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__init__.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* Scott Dixon, Metaphorics, LLC
#-* 
#-*
#Z* -------------------------------------------------------------------

import os
import shutil
import glob
import re
import string
import sys
import time

from chempy import feedback

# "do" is the preferred command for running tinker

def do(command,in_prefix,run_prefix,out_prefix,tokens,capture=None):
   if feedback['tinker']:
      print " "+str(__name__)+': creating temporary files "%s.*"' % (run_prefix)
      print " "+str(__name__)+': launching %s...' % command
      c = 1
      for a in tokens:
         print " "+str(__name__)+': input %d = %s' % (c,a)
         c = c + 1
      if hasattr(sys.stdout,"flush"):
         sys.stdout.flush()
   for a in glob.glob(run_prefix+".*"):
      os.unlink(a)
   for a in glob.glob(out_prefix+".*"):
      os.unlink(a)
   for src in glob.glob(in_prefix+".*"):
      dst = string.split(src,'.')
      dst = run_prefix+'.'+dst[len(dst)-1]
      shutil.copyfile(src,dst)
   if capture==1:
      pipe = os.popen(bin_path+command+"> "+run_prefix+".out","w")      
   elif capture==2:
      pipe = os.popen(bin_path+command+" | tee "+run_prefix+".out","w")      
   else:
      pipe = os.popen(bin_path+command,"w")
   if not pipe:
      print "Error: can't run tinker!!!"
      raise RunError
   for a in tokens:
      pipe.write(a+"\n")
   pipe.close()
# NFS workaround (flushes the directory cache so that glob will work)
   try: os.unlink(".sync")
   except: pass
   f = open(".sync",'w')
   f.close()
#
   for src in glob.glob(run_prefix+".*_2"):
      dst = string.replace(src,'_2','')
      if os.path.exists(dst):
         os.unlink(dst)
#      os.rename(src,dst)    rename can fail over NFS (remote action)
      shutil.copyfile(src,dst)
# sloppy workaround for buggy NFS on linux
      os.unlink(src)
   for src in glob.glob(run_prefix+".*"):
      dst = string.split(src,'.')
      dst = out_prefix+'.'+dst[len(dst)-1]
      if os.path.exists(dst):
         os.unlink(dst)
#      os.rename(src,dst)    rename can fail over NFS (remote action)  
      shutil.copy(src,dst)
      os.unlink(src)
   for a in glob.glob(in_prefix+".*"):
      os.unlink(a)
   if feedback['tinker']:
      print " "+str(__name__)+': %s job complete. ' % command
      print " "+str(__name__)+': creating output files "%s.*"' % (out_prefix)

#  DEPRECATED

prefix = "tinker_run"

def run(command,in_prefix,out_prefix,tokens,capture=None):
   if feedback['tinker']:
      print " "+str(__name__)+': creating temporary files "%s.*"' % (prefix)
      print " "+str(__name__)+': launching %s...' % command
      c = 1
      for a in tokens:
         print " "+str(__name__)+': input %d = %s' % (c,a)
         c = c + 1
      if hasattr(sys.stdout,"flush"):
         sys.stdout.flush()
   for a in glob.glob(prefix+".*"):
      os.unlink(a)
   for a in glob.glob(out_prefix+".*"):
      os.unlink(a)
   for src in glob.glob(in_prefix+".*"):
      dst = string.split(src,'.')
      dst = prefix+'.'+dst[len(dst)-1]
      shutil.copyfile(src,dst)
   if capture:
      pipe = os.popen(bin_path+command+"> "+out_prefix+".out","w")      
   else:
      pipe = os.popen(bin_path+command,"w")
   if not pipe:
      print "Error: can't run tinker!!!"
      raise RunError
   for a in tokens:
      pipe.write(a+"\n")
   pipe.close()
   for src in glob.glob(prefix+".*_2"):
      dst = string.replace(src,'_2','')
      if os.path.exists(dst):
         os.unlink(dst)
#      os.rename(src,dst)    rename can fail over NFS (remote action)  
      shutil.copy(src,dst)
      os.unlink(src)
   for src in glob.glob(prefix+".*"):
      dst = string.split(src,'.')
      dst = out_prefix+'.'+dst[len(dst)-1]
      if os.path.exists(dst):
         os.unlink(dst)
#      os.rename(src,dst)    rename can fail over NFS (remote action)  
      shutil.copy(src,dst)
   if feedback['tinker']:
      print " "+str(__name__)+': %s job complete. ' % command
      print " "+str(__name__)+': creating output files "%s.*"' % (out_prefix)

if os.environ.has_key('TINKER_PATH'):
   base = os.environ['TINKER_PATH']
   bin_path = base + '/bin/'
   params_path = base + '/params/'
elif os.environ.has_key('FREEMOL_ETC'):
   base = os.environ['FREEMOL_ETC'] + '/tinker'
   bin_path = base + '/bin/'
   params_path = base + '/params/'
else:
   base = ''
   bin_path = ''
   params_path = ''

if os.environ.has_key('PYMOL_PATH'):
   pymol_path = os.environ['PYMOL_PATH']
   test_path = pymol_path + '/data/chempy/tinker/'
   if os.path.exists(test_path):
      params_path = test_path


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