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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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