def runADT(*argv, **kw):
"""The main function for running AutoDockTools
"""
import sys
if type(argv) is tuple:
if len(argv) == 0:
argv = None
elif len(argv) == 1:
argv = argv[0]
if type(argv) is not list:
argv = [argv]
else:
argv = list(argv)
if kw.has_key("ownInterpreter"):
ownInterpreter = kw["ownInterpreter"]
else:
if argv is None:
argv = ['AutoDockTools/bin/runADT.py', '-i']
ownInterpreter = False
elif argv[0].endswith('runADT.py') is False:
argv.insert(0, '-i')
argv.insert(0, 'AutoDockTools/bin/runADT.py')
ownInterpreter = False
else:
ownInterpreter = True
optlist, args = getopt.getopt(argv[1:], 'haipsd:c:v:', [
'update', 'help', 'again', 'overwriteLog', 'uniqueLog', 'noLog',
'noGUI', 'die', 'customizer=', 'interactive', 'dmode=', 'cmode=',
'noSplash', 'vision', 'python'
])
help_msg = """usage: pmv <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
--noGUI : start PMV without the Graphical User Interface
-s or --noSplash : turn off Splash Screen
--die : do not start GUI event loop
--customizer file : run the user specified file
--lib packageName : add a libraries of commands
-p or --ipython : create an ipython shell instead of a python shell
-v r or --vision run : run vision networks on the command line
-v o or --vision once : run vision networks and exit PMV
--update [nightly|tested|clear] : update MGLTools
if no arguments are given Update Manager GUI is provided
'nightly': download and install Nightly Builds
'tested' : download and install tested Nightly Builds
'clear' : clear/uninstall all the updates
-d or --dmode modes : specify a display mode
modes can be any a combination of display mode
'cpk' : cpk
'lines': lines
'ss' : secondary structure ribbon
'sb' : sticks and balls
'lic' : licorice
'ms' : molecular surface
'ca' : C-alpha trace
'bt' : backbone trace
'sp' : CA-spline
'sssb' : secondary structure for proteins,
sticks and balls for other residues with bonds
lines for other residues without bonds
-c or --cmode modes : specify a display mode color scheme:
'ca' : color by atom
'cr' : color by residue (RASMOL scheme)
'cc' : color by chain
'cm' : color by molecule
'cdg': color using David Goodsell's scheme
'cs' : color residues using Shapely scheme
'css': color by secondary structure element
example:
display protein as ribbon, non protein as sticks and balls
and color by atom type
adt -i --dmode sssb --cmode cr myprot.pdb
adt -i -m sssb -c cr myprot.pdb
"""
customizer = None
logmode = 'overwrite'
libraries = []
again = 0
interactive = 0
ipython = False
die = 0
gui = True
noSplash = False
dmode = cmode = None
dmodes = [
'cpk', 'lines', 'ss', 'sb', 'lic', 'ms', 'ca', 'bt', 'sp', 'sssb'
]
cmodes = ['ca', 'cr', 'cc', 'cm', 'cdg', 'cs', 'css']
visionarg = None
for opt in optlist:
if opt[0] in ('-h', '--help'):
print help_msg
sys.exit()
elif opt[0] in ('-a', '--again'):
again = 1
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] == '--noGUI':
gui = False
elif opt[0] == '--die':
die = 1
elif opt[0] in ('-s', '--noSplash'):
noSplash = True
elif opt[0] == '--customizer':
customFile = opt[1]
elif opt[0] == '--lib':
libraries.append(opt[1])
elif opt[0] in ('-i', '--interactive'):
interactive = 1
elif opt[0] in ('-p', '--python'):
ipython = True
elif opt[0] in ('-d', '--dmode'):
assert min([mo in dmodes for mo in opt[1].split('|')]) == True
dmode = opt[1]
elif opt[0] in ('-c', '--cmode'):
assert min([mo in cmodes for mo in opt[1].split('|')]) == True
cmode = opt[1]
elif opt[0] == '--update':
try:
from Support.update import Update
except ImportError:
print "Support package is needed to get updates"
break
update = Update()
if 'nightly' in args:
update.latest = 'nightly'
update.getUpdates()
elif 'tested' in args:
update.latest = 'tested'
update.getUpdates()
elif 'clear' in args:
print "Removing all updates"
update.clearUpdates()
else:
waitTk = update.gui()
update.master.wait_variable(waitTk)
elif opt[0] in ('-v', '--vision'):
if opt[1] in ('o', 'once'):
visionarg = 'once'
elif opt[1] in ('r', 'run'):
visionarg = 'run'
else:
print "unknown option %s %s" % tuple(opt)
print help_msg
sys.exit(1)
#import sys
text = 'Python executable : ' + sys.executable + '\n'
if kw.has_key('AdtScriptPath'):
text += 'ADT script : ' + kw['AdtScriptPath'] + '\n'
text += 'MGLTool packages ' + '\n'
from Support.path import path_text, release_path
from Support.version import __version__
from mglutil import __revision__
version = __version__
text += path_text
text += version + ': ' + release_path
path_data = text
print 'Run ADT from ', __path__[0]
# if MGLPYTHONPATH environment variable exists - insert the specified path
# into sys.path
#if os.environ.has_key("MGLPYTHONPATH"):
# if sys.platform == "win32":
# mglPath = split(os.environ["MGLPYTHONPATH"], ";")
# else:
# mglPath = split(os.environ["MGLPYTHONPATH"], ":")
# mglPath.reverse()
# for p in mglPath:
# sys.path.insert(0, os.path.abspath(p))
try:
##################################################################
# Splash Screen
##################################################################
import Pmv
image_dir = os.path.join(Pmv.__path__[0], 'Icons', 'Images')
copyright = """(c) 1999-2011 Molecular Graphics Laboratory, The Scripps Research Institute
ALL RIGHTS RESERVED """
authors = """Authors: Michel F. Sanner, Ruth Huey, Sargis Dallakyan,
Chris Carrillo, Kevin Chan, Sophie Coon, Alex Gillet,
Sowjanya Karnati, William (Lindy) Lindstrom, Garrett M. Morris, Brian Norledge,
Anna Omelchenko, Daniel Stoffler, Vincenzo Tschinke, Guillaume Vareille, Yong Zhao"""
icon = os.path.join(Pmv.__path__[0], 'Icons', '64x64', 'adt.png')
third_party = """Fast Isocontouring, Volume Rendering -- Chandrait Bajaj, UT Austin
Adaptive Poisson Bolzman Solver (APBS) -- Nathan Baker Wash. Univ. St Louis
GL extrusion Library (GLE) -- Linas Vepstas
Secondary Structure Assignment (Stride) -- Patrick Argos EMBL
Mesh Decimation (QSlim 2.0) -- Micheal Garland, Univeristy of Illinois
Tiled Rendering (TR 1.3) -- Brian Paul
GLF font rendering library -- Roman Podobedov
PyMedia video encoder/decoder -- http://pymedia.org"""
title = "AutoDockTools"
#create a root and hide it
try:
from TkinterDnD2 import TkinterDnD
root = TkinterDnD.Tk()
except ImportError:
from Tkinter import Tk
root = Tk()
root.withdraw()
from mglutil.splashregister.splashscreen import SplashScreen
from mglutil.splashregister.about import About
about = About(image_dir=image_dir,
third_party=third_party,
path_data=path_data,
title=title,
version=version,
revision=__revision__,
copyright=copyright,
authors=authors,
icon=icon)
if gui:
splash = SplashScreen(about, noSplash=noSplash)
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer(logMode=logmode,
customizer=customizer,
master=root,
title=title,
withShell=not interactive,
verbose=False,
gui=gui)
mv.browseCommands('autotors41Commands',
commands=None,
package='AutoDockTools')
mv.browseCommands('autoflex41Commands',
commands=None,
package='AutoDockTools')
mv.browseCommands('autogpf41Commands',
commands=None,
package='AutoDockTools')
mv.browseCommands('autodpf41Commands',
commands=None,
package='AutoDockTools')
mv.browseCommands('autostart41Commands',
commands=None,
package='AutoDockTools')
mv.browseCommands('autoanalyze41Commands',
commands=None,
package='AutoDockTools')
#mv.GUI.currentADTBar = 'AutoTools42Bar'
#setADTmode("AD4.0", mv)
setADTmode("AD4.2", mv)
mv.browseCommands('selectionCommands', package='Pmv')
mv.browseCommands('AutoLigandCommand',
package='AutoDockTools',
topCommand=0)
mv.GUI.naturalSize()
mv.customize('_adtrc')
mv.help_about = about
if gui:
font = mv.GUI.ROOT.option_get('font', '*')
mv.GUI.ROOT.option_add('*font', font)
try:
import Vision
mv.browseCommands('visionCommands',
commands=('vision', ),
topCommand=0)
mv.browseCommands('coarseMolSurfaceCommands', topCommand=0)
if hasattr(mv, 'vision') and mv.vision.ed is None:
mv.vision(log=0)
else:
# we address the global variable in vision
Vision.ed = mv.vision.ed
except ImportError:
pass
#show the application after it built
if gui:
splash.finish()
root.deiconify()
globals().update(locals())
if gui:
mv.GUI.VIEWER.suspendRedraw = True
cwd = os.getcwd()
#mv._cwd differs from cwd when 'Startup Directory' userpref is set
os.chdir(mv._cwd)
if dmode is not None or cmode is not None:
# save current list of commands run when a molecule is loaded
addCmds = mv.getOnAddObjectCmd()
# remove them
if dmode is not None:
for c in addCmds:
mv.removeOnAddObjectCmd(c[0])
# set the mode
setdmode(dmode, mv)
if cmode is not None:
# set the mode
setcmode(cmode, mv)
for a in args:
if a[0] == '-': # skip all command line options
continue
elif (a[-10:]
== '_pmvnet.py') or (a[-7:] == '_net.py'): # Vision networks
mv.browseCommands('visionCommands', commands=('vision', ))
if mv.vision.ed is None:
mv.vision()
mv.vision.ed.loadNetwork(a)
if visionarg == 'run' or visionarg == 'once':
mv.vision.ed.softrunCurrentNet_cb()
elif a[-3:] == '.py': # command script
print 'sourcing', a
mv.source(a)
elif a[-4:] in ['.pdb', '.pqr', 'pdbq', 'mol2', '.cif', '.gro'
] or a[-5:] == 'pdbqs' or a[-5:] == 'pdbqt':
mv.readMolecule(a)
elif a in ['clear', 'tested', 'nighlty']:
pass
else:
print 'WARNING: unable to process %s command line argument' % a
if again:
mv.source(".tmp.py")
if dmode is not None or cmode is not None:
# get current list of commands run when a molecule is loaded
cmds = mv.getOnAddObjectCmd()
# remove them
for c in cmds:
mv.removeOnAddObjectCmd(c[0])
# restore original list of commands
for c in addCmds:
apply(mv.addOnAddObjectCmd, c)
if gui:
mv.GUI.VIEWER.suspendRedraw = False
os.chdir(cwd)
if visionarg != 'once':
if ownInterpreter is True:
mod = __import__('__main__')
mod.__dict__.update({'self': mv})
if interactive:
sys.stdin = sys.__stdin__
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
if ipython is True:
try:
# create IPython shell
from IPython.Shell import _select_shell
sh = _select_shell([])(argv=[],
user_ns=mod.__dict__)
sh.mainloop()
except:
import code
try: # hack to really exit code.interact
code.interact(
'AutoDockTools Interactive Shell',
local=mod.__dict__)
except:
pass
else:
import code
try: # hack to really exit code.interact
code.interact('AutoDockTools Interactive Shell',
local=mod.__dict__)
except:
pass
elif not die:
#mv.GUI.pyshell.interp.locals = globals()
if gui:
mv.GUI.pyshell.interp.locals = mod.__dict__
mv.GUI.ROOT.mainloop()
mod.__dict__.pop('self')
else:
ed.master.mainloop()
except:
import traceback
traceback.print_exc()
raw_input("hit enter to continue")
import sys
sys.exit(1)
def runADT(*argv, **kw):
"""The main function for running AutoDockTools
"""
import sys
if type(argv) is tuple:
if len(argv) == 0:
argv = None
elif len(argv) == 1:
argv = argv[0]
if type(argv) is not list:
argv = [argv]
else:
argv = list(argv)
if kw.has_key("ownInterpreter"):
ownInterpreter = kw["ownInterpreter"]
else:
if argv is None:
argv = ['AutoDockTools/bin/runADT.py', '-i']
ownInterpreter = False
elif argv[0].endswith('runADT.py') is False:
argv.insert(0,'-i')
argv.insert(0,'AutoDockTools/bin/runADT.py')
ownInterpreter = False
else:
ownInterpreter = True
optlist, args = getopt.getopt(argv[1:], 'haipsd:c:v:', [
'update', 'help', 'again', 'overwriteLog', 'uniqueLog', 'noLog',
'noGUI', 'die', 'customizer=', 'interactive', 'dmode=', 'cmode=',
'noSplash', 'vision', 'python'] )
help_msg = """usage: pmv <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
--noGUI : start PMV without the Graphical User Interface
-s or --noSplash : turn off Splash Screen
--die : do not start GUI event loop
--customizer file : run the user specified file
--lib packageName : add a libraries of commands
-p or --ipython : create an ipython shell instead of a python shell
-v r or --vision run : run vision networks on the command line
-v o or --vision once : run vision networks and exit PMV
--update [nightly|tested|clear] : update MGLTools
if no arguments are given Update Manager GUI is provided
'nightly': download and install Nightly Builds
'tested' : download and install tested Nightly Builds
'clear' : clear/uninstall all the updates
-d or --dmode modes : specify a display mode
modes can be any a combination of display mode
'cpk' : cpk
'lines': lines
'ss' : secondary structure ribbon
'sb' : sticks and balls
'lic' : licorice
'ms' : molecular surface
'ca' : C-alpha trace
'bt' : backbone trace
'sp' : CA-spline
'sssb' : secondary structure for proteins,
sticks and balls for other residues with bonds
lines for other residues without bonds
-c or --cmode modes : specify a display mode color scheme:
'ca' : color by atom
'cr' : color by residue (RASMOL scheme)
'cc' : color by chain
'cm' : color by molecule
'cdg': color using David Goodsell's scheme
'cs' : color residues using Shapely scheme
'css': color by secondary structure element
example:
display protein as ribbon, non protein as sticks and balls
and color by atom type
adt -i --dmode sssb --cmode cr myprot.pdb
adt -i -m sssb -c cr myprot.pdb
"""
customizer = None
logmode = 'overwrite'
libraries = []
again = 0
interactive = 0
ipython = False
die=0
gui = True
noSplash = False
dmode = cmode = None
dmodes = ['cpk', 'lines', 'ss', 'sb', 'lic', 'ms', 'ca', 'bt', 'sp', 'sssb' ]
cmodes = ['ca', 'cr', 'cc', 'cm', 'cdg', 'cs', 'css']
visionarg = None
for opt in optlist:
if opt[ 0] in ('-h', '--help'):
print help_msg
sys.exit()
elif opt[ 0] in ('-a', '--again'):
again = 1
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] =='--noGUI': gui = False
elif opt[ 0] =='--die': die = 1
elif opt[ 0] in ('-s', '--noSplash'):
noSplash = True
elif opt[ 0] == '--customizer':
customFile = opt[1]
elif opt[ 0] == '--lib':
libraries.append(opt[1])
elif opt[ 0] in ('-i', '--interactive'):
interactive = 1
elif opt[ 0] in ('-p', '--python'):
ipython = True
elif opt[ 0] in ('-d', '--dmode'):
assert min([mo in dmodes for mo in opt[1].split('|')])==True
dmode = opt[1]
elif opt[ 0] in ('-c', '--cmode'):
assert min([mo in cmodes for mo in opt[1].split('|')])==True
cmode = opt[1]
elif opt[0] == '--update':
try:
from Support.update import Update
except ImportError:
print "Support package is needed to get updates"
break
update = Update()
if 'nightly' in args:
update.latest = 'nightly'
update.getUpdates()
elif 'tested' in args:
update.latest = 'tested'
update.getUpdates()
elif 'clear' in args:
print "Removing all updates"
update.clearUpdates()
else:
waitTk = update.gui()
update.master.wait_variable(waitTk)
elif opt[ 0] in ('-v', '--vision'):
if opt[1] in ('o', 'once'):
visionarg = 'once'
elif opt[1] in ('r', 'run'):
visionarg = 'run'
else:
print "unknown option %s %s"%tuple(opt)
print help_msg
sys.exit(1)
#import sys
text = 'Python executable : '+ sys.executable +'\n'
if kw.has_key('AdtScriptPath'):
text += 'ADT script : '+ kw['AdtScriptPath'] +'\n'
text += 'MGLTool packages '+'\n'
from Support.path import path_text, release_path
from Support.version import __version__
from mglutil import __revision__
version = __version__
text += path_text
text += version+': '+release_path
path_data = text
print 'Run ADT from ', __path__[0]
# if MGLPYTHONPATH environment variable exists - insert the specified path
# into sys.path
#if os.environ.has_key("MGLPYTHONPATH"):
# if sys.platform == "win32":
# mglPath = split(os.environ["MGLPYTHONPATH"], ";")
# else:
# mglPath = split(os.environ["MGLPYTHONPATH"], ":")
# mglPath.reverse()
# for p in mglPath:
# sys.path.insert(0, os.path.abspath(p))
try:
##################################################################
# Splash Screen
##################################################################
import Pmv
image_dir = os.path.join( Pmv.__path__[0],'Icons','Images')
copyright = """(c) 1999-2010 Molecular Graphics Laboratory, The Scripps Research Institute
ALL RIGHTS RESERVED """
authors = """Authors: Michel F. Sanner, Ruth Huey, Sargis Dallakyan,
Chris Carrillo, Kevin Chan, Sophie Coon, Alex Gillet,
Sowjanya Karnati, William (Lindy) Lindstrom, Garrett M. Morris, Brian Norledge,
Anna Omelchenko, Daniel Stoffler, Vincenzo Tschinke, Guillaume Vareille, Yong Zhao"""
icon = os.path.join(Pmv.__path__[0],'Icons','64x64','adt.png')
third_party = """Fast Isocontouring, Volume Rendering -- Chandrait Bajaj, UT Austin
Adaptive Poisson Bolzman Solver (APBS) -- Nathan Baker Wash. Univ. St Louis
GL extrusion Library (GLE) -- Linas Vepstas
Secondary Structure Assignment (Stride) -- Patrick Argos EMBL
Mesh Decimation (QSlim 2.0) -- Micheal Garland, Univeristy of Illinois
Tiled Rendering (TR 1.3) -- Brian Paul
GLF font rendering library -- Roman Podobedov
PyMedia video encoder/decoder -- http://pymedia.org"""
title="AutoDockTools"
#create a root and hide it
try:
from TkinterDnD2 import TkinterDnD
root = TkinterDnD.Tk()
except ImportError:
from Tkinter import Tk
root = Tk()
root.withdraw()
from mglutil.splashregister.splashscreen import SplashScreen
from mglutil.splashregister.about import About
about = About(image_dir=image_dir, third_party=third_party,
path_data=path_data, title=title, version=version,
revision=__revision__,
copyright=copyright, authors=authors, icon=icon)
if gui:
splash = SplashScreen(about, noSplash=noSplash)
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer(
logMode=logmode, customizer=customizer, master=root,
title=title, withShell= not interactive, verbose=False, gui=gui)
mv.browseCommands('autotors41Commands', commands = None,
package = 'AutoDockTools')
mv.browseCommands('autoflex41Commands', commands = None,
package = 'AutoDockTools')
mv.browseCommands('autogpf41Commands', commands = None,
package = 'AutoDockTools')
mv.browseCommands('autodpf41Commands', commands = None,
package = 'AutoDockTools')
mv.browseCommands('autostart41Commands', commands = None,
package = 'AutoDockTools')
mv.browseCommands('autoanalyze41Commands', commands = None,
package = 'AutoDockTools')
#mv.GUI.currentADTBar = 'AutoTools42Bar'
#setADTmode("AD4.0", mv)
setADTmode("AD4.2", mv)
mv.browseCommands('selectionCommands', package='Pmv')
mv.browseCommands('AutoLigandCommand', package='AutoDockTools', topCommand=0)
mv.GUI.naturalSize()
mv.customize('_adtrc')
mv.help_about = about
if gui:
font = mv.GUI.ROOT.option_get('font', '*')
mv.GUI.ROOT.option_add('*font', font)
try:
import Vision
mv.browseCommands('visionCommands', commands=('vision',), topCommand=0)
mv.browseCommands('coarseMolSurfaceCommands', topCommand=0)
if hasattr(mv,'vision') and mv.vision.ed is None:
mv.vision(log=0)
else:
# we address the global variable in vision
Vision.ed = mv.vision.ed
except ImportError:
pass
#show the application after it built
if gui:
splash.finish()
root.deiconify()
globals().update(locals())
if gui:
mv.GUI.VIEWER.suspendRedraw = True
cwd = os.getcwd()
#mv._cwd differs from cwd when 'Startup Directory' userpref is set
os.chdir(mv._cwd)
if dmode is not None or cmode is not None:
# save current list of commands run when a molecule is loaded
addCmds = mv.getOnAddObjectCmd()
# remove them
if dmode is not None:
for c in addCmds:
mv.removeOnAddObjectCmd(c[0])
# set the mode
setdmode(dmode, mv)
if cmode is not None:
# set the mode
setcmode(cmode, mv)
for a in args:
if a[0]=='-':# skip all command line options
continue
elif (a[-10:]=='_pmvnet.py') or (a[-7:]=='_net.py'): # Vision networks
mv.browseCommands('visionCommands', commands=('vision',) )
if mv.vision.ed is None:
mv.vision()
mv.vision.ed.loadNetwork(a)
if visionarg == 'run' or visionarg == 'once':
mv.vision.ed.softrunCurrentNet_cb()
elif a[-3:]=='.py': # command script
print 'sourcing', a
mv.source(a)
elif a[-4:] in ['.pdb', '.pqr', 'pdbq', 'mol2', '.cif', '.gro'] or a[-5:]=='pdbqs' or a[-5:]=='pdbqt':
mv.readMolecule(a)
elif a in ['clear', 'tested', 'nighlty']:
pass
else:
print 'WARNING: unable to process %s command line argument'%a
if again:
mv.source(".tmp.py")
if dmode is not None or cmode is not None:
# get current list of commands run when a molecule is loaded
cmds = mv.getOnAddObjectCmd()
# remove them
for c in cmds:
mv.removeOnAddObjectCmd(c[0])
# restore original list of commands
for c in addCmds:
apply( mv.addOnAddObjectCmd, c )
if gui:
mv.GUI.VIEWER.suspendRedraw = False
os.chdir(cwd)
if visionarg != 'once':
if ownInterpreter is True:
mod = __import__('__main__')
mod.__dict__.update({'self':mv})
if interactive:
sys.stdin = sys.__stdin__
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
if ipython is True:
try:
# create IPython shell
from IPython.Shell import _select_shell
sh = _select_shell([])(argv=[], user_ns=mod.__dict__)
sh.mainloop()
except:
import code
try: # hack to really exit code.interact
code.interact( 'AutoDockTools Interactive Shell', local=mod.__dict__)
except:
pass
else:
import code
try: # hack to really exit code.interact
code.interact( 'AutoDockTools Interactive Shell', local=mod.__dict__)
except:
pass
elif not die:
#mv.GUI.pyshell.interp.locals = globals()
if gui:
mv.GUI.pyshell.interp.locals = mod.__dict__
mv.GUI.ROOT.mainloop()
mod.__dict__.pop('self')
else:
ed.master.mainloop()
except:
import traceback
traceback.print_exc()
raw_input("hit enter to continue")
import sys
sys.exit(1)
