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realtime.py

# pymol

from pymol import cmd
from chempy import io
from chempy import feedback
from chempy.bmin.state import State

import threading
import traceback
import os

state = None
model = None

def assign(sele,preserve=0):

   from molobj import MolObj
   from typer import Typer,Rules
   import rules

   result = 1
   
   state = State()

   model = cmd.get_model(sele)
   # now assign atom types

   ruleSet = Rules()

   ruleSet.fromList(rules.mmff_types)
   ruleSet.mappingFromList(rules.mmff_mapping)
   
   mobj = MolObj()
   mobj.fromChemPyModel(model)

   typed = Typer(molObj = mobj)
   
   print " realtime: assigning atom types"
   typed.applyRules(ruleSet)

   c = 0
   for a in typed.getTypes():
      at = model.atom[c]
      if (at.text_type == '??') or (not preserve):
         if a==-99:
            print " warning: unable to assign atom type to atom %d"%c
            result = 0
         else:
            cmd.alter("((%s) and (index %s))" % (sele,at.index),
                      "numeric_type ='%s'" % a)
            if feedback['tinker']:
               print " "+str(__name__)+': %s is a %s' % (at.name,a)
            at.numeric_type = a
      c = c + 1

   sm = 0
   for a in model.atom:
      a.resi = str(a.resi_number)
      sm = sm + a.partial_charge

   return result

def setup(sele,preserve=0):
   
   global state
   global model
   
   state = State()
   model = cmd.get_model(sele)

   sm = 0
   for a in model.atom:
      a.resi = str(a.resi_number)
      sm = sm + a.partial_charge

   state.load_model(model)
   return 1

def check(obj='check'):
   global state
   global model
   
   if not state:
      if not model:
         print " realtime.reload: please run setup first."
      else:
         cmd.load_model(model,obj,1)
   else:
      model = state.model
      cmd.load_model(model,obj,1)

def mini(total_steps=500,
         gradient=0.001,
         interval=100,
         object='rt',
         fix_flag=None,
         rest_flag=None,
         solvation=None,
         finish=None):

   global state
   if not state:
      print " realtime.mini: please run setup first..."
   else:
      model = state.model
      print " realtime.mini: %d atoms total\n" % model.nAtom
      try:
         while total_steps>0:
            total_steps = total_steps - interval
            state.minimize(max_iter=interval,
                           fix_flag=fix_flag,
                           rest_flag=rest_flag,
                           solvation=solvation)
            cmd.delete(object)
            cmd.load_model(state.model,object,1)
            cmd.refresh()
            if finish!=None:
               apply(finish[0],finish[1],finish[2])
      except:
         cmd.load_model(state.model,'ref')
         traceback.print_exc()
      print " realtime.mini: complete."

def mini_threaded(*args,**kwargs):
   t = threading.Thread(target=mini,
                        args=args,
                        kwargs=kwargs)
   t.setDaemon(1)
   t.start()
   




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