[Cctbx-cvs] SF.net SVN: cctbx:[13482] trunk/iotbx/command_line/cablam_annote.py

[<Met...@us...>]

Revision: 13482
          http://cctbx.svn.sourceforge.net/cctbx/?rev=13482&view=rev
Author:   MetalHeadd
Date:     2011-07-13 19:46:43 +0000 (Wed, 13 Jul 2011)

Log Message:
-----------
oops...moved cablam_annote back to mmtbx/command_line

Removed Paths:
-------------
    trunk/iotbx/command_line/cablam_annote.py

Deleted: trunk/iotbx/command_line/cablam_annote.py
===================================================================
--- trunk/iotbx/command_line/cablam_annote.py	2011-07-13 19:40:59 UTC (rev 13481)
+++ trunk/iotbx/command_line/cablam_annote.py	2011-07-13 19:46:43 UTC (rev 13482)
@@ -1,97 +0,0 @@
-# LIBTBX_SET_DISPATCHER_NAME phenix.cablam_annote
-
-from iotbx import pdb
-import libtbx.phil
-import sys, os
-
-master_phil = libtbx.phil.parse("""
-cablam {
-  file_name = None
-    .type = path
-    .multiple = true
-    .short_caption = PDB file
-    .help = '''input coordinate file (pdb)'''
-  kin = False
-    .type = bool
-    .short_caption = generate kinemage output
-    .help = '''generate kinemage output'''
-}
-""", process_includes=True)
-
-def run(args):
-  from mmtbx.cablam import cablam_annote, cablam_math, cablam_res
-  from iotbx import file_reader
-  interpreter = master_phil.command_line_argument_interpreter()
-  pdb_files = []
-  sources = []
-  for arg in args :
-    if os.path.isfile(arg) :
-      input_file = file_reader.any_file(arg)
-      if (input_file.file_type == "pdb") :
-        pdb_files.append(input_file)
-        sources.append(interpreter.process(arg="file_name=\"%s\"" % arg))
-    else :
-      arg_phil = interpreter.process(arg=arg)
-      sources.append(arg_phil)
-  work_phil = master_phil.fetch(sources=sources)
-  work_params = work_phil.extract()
-  if len(work_params.cablam.file_name) == 0 :
-    if len(pdb_files) == 0 :
-      summary = "insert help txt here"
-      raise Usage(summary)
-    else :
-      for pdb_file in pdb_files:
-        work_params.cablam.file_name.append(pdb_file.file_name)
-  params = work_params.cablam
-  #parser = argparse.ArgumentParser()
-  #parser.add_argument('file_or_dir',
-  #  help='the path to the file or directory to be operated on')
-  #parser.add_argument('--kin', action='store_true',
-  #  help='flag to get kinemage output')
-
-  #args = parser.parse_args()
-
-  #if os.path.isdir(args.file_or_dir):
-  #  fileset = os.listdir(args.file_or_dir)
-  #  dirpath = args.file_or_dir
-  #elif os.path.isfile(args.file_or_dir):
-  #  fileset = [args.file_or_dir]
-  #  dirpath = None
-  #else:
-  #  sys.stderr.write("Could not identify valid target file or dir.\n")
-  #  ## print the help section
-  #  sys.exit()
-
-  #for filename in fileset:
-  #  if dirpath: #must add the path if using the listed contents of a dir
-  #    filename = os.path.join(dirpath,filename)
-  #  else:
-  #    pass
-  for filename in params.file_name:
-    pdb_io = pdb.input(filename)
-    pdbid = os.path.basename(filename)
-
-    sys.stderr.write(pdbid+'\n')
-    hierarchy = pdb_io.construct_hierarchy()
-    resdata = cablam_res.construct_linked_residues(
-      hierarchy, targetatoms=["CA","O","C","N"], pdbid=pdbid)
-
-    cablam_math.CApseudos(resdata, dodihedrals=True, doangles=True)
-
-    dsspcodes = ['H','G','I','E','B','S','T','X']
-    for dsspcode in dsspcodes:
-      cablam_annote.annote_dssp_3d(resdata,dsspcode)
-
-    reskeys = resdata.keys()
-    reskeys.sort()
-
-    if resdata:
-      if params.kin:
-        cablam_annote.print_annoted_kin(resdata)
-      else:
-        cablam_annote.print_annoted_text_human(resdata)
-
-#{{{ __main__
-if __name__ == "__main__":
-  run(sys.argv[1:])
-#}}}


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