Source Code for Package Pmv

  1  # $Header: /opt/cvs/python/packages/share1.5/Pmv/__init__.py,v 1.21.2.2 2007/08/12 16:13:15 sargis Exp $ 
  2  # $Id: __init__.py,v 1.21.2.2 2007/08/12 16:13:15 sargis Exp $ 
  3  # this makes this directory a package 
  4   
  5  import sys, os, getopt, time 
  6  from string import split 
  7   
  8 -def setdmode(mode, mv): 
  9      """ 
 10  load display commands for mode and set them as default command for new molecule 
 11  """ 
 12      if mode=='cpk': 
 13          mv.browseCommands('displayCommands', commands=['displayCPK'], 
 14                log=0, package='Pmv') 
 15          mv.addOnAddObjectCmd(mv.displayCPK) 
 16   
 17      elif mode=='lines': 
 18          mv.browseCommands('bondsCommands', 
 19                commands=('buildBondsByDistance',), log=0) 
 20          mv.addOnAddObjectCmd(mv.buildBondsByDistance) 
 21          mv.browseCommands('displayCommands', commands=('ribbon',), log=0) 
 22          mv.addOnAddObjectCmd(mv.displayLines) 
 23   
 24      elif mode=='ss': 
 25          mv.browseCommands('secondaryStructureCommands', 
 26                commands=('ribbon',), log=0) 
 27          mv.addOnAddObjectCmd(mv.ribbon) 
 28   
 29      elif mode=='sb': 
 30          mv.browseCommands('bondsCommands', 
 31                            commands=('buildBondsByDistance',), log=0) 
 32          mv.addOnAddObjectCmd(mv.buildBondsByDistance) 
 33          mv.browseCommands('displayCommands', 
 34                            commands=('displaySticksAndBalls',), log=0) 
 35          mv.addOnAddObjectCmd(mv.displaySticksAndBalls, (), 
 36                               {'cquality':0, 'bquality':0}) 
 37   
 38      elif mode=='lic': 
 39          mv.browseCommands('bondsCommands', 
 40                            commands=('buildBondsByDistance',), log=0) 
 41          mv.addOnAddObjectCmd(mv.buildBondsByDistance) 
 42          mv.browseCommands('displayCommands', 
 43                            commands=('displaySticksAndBalls',), log=0) 
 44          mv.addOnAddObjectCmd(mv.displaySticksAndBalls, (), 
 45                               {'sticksBallsLicorice':'Licorice', 'cquality':0, 'cradius':.2}) 
 46   
 47      elif mode=='ms': 
 48          mv.browseCommands('msmsCommands', commands=('computeMSMS',), log=0) 
 49          mv.browseCommands('msmsCommands', commands=('displayMSMS',), log=0) 
 50          mv.addOnAddObjectCmd(mv.computeMSMS, (), {'density':3.0}) 
 51          mv.addOnAddObjectCmd(mv.displayMSMS) 
 52       
 53      elif mode=='ca': 
 54          mv.browseCommands('traceCommands', commands=('computeTrace',), log=0) 
 55          mv.browseCommands('traceCommands', commands=('extrudeTrace',), log=0) 
 56          mv.browseCommands('traceCommands', commands=('displayTrace',), log=0) 
 57          mv.addOnAddObjectCmd(mv.computeTrace) 
 58          mv.addOnAddObjectCmd(mv.extrudeTrace) 
 59          mv.addOnAddObjectCmd(mv.displayTrace) 
 60   
 61      elif mode=='bt': 
 62          mv.browseCommands('bondsCommands', 
 63                commands=('buildBondsByDistance',), log=0) 
 64          mv.browseCommands('displayCommands', 
 65                commands=('displayBackboneTrace',), log=0) 
 66          mv.addOnAddObjectCmd(mv.displayBackboneTrace, (),  
 67                   {'cquality':0, 'bquality':0, 'cradius':0.25, 
 68                    'bRad':0.33} ) 
 69           
 70      elif mode=='sp': 
 71          mv.browseCommands('splineCommands', commands=('computeSpline',), log=0) 
 72          mv.browseCommands('splineCommands', commands=('extrudeSpline',), log=0) 
 73          mv.browseCommands('splineCommands', 
 74                commands=('displayExtrudedSpline',), log=0) 
 75          mv.addOnAddObjectCmd(mv.computeSpline) 
 76          mv.addOnAddObjectCmd(mv.extrudeSpline) 
 77          mv.addOnAddObjectCmd(mv.displayExtrudedSpline) 
 78   
 79      elif mode=='sssb': 
 80          mv.browseCommands('displayCommands', 
 81                commands=('displaySSSB',), log=0, package='Pmv') 
 82          mv.addOnAddObjectCmd(mv.displaySSSB) 
 83   
 84   
 85 -def setcmode(mode, mv): 
 86      """ 
 87  load color commands for mode and set them as default command for new molecule 
 88  """ 
 89      if mode=='ca': 
 90          mv.browseCommands('colorCommands', commands=('colorByAtomType',), 
 91                log=0, package='Pmv') 
 92          mv.addOnAddObjectCmd(mv.colorByAtomType) 
 93   
 94      elif mode=='cr': 
 95          mv.browseCommands('colorCommands', 
 96                commands=('colorByResidueType',), log=0) 
 97          mv.addOnAddObjectCmd(mv.colorByResidueType) 
 98           
 99      elif mode=='cc': 
100          mv.browseCommands('colorCommands', commands=('colorByChains',), 
101                log=0, package='Pmv') 
102          mv.addOnAddObjectCmd(mv.colorByChains) 
103   
104      elif mode=='cm': 
105          mv.self.browseCommands('colorCommands', commands=('colorByMolecules',), 
106                     log=0, package='Pmv') 
107          mv.addOnAddObjectCmd(mv.colorByMolecules) 
108   
109      elif mode=='cdg': 
110          mv.browseCommands('colorCommands', commands=('colorAtomsUsingDG',), 
111                log=0, package='Pmv') 
112          mv.addOnAddObjectCmd(mv.colorAtomsUsingDG) 
113   
114      elif mode=='cs': 
115          mv.browseCommands('colorCommands', 
116                commands=('colorResiduesUsingShapely',), log=0 ) 
117          mv.addOnAddObjectCmd(mv.colorResiduesUsingShapely) 
118   
119      elif mode=='css': 
120          mv.browseCommands('secondaryStructureCommands', 
121                commands=('colorBySecondaryStructure',), log=0) 
122          mv.addOnAddObjectCmd(mv.colorBySecondaryStructure) 
123   
124   
125  ################################################################## 
126  # Define a bunch of useful methods 
127  ################################################################## 
128 -def ed(): 
129      return self.vision.ed 
130   
131   
132 -def net(): 
133      return self.vision.ed.currentNetwork 
134   
135   
136 -def nodes(): 
137      return self.vision.ed.currentNetwork.nodes 
138   
139   
140 -def startPMV(argv, PmvScriptPath): 
141      """The main function for running PMV""" 
142      import os, sys, pdb 
143      optlist, args = getopt.getopt(argv[1:], 'haid:c:', ['update', 
144                  'help', 'again', 'overwriteLog', 'uniqueLog', 'noLog', 'die', 
145              'customizer=', 'interactive', 'dmode=', 'cmode=', 'noSplash'] ) 
146       
147      help_msg = """usage: pmv <options> 
148              -h or --help       : print this message 
149              -a or --again      : play back lastlog file 
150              --overwriteLog     : overwrite log file 
151              --uniqueLog        : create a log file with a unique name 
152              --noLog            : turn off logging 
153              --noSplash         : turn off Splash Screen 
154              --die              : do not start GUI event loop 
155              --customizer file  : run the user specified file 
156              --lib packageName  : add a libraries of commands 
157       
158          --update [nightly|tested|clear] : update MGLTools 
159                  if no arguments are given Update Manager GUI is provided 
160                  'nightly': download and install Nightly Builds 
161                  'tested' : download and install tested Nightly Builds 
162                  'clear'  : clear/uninstall all the updates       
163       
164          -d or --dmode modes : specify a display mode 
165                  modes can be any a combination of display mode 
166                 'cpk'  : cpk 
167                 'lines': lines 
168                 'ss'   : secondary structure ribbon 
169                 'sb'   : sticks and balls 
170                 'lic'  : licorice 
171                 'ms'   : molecular surface 
172                 'ca'   : C-alpha trace 
173                 'bt'   : backbone trace 
174                 'sp'   : CA-spline 
175                 'sssb' : secondary structure for proteins, 
176                          sticks and balls for other residues with bonds 
177                      lines for other residues without bonds 
178       
179          -c or --cmode modes : specify a dispaly mode 
180                      color scheme: 
181                  'ca' : color by atom 
182                  'cr' : color by residue (RASMOL scheme) 
183                  'cc' : color by chain 
184                  'cm' : color by molecule 
185                  'cdg': color using David Goodsell's scheme 
186                  'cs' : color residues using Shapely scheme 
187                  'css': color by secondary structure element 
188                   
189                example: 
190                display protein as ribbon, non protein as sticks and balls 
191                and color by atom type 
192                   pmv -i --dmode sssb --cmode cr myprot.pdb 
193                   pmv -i -m sssb -c cr myprot.pdb 
194       
195      """ 
196       
197      customizer = None 
198      logmode = 'overwrite' 
199      libraries = [] 
200      again = 0 
201      interactive = 0 
202      die=0 
203      noSplash = False 
204      dmode = cmode = None 
205      dmodes = ['cpk', 'lines', 'ss', 'sb', 'lic', 'ms', 'ca', 'bt', 'sp', 'sssb' ] 
206      cmodes = ['ca', 'cr', 'cc', 'cm', 'cdg', 'cs', 'css'] 
207       
208      for opt in optlist: 
209          if opt[ 0] in ('-h', '--help'): 
210              print help_msg 
211              sys.exit() 
212          elif opt[ 0] in ('-a', '--again'): 
213              again = 1 
214              os.system("mv mvAll.log.py .tmp.py") 
215          elif opt[ 0] =='--overwriteLog': logmode = 'overwrite' 
216          elif opt[ 0] =='--uniqueLog': logmode = 'unique' 
217          elif opt[ 0] =='--noLog': logmode = 'no' 
218          elif opt[ 0] =='--die': die = 1 
219          elif opt[ 0] =='--noSplash': noSplash = True 
220          elif opt[ 0] == '--customizer': 
221              customFile = opt[1] 
222          elif opt[ 0] == '--lib': 
223              libraries.append(opt[1]) 
224          elif opt[ 0] in ('-i', '--interactive'): 
225              interactive = 1 
226          elif opt[ 0] in ('-d', '--dmode'): 
227              assert min([mo in dmodes for mo in opt[1].split('|')])==True 
228              dmode = opt[1] 
229          elif opt[ 0] in ('-c', '--cmode'): 
230              assert min([mo in cmodes for mo in opt[1].split('|')])==True 
231              cmode = opt[1] 
232          elif opt[0] == '--update': 
233              try: 
234                  from Support.update import Update 
235              except ImportError: 
236                  print "Support package is needed to get updates" 
237                  break 
238                   
239              update = Update() 
240              if 'nightly' in args: 
241                  update.latest = 'nightly' 
242                  update.getUpdates() 
243              elif 'tested' in args: 
244                  update.latest     = 'tested' 
245                  update.getUpdates() 
246              elif 'clear' in args: 
247                  print "Removing all updates" 
248                  update.clearUpdates() 
249              else: 
250                  waitTk = update.gui() 
251                  update.master.wait_variable(waitTk) 
252          else: 
253              print "unknown option %s %s"%tuple(opt) 
254              print help_msg 
255              sys.exit(1) 
256       
257      text = 'Python executable     : '+sys.executable+'\n' 
258      text += 'PMV script                : '+PmvScriptPath+'\n' 
259      text += 'MGLTool packages '+'\n' 
260       
261      from Support.path import path_text, release_path 
262      from Support.version import __version__ 
263      version = __version__ 
264      text += path_text 
265      text += version+': '+release_path 
266       
267      path_data = text 
268               
269      import Pmv 
270      print 'Run PMV from ', Pmv.__path__[0] 
271      sys.modules['__main__'] = sys.modules['Pmv'] 
272      # if MGLPYTHONPATH environment variable exists - insert the specified path 
273      # into sys.path 
274       
275      #if os.environ.has_key("MGLPYTHONPATH"): 
276      #    if sys.platform == "win32": 
277      #        mglPath = split(os.environ["MGLPYTHONPATH"], ";") 
278      #    else: 
279      #        mglPath = split(os.environ["MGLPYTHONPATH"], ":") 
280      #    mglPath.reverse() 
281      #    for p in mglPath: 
282      #        sys.path.insert(0, os.path.abspath(p)) 
283           
284      try: 
285          ################################################################## 
286          # Splash Screen 
287          ################################################################## 
288          image_dir = os.path.join( Pmv.__path__[0],'Icons','Images') 
289          copyright = """(c) 1999-2007 Molecular Simulation Laboratory, The Scripps Research Institute 
290      ALL RIGHTS RESERVED """ 
291          authors = """Authors: Michel F. Sanner, Chris Carrillo, Kevin Chan,  
292  Sophie Coon, Sargis Dallakyan, Alex Gillet, Ruth Huey, Sowjanya Karnati,  
293  William (Lindy) Lindstrom, Garrett M. Morris, Brian Norledge, Anna Omelchenko,  
294  Daniel Stoffler, Vincenzo Tschinke, Guillaume Vareille, Yong Zhao""" 
295          icon = os.path.join(Pmv.__path__[0],'Icons','64x64','ss64.png') 
296          third_party = """Fast Isocontouring, Volume Rendering -- Chandrait Bajaj, UT Austin 
297  Adaptive Poisson Bolzman Solver (APBS) -- Nathan Baker Wash. Univ. St Louis 
298  GL extrusion Library (GLE) -- Linas Vepstas 
299  Secondary Structure Assignment (Stride) -- Patrick Argos EMBL 
300  Mesh Decimation (QSlim 2.0) -- Micheal Garland,  Univeristy of Illinois 
301  Tiled Rendering (TR 1.3) -- Brian Paul 
302  GLF font rendering library --  Roman Podobedov 
303  PyMedia video encoder/decoder -- http://pymedia.org""" 
304          title="Python Molecule Viewer" 
305          #create a root and hide it 
306          try: 
307              from TkinterDnD2 import TkinterDnD 
308              root = TkinterDnD.Tk() 
309          except ImportError: 
310              from Tkinter import Tk 
311              root = Tk()     
312          root.withdraw() 
313       
314          from mglutil.splashregister.splashscreen import SplashScreen 
315          from mglutil.splashregister.about import About 
316          about = About(image_dir=image_dir, third_party=third_party, 
317                        path_data=path_data, title=title, version=version,  
318                        copyright=copyright, authors=authors, icon=icon) 
319          splash =  SplashScreen(about, noSplash=noSplash) 
320       
321          from Pmv.moleculeViewer import MoleculeViewer 
322   
323          mv = MoleculeViewer( logMode=logmode, customizer=customizer, master=root, 
324                               title=title, withShell= not interactive, verbose=False) 
325      #                        libraries=libraries) 
326          mv.help_about = about 
327       
328          font = mv.GUI.ROOT.option_get('font', '*') 
329          mv.browseCommands('visionCommands', commands=('vision',), topCommand=0) 
330          mv.browseCommands('coarseMolSurfaceCommands', topCommand=0) 
331          if mv.vision.ed is None: 
332              mv.vision(log=0) 
333              mv.vision(log=0) 
334          mv.GUI.ROOT.option_add('*font', font)     
335          self = mv 
336           
337          #show the application after it built 
338          splash.finish() 
339          root.deiconify() 
340          globals().update(locals()) 
341   
342          mv.GUI.VIEWER.suspendRedraw = True 
343          cwd = os.getcwd()  
344          #mv._cwd differs from cwd when 'Startup Directory' userpref is set 
345          os.chdir(mv._cwd) 
346          if dmode is not None or cmode is not None: 
347              # save current list of commands run when a molecule is loaded 
348              addCmds = mv.getOnAddObjectCmd() 
349          # remove them 
350              if dmode is not None: 
351                  for c in addCmds: 
352                      mv.removeOnAddObjectCmd(c[0]) 
353                  # set the mode 
354                  setdmode(dmode, mv) 
355       
356              if cmode is not None: 
357              # set the mode 
358                  setcmode(cmode, mv) 
359       
360          for a in args: 
361              if a[0]=='-':# skip all command line options 
362                  continue 
363       
364              elif (a[-10:]=='_pmvnet.py') or (a[-7:]=='_net.py'):  # Vision networks 
365                  mv.browseCommands('visionCommands', commands=('vision',) ) 
366                  if mv.vision.ed is None: 
367                      mv.vision() 
368                  mv.vision.ed.loadNetwork(a) 
369       
370              elif a[-3:]=='.py':     # command script 
371                  print 'sourcing', a 
372                  mv.source(a) 
373       
374              elif a[-4:] in ['.pdb', '.pqr', 'pdbq', 'mol2', '.cif', '.gro'] or a[-5:]=='pdbqs' or a[-5:]=='pdbqt': 
375                  mv.readMolecule(a) 
376                   
377              elif a in ['clear', 'tested', 'nighlty']: 
378                  pass 
379               
380              else: 
381                  print 'WARNING: unable to process %s command line argument'%a 
382          if again: 
383              mv.source(".tmp.py") 
384          if dmode is not None or cmode is not None: 
385              # get current list of commands run when a molecule is loaded 
386              cmds = mv.getOnAddObjectCmd() 
387              # remove them 
388              for c in cmds: 
389                  mv.removeOnAddObjectCmd(c[0]) 
390              # restore original list of commands 
391              for c in addCmds: 
392                  apply( mv.addOnAddObjectCmd, c ) 
393       
394          mv.GUI.VIEWER.suspendRedraw = False 
395          os.chdir(cwd) 
396          if interactive: 
397              sys.stdin = sys.__stdin__ 
398              sys.stdout = sys.__stdout__ 
399              sys.stderr = sys.__stderr__ 
400              import code 
401              code.interact( 'PMV Interactive Shell', local=globals() ) 
402          elif not die: 
403              mv.GUI.pyshell.interp.locals = globals() 
404              mv.GUI.ROOT.mainloop() 
405       
406      except: 
407          import traceback 
408          traceback.print_exc() 
409          raw_input("hit enter to continue") 
410          import sys 
411          sys.exit(1) 
412   
413   
414  FlagCheck = 1 
415   
416  CRITICAL_DEPENDENCIES =['Numeric', 'Pmw', 'mglutil', 'ViewerFramework', 'MolKit', 'DejaVu', 'opengltk'] 
417  NONCRITICAL_DEPENDENCIES =['ZSI', 'geomutils', 'UTpackages', 'SpatialLogic', 'bhtree', 'sff', 'PyBabel', 'Volume', 'mslib', 'Vision', 'NetworkEditor', 'ARTK', 'PIL', 'symserv','QSlimLib', 'AutoDockTools', 'PyMead', 'isocontour','Support'] 
418