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realtime.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* Scott Dixon, Metaphorics, LLC
#-* 
#-*
#Z* -------------------------------------------------------------------


# pymol

from pymol import cmd

from chempy import io
from chempy import protein,hetatm
from chempy import feedback
from chempy import protein_amber99
from chempy import tinker
from chempy.tinker import keyword
from chempy.tinker.amber import Parameters,Topology,Subset
from chempy.tinker.state import State

import os

state = None
model = None

def assign(sele,preserve=0):

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

   global state
   global model

   result = 1
   
   state = State()

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

   ruleSet = Rules()

#   ruleSet.fromList(rules.amber_types)
   ruleSet.fromList(rules.simple_types)

   mobj = MolObj()
   mobj.fromChemPyModel(model)

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

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

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

   print " lig: net charge on ligand  is %8.4f\n" % sm

   return result

#   param = Parameters(tinker.params_path+"parm99_wld.dat")
#   param = Parameters(tinker.params_path+"simple_parm.dat")
#   param = Parameters("simple_parm.dat")

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

   print " lig: net charge on ligand  is %8.4f\n" % sm

#   param = Parameters(tinker.params_path+"parm99_wld.dat")
   param = Parameters(tinker.params_path+"parm99_simple.dat")
   topo = Topology(model)

   subset = Subset(param,topo)

   if(subset.complete()):
      subset.write_tinker_prm("realtime.prm")

      state.params = "realtime.prm"

      state.load_model(model)
      return 1
   else:
      subset.dump_missing()
      model = model
      state = None
      return 0

def dyna(steps,iter=1):

   global state

   if not state:
      print " realtime.dyna: please run setup first."
   else:
      state.echo = 0

      model = state.model

      print " realtime.dyna: %d atoms total\n" % model.nAtom

      xtra_kw = []

      xtra_kw.extend(keyword.get_inactive(model,3))
      xtra_kw.extend(keyword.get_restrain_positions(model,2,0,10))
      xtra_kw.extend(keyword.get_restrain_positions(model,5,0.5,1))
      xtra_kw.extend(keyword.get_inactive(model,6))

      state.keywords['chg-cutoff'] = 10.0
      state.keywords['vdw-cutoff'] = 7.00
      state.keywords['lights'] = ''
      state.keywords['restrainterm'] = ''

      for x in range(0,iter):
         state.dynamics(steps=steps,timestep=1,kw=xtra_kw)
         if not len(state.summary):
            break
         for a in state.summary:
            print a
         cmd.load_model(model,'dyna')
         cmd.ending()
         cmd.refresh()
      io.pkl.toFile("realtime.pkl")
      print " realtime.dyna: terminated after %d steps." % state.counter

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_step=100,gradient=0.001,interval=100,obj='rt'):

   global state

   if not state:
      print " realtime.mini: please run setup first."
   else:
      state.echo = 0

      model = state.model

      print " realtime.mini: %d atoms total\n" % model.nAtom

      xtra_kw = []

      xtra_kw.extend(keyword.get_inactive(model,3))
      xtra_kw.extend(keyword.get_restrain_positions(model,2,0,10))
      xtra_kw.extend(keyword.get_restrain_positions(model,5,0.5,1))
      xtra_kw.extend(keyword.get_inactive(model,6))

      state.keywords['chg-cutoff'] = 10.0
      state.keywords['vdw-cutoff'] = 7.00
      state.keywords['lights'] = ''
      state.keywords['restrainterm'] = ''

      iter = total_step/interval
      for x in range(0,iter):
         state.minimize(gradient=gradient,max_iter=interval,kw=xtra_kw)
         cmd.delete(obj)
         cmd.load_model(model,obj,1)
         cmd.refresh()
         if not len(state.summary):
            break
         for a in state.summary:
            print a
         if state.summary[-1][7]=='SmallGrad':
            break;         
      io.pkl.toFile(model,"realtime.pkl")
      print " realtime.mini: terminated after %d steps." % state.counter





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