Python AtomSet.full_name方法代碼示例

# 需要導入模塊: from MolKit.molecule import AtomSet [as 別名]
# 或者: from MolKit.molecule.AtomSet import full_name [as 別名]
 def buildCloseContactAtoms(self, percentCutoff, ligand, comment="USER AD> "):
     pairDict = self.distanceSelector.select(ligand.allAtoms,
                     self.macro_atoms, percentCutoff=percentCutoff)
     self.pairDict = pairDict
     #reset here
     lig_close_ats = AtomSet()
     macro_close_ats = AtomSet()
     cdict = {}
     for k,v in pairDict.items():
         if len(v):
             cdict[k] = 1
         for at in v:
             if at not in macro_close_ats:
                 cdict[at] = 1
     closeAtoms = AtomSet(cdict.keys())
     lig_close_ats = closeAtoms.get(lambda x: x.top==ligand).uniq()
     #ligClAtStr = lig_close_ats.full_name()
     ligClAtStr = comment + "lig_close_ats: %d\n" %( len(lig_close_ats))
     if len(lig_close_ats):
         ligClAtStr += comment + "%s\n" %( lig_close_ats.full_name())
     macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms).uniq()
     macroClAtStr = comment + "macro_close_ats: %d\n" %( len(macro_close_ats))
     if len(macro_close_ats):
         macroClAtStr += comment + "%s\n" %( macro_close_ats.full_name())
     #macroClAtStr = "macro_close_ats: " + len(macro_close_ats)+"\n" +macro_close_ats.full_name()
     rdict = self.results
     rdict['lig_close_atoms'] = lig_close_ats
     rdict['macro_close_atoms'] = macro_close_ats
     if self.verbose: print "macroClAtStr=", macroClAtStr
     if self.verbose: print "ligClAtStr=", ligClAtStr
     if self.verbose: print "returning "+ macroClAtStr + '==' + ligClAtStr
     return  macroClAtStr , ligClAtStr

# 需要導入模塊: from MolKit.molecule import AtomSet [as 別名]
# 或者: from MolKit.molecule.AtomSet import full_name [as 別名]
 def setupUndoAfter(self, ats, angle,**kw):
     #no atoms, <4 atoms, 
     aSet = AtomSet(self.atomList)
     self.undoMenuString = self.name
     if len(self.atomList)==0:
         undoCmd = 'self.setTorsionGC.atomList=[]; self.setTorsionGC.update()'
     elif len(self.atomList)<4:
         #need to step back here
         undoCmd = 'self.setTorsionGC.atomList=self.setTorsionGC.atomList[:-1]; self.setTorsionGC.update()'
     elif self.origValue==self.oldValue:
         return
     else:
         restoreAngle = self.origValue
         self.undoNow = 1
         undoCmd = 'self.setTorsionGC(\''+ aSet.full_name()+ '\',' + str(restoreAngle) + ', topCommand=0)'
     self.vf.undo.addEntry((undoCmd), (self.name))

# 需要導入模塊: from MolKit.molecule import AtomSet [as 別名]
# 或者: from MolKit.molecule.AtomSet import full_name [as 別名]
class AddBondsGUICommand(MVCommand, MVAtomICOM):
    """
    The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them. To use this command you need first to load it into PMV. Then you can find the entry 'addBonds' under the Edit menu. To add bonds  you just need to pick on the 2 atoms you want to bind. If you drag select  a bunch of atoms, the command will buildBondsByDistance between them.This command is undoable.
   \nPackage : Pmv
   \nModule  : bondsCommands
   \nClass   : AddBondsGUICommand
   \nCommand : addBondsGC
   \nSynopsis:\n
        None<-addBondsGC(atoms)\n
    \nRequired Arguments:\n    
        atoms  : atom(s)\n
    """
    
    def __init__(self, func=None):
        MVCommand.__init__(self, func)
        MVAtomICOM.__init__(self)
        self.atomList = AtomSet([])
        self.undoAtList = AtomSet([])
        self.labelStrs = []


    def onRemoveObjectFromViewer(self, obj):
        removeAts = AtomSet([])
        for at in self.atomList:
            if at in obj.allAtoms:
                removeAts.append(at)
        self.atomList = self.atomList - removeAts
        removeAts = AtomSet([])
        for at in self.undoAtList:
            if at in obj.allAtoms:
                removeAts.append(at)
        self.undoAtList = self.undoAtList - removeAts
        self.update()

       
    def onAddCmdToViewer(self):
        if not self.vf.commands.has_key('setICOM'):
            self.vf.loadCommand('interactiveCommands', 'setICOM', 'Pmv',
                                topCommand=0) 
        if not self.vf.commands.has_key('addBonds'):
            self.vf.loadCommand('bondsCommands', 'addBonds', 'Pmv',
                                topCommand=0) 
        if not self.vf.commands.has_key('removeBondsGC'):
            self.vf.loadCommand('bondsCommands', 'removeBondsGC', 'Pmv',
                                topCommand=0) 
        self.masterGeom = Geom('addBondsGeom',shape=(0,0), 
                               pickable=0, protected=True)
        self.masterGeom.isScalable = 0
        self.spheres = Spheres(name='addBondsSpheres', shape=(0,3),
                               inheritMaterial=0,
                               radii=0.2, quality=15,
                               materials = ((1.,1.,0.),), protected=True) 
        if not self.vf.commands.has_key('labelByExpression'):
            self.vf.loadCommand('labelCommands', 
                                ['labelByExpression',], 'Pmv', topCommand=0)
        if self.vf.hasGui:
            miscGeom = self.vf.GUI.miscGeom
            self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
            self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)


    def __call__(self, atoms, **kw):
        """None<-addBondsGC(atoms)
           \natoms  : atom(s)"""
        if type(atoms) is StringType:
            self.nodeLogString = "'"+atoms+"'"
        ats = self.vf.expandNodes(atoms)
        if not len(ats): return 'ERROR'
        return apply(self.doitWrapper, (ats,), kw)


    def doit(self, ats):
        if len(ats)>2:
            if len(self.atomList):
                atSet = ats + self.atomList
            else: atSet = ats
            parent = atSet[0].parent
            parent.buildBondsByDistanceOnAtoms(atSet)
            self.atomList = AtomSet([])
            self.update(True)
        else:
            lenAts = len(self.atomList)
            last = None
            if lenAts:
                last = self.atomList[-1]
                top = self.atomList[0].top
            for at in ats:
                #check for repeats of same atom
                if lenAts and at==last:
                    continue
                #lenAts = len(self.atomList)
                #if lenAts and at==self.atomList[-1]:
                #    continue
                if lenAts and at.top!=self.atomList[-1].top:
                    msg = "intermolecular bond to %s disallowed"%(at.full_name())
                    self.warningMsg(msg)
                self.atomList.append(at)
                self.undoAtList.append(at)
                lenAts = len(self.atomList)
            self.update(True)
#.........這裏部分代碼省略.........