From c445be692c1f8ae2ed75abd5f3e39607c3adf6e3 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 18 Jan 2023 10:25:58 +0100
Subject: [PATCH] feat: SCHWED-5783 document assumptions better
---
modules/mol/alg/pymod/ligand_scoring.py | 51 +++++++++++++++----------
1 file changed, 30 insertions(+), 21 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index d38873290..84d1291ac 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -4,6 +4,7 @@ import numpy as np
import networkx
from ost import mol
+from ost import LogError, LogWarning, LogScript, LogInfo, LogVerbose, LogDebug
from ost.mol.alg import chain_mapping
@@ -18,21 +19,36 @@ class LigandScorer:
(e.g. use ``pip install numpy networkx``)
Mostly expects cleaned up structures (you can use the
- :class:`~ost.mol.alg.scoring.Scorer` outputs for that).
+ :class:`~ost.mol.alg.scoring.Scorer` outputs for that). In addition,
+ you probably want to remove hydrogen atoms from the structures before
+ calling this function. You can do this easily with a selection:
+
+ target_noH = target.Select("ele != H")
+ model_noH = model.Select("ele != H")
+ LigandScorer(model_noH, target_noH, ...)
+
+ Make sure to remove hydrogen atoms from the ligands too.
+
+ The class generally assumes that the
+ :attr:`~ost.mol.ResidueHandle.is_ligand` property is properly set on all
+ the ligand atoms, and only ligand atoms. 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.
: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.
+ input. Hydrogen atoms are kept.
: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.
+ is performed on the input. Hydrogen atoms are kept.
:type target: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param model_ligands: Model ligands, as a list of
- :class:`ost.mol.ResidueHandle` belonging to the model
+ :class:`~ost.mol.ResidueHandle` belonging to the model
entity. Can be instantiated with either a :class:list of
- :class:`ost.mol.ResidueHandle`/:class:`ost.mol.ResidueView`
+ :class:`~ost.mol.ResidueHandle`/:class:`ost.mol.ResidueView`
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`
@@ -40,9 +56,9 @@ class LigandScorer:
entities loaded from mmCIF).
:type model_ligands: :class:`list`
:param target_ligands: Target ligands, as a list of
- :class:`ost.mol.ResidueHandle` belonging to the target
+ :class:`~ost.mol.ResidueHandle` belonging to the target
entity. Can be instanciated either a :class:list of
- :class:`ost.mol.ResidueHandle`/:class:`ost.mol.ResidueView`
+ :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
@@ -141,7 +157,9 @@ class LigandScorer:
if mol.InSequence(residue, residue.next):
raise RuntimeError("Connected residues in non polymer "
"chain %s" % (chain.name))
+ residue.SetIsLigand(True) # just in case
extracted_ligands.append(residue)
+ LogVerbose("Detected residue %s as ligand" % residue)
return extracted_ligands
@staticmethod
@@ -156,17 +174,6 @@ class LigandScorer:
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 = []
@@ -186,7 +193,7 @@ class LigandScorer:
handle.number, handle.chain.name)
raise RuntimeError(msg)
- # Instanciate the editor
+ # Instantiate the editor
if new_editor is None:
new_editor = new_entity.EditXCS()
@@ -196,7 +203,6 @@ class LigandScorer:
new_chain = new_editor.InsertChain(handle.chain.name)
# Add the residue with its original residue number
new_res = new_editor.AppendResidue(new_chain, handle, deep=True)
- new_res.SetIsLigand(True)
return new_res
def _process_ligand_residue(res):
@@ -207,6 +213,7 @@ class LigandScorer:
else:
# Residue is not part of the entity, need to copy it first
new_res = _copy_residue(res.handle)
+ new_res.SetIsLigand(True)
return new_res
for ligand in ligands:
@@ -285,7 +292,9 @@ class LigandScorer:
def ResidueToGraph(residue):
- """Return a NetworkX graph representation of the residue."""
+ """Return a NetworkX graph representation of the residue.
+
+ Nodes are labeled with the Atom's :attr:`~ost.mol.AtomHandle.element`"""
nxg = networkx.Graph()
nxg.add_nodes_from([a.name for a in residue.atoms], element=[a.element for a in residue.atoms])
# This will list all edges twice - once for every atom of the pair.
--
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