From 8297d991fae8d67e4e37f0397ade6645dde4cfc4 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 6 Apr 2010 14:25:45 +0000
Subject: [PATCH] move DSSP bindings from internal to main repo
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1930 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/CMakeLists.txt | 2 +-
modules/bindings/pymod/dssp.py | 182 ++++++++++++++++++++++++++
2 files changed, 183 insertions(+), 1 deletion(-)
create mode 100644 modules/bindings/pymod/dssp.py
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index 5dd7a1cc9..c17cb439f 100644
--- a/modules/bindings/pymod/CMakeLists.txt
+++ b/modules/bindings/pymod/CMakeLists.txt
@@ -1 +1 @@
-pymod(NAME bindings PY __init__.py lga.py hbplus.py msms.py tmtools.py)
+pymod(NAME bindings PY __init__.py lga.py hbplus.py msms.py tmtools.py dssp.py)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
new file mode 100644
index 000000000..6594d639b
--- /dev/null
+++ b/modules/bindings/pymod/dssp.py
@@ -0,0 +1,182 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+"""
+Utility functions to load secondary structure information from DSSP files
+and assign them to entities.
+
+Authors: Pascal Benkert, Marco Biasini
+"""
+
+import os
+import tempfile
+
+from ost import io,mol
+from ost import settings
+
+
+def _SkipHeader(stream):
+ line=stream.readline()
+ while line:
+ if line.strip().find('#')==0:
+ return True
+ line=stream.readline()
+ return False
+
+
+def _ExecuteDSSP(path, temp_dir=None):
+ # use of mktemp is a safty problem (use mkstemp and provide file handle to
+ # subsequent process
+ temp_dssp_path=tempfile.mktemp(suffix=".out",prefix="dssp", dir=temp_dir)
+ dssp_abs_path=settings.Locate('dssp', env_name='DSSP_EXECUTABLE')
+ status = os.system(dssp_abs_path+" "+path+" 2>/dev/null 1> "+temp_dssp_path)
+ return temp_dssp_path
+
+
+def _CalcRelativeSA(residue_type, absolute_sa):
+ solvent_max_list=[118,317,238,243,183,262,286,154,258,228,
+ 243,278,260,271,204,234,206,300,303,216] #TODO: source?
+ residue_indices = "ARNDCQEGHILKMFPSTWYV"
+ if residue_type.islower()==True:
+ residue_type='C'
+ if residue_indices.find(residue_type)==-1:
+ raise RuntimeError('residue %s is a non-standard residue' %(residue_type))
+ else:
+ rel=float(absolute_sa)/(solvent_max_list[residue_indices.find(residue_type)])
+ return rel
+
+
+def AssignDSSP(ent, pdb_path="", extract_burial_status_flag=0, tmp_dir=None):
+ entity_saved_flag = 0
+ if pdb_path=="":
+ # use of mktemp is a safty problem (use mkstemp and provide file handle to
+ # subsequent process
+ pdb_path=tempfile.mktemp(suffix=".pdb",prefix="temp_entity",
+ dir=tmp_dir)
+ io.SaveEntity(ent, pdb_path)
+ entity_saved_flag = 1
+
+ #TODO: exception handling (currently errors occuring here
+ # are handled in the parser LoadDSSP)
+ temp_dssp_path=_ExecuteDSSP(pdb_path)
+
+ # assign DSSP to entity
+ try:
+ LoadDSSP(temp_dssp_path, ent, extract_burial_status_flag,
+ entity_saved_flag)
+ except Exception, e:
+ # clean up
+ print "Exception in DSSP:", e
+ if entity_saved_flag == 1:
+ os.remove(pdb_path)
+ os.remove(temp_dssp_path)
+ raise RuntimeError(e)
+
+ # clean up
+ #print pdb_path, temp_dssp_path
+ if entity_saved_flag == 1:
+ os.remove(pdb_path)
+ os.remove(temp_dssp_path)
+
+ return ent
+
+
+
+def LoadDSSP(file_name, model, extract_burial_status_flag=0,
+ entity_saved_flag=0, calculate_relative_sa=True):
+ if model.IsValid() == 0:
+ print "DSSP: model is not valid"
+ stream=open(file_name)
+ if not _SkipHeader(stream):
+ stream.close()
+ raise RuntimeError('Ill-formatted DSSP file')
+
+ for line in stream:
+ num=line[6:10].strip()
+ ins_code=line[10].strip()
+ chain_name=line[11]
+ solvent_accessibility=float(line[34:39].strip())
+ #solvent_accessibility=line[34:39].strip()
+ amino_acid=line[13]
+ #print line
+
+
+ if isinstance(model,mol.ChainView):
+ chain=model
+ else:
+ chain=model.FindChain(chain_name)
+
+ if not chain.IsValid():
+ continue
+ if num=='':
+ continue
+ residue=None
+ try:
+ if ins_code == "":
+ residue=chain.FindResidue(mol.ResNum(int(num)))
+ else:
+ residue=chain.FindResidue(mol.ResNum(int(num),ins_code))
+
+ # set property "burial status:
+ if extract_burial_status_flag == 1:
+ #set default (dummy) burial status for incomplete residues:
+ residue.SetGenericStringProperty("burial_status", 'X')
+
+ #handle seleno-methionine appearing as amino acid 'X' in DSSP:
+ if residue.name=="MSE" and amino_acid=='X':
+ amino_acid='M'
+
+ residue.SetGenericFloatProperty("solvent_accessibility",
+ solvent_accessibility)
+ if calculate_relative_sa:
+ relative_sa=_CalcRelativeSA(amino_acid,solvent_accessibility)
+ residue.SetGenericFloatProperty("relative_solvent_accessibility",
+ relative_sa)
+ if relative_sa < 0.25:
+ residue.SetGenericStringProperty("burial_status", 'b')
+ else:
+ residue.SetGenericStringProperty("burial_status", 'e')
+ except Exception, e:
+ print "ERROR:",e
+ continue
+
+ rtype=line[16:17]
+ rt=mol.SecStructure.COIL
+ if rtype=='H':
+ rt=mol.SecStructure.ALPHA_HELIX
+ elif rtype=='E':
+ rt=mol.SecStructure.EXTENDED
+ elif rtype=='B':
+ rt=mol.SecStructure.BETA_BRIDGE
+ elif rtype=='S':
+ rt=mol.SecStructure.BEND
+ elif rtype=='T':
+ rt=mol.SecStructure.TURN
+ elif rtype=='I':
+ rt=mol.SecStructure.PI_HELIX
+ elif rtype=='G':
+ rt=mol.SecStructure.THREE_TEN_HELIX
+ # for corrupted DSSP files. Catch in calling routine:
+ if residue.IsValid() == 0:
+ #Todo: if residues with occupancy 0 have been removed before
+ #using a selection statement, they are missed here
+ #IMPORTANT: asign DSSP before any selections
+ stream.close()
+ raise RuntimeError('Ill-formatted DSSP file: invalid residue')
+ residue.SetSecStructure(mol.SecStructure(rt))
+ stream.close()
--
GitLab