Added binding for a structural alignment tool 3DComb

modules/bindings/pymod/CMakeLists.txt

@@ -13,5 +13,6 @@ blast.py
 cadscore.py
 kclust.py
 ialign.py
+align_3dcomb.py
 )
 pymod(NAME bindings PY ${OST_BINDINGS})

modules/bindings/pymod/__init__.py

@@ -7,3 +7,4 @@ from ost.bindings import naccess
 from ost.bindings import hbplus
 from ost.bindings import clustalw
 from ost.bindings import cadscore
+from ost.bindings import align_3dcomb

modules/bindings/pymod/align_3dcomb.py

+"""
+3DCOMB module
+
+Author: Niklaus Johner
+
+This module is for structural alignment from OpenStructure using the external program 3DCOMB.
+
+How To Use This Module:
+ 1. Import it (e.g. as "from ost.bindings import align_3dcomb")
+ 2. Use it (e.g. as "alignment,transformation_list = align_3dcomb.AlignStructures(view_list)")
+
+Requirement:
+ - 3DCOMB installed
+"""
+
+from ost.bindings import utils
+import subprocess,os
+from ost import settings
+from ost import io
+import ost
+import ost.geom
+
+def _GetExecutable(comb_exe, comb_env):
+  """
+    Function to check if 3DCOMB executable is present
+    
+    :param comb_exe: Explicit path to 3DCOMB executable
+    :param msms_env: Environment variable pointing to 3DCOMB executable
+    :returns: Path to the executable
+    :raises:  :class:`~ost.FileNotFound` if executable is not found
+    """
+  return settings.Locate(['3DCOMB_linux','3DCOMB_win.exe'], explicit_file_name=comb_exe,
+                         env_name=comb_env)
+
+def _SetupFiles(structure_list):
+  """
+    Setup files for MSMS calculation in temporary directory
+    
+    :param structure_list: A list of EntityView that will be aligned.\
+      each EntityView should contain a single chain and each residue needs to have a CA atom.
+    :returns: calss:settings.TempDir
+    :raises:  class:`RuntimeError` if on of the Views is not valid
+  """
+  
+  #write out temporary pdb files
+  if not all([ev.IsValid() for ev in structure_list]):
+    raise RuntimeError, "Invalid EntityView in structure_list"
+  tpd=utils.TempDirWithFiles(structure_list)
+  
+  #Write out the file containing the list of all structures
+  outfile=open(os.path.join(tpd.dirname,'list'),'w')
+  outfile.write('\n'.join(tpd.files))
+  outfile.close()
+  return tpd
+
+
+def _Run3DCOMB(command,tpd):
+  """
+    Run the 3DCOMB alignment command
+    
+    This functions starts the external 3DCOMB executable and returns the stdout of
+    3DCOMB.
+    
+    :param command:          Command to execute
+    :returns:                 stdout of 3DCOMB
+    :raises:              :class:`CalledProcessError` for non-zero return value
+    """
+  outname=os.path.join(tpd.dirname,'align.out')
+  outfile=open(outname,'w')
+  returncode=subprocess.call(command, shell=True, stdout=outfile)
+  outfile.close()
+  #check for successful completion of 3DCOMB
+  if returncode!=0:
+    print "WARNING: 3DCOMB error\n"
+    raise subprocess.CalledProcessError
+  return returncode
+
+def _ParseOutput(tpd):
+  #Read Alignment
+  ali=io.LoadAlignment(os.path.join(tpd.dirname,'list.ali'),'fasta')
+  for i in range(ali.GetCount()):
+    ali.SetSequenceName(i,'struc{0}'.format(i))
+  #Read Transformations
+  f=open(os.path.join(tpd.dirname,'list.rmt'),'r')
+  Tl=[]
+  for l in f:
+    if l.startswith('>'):
+      fl=ost.FloatList()
+      for i in range(3):
+        l=f.next()
+        sl=l.split(',')
+        fl.extend([float(el) for el in sl[0].split()+[sl[1]]])
+      fl.extend([0,0,0,1])
+      T=ost.geom.Transform()
+      M=ost.geom.Mat4(*fl)
+      T.SetMatrix(M)
+      Tl.append(T)
+  #Read standard output
+  outfile=open(os.path.join(tpd.dirname,'align.out'),'r')
+  results={}
+  for line in outfile:
+    if line.startswith('Objective function value is'):results['objective_function']=float(line.split()[-1])
+    if line.startswith('CORE_LEN'):
+      l=line.split(',')
+      for el in l:
+        s=el.split('=')
+        results[s[0]]=float(s[1])
+  return ali,Tl,results
+
+
+def AlignStructures(structure_list,apply_transform=False,name_list=None,comb_exe=None,comb_env=None):
+  comb_executable=_GetExecutable(comb_exe, comb_env)
+  tpd=_SetupFiles(structure_list)
+  command=' '.join([comb_executable,os.path.join(tpd.dirname,'list')])
+  returncode=_Run3DCOMB(command,tpd)
+  try:ali,Tl,results=_ParseOutput(tpd)
+  except:
+    print 'could not parse output'
+    raise RuntimeError
+  if apply_transform:
+    for T,ev in zip(Tl,structure_list):
+      ev.handle.FixTransform()
+      ev.handle.SetTransform(T)
+  tpd.Cleanup()
+  return ali,Tl,results
+
+
+
+