From 5bfa7dc7ef40ceff006294acf539e2a8eb303f56 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 22 Sep 2023 18:21:32 +0200
Subject: [PATCH] USalign: pass custom chain mapping as -chainmap argument
---
modules/bindings/pymod/tmtools.py | 21 ++++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 29dcb8c40..c16b1acdf 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -32,7 +32,7 @@ import subprocess, os, tempfile, platform
import ost
from ost import settings, io, geom, seq
-def _SetupFiles(models):
+def _SetupFiles(models, custom_chain_mapping = None):
# create temporary directory
tmp_dir_name=tempfile.mkdtemp()
dia = 'PDB'
@@ -46,6 +46,9 @@ def _SetupFiles(models):
dia = 'CHARMM'
break;
io.SavePDB(model, os.path.join(tmp_dir_name, 'model%02d.pdb' % (index+1)), dialect=dia)
+ if custom_chain_mapping is not None:
+ with open(os.path.join(tmp_dir_name, "custom_mapping.txt"), 'w') as fh:
+ fh.write('\n'.join([f"{mdl_ch}\t{ref_ch}" for ref_ch, mdl_ch in custom_chain_mapping.items()]))
return tmp_dir_name
def _CleanupFiles(dir_name):
@@ -183,6 +186,9 @@ def _RunUSAlign(usalign, tmp_dir):
mat_filename = os.path.join(tmp_dir, "mat.txt")
usalign_path=settings.Locate('USalign', explicit_file_name=usalign)
command = f"{usalign_path} {model1_filename} {model2_filename} -mm 1 -ter 0 -m {mat_filename}"
+ custom_mapping = os.path.join(tmp_dir, "custom_mapping.txt")
+ if os.path.exists(custom_mapping):
+ command += f" -chainmap {custom_mapping}"
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
stdout,_=ps.communicate()
lines=stdout.decode().splitlines()
@@ -319,7 +325,7 @@ def TMScore(model1, model2, tmscore=None):
return result
-def USAlign(model1, model2, usalign=None):
+def USAlign(model1, model2, usalign=None, custom_chain_mapping=None):
"""
Performs a sequence independent superposition of model1 onto model2, the
reference. Can deal with multimeric complexes and RNA.
@@ -334,13 +340,22 @@ def USAlign(model1, model2, usalign=None):
:type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param usalign: If not None, the path to the USalign executable. Searches
for executable with name ``USalign`` in PATH if not given.
+ :param custom_chain_mapping: Custom chain mapping that is passed as -chainmap
+ to USalign executable. Raises an error is this
+ is not supported by the USalign executable you're
+ using (introduced in July 2023).
+ It's a dict with reference chain names as key
+ (model2) and model chain names as values
+ (model1).
+ :type custom_chain_mapping: :class:`dict`
:returns: The result of the superposition
:rtype: :class:`ost.bindings.MMAlignResult`
:raises: :class:`~ost.settings.FileNotFound` if executable could not be located.
:raises: :class:`RuntimeError` if the superposition failed
"""
- tmp_dir_name=_SetupFiles((model1, model2))
+ tmp_dir_name=_SetupFiles((model1, model2),
+ custom_chain_mapping=custom_chain_mapping)
result=_RunUSAlign(usalign, tmp_dir_name)
model1.handle.EditXCS().ApplyTransform(result.transform)
_CleanupFiles(tmp_dir_name)
--
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