def __init__(self, target=None, # Tk container
name = 'Embedded camera',
debug = 0,
):
self.debug = debug
if self.debug:
print "EmbeddedMolViewer __init__> ", target
self.target = target
self.PMV_win = Toplevel()
self.PMV_win.withdraw()
VFGUI.hasDnD2 = False
print "\n=========================================="
print " Initializing PMV..."
self.mv = MoleculeViewer(logMode = 'overwrite', master=self.PMV_win, # customizer='custom_pmvrc',
title='[embedded viewer]',
withShell=False,
verbose=False, gui = True, guiVisible=1)
self.VIEWER = self.mv.GUI.VIEWER
self.GUI = self.mv.GUI
self.VIEWER.cameras[0].suspendRedraw = 1 # stop updating the main Pmv camera
self._pmv_visible = False
self.cameras = {} # 'name' {'obj' : pmv_obj, 'structures': [mol1_obj, mol2_obj, ....], }
self.cameras['pmv'] = { 'obj' :self.VIEWER.cameras[0],
'structures' : [],
}
self.cameraslist = ['pmv'] # name0, name1, name2
# keep the order in which cameras are added
self.target = target
print " [ DONE ]"
print "==========================================\n"
self.initStyles()
if self.target:
self.addCamera(target = self.targer, name=name)
def setUp(self):
from Pmv.moleculeViewer import MoleculeViewer
self.mv = MoleculeViewer(customizer='./.empty',
logMode='overwrite',
withShell=0)
self.mv.loadCommand('fileCommands', 'readMolecule', 'Pmv')
self.mv.loadCommand('deleteCommands', 'deleteMol', 'Pmv')
self.mv.loadCommand("bondsCommands", "buildBondsByDistance", "Pmv")
self.mv.setOnAddObjectCommands(
['buildBondsByDistance', 'displayLines'], log=0)
self.mv.loadModule("interactiveCommands", 'Pmv')
# Don't want to trap exceptions and errors...
# the user pref is set to 1 by
# default
self.mv.setUserPreference(('trapExceptions', '0'), log=0)
self.mv.setUserPreference(('warningMsgFormat', 'printed'), log=0)
self.mv.loadModule('displayCommands', 'Pmv')
def setUp(self):
from Pmv.moleculeViewer import MoleculeViewer
self.mv = MoleculeViewer(customizer = './.empty',
logMode = 'overwrite', withShell=0)
self.mv.loadCommand('fileCommands', 'readMolecule', 'Pmv')
self.mv.loadCommand('deleteCommands','deleteMol', 'Pmv')
self.mv.loadCommand("bondsCommands", "buildBondsByDistance", "Pmv")
self.mv.setOnAddObjectCommands(['buildBondsByDistance',
'displayLines'], log=0)
self.mv.loadModule("interactiveCommands", 'Pmv')
# Don't want to trap exceptions and errors...
# the user pref is set to 1 by
# default
self.mv.setUserPreference(('trapExceptions', '0'), log = 0)
self.mv.setUserPreference(('warningMsgFormat', 'printed'), log = 0)
self.mv.loadModule('displayCommands', 'Pmv')
## if hasattr(atom, 'segID'):
## atom.segID = a[1].segID
## atom.hetatm = 0
## atom.alternate = []
## atom.element = 'H'
## atom.number = -1
## atom.occupancy = 1.0
## atom.conformation = 0
## atom.temperatureFactor = 0.0
## atom.babel_atomic_number = a[2]
## atom.babel_type = a[3]
## atom.babel_organic=1
## bond = Bond( a[1], atom )
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer()
mv.addMolecule(mol)
mol.bondsflag = 1
mv.lines(mol)
v = []
l = []
g = mv.Mols[0].geomContainer.geoms['lines']
vc = len(g.vertexSet)
scale = [0, 1, -1, 2, -2, 3, -3, 4, -4]
add = -1
## for b in bonds:
## if b.bondOrder>1:
## b.bondOrder = 5
## break
import math
from Pmv.moleculeViewer import MoleculeViewer
from ViewerFramework.VF import LogEvent
from pdb_c4d import *
#from Pmv.displayCommands import BindGeomToMolecularFragment
from ViewerFramework.clientsCommands import Pmv_client
from c4d import plugins
from c4d import documents
import c4d
scene = doc = documents.get_active_document()
self = MoleculeViewer(logMode = 'overwrite', customizer=None, master=None,title='toto', withShell= 0,verbose=False, gui = False)
self.abclogfiles=open('abclog','w')
self.pmvstderr=open('pmvstderr','w')
sys.stderr=self.pmvstderr
self.addCommand(Pmv_client(), 'client', None)
#self.addCommand(BindGeomToMolecularFragment(), 'bindGeomToMolecularFragment', None)
self.client.setDriver('c4d')
self.registerListener(LogEvent, self.client.handleLogEvent)
self.armObj = None
self.browseCommands('fileCommands', package="Pmv", topCommand=0)
com=True
cpk=False
coarse=False
sym=False
def startMoleculeViewer():
global mv
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer(customizer='./.empty',
logMode='overwrite',
withShell=0)
mv.setUserPreference(('trapExceptions', '0'), log=0)
mv.setUserPreference(('warningMsgFormat', 'printed'), log=0)
mv.loadCommand('fileCommands', 'readMolecule', 'Pmv')
mv.loadCommand('deleteCommands', 'deleteMol', 'Pmv')
mv.loadCommand("bondsCommands", "buildBondsByDistance", "Pmv")
mv.setOnAddObjectCommands(['buildBondsByDistance', 'displayLines'], log=0)
mv.loadModule("interactiveCommands", 'Pmv')
mv.loadModule('secondaryStructureCommands', 'Pmv')
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 startMoleculeViewer():
global mv
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer(customizer = './.empty', logMode = 'overwrite')
mv.setUserPreference(('trapExceptions', '0'), log = 0)
mv.setUserPreference(('warningMsgFormat', 'printed'), log = 0)
mv.loadCommand('fileCommands', 'readMolecule', 'Pmv')
mv.loadCommand('deleteCommands','deleteMol', 'Pmv')
mv.loadCommand("bondsCommands", "buildBondsByDistance", "Pmv")
mv.setOnAddObjectCommands(['buildBondsByDistance','displayLines'], log=0)
mv.loadModule("interactiveCommands", 'Pmv')
mv.loadModule('secondaryStructureCommands', 'Pmv')
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)
## if hasattr(atom, 'segID'):
## atom.segID = a[1].segID
## atom.hetatm = 0
## atom.alternate = []
## atom.element = 'H'
## atom.number = -1
## atom.occupancy = 1.0
## atom.conformation = 0
## atom.temperatureFactor = 0.0
## atom.babel_atomic_number = a[2]
## atom.babel_type = a[3]
## atom.babel_organic=1
## bond = Bond( a[1], atom )
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer()
mv.addMolecule(mol)
mol.bondsflag = 1
mv.lines( mol )
v = []
l = []
g = mv.Mols[0].geomContainer.geoms['lines']
vc = len(g.vertexSet)
scale = [0, 1, -1, 2, -2, 3, -3, 4, -4]
add = -1
## for b in bonds:
## if b.bondOrder>1:
## b.bondOrder = 5
## break
class EmbeddedMolViewer:
def __init__(self, target=None, # Tk container
name = 'Embedded camera',
debug = 0,
):
self.debug = debug
if self.debug:
print "EmbeddedMolViewer __init__> ", target
self.target = target
self.PMV_win = Toplevel()
self.PMV_win.withdraw()
VFGUI.hasDnD2 = False
print "\n=========================================="
print " Initializing PMV..."
self.mv = MoleculeViewer(logMode = 'overwrite', master=self.PMV_win, # customizer='custom_pmvrc',
title='[embedded viewer]',
withShell=False,
verbose=False, gui = True, guiVisible=1)
self.VIEWER = self.mv.GUI.VIEWER
self.GUI = self.mv.GUI
self.VIEWER.cameras[0].suspendRedraw = 1 # stop updating the main Pmv camera
self._pmv_visible = False
self.cameras = {} # 'name' {'obj' : pmv_obj, 'structures': [mol1_obj, mol2_obj, ....], }
self.cameras['pmv'] = { 'obj' :self.VIEWER.cameras[0],
'structures' : [],
}
self.cameraslist = ['pmv'] # name0, name1, name2
# keep the order in which cameras are added
self.target = target
print " [ DONE ]"
print "==========================================\n"
self.initStyles()
if self.target:
self.addCamera(target = self.targer, name=name)
def initStyles(self):
""" initialize styles dictionary """
#color_cb = CallbackFunction(self.mv.colorByAtomType, (['lines', 'balls', 'sticks'], log=0) )
#self.styles ={ 'default' : [ color_cb ] }
# XXX WHAT TO DO?
pass
def togglepmv(self, event=None):
""" toggle between visible and hidden pmv"""
if self._pmv_visible:
self._hidePmv()
else:
self._showPmv()
def _showPmv(self, event=None):
""" stop all cams and restore the underlying
pmv session
"""
if self.debug:
print "_showPmv> called"
print "ACTIVE CAMS", self.activeCams()
self._pmv_suspended_cams = self.activeCams()
self.activateCam(['pmv'], only=1, mols=True)
self._pmv_visible = True
self.mv.GUI.ROOT.deiconify()
def _hidePmv(self, event=None):
""" stop Pmv camera, minimize Pmv and
restore previously disabled cams
"""
self.VIEWER.cameras[0].suspendRedraw = 1 # stop updating the main Pmv camera
self._pmv_visible = False
self.mv.GUI.ROOT.withdraw()
self.activateCam(self._pmv_suspended_cams, only=1, mols=True)
def addCamera(self,target,name = '', depth=True, bgcolor=(0., 0., 0.)):
""" add a new camera 'name' bound to 'target'"""
if self.debug: print "adding another camera"
if name in self.cameraslist:
print "Camera [%s] already exist!", name
return
cam_obj = self.VIEWER.AddCamera(master=target) # the next ones will be added)
if depth:
cam_obj.fog.Set(enabled=1)
cam_obj.backgroundColor = ( bgcolor + (1.0,) )
cam_obj.Redraw()
self.cameraslist.append(name)
self.cameras[name] = { 'obj':cam_obj, 'structures' : [] }
return cam_obj
def delCamera(self, idx=None, name=None, mols=True):
""" delete camera by index or by name; by default all molecules
loaded in a given camera are loaded
"""
if self.debug: print "delcamera", idx, name
if idx == None and name == None:
print "delete camera by name or by idx!"
return
if idx == 0 or len(self.VIEWER.cameras) == 1:
print "cowardly refusing to delete the main Pmv camera...(returning)"
return
self.VIEWER.DeleteCamera(idx)
name = self.cameraslist.pop(idx)
if mols:
for s in self.cameras[name]['structures']:
self.mv.deleteMol(s)
# delete all objects from this camera
self.nukeCamMols(name)
# delete camera
del self.cameras[name]
def activeCams(self):
""" return list of active cameras"""
active = []
#active = [ name for name in self.cameras.keys() if self.cameras[name]['obj'].suspendRedraw == 0 ]
for c in self.cameras.keys():
if not self.cameras[c]['obj'].suspendRedraw:
active.append(c)
return active
def cams(self):
""" return the list of all camera names"""
return self.cameras.keys()
def cameraByName(self, name): #, attribute='obj'):
""" retrieve camera object by name
None, if camera doesn't exist
"""
cam = self.cameras.get(name, None)
if not cam == None:
return cam['obj']
else:
return None
def cameraStructures(self, name):
""" return all mols loaded in this camera"""
return self.cameras[name]['structures']
def activateCam(self, namelist=[], only=1, mols=True):
""" activate redraw on selected camera and disabling
(by default) other cameras
"""
# - reactivate this camera
if self.debug: print "activatecam> namelist", namelist
for c in self.cameras.keys():
if c in namelist:
for s in self.cameras[c]['structures']:
# XXX ASK MICHEL
if isinstance(s, Molecule):
s = s.geomContainer.geoms['master']
s.Set(visible=True) #,redraw=False)
self.cameras[c]['obj'].Redraw()
self.cameras[c]['obj'].suspendRedraw = 0
elif only:
self.cameras[c]['obj'].suspendRedraw = 1
# hide molecules loaded in this camera
for s in self.cameras[c]['structures']:
if isinstance(s, Molecule):
s = s.geomContainer.geoms['master']
s.Set(visible=False) #,redraw=False)
def deactivateCam(self, namelist=[]):
""" disable redraw update in cameras"""
self.VIEWER.redrawLock.acquire()
if len(namelist) == 0:
namelist = self.cameras.keys()
for c in namelist:
self.cameras[c]['obj'].suspendRedraw = 1
self.VIEWER.redrawLock.release()
def loadMolWithStyle(self, molfile, style='default'):
""" load molecules with representation style
"""
mol = self.mv.readMolecule(molfile, modelsAs='conformations')
return mol
def loadInCamera(self, molfile, camera, style='default'):
""" load molecule in selected camera
and apply optional repr.style
"""
mol = self.loadMolWithStyle(molfile, style=style)[0]
self.cameras[camera]['structures'].append(mol)
return mol
def deleteInCamera(self, molobj, camera):
""" delete an object from a camera"""
m = """
#######################################
###
###
### PROBLEMATIC DELETION! ASK MICHEL
### ISSUE WITH DELETING FILES
###
###
#######################################"""
#print m
#print "LIST OF STRUCTURES", self.cameras[camera]['structures']
self.mv.deleteMol(molobj)
self.cameras[camera]['structures'] = [ x for x in self.cameras[camera]['structures'] if not x == molobj ]
return
idx = self.cameras[camera]['structures'].index(molobj)
d = self.cameras[camera]['structures'].pop(idx)
try:
self.mv.deleteMol(d)
except:
print "TRYING TO DELETE MOLECULE %s RAISED ERROR!" % d
def nukeCamMols(self, camera):
""" delete all molecules from a cam"""
for m in self.cameras[camera]['structures']:
self.mv.deleteMol(m)
self.cameras[camera]['structures'] = []
def centerView(self, item=None):
""" center the view on specified target
if target is None, reset the view
on all mols
"""
root = self.VIEWER.rootObject
if item == None:
item = root
self.VIEWER.toggleTransformRootOnly(False)
self.VIEWER.SetCurrentObject(item)
#self.VIEWER.Reset_cb()
self.VIEWER.Normalize_cb()
self.VIEWER.toggleTransformRootOnly(True)
self.VIEWER.Center_cb()
self.VIEWER.SetCurrentObject(root)
def setUp(self):
global mv
if mv is None:
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer(customizer='./.empty',
logMode='no',
withShell=False,
verbose=False)
mv.browseCommands('fileCommands', package="Pmv", topCommand=0)
mv.browseCommands('bondsCommands', package='Pmv', topCommand=0)
mv.browseCommands('colorCommands', package='Pmv', topCommand=0)
mv.browseCommands('deleteCommands', package='Pmv', topCommand=0)
mv.browseCommands('displayCommands',
commands=[
'displaySticksAndBalls',
'undisplaySticksAndBalls', 'displayCPK',
'undisplayCPK', 'displayLines',
'undisplayLines', 'displayBackboneTrace',
'undisplayBackboneTrace', 'DisplayBoundGeom'
],
package='Pmv',
topCommand=0)
mv.setOnAddObjectCommands(
['buildBondsByDistance', 'displayLines', 'colorByAtomType'],
topCommand=0)
#mv.loadModule("interactiveCommands", 'Pmv')
mv.loadCommand("visionCommands", "vision", "Pmv")
# Don't want to trap exceptions and errors... the user pref is set to 1 by
# default
#mv.setUserPreference(('trapExceptions', '0'), log = 0)
mv.setUserPreference(('warningMsgFormat', 'printed'), log=0)
self.mv = mv
