From 2ac197c7982a7e0545d8a14476c387a5ab24f0ef Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 15 Apr 2010 13:19:49 +0000
Subject: [PATCH] parse and return detailed info for tmalign
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2015 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/tmtools.py | 21 ++++++++++++++++-----
1 file changed, 16 insertions(+), 5 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 76abc5324..b8ab2a261 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -41,8 +41,19 @@ def _SetupFiles(models):
def _CleanupFiles(dir_name):
import shutil
shutil.rmtree(dir_name)
-
+
+class TMAlignResult:
+ def __init__(self, rmsd, tm_score, aligned_length, transform):
+ self.rmsd=rmsd
+ self.tm_score=tm_score
+ self.aligned_length=aligned_length
+ self.transform=transform
+
def _ParseTmAlign(lines):
+ info_line=lines[11].split(',')
+ aln_length=float(info_line[0].split('=')[1].strip())
+ rmsd=float(info_line[1].split('=')[1].strip())
+ tm_score=float(info_line[2].split('=')[1].strip())
tf1=[float(i.strip()) for i in lines[15].split()]
tf2=[float(i.strip()) for i in lines[16].split()]
tf3=[float(i.strip()) for i in lines[17].split()]
@@ -50,7 +61,7 @@ def _ParseTmAlign(lines):
tf2[4], tf3[2], tf3[3], tf3[4])
tf=geom.Mat4(rot)
tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
- return tf
+ return TMAlignResult(rmsd, aln_length, tm_score, tf)
def _RunTmAlign(tmalign, tmp_dir):
tmalign_path=settings.Locate('tmalign', explicit_file_name=tmalign)
@@ -108,10 +119,10 @@ def TMAlign(model1, model2, tmalign=None):
Run tmalign on two protein structures
"""
tmp_dir_name=_SetupFiles((model1, model2))
- tf=_RunTmAlign(tmalign, tmp_dir_name)
- model1.handle.RequestXCSEditor().ApplyTransform(tf)
+ result=_RunTmAlign(tmalign, tmp_dir_name)
+ model1.handle.RequestXCSEditor().ApplyTransform(result.transform)
_CleanupFiles(tmp_dir_name)
-
+ return result
def TMScore(model1, model2, tmscore=None):
"""
Run tmscore on two protein structures
--
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