def setupMV(self):
self.mv.browseCommands('fileCommands', package="Pmv", topCommand=0)
self.mv.browseCommands('bondsCommands', package='Pmv', topCommand=0)
self.mv.browseCommands('deleteCommands', package='Pmv', topCommand=0)
self.mv.browseCommands('displayCommands',
commands=[
'displaySticksAndBalls',
'undisplaySticksAndBalls', 'displayCPK',
'undisplayCPK', 'displayLines',
'undisplayLines', 'displayBackboneTrace',
'undisplayBackboneTrace', 'DisplayBoundGeom'
],
package='Pmv',
topCommand=0)
self.mv.browseCommands('editCommands', package='Pmv', topCommand=0)
self.mv.browseCommands("secondaryStructureCommands",
package="Pmv",
topCommand=0)
self.mv.browseCommands('beadedRibbonsCommands',
package="ePMV",
topCommand=0)
self.mv.browseCommands("splineCommands", package="Pmv", topCommand=0)
self.mv.browseCommands("coarseMolSurfaceCommands",
package="Pmv",
topCommand=0)
self.mv.browseCommands('msmsCommands',
commands=[
'computeMSMS',
'displayMSMS',
'undisplayMSMS',
'readMSMS',
'saveMSMS',
'computeSESAndSASArea',
],
package='Pmv',
topCommand=0)
self.mv.browseCommands('selectionCommands',
commands=[
'select', 'deselect', 'clearSelection',
'saveSet', 'invertSelection', 'selectSet',
'selectFromString', 'directSelect',
'selectHeteroAtoms'
],
package='Pmv',
topCommand=0)
self.mv.browseCommands('APBSCommands_2x',
package='ePMV.pmv_dev',
topCommand=0)
self.mv.browseCommands('colorCommands',
package='ePMV.pmv_dev',
topCommand=0)
self.mv.browseCommands('buildDNACommands',
package='ePMV.pmv_dev',
topCommand=0) #commands=['buildDNA']
self.mv.browseCommands('repairCommands', package='Pmv', topCommand=0)
self.mv.browseCommands("dejaVuCommands",
package="ViewerFramework",
topCommand=0)
self.mv.browseCommands('displayCommands',
commands=['showMolecules'],
package='Pmv',
topCommand=0)
self.mv.browseCommands('helpCommands', package='Pmv', topCommand=0)
self.mv.browseCommands('superimposeCommandsNew',
package='Pmv',
topCommand=0)
self.mv.browseCommands('setangleCommands', package='Pmv', topCommand=0)
self.mv.setUserPreference(('Transformation Logging', 'final'),
topCommand=0)
self.mv.setUserPreference(('Show Progress Bar', 'show'), topCommand=0)
self.mv.setUserPreference(('Sharp Color Boundaries for MSMS', 'blur'),
topCommand=0)
self.mv.browseCommands('serverCommands',
commands=[
'startServer', 'connectToServer',
'StartWebControlServer'
],
package='ViewerFramework',
topCommand=0)
self.mv.addCommand(BindGeomToMolecularFragment(),
'bindGeomToMolecularFragment', None)
self.mv.browseCommands('trajectoryCommands',
commands=['openTrajectory'],
log=0,
package='Pmv')
self.mv.addCommand(PlayTrajectoryCommand(), 'playTrajectory', None)
self.mv.addCommand(addGridCommand(), 'addGrid', None)
self.mv.addCommand(readAnyGrid(), 'readAny', None)
self.mv.addCommand(IsocontourCommand(), 'isoC', None)
#define the listener
if self.host is not None:
self.mv.registerListener(DeleteGeomsEvent, self.updateGeom)
self.mv.registerListener(AddGeomsEvent, self.updateGeom)
self.mv.registerListener(EditGeomsEvent, self.updateGeom)
self.mv.registerListener(AfterDeleteAtomsEvent, self.updateModel)
self.mv.registerListener(BeforeDeleteMoleculesEvent,
self.updateModel)
self.mv.addCommand(epmvAdaptor.loadMoleculeInHost(self),
'_loadMol', None)
#self.mv.embedInto(self.host,debug=0)
self.mv.embeded = True
#compatibility with PMV
self.mv.Grid3DReadAny = self.mv.readAny
#mv.browseCommands('superimposeCommandsNew', package='Pmv', topCommand=0)
self.mv.userpref['Read molecules as']['value'] = 'conformations'
self.mv.setUserPreference((
'Read molecules as',
'conformations',
),
log=0)
self.mv.setUserPreference((
'Number of Undo',
'0',
), redraw=0, log=1)
self.mv.setUserPreference((
'Save Perspective on Exit',
'no',
), log=0)
self.mv.setUserPreference((
'Transformation Logging',
'no',
), log=0)
#should add some user preferece and be able to save it
#recentFiles Folder
rcFile = self.mv.rcFolder
if rcFile:
rcFile += os.sep + 'Pmv' + os.sep + "recent.pkl"
self.mv.recentFiles = RecentFiles(self.mv,
None,
filePath=rcFile,
index=0)
else:
print("no rcFolder??")
#this create mv.hostapp which handle server/client and log event system
#NOTE : need to test it in the latest version
# if not self.useLog :
# self.mv.hostApp.driver.useEvent = True
self.mv.iTraj = {}
self.funcColor = [
self.mv.colorByAtomType, self.mv.colorAtomsUsingDG,
self.mv.colorByResidueType, self.mv.colorResiduesUsingShapely,
self.mv.colorBySecondaryStructure, self.mv.colorByChains,
self.mv.colorByDomains, self.mv.color, self.mv.colorByProperty
]
self.fTypeToFc = {
"ByAtom": 0,
"AtomsU": 1,
"ByResi": 2,
"Residu": 3,
"BySeco": 4,
"ByChai": 5,
"ByDoma": 6,
"": 7,
"ByPropN": 8,
"ByPropT": 9,
"ByPropS": 10
}
self.mv.host = self.host
def setupMV(self):
self.mv.browseCommands('fileCommands', package="Pmv", topCommand=0)
self.mv.browseCommands('bondsCommands',package='Pmv', topCommand=0)
self.mv.browseCommands('deleteCommands',package='Pmv', topCommand=0)
self.mv.browseCommands('displayCommands',
commands=['displaySticksAndBalls','undisplaySticksAndBalls',
'displayCPK', 'undisplayCPK',
'displayLines','undisplayLines',
'displayBackboneTrace','undisplayBackboneTrace',
'DisplayBoundGeom'], package='Pmv', topCommand=0)
self.mv.browseCommands('editCommands',package='Pmv', topCommand=0)
self.mv.browseCommands("secondaryStructureCommands", package="Pmv", topCommand=0)
self.mv.browseCommands('beadedRibbonsCommands', package="ePMV", topCommand=0)
self.mv.browseCommands("splineCommands", package="Pmv", topCommand=0)
self.mv.browseCommands("coarseMolSurfaceCommands", package="Pmv", topCommand=0)
self.mv.browseCommands('msmsCommands',
commands=['computeMSMS','displayMSMS', 'undisplayMSMS',
'readMSMS', 'saveMSMS', 'computeSESAndSASArea',],
package='Pmv', topCommand=0)
self.mv.browseCommands('selectionCommands', commands=['select', 'deselect',
'clearSelection', 'saveSet',
'invertSelection',
'selectSet',
'selectFromString',
'directSelect','selectHeteroAtoms'],
package='Pmv', topCommand=0)
self.mv.browseCommands('APBSCommands_2x', package='ePMV.pmv_dev', topCommand=0)
self.mv.browseCommands('colorCommands',package='ePMV.pmv_dev', topCommand=0)
self.mv.browseCommands('buildDNACommands',package='ePMV.pmv_dev', topCommand=0)#commands=['buildDNA']
self.mv.browseCommands('repairCommands', package='Pmv', topCommand=0)
self.mv.browseCommands("dejaVuCommands", package="ViewerFramework", topCommand=0)
self.mv.browseCommands('displayCommands',
commands=['showMolecules'],
package='Pmv', topCommand=0)
self.mv.browseCommands('helpCommands',package ='Pmv', topCommand =0)
self.mv.browseCommands('superimposeCommandsNew', package='Pmv', topCommand=0)
self.mv.browseCommands('setangleCommands', package='Pmv', topCommand=0)
self.mv.setUserPreference(('Transformation Logging', 'final'), topCommand=0)
self.mv.setUserPreference(('Show Progress Bar', 'show'), topCommand=0)
self.mv.setUserPreference(('Sharp Color Boundaries for MSMS', 'blur'), topCommand=0)
self.mv.browseCommands('serverCommands', commands=[
'startServer', 'connectToServer', 'StartWebControlServer'],
package='ViewerFramework', topCommand=0)
self.mv.addCommand(BindGeomToMolecularFragment(), 'bindGeomToMolecularFragment', None)
self.mv.browseCommands('trajectoryCommands',commands=['openTrajectory'],log=0,package='Pmv')
self.mv.addCommand(PlayTrajectoryCommand(),'playTrajectory',None)
self.mv.addCommand(addGridCommand(),'addGrid',None)
self.mv.addCommand(readAnyGrid(),'readAny',None)
self.mv.addCommand(IsocontourCommand(),'isoC',None)
#define the listener
if self.host is not None :
self.mv.registerListener(DeleteGeomsEvent, self.updateGeom)
self.mv.registerListener(AddGeomsEvent, self.updateGeom)
self.mv.registerListener(EditGeomsEvent, self.updateGeom)
self.mv.registerListener(AfterDeleteAtomsEvent, self.updateModel)
self.mv.registerListener(BeforeDeleteMoleculesEvent,self.updateModel)
self.mv.addCommand(epmvAdaptor.loadMoleculeInHost(self),'_loadMol',None)
#self.mv.embedInto(self.host,debug=0)
self.mv.embeded = True
#compatibility with PMV
self.mv.Grid3DReadAny = self.mv.readAny
#mv.browseCommands('superimposeCommandsNew', package='Pmv', topCommand=0)
self.mv.userpref['Read molecules as']['value']='conformations'
self.mv.setUserPreference(('Read molecules as', 'conformations',), log=0)
self.mv.setUserPreference(('Number of Undo', '0',), redraw=0, log=1)
self.mv.setUserPreference(('Save Perspective on Exit', 'no',), log=0)
self.mv.setUserPreference(('Transformation Logging', 'no',), log=0)
#should add some user preferece and be able to save it
#recentFiles Folder
rcFile = self.mv.rcFolder
if rcFile:
rcFile += os.sep + 'Pmv' + os.sep + "recent.pkl"
self.mv.recentFiles = RecentFiles(self.mv, None, filePath=rcFile,index=0)
else :
print("no rcFolder??")
#this create mv.hostapp which handle server/client and log event system
#NOTE : need to test it in the latest version
# if not self.useLog :
# self.mv.hostApp.driver.useEvent = True
self.mv.iTraj={}
self.funcColor = [self.mv.colorByAtomType,
self.mv.colorAtomsUsingDG,
self.mv.colorByResidueType,
self.mv.colorResiduesUsingShapely,
self.mv.colorBySecondaryStructure,
self.mv.colorByChains,
self.mv.colorByDomains,
self.mv.color,
self.mv.colorByProperty]
self.fTypeToFc = {"ByAtom":0,"AtomsU":1,"ByResi":2,"Residu":3,
"BySeco":4,"ByChai":5,"ByDoma":6,"":7,
"ByPropN":8,"ByPropT":9,"ByPropS":10}
self.mv.host = self.host