From c1ab3a0367c1dbd67175308d082a3760ac477f56 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <mariva00@kb-eliot.(none)>
Date: Fri, 5 Oct 2012 16:35:45 +0200
Subject: [PATCH] Bindings for CAD score.
First version. Only AA contacts, the most interesting. Easily expandable.
---
modules/bindings/pymod/CMakeLists.txt | 1 +
modules/bindings/pymod/__init__.py | 4 +-
modules/bindings/pymod/cadscore.py | 154 ++++++++++++++++++++++++++
3 files changed, 158 insertions(+), 1 deletion(-)
create mode 100644 modules/bindings/pymod/cadscore.py
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index 89244b23f..8cd78a87c 100644
--- a/modules/bindings/pymod/CMakeLists.txt
+++ b/modules/bindings/pymod/CMakeLists.txt
@@ -9,5 +9,6 @@ clustalw.py
utils.py
naccess.py
blast.py
+cadscore.py
)
pymod(NAME bindings PY ${OST_BINDINGS})
diff --git a/modules/bindings/pymod/__init__.py b/modules/bindings/pymod/__init__.py
index 388a6054e..e7f855fe8 100644
--- a/modules/bindings/pymod/__init__.py
+++ b/modules/bindings/pymod/__init__.py
@@ -4,4 +4,6 @@ from ost.bindings import blast
from ost.bindings import tmtools
from ost.bindings import naccess
from ost.bindings import hbplus
-from ost.bindings import clustalw
\ No newline at end of file
+from ost.bindings import clustalw
+from ost.bindings import cadscore
+
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
new file mode 100644
index 000000000..fdaef13a9
--- /dev/null
+++ b/modules/bindings/pymod/cadscore.py
@@ -0,0 +1,154 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2009 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+#------------------------------------------------------------------------------
+"""
+Wrapper for the CAD score.
+
+References:
+
+Olechnovic K, Kulberkyte E, Venclovas C., CAD-score: A new contact area
+difference-based function for evaluation of protein structural models
+Proteins. 2012 Aug 30. [Epub ahead of print]
+
+Authors: Valerio Mariani, Alessandro Barbato
+"""
+
+import subprocess, os, tempfile, platform
+from ost import settings, io
+
+def _SetupFiles(model,reference):
+ # create temporary directory
+ tmp_dir_name=tempfile.mkdtemp()
+ dia = 'PDB'
+ for chain in model.chains:
+ if chain.name==" ":
+ raise RuntimeError("One of the chains in the model has no name. Cannot calculate CAD score")
+ if len(chain.name) > 1:
+ dia = 'CHARMM'
+ break;
+ for res in chain.residues:
+ if len(res.name) > 3:
+ dia = 'CHARMM'
+ break;
+ io.SavePDB(model, os.path.join(tmp_dir_name, 'model.pdb'), dialect=dia)
+ dia = 'PDB'
+ for chain in reference.chains:
+ if chain.name==" ":
+ raise RuntimeError("One of the chains in the reference has no name. Cannot calculate CAD score")
+ if len(chain.name) > 1:
+ dia = 'CHARMM'
+ break;
+ for res in chain.residues:
+ if len(res.name) > 3:
+ dia = 'CHARMM'
+ break;
+ io.SavePDB(reference, os.path.join(tmp_dir_name, 'reference.pdb'),dialect=dia)
+ return tmp_dir_name
+
+def _CleanupFiles(dir_name):
+ import shutil
+ shutil.rmtree(dir_name)
+
+
+class CADResult:
+ """
+ Holds the result of running CAD
+
+ .. attribute:: globalAA
+
+ The global CAD's atom-atom (AA) score
+
+ .. attribute:: localAA
+
+ Dictionary containing local CAD's atom-atom (AA) scores.
+
+ :type: dictionary (key: chain.resnum (e.g.: A.24), value: CAD local AA score (see CAD Documentation online)
+ """
+ def __init__(self, globalAA, localAA):
+ self.globalAA=globalAA
+ self.localAA=localAA
+
+def _ParseCADGlobal(lines):
+ interesting_lines=lines[1]
+ aa=float(interesting_lines.split()[10])
+ return aa
+
+def _ParseCADLocal(lines):
+ local_aa_dict={}
+ for lin in lines[11:]:
+ items=lin.split()
+ chain=items[0]
+ resnum=int(items[1])
+ key=chain+'.'+str(resnum)
+ aa=float(items[2])
+ local_aa_dict[key]=aa
+ return local_aa_dict
+
+def _RunCAD(max_iter, tmp_dir):
+ model_filename=os.path.join(tmp_dir, 'model.pdb')
+ reference_filename=os.path.join(tmp_dir, 'reference.pdb')
+ if platform.system() == "Windows":
+ raise RuntimeError('CAD score not available on Windows')
+ else:
+ cad_calc_path=settings.Locate('CADscore_calc.bash')
+ cad_read_g_path=settings.Locate('CADscore_read_global_scores.bash')
+ cad_read_l_path=settings.Locate('CADscore_read_local_scores.bash')
+ command1="\"%s\" -o %i -m \"%s\" -t \"%s\" -D \"%s\"" %(cad_calc_path, max_iter, model_filename, reference_filename, os.path.join(tmp_dir,"cadtemp"))
+ command2="\"%s\" -D \"%s\"" %(cad_read_g_path, os.path.join(tmp_dir,"cadtemp"))
+ command3="\"%s\" -m \"%s\" -t \"%s\" -D \"%s\" -c AA" %(cad_read_l_path, model_filename, reference_filename,os.path.join(tmp_dir,"cadtemp"))
+ ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
+ ps1.wait()
+ ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
+ ps2.wait()
+ lines=ps2.stdout.readlines()
+ try:
+ globalAA=_ParseCADGlobal(lines)
+ except:
+ raise RuntimeError("CAD calculation failed")
+ ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
+ ps3.wait()
+ lines=ps3.stdout.readlines()
+ try:
+ localAA=_ParseCADLocal(lines)
+ except:
+ raise RuntimeError("CAD calculation failed")
+
+ return CADResult(globalAA,localAA)
+
+
+def CADScore(model, reference, max_iter=300):
+ """
+ Calculates global and local atom-atom (AA) CAD Scores
+
+
+ :param model: The model structure.
+ :type model: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param reference: The reference structure
+ :type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param max_iter: Optional. The maximum number of iteration for the tessellation algorithm before giving up. By default 300
+ :returns: The result of the CAD score calculation
+ :rtype: :class:`CADResult`
+
+ :raises: :class:`~ost.settings.FileNotFound` if any of the CAD score exacutables could not be located.
+ :raises: :class:`RuntimeError` if the calculation failed
+ """
+ tmp_dir_name=_SetupFiles(model, reference)
+ result=_RunCAD(max_iter, tmp_dir_name)
+ _CleanupFiles(tmp_dir_name)
+ return result
+
--
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