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#!/usr/bin/python
#
import sys, getopt
optlist, args = getopt.getopt(sys.argv[1:], 'hai', [
'help', 'again', 'overwriteLog', 'uniqueLog', 'noLog', 'die',
'customizer=', 'interactive'] )
help_msg = """usage: %s <options>
-h or --help : print this message
-a or --again : play back lastlog file
--overwriteLog : overwrite log file
--uniqueLog : create a log file with a unique name
--noLog : turn off logging
--die : do not start GUI event loop
--customizer file : run the user specified file
--lib packageName : add a libraries of commands""" % sys.argv[0]
customizer = None
logmode = 'overwrite'
libraries = []
again = 0
interactive = 0
die=0
for opt in optlist:
if opt[ 0] in ('-h', '--help'):
print help_msg
sys.exit()
elif opt[ 0] in ('-a', '--again'):
again = 1
import os
os.system("mv mvAll.log.py .tmp.py")
elif opt[ 0] =='--overwriteLog': logmode = 'overwrite'
elif opt[ 0] =='--uniqueLog': logmode = 'unique'
elif opt[ 0] =='--noLog': logmode = 'no'
elif opt[ 0] =='--die': die = 1
elif opt[ 0] == '--customizer':
customFile = opt[1]
elif opt[ 0] == '--lib':
libraries.append(opt[1])
elif opt[ 0] in ('-i', '--interactive'):
interactive = 1
else:
print "unknown option %s %s"%tuple(opt)
print help_msg
sys.exit( 1)
sys.path.insert(0, '.')
try:
import AutoDockTools
print 'Run AutoDockTools from', AutoDockTools.__path__[0]
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer( title='AutoDockTools3',
logMode=logmode, customizer=customizer,
withShell= not interactive)
# libraries=libraries)
atorsList = [ 'ADtors_readLigand', 'ADtors_chooseLigand',
'ADtors_setRoot', 'ADtors_autoRoot', 'ADtors_markRoot',
'ADtors_defineRotBonds', 'ADtors_setBondRotatableFlag',
'ADtors_limitTorsionsGC', 'ADtors_limitTorsions',
'ADtors_changePlanarCarbonsToA', 'ADtors_changeAromaticCarbonsToC',
'ADtors_setCarbonNames', 'ADtors_changePlanarityCriteria',
'ADtors_rigidLigand', 'ADtors_writeFormattedPDBQ',
'ADtors_showRootSphere', 'ADtors_automaticLigandFormatting']
mv.browseCommands('autotorsCommands', commands=atorsList, package='AutoDockTools')
gpfList = [ 'ADgpf_initMacro','ADgpf_initMacro',
'ADgpf_readMacromolecule',
'ADgpf_chooseMacromolecule',
'ADgpf_addSolvationParameters',
'ADgpf_checkMacroTypes',
'ADgpf_initLigand', 'ADgpf_setMapTypes',
'ADgpf_readFormattedLigand', 'ADgpf_chooseFormattedLigand',
'ADgpf_selectCenter', 'ADgpf_setGrid', 'ADgpf_setGpo',
'ADgpf_writeGPF', 'ADgpf_editGPF']
#'ADgpf_setOtherOptions', 'ADgpf_setUpCovalentMap',
mv.browseCommands('autogpfCommands', commands=gpfList, package='AutoDockTools')
dpfList = ['ADdpf_read', 'ADdpf_readMacromolecule',
'ADdpf_readFormattedLigand', 'ADdpf_chooseFormattedLigand',
'ADdpf_initLigand', 'ADdpf_setDpo',
'ADdpf_setSAparameters',
'ADdpf_setGAparameters', 'ADdpf_setLSparameters',
'ADdpf_setDockingParameters', 'ADdpf_writeSA',
'ADdpf_writeGA', 'ADdpf_writeLS', 'ADdpf_writeGALS',
'ADdpf_edit' ]
mv.browseCommands('autodpfCommands', commands=dpfList, package='AutoDockTools')
mv.browseCommands('autostartCommands', package='AutoDockTools')
mv.browseCommands('autoanalyzeCommands', package='AutoDockTools')
# Here just the time to fix the loadCommands
mv.browseCommands('selectionCommands', package='Pmv')
#mv.customize('_adtrc')
self=mv
for a in args:
print a
if a[0]=='-':# skip all command line options
continue
elif a[-7:]=='_net.py': # Vision networks
mv.browseCommands('visionCommands', commands=('vision',) )
if mv.vision.ed is None:
mv.vision()
mv.vision.ed.loadNetwork(a)
elif a[-3:]=='.py': # command script
print 'sourcing', a
mv.source(a)
elif a[-4:] in ['.pdb', '.pqr', 'pdbq', 'mol2'] or a[-5:]=='pdbqs':
mv.readMolecule(a)
else:
print 'WARNING: unable to process %s command line argument'%a
if again:
mv.source(".tmp.py")
##################################################################
# Set the Python Shell
##################################################################
if interactive:
sys.stdin = sys.__stdin__
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
import code
code.interact( 'AutoDockTools Interactive Shell', local=globals() )
elif not die:
mv.GUI.ROOT.mainloop()
except:
import traceback
traceback.print_exc()
raw_input("hit enter to continue")
import sys
sys.exit( 1)
import sys, getopt
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