Source Code for Module rdkit.Chem.PyMol

  1  # $Id: PyMol.py 997 2009-02-25 06:12:43Z glandrum $ 
  2  # 
  3  # Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """ uses pymol to interact with molecules 
  8   
  9  """ 
 10  from rdkit import Chem 
 11  import xmlrpclib,os 
 12   
 13   
 14  _server=None 
 15 -class MolViewer(object): 
 16 -  def __init__(self,host=None,port=9123,force=0,**kwargs): 
 17      global _server 
 18      if not force and _server is not None: 
 19        self.server=_server 
 20      else: 
 21        if not host: 
 22          host=os.environ.get('PYMOL_RPCHOST','localhost') 
 23        _server=None 
 24        serv = xmlrpclib.Server('http://%s:%d'%(host,port)) 
 25        serv.ping() 
 26        _server = serv 
 27        self.server=serv 
 28      self.InitializePyMol() 
 29       
 30 -  def InitializePyMol(self): 
 31      """ does some initializations to set up PyMol according to our 
 32      tastes 
 33   
 34      """ 
 35      self.server.do('set valence,1') 
 36      self.server.do('set stick_rad,0.15') 
 37      self.server.do('set mouse_selection_mode,0') 
 38      self.server.do('set line_width,2') 
 39      self.server.do('set selection_width,10') 
 40      self.server.do('set auto_zoom,0') 
 41       
 42   
 43 -  def DeleteAll(self): 
 44      " blows out everything in the viewer " 
 45      self.server.deleteAll() 
 46   
 47 -  def DeleteAllExcept(self,excludes): 
 48      " deletes everything except the items in the provided list of arguments " 
 49      allNames = self.server.getNames('*',False) 
 50      for nm in allNames: 
 51        if nm not in excludes: 
 52          self.server.deleteObject(nm) 
 53   
 54 -  def LoadFile(self,filename,name,showOnly=False): 
 55      """ calls pymol's "load" command on the given filename; the loaded object 
 56      is assigned the name "name" 
 57      """ 
 58      if showOnly: 
 59        self.DeleteAll() 
 60      id = self.server.loadFile(filename,name) 
 61      return id 
 62   
 63 -  def ShowMol(self,mol,name='molecule',showOnly=True,highlightFeatures=[], 
 64                molB="",confId=-1,zoom=True): 
 65      """ special case for displaying a molecule or mol block """ 
 66     
 67      if not molB: 
 68        molB = Chem.MolToMolBlock(mol,confId=confId) 
 69      server = self.server 
 70      if not zoom: 
 71        self.server.do('view rdinterface,store') 
 72      if showOnly: 
 73        self.DeleteAll() 
 74      id = server.loadMolBlock(molB,name) 
 75      if highlightFeatures: 
 76        nm = name+'-features' 
 77        conf = mol.GetConformer(confId) 
 78        for feat in highlightFeatures: 
 79          pt = [0.0,0.0,0.0] 
 80          for idx in feat: 
 81            loc = conf.GetAtomPosition(idx) 
 82            pt[0] += loc[0]/len(feat) 
 83            pt[1] += loc[1]/len(feat) 
 84            pt[2] += loc[2]/len(feat) 
 85          server.sphere(pt,0.2,(1,1,1),nm) 
 86      if zoom: 
 87        server.zoom('visible') 
 88      else: 
 89        self.server.do('view rdinterface,recall') 
 90      return id 
 91   
 92 -  def GetSelectedAtoms(self,whichSelection=None): 
 93      " returns the selected atoms " 
 94      if not whichSelection: 
 95        sels = self.server.getNames('selections') 
 96        if sels: 
 97          whichSelection = sels[-1] 
 98        else: 
 99          whichSelection=None 
100      if whichSelection:    
101        items = self.server.index(whichSelection) 
102      else: 
103        items = [] 
104      return items 
105   
106   
107 -  def SelectAtoms(self,itemId,atomIndices,selName='selection'): 
108      " selects a set of atoms " 
109      ids = '(id ' 
110      ids += ','.join(['%d'%(x+1) for x in atomIndices]) 
111      ids += ')' 
112      cmd = 'select %s,%s and %s'%(selName,ids,itemId) 
113      self.server.do(cmd) 
114     
115 -  def HighlightAtoms(self,indices,where,extraHighlight=False): 
116      " highlights a set of atoms "  
117      if extraHighlight: 
118        idxText = ','.join(['%s and (id %d)'%(where,x) for x in indices]) 
119        self.server.do('edit %s'%idxText) 
120      else: 
121        idxText = ' or '.join(['id %d'%x for x in indices]) 
122        self.server.do('select selection, %s and (%s)'%(where,idxText)) 
123   
124 -  def SetDisplayStyle(self,obj,style=''): 
125      " change the display style of the specified object " 
126      self.server.do('hide everything,%s'%(obj,)) 
127      if style: 
128        self.server.do('show %s,%s'%(style,obj)) 
129   
130 -  def SelectProteinNeighborhood(self,aroundObj,inObj,distance=5.0, 
131                                  name='neighborhood',showSurface=False): 
132      """ selects the area of a protein around a specified object/selection name; 
133      optionally adds a surface to that """ 
134      self.server.do('select %(name)s,byres (%(aroundObj)s around %(distance)f) and %(inObj)s'%locals()) 
135       
136   
137      if showSurface: 
138        self.server.do('show surface,%s'%name) 
139        self.server.do('disable %s'%name) 
140   
141 -  def AddPharmacophore(self,locs,colors,label,sphereRad=0.5): 
142      " adds a set of spheres " 
143      self.server.do('view rdinterface,store') 
144      self.server.resetCGO(label) 
145      for i,loc in enumerate(locs): 
146        self.server.sphere(loc,sphereRad,colors[i],label,1) 
147      self.server.do('enable %s'%label) 
148      self.server.do('view rdinterface,recall') 
149       
150   
151 -  def SetDisplayUpdate(self,val): 
152      if not val: 
153        self.server.do('set defer_update,1') 
154      else: 
155        self.server.do('set defer_update,0') 
156   
157 -  def GetAtomCoords(self,sels): 
158      " returns the coordinates of the selected atoms "  
159      res = {} 
160      for label,idx in sels: 
161        coords = self.server.getAtomCoords('(%s and id %d)'%(label,idx)) 
162        res[(label,idx)] = coords 
163      return res 
164   
165 -  def HideAll(self): 
166      self.server.do('disable all') 
167 -  def HideObject(self,objName): 
168      self.server.do('disable %s'%objName) 
169 -  def DisplayObject(self,objName): 
170      self.server.do('enable %s'%objName) 
171   
172 -  def Redraw(self): 
173      self.server.do('refresh') 
174 -  def Zoom(self,objName): 
175      self.server.zoom(objName) 
176   
177 -  def DisplayHBonds(self,objName,molName,proteinName, 
178                      molSelText='(%(molName)s)', 
179                      proteinSelText='(%(proteinName)s and not het)'): 
180      " toggles display of h bonds between the protein and a specified molecule " 
181      cmd = "delete %(objName)s;\n" 
182      cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",mode=2;\n" 
183      cmd += "enable %(objName)s;" 
184      cmd = cmd%locals() 
185   
186      self.server.do(cmd) 
187   
188 -  def DisplayCollisions(self,objName,molName,proteinName,distCutoff=3.0, 
189                          color='red', 
190                          molSelText='(%(molName)s)', 
191                          proteinSelText='(%(proteinName)s and not het)'): 
192      " toggles display of collisions between the protein and a specified molecule " 
193      cmd = "delete %(objName)s;\n" 
194      cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",%(distCutoff)f,mode=0;\n" 
195      cmd += """enable %(objName)s 
196      color %(color)s, %(objName)s""" 
197      cmd = cmd%locals() 
198      self.server.do(cmd) 
199