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state.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* -------------------------------------------------------------------

from chempy import tinker,io,feedback
from chempy.tinker import keyword
import copy
import string

class State:

   def __init__(self):
      if feedback['verbose']:
         print ' '+str(self.__class__)+': created.'
      self.prefix = 'tinker'
      self.params = tinker.params_path+'chempy.prm'

      self.default = {}
      self.default['timestep'] = 1.0
      self.default['temperature'] = 300.0

      self.keywords = {}
      self.keywords['verbose'] = ''
      self.keywords['cutoff'] = 8.0      
      self.keywords['randomseed'] = 1234567890

      self.mapping = None
      self.echo = 0
      self.model = None
      self.reset_fragile()
      self.counter = 0

   def reset_fragile(self):
      self.restart = None
      self.frames = None
      
   def __write_keys(self,list):
      f=open(self.prefix+"_inp.key",'w')
      f.writelines(list)
      f.close()

   def analyze(self,kw=None,summary=1):
      if feedback['actions']:
         print ' '+str(self.__class__)+': starting energy run...'
      io.xyz.toFile(self.model,self.prefix+"_inp.xyz",
                    mapping = self.mapping)
      kw_list = [ "parameters "+self.params+"\n" ]
      for a in self.keywords.keys():
         kw_list.append("%s %s\n" % ( a,str(self.keywords[a])))
      kw_list.extend(keyword.get_partial_charge(self.model))
      if kw:
         kw_list.extend(kw)
      self.__write_keys(kw_list)
      tinker.do('analyze',
                self.prefix+"_inp",
                self.prefix+"_run",
                self.prefix+"_out",
                [ tinker.prefix,
                  'E',],
                capture = 1 + self.echo )
      if summary:
# get energy information from output file
         f = open(self.prefix+"_out.out")
         self.summary = []
         flag = 0
         while 1:
            lin = f.readline()
            if not lin: break
            if not flag:
               if lin[0:25]==' Total Potential Energy :':
                  self.summary.append([
                     string.strip(lin[0:23]),
                     float(lin[25:49])])
                  flag = 1
            else:
               tok = string.split(string.strip(lin))
               if len(tok):
                  if(tok[0]!='Energy'):
                     self.summary.append([
                        string.strip(lin[0:23]),
                        float(lin[25:49]),
                        int(lin[49:64])])
         f.close()
      else:
         self.summary = None
      if len(self.summary):
          self.energy = self.summary[0][1]
      else:
          self.energy = None

   def minimize(self,gradient=0.1,max_iter=100,
                kw=None,summary=1):
      if feedback['actions']:
         print ' '+str(self.__class__)+': starting minimization run...'
      io.xyz.toFile(self.model,self.prefix+"_inp.xyz")
      self.counter = self.counter + max_iter
      kw_list = [ "parameters "+self.params+"\n" ]
      for a in self.keywords.keys():
         kw_list.append("%s %s\n" % ( a,str(self.keywords[a])))
      kw_list.extend(keyword.get_partial_charge(self.model))
      if kw:
         kw_list.extend(kw)
      kw_list.append("overwrite\n")
      kw_list.append("maxiter %d\n" % max_iter)
      self.__write_keys(kw_list)
      tinker.do('minimize',
                self.prefix+"_inp",
                self.prefix+"_run",
                self.prefix+"_out",
                [ tinker.prefix,
                  str(gradient),],
                capture = 1 + self.echo )
      io.xyz.updateFromFile(self.model,self.prefix+"_out.xyz")
      self.restart = None
      if summary:
# get energy information from output file
         f = open(self.prefix+"_out.out")
         step = 1
         flag = 0
         self.summary = []
         while 1:
            lin = f.readline()
            if not lin: break
            if not flag:
               if (lin[0:9]==' CG Iter ' or
                   lin[0:9]==' QN Iter '):
                  f.readline() # skip blank
                  flag = 1
            else:
               try:
                  if int(lin[0:6])==step:
                     step = step + 1
                     self.summary.append([
                        int(lin[0:6]),
                        float(lin[6:19]),
                        float(lin[19:30]),
                        float(lin[30:41]),
                        float(lin[41:51]),
                        float(lin[51:60]),
                        int(lin[60:67]),
                        string.strip(lin[67:])])
               except ValueError:
                  pass
         f.close()
      else:
         self.summary = None
      if len(self.summary):
          self.energy = self.summary[-1][1]
      else:
          self.energy = None
         
   def dynamics(self,steps=100,
                timestep=None,
                interval=None,
                temperature=None,
                kw=None,summary=1):
      if feedback['actions']:
         print ' '+str(self.__class__)+': starting dynamics run...'
      io.xyz.toFile(self.model,self.prefix+"_inp.xyz")
      self.counter = self.counter + steps * timestep
# if restart is available, then use it.
      if self.restart:
         f = open(self.prefix+"_inp.dyn","w")
         f.writelines(self.restart)
         f.close()
         if feedback['actions']:
            print ' '+str(self.__class__)+': using restart information...'
#         
      kw_list = [ "parameters "+self.params+"\n" ]
      for a in self.keywords.keys():
         kw_list.append("%s %s\n" % ( a,str(self.keywords[a])))
      kw_list.extend(keyword.get_partial_charge(self.model))
      if kw:
         kw_list.extend(kw)
      kw_list.append("archive\n")
      self.__write_keys(kw_list)
      if not timestep:
         timestep = self.default['timestep']
      if not temperature:
         temperature = self.default['temperature']
      if not interval:
         interval = (timestep*steps)/1000.0
      else:
         interval = interval/1000.0
      tinker.do('dynamic',
                self.prefix+"_inp",
                self.prefix+"_run",
                self.prefix+"_out",
                [ tinker.prefix,
                  str(steps),
                  str(timestep),
                  str(interval),
                  str(temperature)],
                capture = 1 + self.echo )
      self.frames = io.arc.fromFile(self.prefix+"_out.arc")
      if len(self.frames):
         c = 0
         atm = self.model.atom
         for a in self.frames[-1]:
            atm[c].coord = copy.deepcopy(a)
            c = c + 1
# get restart information
      f = open(self.prefix+"_out.dyn")
      self.restart = f.readlines()
      f.close()
# get energy information from output file
      if summary:
         f = open(self.prefix+"_out.out")
         step = 1
         flag = 0
         self.summary = []
         while 1:
            lin = f.readline()
            if not lin: break
            if not flag:
               if lin[0:12]=='    MD Step ':
                  f.readline() # skip blank
                  flag = 1
            else:
               try:
                  if int(lin[0:10])==step:
                     step = step + 1
                     self.summary.append([
                        int(lin[0:10]),
                        float(lin[10:24]),
                        float(lin[24:38]),
                        float(lin[38:50]),
                        float(lin[50:61])])
               except ValueError:
                  pass
         f.close()
      else:
         self.summary = None
      if len(self.summary):
         self.energy = self.summary[-1][1]
      else:
         self.energy = None

      
   def load_model(self,a):
      if feedback['verbose']:
         print ' '+str(self.__class__)+': new model loaded.'
      self.model = a
      self.reset_fragile()






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