From 656b852ba7cfacd8e81449538c31de3e835c0d0d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 19 Apr 2022 14:10:45 +0200
Subject: [PATCH] lDDT: code cleanups
---
modules/mol/alg/pymod/lddt.py | 93 ++++++++++++++++++++---------------
1 file changed, 52 insertions(+), 41 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index c14ea43a2..7fba7a74c 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -638,10 +638,53 @@ class lDDTScorer:
No distance related members - see _SetupDistances
"""
+ residue_numbers = self._GetTargetResidueNumbers(self.target,
+ seqres_mapping)
+ current_idx = 0
+ for chain in self.target.chains:
+ ch_name = chain.GetName()
+ self.chain_names.append(ch_name)
+ self.chain_start_indices.append(current_idx)
+ self.chain_res_start_indices.append(len(self.compound_names))
+ for r, rnum in zip(chain.residues, residue_numbers[ch_name]):
+ 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,
+ calpha)
+
+ self.res_start_indices.append(current_idx)
+ self.res_mapper[(ch_name, rnum)] = len(self.compound_names)
+ self.compound_names.append(r.name)
+ self.res_resnums.append(rnum)
+
+ atoms = [r.FindAtom(an) for an in self.compound_anames[r.name]]
+ for a in atoms:
+ if a.IsValid():
+ self.atom_indices[a.handle.GetHashCode()] = current_idx
+ current_idx += 1
+
+ if r.name in self.compound_symmetric_atoms:
+ for sym_tuple in self.compound_symmetric_atoms[r.name]:
+ for a_idx in sym_tuple:
+ a = atoms[a_idx]
+ if a.IsValid():
+ hashcode = a.handle.GetHashCode()
+ self.symmetric_atoms.add(
+ self.atom_indices[hashcode]
+ )
+ self.n_atoms = current_idx
+
+
+ def _GetTargetResidueNumbers(self, target, seqres_mapping):
+ """Returns residue numbers for each chain in target as dict
+
+ They're either directly extracted from the raw residue number
+ from the structure or from user provided alignments
+ """
residue_numbers = dict()
- for ch in self.target.chains:
+ for ch in target.chains:
ch_name = ch.GetName()
- self.chain_names.append(ch_name)
rnums = list()
if ch_name in seqres_mapping:
seqres = seqres_mapping[ch_name].GetSequence(0).GetString()
@@ -685,39 +728,7 @@ class lDDTScorer:
)
assert len(rnums) == len(ch.residues)
residue_numbers[ch_name] = rnums
-
- current_idx = 0
- for chain in self.target.chains:
- ch_name = chain.GetName()
- self.chain_start_indices.append(current_idx)
- self.chain_res_start_indices.append(len(self.compound_names))
- for r, rnum in zip(chain.residues, residue_numbers[ch_name]):
- 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,
- calpha)
-
- self.res_start_indices.append(current_idx)
- self.res_mapper[(ch_name, rnum)] = len(self.compound_names)
- self.compound_names.append(r.name)
- self.res_resnums.append(rnum)
-
- atoms = [r.FindAtom(an) for an in self.compound_anames[r.name]]
- for a in atoms:
- if a.IsValid():
- self.atom_indices[a.handle.GetHashCode()] = current_idx
- current_idx += 1
-
- for sym_tuple in self.compound_symmetric_atoms[r.name]:
- for a_idx in sym_tuple:
- a = atoms[a_idx]
- if a.IsValid():
- hashcode = a.handle.GetHashCode()
- self.symmetric_atoms.add(
- self.atom_indices[hashcode]
- )
- self.n_atoms = current_idx
+ return residue_numbers
def _SetupCompound(self, r, compound_lib, symmetry_settings, calpha):
"""fill self.compound_anames/self.compound_symmetric_atoms
@@ -735,22 +746,22 @@ class lDDTScorer:
for atom_spec in compound.GetAtomSpecs():
if atom_spec.element not in ["H", "D"]:
atom_names.append(atom_spec.name)
- self.compound_anames[r.name] = atom_names
if r.name in symmetry_settings.symmetric_compounds:
for pair in symmetry_settings.symmetric_compounds[r.name]:
try:
- a = self.compound_anames[r.name].index(pair[0])
- b = self.compound_anames[r.name].index(pair[1])
+ a = atom_names.index(pair[0])
+ b = atom_names.index(pair[1])
except:
msg = f"Could not find symmetric atoms "
msg += f"({pair[0]}, {pair[1]}) for {r.name} "
msg += f"as specified in SymmetrySettings in "
msg += f"compound from component dictionary. "
- msg += f"Atoms in compound: "
- msg += f"{self.compound_anames[r.name]}"
+ msg += f"Atoms in compound: {atom_names}"
raise RuntimeError(msg)
symmetric_atoms.append((a, b))
- self.compound_symmetric_atoms[r.name] = symmetric_atoms
+ self.compound_anames[r.name] = atom_names
+ if len(symmetric_atoms) > 0:
+ self.compound_symmetric_atoms[r.name] = symmetric_atoms
def _SetupDistances(self):
"""Compute distance related members of lDDTScorer
--
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