Source Code for Module Chem.PyMol

  1  # $Id: PyMol.py 2 2006-05-06 22:54:39Z glandrum $
 
  2  #
 
  3  # Copyright (C) 2004-2006 Rational Discovery LLC
 
  4  #
 
  5  #   @@ All Rights Reserved  @@
 
  6  #
 
  7  """ uses pymol to interact with molecules
 
  8  
 
  9  """ 
 10  import Chem 
 11  import xmlrpclib 
 12  
 
 13  
 
 14  _server=None 
 15 -class MolViewer(object): 
 16 -  def __init__(self,host='localhost',port=9123,force=0,**kwargs): 
 17      global _server 
 18      if not force and _server is not None: 
 19        self.server=_server 
 20      else: 
 21        _server=None 
 22        serv = xmlrpclib.Server('http://%s:%d'%(host,port)) 
 23        serv.ping() 
 24        _server = serv 
 25        self.server=serv 
 26      self.InitializePyMol() 
 27      
 
 28 -  def InitializePyMol(self): 
 29      """ does some initializations to set up PyMol according to our
 
 30      tastes
 
 31  
 
 32      """ 
 33      self.server.do('set valence,1') 
 34      self.server.do('set stick_rad,0.15') 
 35      self.server.do('set mouse_selection_mode,0') 
 36      self.server.do('set line_width,2') 
 37      self.server.do('set selection_width,10') 
 38      self.server.do('set auto_zoom,0') 
 39      
 
 40  
 
 41 -  def DeleteAll(self): 
 42      self.server.deleteAll() 
 43  
 
 44 -  def DeleteAllExcept(self,excludes): 
 45      allNames = self.server.getNames('*',False) 
 46      for nm in allNames: 
 47        if nm not in excludes: 
 48          self.server.deleteObject(nm) 
 49  
 
 50 -  def LoadFile(self,filename,name,showOnly=False): 
 51      if showOnly: 
 52        self.DeleteAll() 
 53      id = self.server.loadFile(filename,name) 
 54      return id 
 55  
 
 56 -  def ShowMol(self,mol,name='molecule',showOnly=True,highlightFeatures=[],
 
 57                molB="",confId=-1,zoom=True): 
 58      """ special case for displaying a molecule or mol block """ 
 59    
 
 60      if not molB: 
 61        molB = Chem.MolToMolBlock(mol,confId=confId) 
 62      server = self.server 
 63      if not zoom: 
 64        self.server.do('view rdinterface,store') 
 65      if showOnly: 
 66        self.DeleteAll() 
 67      id = server.loadMolBlock(molB,name) 
 68      if highlightFeatures: 
 69        nm = name+'-features' 
 70        conf = mol.GetConformer(confId) 
 71        for feat in highlightFeatures: 
 72          pt = [0.0,0.0,0.0] 
 73          for idx in feat: 
 74            loc = conf.GetAtomPosition(idx) 
 75            pt[0] += loc[0]/len(feat) 
 76            pt[1] += loc[1]/len(feat) 
 77            pt[2] += loc[2]/len(feat) 
 78          server.sphere(pt,0.2,(1,1,1),nm) 
 79      if zoom: 
 80        server.zoom('visible') 
 81      else: 
 82        self.server.do('view rdinterface,recall') 
 83      return id 
 84 -  def GetSelectedAtoms(self,whichSelection=None): 
 85      if not whichSelection: 
 86        sels = self.server.getNames('selections') 
 87        if sels: 
 88          whichSelection = sels[-1] 
 89        else: 
 90          whichSelection=None 
 91      if whichSelection:    
 92        items = self.server.index(whichSelection) 
 93      else: 
 94        items = [] 
 95      return items 
 96  
 
 97  
 
 98 -  def SelectAtoms(self,itemId,atomIndices,selName='selection'): 
 99      ids = '(id ' 
100      ids += ','.join(['%d'%(x+1) for x in atomIndices]) 
101      ids += ')' 
102      cmd = 'select %s,%s and %s'%(selName,ids,itemId) 
103      self.server.do(cmd) 
104    
 
105 -  def HighlightAtoms(self,indices,where,extraHighlight=False): 
106      if extraHighlight: 
107        idxText = ','.join(['%s and (id %d)'%(where,x) for x in indices]) 
108        self.server.do('edit %s'%idxText) 
109      else: 
110        idxText = ' or '.join(['id %d'%x for x in indices]) 
111        self.server.do('select selection, %s and (%s)'%(where,idxText)) 
112  
 
113 -  def SetDisplayStyle(self,obj,style=''): 
114      self.server.do('hide everything,%s'%(obj,)) 
115      if style: 
116        self.server.do('show %s,%s'%(style,obj)) 
117  
 
118 -  def SelectProteinNeighborhood(self,aroundObj,inObj,distance=5.0,
 
119                                  name='neighborhood',showSurface=False): 
120      self.server.do('select %(name)s,byres (%(aroundObj)s around %(distance)f) and %(inObj)s'%locals()) 
121  
 
122      if showSurface: 
123        self.server.do('show surface,%s'%name) 
124        self.server.do('disable %s'%name) 
125  
 
126  
 
127 -  def AddPharmacophore(self,locs,colors,label,sphereRad=0.5): 
128      self.server.do('view rdinterface,store') 
129      self.server.resetCGO(label) 
130      for i,loc in enumerate(locs): 
131        self.server.sphere(loc,sphereRad,colors[i],label,1) 
132      self.server.do('enable %s'%label) 
133      self.server.do('view rdinterface,recall') 
134      
 
135  
 
136 -  def SetDisplayUpdate(self,val): 
137      if not val: 
138        self.server.do('set defer_update,1') 
139      else: 
140        self.server.do('set defer_update,0') 
141  
 
142        
 
143 -  def GetAtomCoords(self,sels): 
144      res = {} 
145      for label,idx in sels: 
146        coords = self.server.getAtomCoords('(%s and id %d)'%(label,idx)) 
147        res[(label,idx)] = coords 
148        print 'grab:',label,idx,coords 
149      return res 
150  
 
151 -  def HideAll(self): 
152      self.server.do('disable all') 
153 -  def HideObject(self,objName): 
154      self.server.do('disable %s'%objName) 
155 -  def DisplayObject(self,objName): 
156      self.server.do('enable %s'%objName) 
157  
 
158 -  def Redraw(self): 
159      self.server.do('refresh') 
160 -  def Zoom(self,objName): 
161      self.server.zoom(objName) 
162  
 
163 -  def DisplayHBonds(self,objName,molName,proteinName,
 
164                      molSelText='(%(molName)s)',
 
165                      proteinSelText='(%(proteinName)s and not het)'): 
166      cmd = "delete %(objName)s;\n" 
167      cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",mode=2;\n" 
168      cmd += "enable %(objName)s;" 
169      cmd = cmd%locals() 
170  
 
171      self.server.do(cmd) 
172  
 
173 -  def DisplayCollisions(self,objName,molName,proteinName,distCutoff=3.0,
 
174                          color='red',
 
175                          molSelText='(%(molName)s)',
 
176                          proteinSelText='(%(proteinName)s and not het)'): 
177      cmd = "delete %(objName)s;\n" 
178      cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",%(distCutoff)f,mode=0;\n" 
179      cmd += """enable %(objName)s
 
180      color %(color)s, %(objName)s""" 
181      cmd = cmd%locals() 
182      self.server.do(cmd) 
183