Source Code for Module rdkit.Chem.PyMol

  1  # $Id: PyMol.py 1528 2010-09-26 17:04:37Z glandrum $ 
  2  # 
  3  # Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved @@ 
  6  #  This file is part of the RDKit. 
  7  #  The contents are covered by the terms of the BSD license 
  8  #  which is included in the file license.txt, found at the root 
  9  #  of the RDKit source tree. 
 10  # 
 11  """ uses pymol to interact with molecules 
 12   
 13  """ 
 14  from rdkit import Chem 
 15  import xmlrpclib,os 
 16   
 17   
 18  _server=None 
 19 -class MolViewer(object): 
 20 -  def __init__(self,host=None,port=9123,force=0,**kwargs): 
 21      global _server 
 22      if not force and _server is not None: 
 23        self.server=_server 
 24      else: 
 25        if not host: 
 26          host=os.environ.get('PYMOL_RPCHOST','localhost') 
 27        _server=None 
 28        serv = xmlrpclib.Server('http://%s:%d'%(host,port)) 
 29        serv.ping() 
 30        _server = serv 
 31        self.server=serv 
 32      self.InitializePyMol() 
 33       
 34 -  def InitializePyMol(self): 
 35      """ does some initializations to set up PyMol according to our 
 36      tastes 
 37   
 38      """ 
 39      self.server.do('set valence,1') 
 40      self.server.do('set stick_rad,0.15') 
 41      self.server.do('set mouse_selection_mode,0') 
 42      self.server.do('set line_width,2') 
 43      self.server.do('set selection_width,10') 
 44      self.server.do('set auto_zoom,0') 
 45       
 46   
 47 -  def DeleteAll(self): 
 48      " blows out everything in the viewer " 
 49      self.server.deleteAll() 
 50   
 51 -  def DeleteAllExcept(self,excludes): 
 52      " deletes everything except the items in the provided list of arguments " 
 53      allNames = self.server.getNames('*',False) 
 54      for nm in allNames: 
 55        if nm not in excludes: 
 56          self.server.deleteObject(nm) 
 57   
 58 -  def LoadFile(self,filename,name,showOnly=False): 
 59      """ calls pymol's "load" command on the given filename; the loaded object 
 60      is assigned the name "name" 
 61      """ 
 62      if showOnly: 
 63        self.DeleteAll() 
 64      id = self.server.loadFile(filename,name) 
 65      return id 
 66   
 67 -  def ShowMol(self,mol,name='molecule',showOnly=True,highlightFeatures=[], 
 68                molB="",confId=-1,zoom=True): 
 69      """ special case for displaying a molecule or mol block """ 
 70     
 71      if not molB: 
 72        molB = Chem.MolToMolBlock(mol,confId=confId) 
 73      server = self.server 
 74      if not zoom: 
 75        self.server.do('view rdinterface,store') 
 76      if showOnly: 
 77        self.DeleteAll() 
 78      id = server.loadMolBlock(molB,name) 
 79      if highlightFeatures: 
 80        nm = name+'-features' 
 81        conf = mol.GetConformer(confId) 
 82        for feat in highlightFeatures: 
 83          pt = [0.0,0.0,0.0] 
 84          for idx in feat: 
 85            loc = conf.GetAtomPosition(idx) 
 86            pt[0] += loc[0]/len(feat) 
 87            pt[1] += loc[1]/len(feat) 
 88            pt[2] += loc[2]/len(feat) 
 89          server.sphere(pt,0.2,(1,1,1),nm) 
 90      if zoom: 
 91        server.zoom('visible') 
 92      else: 
 93        self.server.do('view rdinterface,recall') 
 94      return id 
 95   
 96 -  def GetSelectedAtoms(self,whichSelection=None): 
 97      " returns the selected atoms " 
 98      if not whichSelection: 
 99        sels = self.server.getNames('selections') 
100        if sels: 
101          whichSelection = sels[-1] 
102        else: 
103          whichSelection=None 
104      if whichSelection:    
105        items = self.server.index(whichSelection) 
106      else: 
107        items = [] 
108      return items 
109   
110   
111 -  def SelectAtoms(self,itemId,atomIndices,selName='selection'): 
112      " selects a set of atoms " 
113      ids = '(id ' 
114      ids += ','.join(['%d'%(x+1) for x in atomIndices]) 
115      ids += ')' 
116      cmd = 'select %s,%s and %s'%(selName,ids,itemId) 
117      self.server.do(cmd) 
118     
119 -  def HighlightAtoms(self,indices,where,extraHighlight=False): 
120      " highlights a set of atoms "  
121      if extraHighlight: 
122        idxText = ','.join(['%s and (id %d)'%(where,x) for x in indices]) 
123        self.server.do('edit %s'%idxText) 
124      else: 
125        idxText = ' or '.join(['id %d'%x for x in indices]) 
126        self.server.do('select selection, %s and (%s)'%(where,idxText)) 
127   
128 -  def SetDisplayStyle(self,obj,style=''): 
129      " change the display style of the specified object " 
130      self.server.do('hide everything,%s'%(obj,)) 
131      if style: 
132        self.server.do('show %s,%s'%(style,obj)) 
133   
134 -  def SelectProteinNeighborhood(self,aroundObj,inObj,distance=5.0, 
135                                  name='neighborhood',showSurface=False): 
136      """ selects the area of a protein around a specified object/selection name; 
137      optionally adds a surface to that """ 
138      self.server.do('select %(name)s,byres (%(aroundObj)s around %(distance)f) and %(inObj)s'%locals()) 
139       
140   
141      if showSurface: 
142        self.server.do('show surface,%s'%name) 
143        self.server.do('disable %s'%name) 
144   
145 -  def AddPharmacophore(self,locs,colors,label,sphereRad=0.5): 
146      " adds a set of spheres " 
147      self.server.do('view rdinterface,store') 
148      self.server.resetCGO(label) 
149      for i,loc in enumerate(locs): 
150        self.server.sphere(loc,sphereRad,colors[i],label,1) 
151      self.server.do('enable %s'%label) 
152      self.server.do('view rdinterface,recall') 
153       
154   
155 -  def SetDisplayUpdate(self,val): 
156      if not val: 
157        self.server.do('set defer_update,1') 
158      else: 
159        self.server.do('set defer_update,0') 
160   
161 -  def GetAtomCoords(self,sels): 
162      " returns the coordinates of the selected atoms "  
163      res = {} 
164      for label,idx in sels: 
165        coords = self.server.getAtomCoords('(%s and id %d)'%(label,idx)) 
166        res[(label,idx)] = coords 
167      return res 
168   
169 -  def HideAll(self): 
170      self.server.do('disable all') 
171 -  def HideObject(self,objName): 
172      self.server.do('disable %s'%objName) 
173 -  def DisplayObject(self,objName): 
174      self.server.do('enable %s'%objName) 
175   
176 -  def Redraw(self): 
177      self.server.do('refresh') 
178 -  def Zoom(self,objName): 
179      self.server.zoom(objName) 
180   
181 -  def DisplayHBonds(self,objName,molName,proteinName, 
182                      molSelText='(%(molName)s)', 
183                      proteinSelText='(%(proteinName)s and not het)'): 
184      " toggles display of h bonds between the protein and a specified molecule " 
185      cmd = "delete %(objName)s;\n" 
186      cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",mode=2;\n" 
187      cmd += "enable %(objName)s;" 
188      cmd = cmd%locals() 
189   
190      self.server.do(cmd) 
191   
192 -  def DisplayCollisions(self,objName,molName,proteinName,distCutoff=3.0, 
193                          color='red', 
194                          molSelText='(%(molName)s)', 
195                          proteinSelText='(%(proteinName)s and not het)'): 
196      " toggles display of collisions between the protein and a specified molecule " 
197      cmd = "delete %(objName)s;\n" 
198      cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",%(distCutoff)f,mode=0;\n" 
199      cmd += """enable %(objName)s 
200      color %(color)s, %(objName)s""" 
201      cmd = cmd%locals() 
202      self.server.do(cmd) 
203