a residue with the same chain name and
+ residue number than an explicitly passed model
+ or target ligand exits in the structure,
+ and `rename_ligand_chain` is False, a
+ RuntimeError will be raised. If
+ `rename_ligand_chain` is True, the ligand will
+ be moved to a new chain instead, and the move
+ will be logged to the console with SCRIPT
+ level.
+ :type rename_ligand_chain: :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.
@@ -158,6 +168,7 @@ class LigandScorer:
"""
def __init__(self, model, target, model_ligands=None, target_ligands=None,
resnum_alignments=False, check_resnames=True,
+ rename_ligand_chain=False,
chain_mapper=None, substructure_match=False,
radius=4.0, lddt_pli_radius=6.0, lddt_bs_radius=10.0,
binding_sites_topn=100000):
@@ -180,7 +191,9 @@ class LigandScorer:
if target_ligands is None:
self.target_ligands = self._extract_ligands(self.target)
else:
- self.target_ligands = self._prepare_ligands(self.target, target, target_ligands)
+ self.target_ligands = self._prepare_ligands(self.target, target,
+ target_ligands,
+ rename_ligand_chain)
if len(self.target_ligands) == 0:
raise ValueError("No ligands in the target")
@@ -188,13 +201,16 @@ class LigandScorer:
if model_ligands is None:
self.model_ligands = self._extract_ligands(self.model)
else:
- self.model_ligands = self._prepare_ligands(self.model, model, model_ligands)
+ self.model_ligands = self._prepare_ligands(self.model, model,
+ model_ligands,
+ rename_ligand_chain)
if len(self.model_ligands) == 0:
raise ValueError("No ligands in the model")
self._chain_mapper = chain_mapper
self.resnum_alignments = resnum_alignments
self.check_resnames = check_resnames
+ self.rename_ligand_chain = rename_ligand_chain
self.substructure_match = substructure_match
self.radius = radius
self.lddt_pli_radius = lddt_pli_radius
@@ -266,7 +282,7 @@ class LigandScorer:
return extracted_ligands
@staticmethod
- def _prepare_ligands(new_entity, old_entity, ligands):
+ def _prepare_ligands(new_entity, old_entity, ligands, rename_chain):
"""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.
@@ -283,27 +299,40 @@ class LigandScorer:
next_chain_num = 1
new_editor = None
- def _copy_residue(handle):
+ def _copy_residue(handle, rename_chain):
""" Copy the residue handle into the new chain.
Return the new residue handle."""
nonlocal next_chain_num, new_editor
- # Does a residue with the same name already exist?
- already_exists = new_entity.FindResidue(handle.chain.name,
- handle.number).IsValid()
- if already_exists:
- msg = "A residue number %s already exists in chain %s" % (
- handle.number, handle.chain.name)
- raise RuntimeError(msg)
-
# Instantiate the editor
if new_editor is None:
new_editor = new_entity.EditXCS()
- # Get or create the chain
new_chain = new_entity.FindChain(handle.chain.name)
if not new_chain.IsValid():
new_chain = new_editor.InsertChain(handle.chain.name)
+ else:
+ # Does a residue with the same name already exist?
+ already_exists = new_chain.FindResidue(handle.number).IsValid()
+ if already_exists:
+ if rename_chain:
+ chain_ext = 2 # Extend the chain name by this
+ while True:
+ new_chain_name = handle.chain.name + "_" + str(chain_ext)
+ new_chain = new_entity.FindChain(new_chain_name)
+ if new_chain.IsValid():
+ chain_ext += 1
+ continue
+ else:
+ new_chain = new_editor.InsertChain(new_chain_name)
+ break
+ LogScript("Moved ligand residue %s to new chain %s" % (
+ handle.qualified_name, new_chain.name))
+ else:
+ msg = "A residue number %s already exists in chain %s" % (
+ handle.number, handle.chain.name)
+ raise RuntimeError(msg)
+
# Add the residue with its original residue number
new_res = new_editor.AppendResidue(new_chain, handle, deep=True)
for old_atom in handle.atoms:
@@ -313,7 +342,7 @@ class LigandScorer:
new_editor.Connect(new_first, new_second)
return new_res
- def _process_ligand_residue(res):
+ def _process_ligand_residue(res, rename_chain):
"""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
@@ -321,7 +350,7 @@ class LigandScorer:
LogVerbose("Ligand residue %s already in entity" % res.handle.qualified_name)
else:
# Residue is not part of the entity, need to copy it first
- new_res = _copy_residue(res.handle)
+ new_res = _copy_residue(res.handle, rename_chain)
LogVerbose("Copied ligand residue %s" % res.handle.qualified_name)
new_res.SetIsLigand(True)
return new_res
@@ -329,10 +358,10 @@ class LigandScorer:
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)
+ new_residue = _process_ligand_residue(residue, rename_chain)
extracted_ligands.append(new_residue)
elif isinstance(ligand, mol.ResidueHandle) or isinstance(ligand, mol.ResidueView):
- new_residue = _process_ligand_residue(ligand)
+ new_residue = _process_ligand_residue(ligand, rename_chain)
extracted_ligands.append(new_residue)
else:
raise RuntimeError("Ligands should be given as Entity or Residue")