def run():
parser = getRefineParser()
(options, _args) = parser.parse_args()
if options.verbosity >= 0 and options.verbosity <= 9:
cing.verbosity = options.verbosity
else:
nTerror("set verbosity is outside range [0-9] at: " +
options.verbosity)
nTerror("Ignoring setting")
# end if
# From this point on code may be executed that will go through the appropriate verbosity filtering
nTdebug("options: %s" % str(options))
#------------------------------------------------------------------------------
# Documentation
#------------------------------------------------------------------------------
if options.doc:
parser.print_help(file=sys.stdout)
nTmessage("%s\n", __doc__)
return
#end if
#------------------------------------------------------------------------------
#check for the required project, name option
parser.check_required('--name')
parser.check_required('--project')
project = Project.open(options.project, status='old',
restore=1) #DEFAULT 0
if project == None:
nTerror("Failed to get a project")
return True
#end if
basePath = project.path(project.directories.refine, options.name)
# nTdebug("basePath: " + basePath)
#------------------------------------------------------------------------------
# Setup
#------------------------------------------------------------------------------
parameters = None
if options.doSetup:
parameters = doSetup(config, project, basePath, options)
# return # We had like to continue in new setup. So don't exit here.
#end if
#------------------------------------------------------------------------------
# Some output
#------------------------------------------------------------------------------
nTmessage("==> Reading configuration")
nTmessage('refinePath: %s', config.refinePath)
nTmessage('xplor: %s', config.XPLOR)
nTmessage("parameterFiles: %s", config.parameterFiles)
nTmessage("topologyFiles: %s", config.topologyFiles)
if (options.fullRefine or options.fullAnneal
or options.fullAnnealAndRefine):
if options.doSetup:
nTerror(
"Setup was done but fullXXX would do it again. Just run fullXXXX again without setup please."
)
sys.exit(1)
# end if
else:
#------------------------------------------------------------------------------
# read parameters file
#------------------------------------------------------------------------------
if not parameters:
# nTdebug('==> will read parameters')
parameters = getParameters(basePath, 'parameters')
# nTdebug('==> parameters\n%s\n', str(parameters))
nTmessage('==> Read parameters')
# end if
setParametersFromOptions(
project, options, parameters
) # Do here for the first time and every time refine is called.
nTmessage(
'==> Done transferring some options from commandline to parameters (again)'
)
parameters.basePath = basePath
if parameters.name != options.name:
nTwarning("parameters.name (%s) != options.name (%s)" %
(parameters.name, options.name))
# end if
# end if
#------------------------------------------------------------------------------
# Action selection
#------------------------------------------------------------------------------
if options.doPSF:
generatePSF(config, project, parameters, options.doPrint)
elif options.generateTemplate:
generateTemplate(config, project, parameters, options.doPrint)
elif options.doAnneal:
anneal(config, project, parameters, options.doPrint)
elif options.doAnalyze:
analyze(config, project, parameters, options.doPrint)
elif options.doRefine:
refine(config, project, parameters, options.doPrint)
elif options.doParse:
_results = parseOutput(config, project, parameters)
elif options.doImport:
importFrom(config, project, parameters)
elif options.fullAnneal:
if not fullAnneal(config, project, options):
nTerror("Failed fullAnneal")
elif options.fullRefine:
if not fullRefine(config, project, parameters, options):
nTerror("Failed fullRefine")
elif options.fullAnnealAndRefine:
if not fullAnnealAndRefine(config, project, options):
nTerror("Failed fullAnnealAndRefine")
else:
if not options.doSetup:
nTerror('refine.py, invalid options combinations:\n%s' %
str(options))
return True
else:
nTmessage("Done after setup.")
#end if
if options.ipython:
startIpythonShell()
def yasaraShell(project):
if not cing.yasaradir:
nTcodeerror('yasaraShell: please put a proper yasara.py module on PYTHONPATH first (check yasaradir!)')
exit(1)
# shortcuts
f = pformat #@UnusedVariable # pylint: disable=W0612
p = project #@UnusedVariable # pylint: disable=W0612
mol = project.molecule #@UnusedVariable # pylint: disable=W0612
def commands(): # pylint: disable=W0612
cmds = ['commands', 'colorByResidue', 'colorGF', 'colorJanin', 'colorROG', 'colorWhatif',
'getSelectedResidue', 'hud', 'loadPDB', 'screenDump', 'showHtml']
cmds.sort()
for c in cmds:
nTmessage( c )
#end for
#end def
def loadPDB(model = None):
"""
Load project.molecule model [0,modelCount-1] or all models if None
"""
if not project.molecule:
nTerror('loadPDB: no molecule defined')
return True
if model == None or model == 'all':
path = project.moleculePath('yasara', sprintf('%s.pdb', project.molecule.name))
model = None
else:
path = project.moleculePath('yasara', sprintf('%s_%s.pdb', project.molecule.name, model))
project.molecule.toPDBfile(path, model = model)
nTmessage('loadPDB: %s' % path)
LoadPDB(os.path.abspath(path))
Style('Ribbon', 'off')
#end def
# alternate names
loadpdb = loadPDB #@UnusedVariable # pylint: disable=W0612
loadPdb = loadPDB #@UnusedVariable # pylint: disable=W0612
def colorROG(object = 1): # pylint: disable=W0612
"""
Color residues according to Cing ROG score
"""
Console('off')
ColorRes('object ' + str(object), 'Gray')
yasaraColorDict = dict(green = 240, orange = 150, red = 120)
for res in project.molecule.allResidues():
cmd = sprintf('object %s residue %d,%s', object, res.resNum, yasaraColorDict[res.rogScore.colorLabel])
ColorRes(cmd)
#end for
Console('on')
#end def
def colorGF(object = 1, minValue = -3.0, maxValue = 1.0): # pylint: disable=W0612
"""
Color residues according to Procheck gf score
"""
colorByResidue(['procheck', 'gf'],
minValue = minValue, maxValue = maxValue,
reverseColorScheme = True
)
#end def
def colorWhatif(checkId, object = 1, minValue = -4.0, maxValue = 1.0, reverseColorScheme = True):
"""
Color according to Whatif checkId score
"""
Console('off')
objectStr = 'object ' + str(object)
ColorRes(objectStr, 'Gray')
PropRes(objectStr, -999)
if reverseColorScheme:
ColorPar('Property ', 'Min', 'red', minValue)
ColorPar('Property ', 'Max', 'blue', maxValue)
else:
ColorPar('Property ', 'Min', 'blue', minValue)
ColorPar('Property ', 'Max', 'red', maxValue)
for res in project.molecule.allResidues():
list = getDeepByKeysOrAttributes(res, WHATIF_STR, checkId, VALUE_LIST_STR)
if list:
value, _sd, _n = list.average()
if value != None and not isNaN(value):
PropRes(sprintf('object %s Residue %d', object, res.resNum), value)
#end if
#end if
#end for
ColorRes(objectStr, 'Property')
Console('on')
#end def
def colorRama(object = 1): # pylint: disable=W0612
"""
Color according to Whatif ramachandran score
"""
colorWhatif('ramachandran', object = object, minValue = -1.5, maxValue = 1.0)
def colorJanin(object = 1): # pylint: disable=W0612
"""
Color according to Whatif janin score
"""
colorWhatif('janin', object = object, minValue = -1.5, maxValue = 1.0)
def colorByResidue(keys, object = 1,
minValue = 0.0, maxValue = 1.0, reverseColorScheme = False
):
Console('off')
objectStr = 'object ' + str(object)
ColorRes(objectStr, 'Gray')
PropRes(objectStr, -999)
#end if
if reverseColorScheme:
ColorPar('Property ', 'Min', 'red', minValue)
ColorPar('Property ', 'Max', 'blue', maxValue)
else:
ColorPar('Property ', 'Min', 'blue', minValue)
ColorPar('Property ', 'Max', 'red', maxValue)
for res in project.molecule.allResidues():
value = getDeepByKeysOrAttributes(res, *keys)
# if res.has_key(property) and res[property] != None and not isNaN(res[property]):
if value != None and not isNaN(value):
PropRes(sprintf('object %s Residue %d', object, res.resNum), value)
#end for
ColorRes(objectStr, 'Property')
Console('on')
#end def
def getSelectedResidue():
"""
Get the residue that is selected in yasara
"""
atomId = MarkAtom()[0]
if int(atomId) == 0:
nTerror('getSelectedResidue: nothing selected')
return None
a = Atom('atom ' + str(atomId))
fields = str(a).split()
atmName = fields[2]
resName = fields[3]
chainName = fields[4]
resNum = int(fields[5])
nTmessage( 'Selected:', chainName, resName, resNum, atmName )
nameTuple = (project.molecule.name, chainName, resNum, None, None, None, IUPAC)
#print nameTuple
res = project.molecule.decodeNameTuple(nameTuple)
#print res
return res
#end def
def showHtml():
"""
Show the html page of the selected residue
"""
res = getSelectedResidue()
if not res:
nTerror('showHtml: invalid residue')
path = os.path.abspath(project.htmlPath('Molecule', res.chain.name, res.name, 'index.html'))
nTmessage( 'showHtml: %s' % path )
webbrowser.open('file://' + path) #@UndefinedVariable
#end def
showhtml = showHtml #@UnusedVariable # pylint: disable=W0612
def screenDump(fileName, hideHUD = True):
"""
Make a screen dump; optionally hide HUD temporarily (default True)
"""
path = project.moleculePath('yasara', fileName)
if hideHUD:
hud('off')
nTmessage( 'screenDump to: %s' % path )
SaveBmp(path)
hud('on')
#end def
screendump = screenDump #@UnusedVariable # pylint: disable=W0612
def hud(toggle):
"""
Toggle HUD on/off
"""
if toggle == 'off':
HUD('off', 'on')
else:
HUD('obj', 'on')
#end def
startIpythonShell(
in_template = sprintf('yasara (%s) \#> ', project.name),
banner = '--------Dropping to yasara--------',
exit_msg='--------Leaving yasara--------'
)
def run():
parser = getRefineParser()
(options, _args) = parser.parse_args()
if options.verbosity >= 0 and options.verbosity <= 9:
cing.verbosity = options.verbosity
else:
nTerror("set verbosity is outside range [0-9] at: " + options.verbosity)
nTerror("Ignoring setting")
# end if
# From this point on code may be executed that will go through the appropriate verbosity filtering
nTdebug("options: %s" % str(options))
#------------------------------------------------------------------------------
# Documentation
#------------------------------------------------------------------------------
if options.doc:
parser.print_help(file=sys.stdout)
nTmessage("%s\n", __doc__)
return
#end if
#------------------------------------------------------------------------------
#check for the required project, name option
parser.check_required('--name')
parser.check_required('--project')
project = Project.open(options.project, status='old',
restore=1) #DEFAULT 0
if project == None:
nTerror("Failed to get a project")
return True
#end if
basePath = project.path(project.directories.refine, options.name)
# nTdebug("basePath: " + basePath)
#------------------------------------------------------------------------------
# Setup
#------------------------------------------------------------------------------
parameters = None
if options.doSetup:
parameters = doSetup(config, project, basePath, options)
# return # We had like to continue in new setup. So don't exit here.
#end if
#------------------------------------------------------------------------------
# Some output
#------------------------------------------------------------------------------
nTmessage("==> Reading configuration")
nTmessage('refinePath: %s', config.refinePath)
nTmessage('xplor: %s', config.XPLOR)
nTmessage("parameterFiles: %s", config.parameterFiles)
nTmessage("topologyFiles: %s", config.topologyFiles)
if ( options.fullRefine or options.fullAnneal or options.fullAnnealAndRefine):
if options.doSetup:
nTerror("Setup was done but fullXXX would do it again. Just run fullXXXX again without setup please.")
sys.exit(1)
# end if
else:
#------------------------------------------------------------------------------
# read parameters file
#------------------------------------------------------------------------------
if not parameters:
# nTdebug('==> will read parameters')
parameters = getParameters( basePath, 'parameters')
# nTdebug('==> parameters\n%s\n', str(parameters))
nTmessage('==> Read parameters')
# end if
setParametersFromOptions(project, options, parameters) # Do here for the first time and every time refine is called.
nTmessage('==> Done transferring some options from commandline to parameters (again)')
parameters.basePath = basePath
if parameters.name != options.name:
nTwarning("parameters.name (%s) != options.name (%s)" % ( parameters.name, options.name) )
# end if
# end if
#------------------------------------------------------------------------------
# Action selection
#------------------------------------------------------------------------------
if options.doPSF:
generatePSF(config, project, parameters, options.doPrint)
elif options.generateTemplate:
generateTemplate(config, project, parameters, options.doPrint)
elif options.doAnneal:
anneal(config, project, parameters, options.doPrint)
elif options.doAnalyze:
analyze(config, project, parameters, options.doPrint )
elif options.doRefine:
refine(config, project, parameters, options.doPrint)
elif options.doParse:
_results = parseOutput(config, project, parameters)
elif options.doImport:
importFrom(config, project, parameters)
elif options.fullAnneal:
if not fullAnneal(config, project, options):
nTerror("Failed fullAnneal")
elif options.fullRefine:
if not fullRefine(config, project, parameters, options):
nTerror("Failed fullRefine")
elif options.fullAnnealAndRefine:
if not fullAnnealAndRefine( config, project, options):
nTerror("Failed fullAnnealAndRefine")
else:
if not options.doSetup:
nTerror('refine.py, invalid options combinations:\n%s' % str(options))
return True
else:
nTmessage("Done after setup.")
#end if
if options.ipython:
startIpythonShell()
def yasaraShell(project):
if not cing.yasaradir:
nTcodeerror('yasaraShell: please put a proper yasara.py module on PYTHONPATH first (check yasaradir!)')
exit(1)
# shortcuts
f = pformat #@UnusedVariable # pylint: disable=W0612
p = project #@UnusedVariable # pylint: disable=W0612
mol = project.molecule #@UnusedVariable # pylint: disable=W0612
def commands(): # pylint: disable=W0612
cmds = ['commands', 'colorByResidue', 'colorGF', 'colorJanin', 'colorROG', 'colorWhatif',
'getSelectedResidue', 'hud', 'loadPDB', 'screenDump', 'showHtml']
cmds.sort()
for c in cmds:
nTmessage( c )
#end for
#end def
def loadPDB(model = None):
"""
Load project.molecule model [0,modelCount-1] or all models if None
"""
if not project.molecule:
nTerror('loadPDB: no molecule defined')
return True
if model == None or model == 'all':
path = project.moleculePath('yasara', sprintf('%s.pdb', project.molecule.name))
model = None
else:
path = project.moleculePath('yasara', sprintf('%s_%s.pdb', project.molecule.name, model))
project.molecule.toPDBfile(path, model = model)
nTmessage('loadPDB: %s' % path)
LoadPDB(os.path.abspath(path))
Style('Ribbon', 'off')
#end def
# alternate names
loadpdb = loadPDB #@UnusedVariable # pylint: disable=W0612
loadPdb = loadPDB #@UnusedVariable # pylint: disable=W0612
def colorROG(object = 1): # pylint: disable=W0612
"""
Color residues according to Cing ROG score
"""
Console('off')
ColorRes('object ' + str(object), 'Gray')
yasaraColorDict = dict(green = 240, orange = 150, red = 120)
for res in project.molecule.allResidues():
cmd = sprintf('object %s residue %d,%s', object, res.resNum, yasaraColorDict[res.rogScore.colorLabel])
ColorRes(cmd)
#end for
Console('on')
#end def
def colorGF(object = 1, minValue = -3.0, maxValue = 1.0): # pylint: disable=W0612
"""
Color residues according to Procheck gf score
"""
colorByResidue(['procheck', 'gf'],
minValue = minValue, maxValue = maxValue,
reverseColorScheme = True
)
#end def
def colorWhatif(checkId, object = 1, minValue = -4.0, maxValue = 1.0, reverseColorScheme = True):
"""
Color according to Whatif checkId score
"""
Console('off')
objectStr = 'object ' + str(object)
ColorRes(objectStr, 'Gray')
PropRes(objectStr, -999)
if reverseColorScheme:
ColorPar('Property ', 'Min', 'red', minValue)
ColorPar('Property ', 'Max', 'blue', maxValue)
else:
ColorPar('Property ', 'Min', 'blue', minValue)
ColorPar('Property ', 'Max', 'red', maxValue)
for res in project.molecule.allResidues():
list = getDeepByKeysOrAttributes(res, WHATIF_STR, checkId, VALUE_LIST_STR)
if list:
value, _sd, _n = list.average()
if value != None and not isNaN(value):
PropRes(sprintf('object %s Residue %d', object, res.resNum), value)
#end if
#end if
#end for
ColorRes(objectStr, 'Property')
Console('on')
#end def
def colorRama(object = 1): # pylint: disable=W0612
"""
Color according to Whatif ramachandran score
"""
colorWhatif('ramachandran', object = object, minValue = -1.5, maxValue = 1.0)
def colorJanin(object = 1): # pylint: disable=W0612
"""
Color according to Whatif janin score
"""
colorWhatif('janin', object = object, minValue = -1.5, maxValue = 1.0)
def colorByResidue(keys, object = 1,
minValue = 0.0, maxValue = 1.0, reverseColorScheme = False
):
Console('off')
objectStr = 'object ' + str(object)
ColorRes(objectStr, 'Gray')
PropRes(objectStr, -999)
#end if
if reverseColorScheme:
ColorPar('Property ', 'Min', 'red', minValue)
ColorPar('Property ', 'Max', 'blue', maxValue)
else:
ColorPar('Property ', 'Min', 'blue', minValue)
ColorPar('Property ', 'Max', 'red', maxValue)
for res in project.molecule.allResidues():
value = getDeepByKeysOrAttributes(res, *keys)
# if res.has_key(property) and res[property] != None and not isNaN(res[property]):
if value != None and not isNaN(value):
PropRes(sprintf('object %s Residue %d', object, res.resNum), value)
#end for
ColorRes(objectStr, 'Property')
Console('on')
#end def
def getSelectedResidue():
"""
Get the residue that is selected in yasara
"""
atomId = MarkAtom()[0]
if int(atomId) == 0:
nTerror('getSelectedResidue: nothing selected')
return None
a = Atom('atom ' + str(atomId))
fields = str(a).split()
atmName = fields[2]
resName = fields[3]
chainName = fields[4]
resNum = int(fields[5])
nTmessage( 'Selected:', chainName, resName, resNum, atmName )
nameTuple = (project.molecule.name, chainName, resNum, None, None, None, IUPAC)
#print nameTuple
res = project.molecule.decodeNameTuple(nameTuple)
#print res
return res
#end def
def showHtml():
"""
Show the html page of the selected residue
"""
res = getSelectedResidue()
if not res:
nTerror('showHtml: invalid residue')
path = os.path.abspath(project.htmlPath('Molecule', res.chain.name, res.name, 'index.html'))
nTmessage( 'showHtml: %s' % path )
webbrowser.open('file://' + path) #@UndefinedVariable
#end def
showhtml = showHtml #@UnusedVariable # pylint: disable=W0612
def screenDump(fileName, hideHUD = True):
"""
Make a screen dump; optionally hide HUD temporarily (default True)
"""
path = project.moleculePath('yasara', fileName)
if hideHUD:
hud('off')
nTmessage( 'screenDump to: %s' % path )
SaveBmp(path)
hud('on')
#end def
screendump = screenDump #@UnusedVariable # pylint: disable=W0612
def hud(toggle):
"""
Toggle HUD on/off
"""
if toggle == 'off':
HUD('off', 'on')
else:
HUD('obj', 'on')
#end def
startIpythonShell(
in_template = sprintf('yasara (%s) \#> ', project.name),
banner = '--------Dropping to yasara--------',
exit_msg='--------Leaving yasara--------'
)
