remove 3dcomb binding as it is broken with latest code

checked with: https://github.com/realbigws/DeepAlign
commit: cff7c39c89c6706858532b55567083823a0f2657

modules/bindings/pymod/CMakeLists.txt

@@ -13,7 +13,6 @@ blast.py
 cadscore.py
 kclust.py
 ialign.py
-align_3dcomb.py
 )
 
 set(OST_BINDINGS_PYMOD_SOURCES

modules/bindings/pymod/__init__.py

@@ -7,5 +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
 from ._ost_bindings import *

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=next(f)
-        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
-
-
-
-