Source Code for Module AutoDockTools.VisionInterface.recluster

  1  ######################################################################## 
  2  # 
  3  #    Vision Macro - Python source code - file generated by vision 
  4  #    Tuesday 25 July 2006 11:59:24  
  5  #     
  6  #       The Scripps Research Institute (TSRI) 
  7  #       Molecular Graphics Lab 
  8  #       La Jolla, CA 92037, USA 
  9  # 
 10  # Copyright: Daniel Stoffler, Michel Sanner and TSRI 
 11  #    
 12  # revision: Guillaume Vareille 
 13  #   
 14  ######################################################################### 
 15  # 
 16  # $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/VisionInterface/recluster.py,v 1.1 2006/07/25 23:35:30 rhuey Exp $ 
 17  # 
 18  # $Id: recluster.py,v 1.1 2006/07/25 23:35:30 rhuey Exp $ 
 19  # 
 20   
 21  from NetworkEditor.macros import MacroNode 
 22 -class recluster(MacroNode): 
 23   
 24 -    def __init__(self, constrkw={}, name='recluster', **kw): 
 25          kw['name'] = name 
 26          apply( MacroNode.__init__, (self,), kw) 
 27   
 28 -    def beforeAddingToNetwork(self, net): 
 29          MacroNode.beforeAddingToNetwork(self, net) 
 30          ## loading libraries ## 
 31          from MolKit.VisionInterface.MolKitNodes import molkitlib 
 32          net.editor.addLibraryInstance(molkitlib,"MolKit.VisionInterface.MolKitNodes", "molkitlib") 
 33   
 34          from Vision.StandardNodes import stdlib 
 35          net.editor.addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib") 
 36   
 37   
 38 -    def afterAddingToNetwork(self): 
 39          from NetworkEditor.macros import MacroNode 
 40          MacroNode.afterAddingToNetwork(self) 
 41          ## loading libraries ## 
 42          from MolKit.VisionInterface.MolKitNodes import molkitlib 
 43          from Vision.StandardNodes import stdlib 
 44          ## building macro network ## 
 45          recluster_11 = self 
 46          from traceback import print_exc 
 47   
 48          ## loading libraries ## 
 49          from MolKit.VisionInterface.MolKitNodes import molkitlib 
 50          self.macroNetwork.getEditor().addLibraryInstance(molkitlib,"MolKit.VisionInterface.MolKitNodes", "molkitlib") 
 51   
 52          from Vision.StandardNodes import stdlib 
 53          self.macroNetwork.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib") 
 54   
 55          try: 
 56              ## saving node input Ports ## 
 57              input_Ports_12 = self.macroNetwork.ipNode 
 58              input_Ports_12.move(172, 137) 
 59          except: 
 60              print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork" 
 61              print_exc() 
 62              input_Ports_12=None 
 63   
 64          try: 
 65              ## saving node output Ports ## 
 66              output_Ports_13 = self.macroNetwork.opNode 
 67              output_Ports_13.move(172, 479) 
 68          except: 
 69              print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork" 
 70              print_exc() 
 71              output_Ports_13=None 
 72   
 73          try: 
 74              ## saving node Docking ## 
 75              from Vision.StandardNodes import Generic 
 76              Docking_16 = Generic(constrkw = {}, name='Docking', library=stdlib) 
 77              self.macroNetwork.addNode(Docking_16,189,250) 
 78              apply(Docking_16.addInputPort, (), {'name': 'docking_logs', 'cast': True, 'datatype': 'list', 'balloon': 'list of docking log files to be read into as a single Docking', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'}) 
 79              apply(Docking_16.addInputPort, (), {'name': 'rmsTool', 'cast': True, 'datatype': 'None', 'balloon': 'rmsTool to be used for clustering', 'required': False, 'height': 8, 'width': 12, 'shape': 'diamond', 'color': 'white'}) 
 80              apply(Docking_16.addOutputPort, (), {'name': 'docking', 'datatype': 'None', 'balloon': 'docking instance', 'height': 8, 'width': 12, 'shape': 'diamond', 'color': 'white'}) 
 81              code = """def doit(self, docking_logs, rmsTool): 
 82          from AutoDockTools.Docking import Docking 
 83          d = Docking() 
 84          for f in docking_logs: 
 85                  d.readDlg(f) 
 86          d.clusterer.rmsTool = rmsTool 
 87          self.outputData(docking = d)            
 88                       
 89           
 90  ## to ouput data on port docking use 
 91  ## self.outputData(docking=data) 
 92   
 93   
 94  """ 
 95              Docking_16.configure(function=code) 
 96          except: 
 97              print "WARNING: failed to restore Generic named Docking in network self.macroNetwork" 
 98              print_exc() 
 99              Docking_16=None 
100   
101          try: 
102              ## saving node rmsTool ## 
103              from Vision.StandardNodes import Generic 
104              rmsTool_17 = Generic(constrkw = {}, name='rmsTool', library=stdlib) 
105              self.macroNetwork.addNode(rmsTool_17,206,197) 
106              apply(rmsTool_17.addInputPort, (), {'name': 'crds', 'cast': True, 'datatype': 'coordinates3D', 'balloon': 'coordinates to use as reference for rms calculation.', 'height': 8, 'width': 12, 'shape': 'rect', 'color': 'green'}) 
107              apply(rmsTool_17.addOutputPort, (), {'name': 'rmsTool', 'datatype': 'None', 'balloon': 'rmsTool created using crds as reference', 'height': 8, 'width': 12, 'shape': 'diamond', 'color': 'white'}) 
108              code = """def doit(self, crds): 
109          from  mglutil.math.rmsd  import RMSDCalculator 
110          rmsTool = RMSDCalculator(crds) 
111          self.outputData(rmsTool = rmsTool) 
112           
113  """ 
114              rmsTool_17.configure(function=code) 
115          except: 
116              print "WARNING: failed to restore Generic named rmsTool in network self.macroNetwork" 
117              print_exc() 
118              rmsTool_17=None 
119   
120          try: 
121              ## saving node Read Molecule ## 
122              from MolKit.VisionInterface.MolKitNodes import ReadMolecule 
123              Read_Molecule_18 = ReadMolecule(constrkw = {}, name='Read Molecule', library=molkitlib) 
124              self.macroNetwork.addNode(Read_Molecule_18,243,16) 
125              apply(Read_Molecule_18.inputPortByName['filename'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'}) 
126              apply(Read_Molecule_18.outputPortByName['MolSets'].configure, (), {'color': '#c64e70', 'shape': 'oval'}) 
127              Read_Molecule_18.inputPortByName['filename'].widget.set("ind.pdbqt", run=False) 
128          except: 
129              print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork" 
130              print_exc() 
131              Read_Molecule_18=None 
132   
133          try: 
134              ## saving node Index ## 
135              from Vision.StandardNodes import Index 
136              Index_19 = Index(constrkw = {}, name='Index', library=stdlib) 
137              self.macroNetwork.addNode(Index_19,243,66) 
138              apply(Index_19.inputPortByName['data'].configure, (), {'datatype': 'MoleculeSet', 'cast': True, 'shape': 'oval', 'color': '#c64e70'}) 
139              apply(Index_19.inputPortByName['index'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'}) 
140              apply(Index_19.outputPortByName['data'].configure, (), {'color': 'white', 'shape': 'diamond'}) 
141          except: 
142              print "WARNING: failed to restore Index named Index in network self.macroNetwork" 
143              print_exc() 
144              Index_19=None 
145   
146          try: 
147              ## saving node Get allAtoms.coords ## 
148              from Vision.StandardNodes import GetAttr 
149              Get_allAtoms_coords_20 = GetAttr(constrkw = {}, name='Get allAtoms.coords', library=stdlib) 
150              self.macroNetwork.addNode(Get_allAtoms_coords_20,243,115) 
151              apply(Get_allAtoms_coords_20.inputPortByName['objects'].configure, (), {'color': 'white', 'cast': True, 'shape': 'diamond'}) 
152              apply(Get_allAtoms_coords_20.inputPortByName['attr'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'}) 
153              apply(Get_allAtoms_coords_20.outputPortByName['attrs'].configure, (), {'color': 'cyan', 'shape': 'oval'}) 
154              apply(Get_allAtoms_coords_20.inputPortByName['attr'].widget.configure, (), {'choices': ('AAradii', 'AtomRadiiPatterns', 'NodesFromName', 'ROOT', 'TORSDOF', '_MarkTree', '__cmp__', '__doc__', '__eq__', '__hash__', '__init__', '__module__', '__ne__', '__repr__', '__str__', '_atomRadius', '_copyNode', '_copy_atom_attr', '_fit_atom_into_tree', '_numberOfDeletedNodes', 'addBond', 'adopt', 'allAtoms', 'assignUniqIndex', 'atmNum', 'attach_nonbonded_fragments', 'bonds', 'bondsflag', 'buildBondsBhtree', 'buildBondsByDistance', 'buildBondsByDistanceOnAtoms', 'buildBrokenBonds', 'chains', 'childByName', 'children', 'childrenName', 'childrenSetClass', 'closerThan', 'compare', 'compiled_patterns', 'configureProgressBar', 'copy', 'defaultRadii', 'deleteSubTree', 'dump', 'elementType', 'findLevels', 'findType', 'full_name', 'get', 'getAtoms', 'getCenter', 'getNext', 'getParentOfType', 'getPrevious', 'getRoot', 'getTypeList', 'hasBonds', 'hasSS', 'isAbove', 'isBelow', 'levels', 'makeNameUniq', 'merge', 'mergeNPH', 'name', 'ndihe', 'p', 'parent', 'parser', 'read', 'remove', 'removeAllHydrogens', 'removeBond', 'secondaryStructure', 'secondaryStructureFromFile', 'secondaryStructureFromStride', 'setClass', 'split', 'subTree', 'top', 'torTree', 'updateProgressBar', 'write')}) 
155              Get_allAtoms_coords_20.inputPortByName['attr'].widget.set("allAtoms.coords", run=False) 
156              apply(Get_allAtoms_coords_20.configure, (), {'expanded': True}) 
157          except: 
158              print "WARNING: failed to restore GetAttr named Get allAtoms.coords in network self.macroNetwork" 
159              print_exc() 
160              Get_allAtoms_coords_20=None 
161   
162          try: 
163              ## saving node Get clusterer ## 
164              from Vision.StandardNodes import GetAttr 
165              Get_clusterer_21 = GetAttr(constrkw = {}, name='Get clusterer', library=stdlib) 
166              self.macroNetwork.addNode(Get_clusterer_21,189,306) 
167              apply(Get_clusterer_21.inputPortByName['objects'].configure, (), {'color': 'white', 'cast': True, 'shape': 'diamond'}) 
168              apply(Get_clusterer_21.inputPortByName['attr'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'}) 
169              apply(Get_clusterer_21.outputPortByName['attrs'].configure, (), {'color': 'cyan', 'shape': 'oval'}) 
170              apply(Get_clusterer_21.inputPortByName['attr'].widget.configure, (), {'choices': ('__doc__', '__init__', '__module__', 'addConformations', 'ch', 'clusterer', 'clusterer_dict', 'defaultParser', 'dlo_list', 'flex_res', 'ligMol', 'parser', 'readDlg', 'readEntropiaResults', 'readXMLResults', 'set_ligand', 'version', 'warnings', 'writeConformation', 'write_current_conformation')}) 
171              Get_clusterer_21.inputPortByName['attr'].widget.set("clusterer", run=False) 
172              apply(Get_clusterer_21.configure, (), {'expanded': True}) 
173          except: 
174              print "WARNING: failed to restore GetAttr named Get clusterer in network self.macroNetwork" 
175              print_exc() 
176              Get_clusterer_21=None 
177   
178          try: 
179              ## saving node Index ## 
180              from Vision.StandardNodes import Index 
181              Index_22 = Index(constrkw = {}, name='Index', library=stdlib) 
182              self.macroNetwork.addNode(Index_22,188,383) 
183              apply(Index_22.inputPortByName['data'].configure, (), {'datatype': 'list', 'cast': True, 'shape': 'oval', 'color': 'cyan'}) 
184              apply(Index_22.inputPortByName['index'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'}) 
185              apply(Index_22.outputPortByName['data'].configure, (), {'color': 'white', 'shape': 'diamond'}) 
186          except: 
187              print "WARNING: failed to restore Index named Index in network self.macroNetwork" 
188              print_exc() 
189              Index_22=None 
190   
191          try: 
192              ## saving node make clustering ## 
193              from Vision.StandardNodes import Generic 
194              make_clustering_23 = Generic(constrkw = {}, name='make clustering', library=stdlib) 
195              self.macroNetwork.addNode(make_clustering_23,189,432) 
196              apply(make_clustering_23.addInputPort, (), {'name': 'clusterer', 'cast': True, 'datatype': 'None', 'balloon': 'clusterer which will make the new clustering', 'height': 8, 'width': 12, 'shape': 'diamond', 'color': 'white'}) 
197              apply(make_clustering_23.addInputPort, (), {'name': 'tolerance', 'cast': True, 'datatype': 'float', 'balloon': 'rms tolerance for the new clustering', 'height': 12, 'width': 12, 'shape': 'circle', 'color': 'green'}) 
198              apply(make_clustering_23.addOutputPort, (), {'name': 'clustering', 'datatype': 'None', 'balloon': 'clustering at newest rms', 'height': 8, 'width': 12, 'shape': 'diamond', 'color': 'white'}) 
199              code = """def doit(self, clusterer, tolerance): 
200          clusterer.make_clustering(tolerance) 
201          self.outputData(clustering = clusterer.clustering_dict[tolerance]) 
202  """ 
203              make_clustering_23.configure(function=code) 
204          except: 
205              print "WARNING: failed to restore Generic named make clustering in network self.macroNetwork" 
206              print_exc() 
207              make_clustering_23=None 
208   
209          try: 
210              ## saving node Dial ## 
211              from Vision.StandardNodes import DialNE 
212              Dial_24 = DialNE(constrkw = {}, name='Dial', library=stdlib) 
213              self.macroNetwork.addNode(Dial_24,233,380) 
214              apply(Dial_24.inputPortByName['dial'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'}) 
215              apply(Dial_24.inputPortByName['mini'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'}) 
216              apply(Dial_24.inputPortByName['maxi'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'}) 
217              apply(Dial_24.outputPortByName['value'].configure, (), {'color': 'green', 'shape': 'circle'}) 
218              Dial_24.inputPortByName['dial'].widget.set(3.0, run=False) 
219              apply(Dial_24.configure, (), {'expanded': False}) 
220          except: 
221              print "WARNING: failed to restore DialNE named Dial in network self.macroNetwork" 
222              print_exc() 
223              Dial_24=None 
224   
225          self.macroNetwork.freeze() 
226   
227          ## saving connections for network recluster ## 
228          if rmsTool_17 is not None and Docking_16 is not None: 
229              try: 
230                  self.macroNetwork.connectNodes( 
231                      rmsTool_17, Docking_16, "rmsTool", "rmsTool", blocking=True) 
232              except: 
233                  print "WARNING: failed to restore connection between rmsTool_17 and Docking_16 in network self.macroNetwork" 
234          if Read_Molecule_18 is not None and Index_19 is not None: 
235              try: 
236                  self.macroNetwork.connectNodes( 
237                      Read_Molecule_18, Index_19, "MolSets", "data", blocking=True) 
238              except: 
239                  print "WARNING: failed to restore connection between Read_Molecule_18 and Index_19 in network self.macroNetwork" 
240          if Index_19 is not None and Get_allAtoms_coords_20 is not None: 
241              try: 
242                  self.macroNetwork.connectNodes( 
243                      Index_19, Get_allAtoms_coords_20, "data", "objects", blocking=True) 
244              except: 
245                  print "WARNING: failed to restore connection between Index_19 and Get_allAtoms_coords_20 in network self.macroNetwork" 
246          if Get_allAtoms_coords_20 is not None and rmsTool_17 is not None: 
247              try: 
248                  self.macroNetwork.connectNodes( 
249                      Get_allAtoms_coords_20, rmsTool_17, "attrs", "crds", blocking=True) 
250              except: 
251                  print "WARNING: failed to restore connection between Get_allAtoms_coords_20 and rmsTool_17 in network self.macroNetwork" 
252          if Docking_16 is not None and Get_clusterer_21 is not None: 
253              try: 
254                  self.macroNetwork.connectNodes( 
255                      Docking_16, Get_clusterer_21, "docking", "objects", blocking=True) 
256              except: 
257                  print "WARNING: failed to restore connection between Docking_16 and Get_clusterer_21 in network self.macroNetwork" 
258          if Get_clusterer_21 is not None and Index_22 is not None: 
259              try: 
260                  self.macroNetwork.connectNodes( 
261                      Get_clusterer_21, Index_22, "attrs", "data", blocking=True) 
262              except: 
263                  print "WARNING: failed to restore connection between Get_clusterer_21 and Index_22 in network self.macroNetwork" 
264          if Index_22 is not None and make_clustering_23 is not None: 
265              try: 
266                  self.macroNetwork.connectNodes( 
267                      Index_22, make_clustering_23, "data", "clusterer", blocking=True) 
268              except: 
269                  print "WARNING: failed to restore connection between Index_22 and make_clustering_23 in network self.macroNetwork" 
270          if Dial_24 is not None and make_clustering_23 is not None: 
271              try: 
272                  self.macroNetwork.connectNodes( 
273                      Dial_24, make_clustering_23, "value", "tolerance", blocking=True) 
274              except: 
275                  print "WARNING: failed to restore connection between Dial_24 and make_clustering_23 in network self.macroNetwork" 
276          output_Ports_13 = self.macroNetwork.opNode 
277          if make_clustering_23 is not None and output_Ports_13 is not None: 
278              try: 
279                  self.macroNetwork.connectNodes( 
280                      make_clustering_23, output_Ports_13, "clustering", "new", blocking=True) 
281              except: 
282                  print "WARNING: failed to restore connection between make_clustering_23 and output_Ports_13 in network self.macroNetwork" 
283          input_Ports_12 = self.macroNetwork.ipNode 
284          if input_Ports_12 is not None and Docking_16 is not None: 
285              try: 
286                  self.macroNetwork.connectNodes( 
287                      input_Ports_12, Docking_16, "new", "docking_logs", blocking=True) 
288              except: 
289                  print "WARNING: failed to restore connection between input_Ports_12 and Docking_16 in network self.macroNetwork" 
290          self.macroNetwork.unfreeze() 
291   
292          recluster_11.shrink() 
293   
294          ## reset modifications ## 
295          recluster_11.resetTags() 
296          recluster_11.buildOriginalList() 
297