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state.py

from chempy import bmin,feedback
from chempy import io

import os
import re
import getpass # for getuser()

class State:

   def __init__(self):
      if feedback['verbose']:
         print ' '+str(self.__class__)+': created.'
      self.default = {}
      self.echo = 0
      self.model = None
      self.counter = 0
      self.prefix = "bmintmp"
      
   def minimize(self,max_iter=100,fix_flag=None,rest_flag=None,
                rest_coeff = 100.0,solvation=None):
      if feedback['actions']:
         print ' '+str(self.__class__)+': starting minimization run...'
      io.mmd.toFile(self.model,self.prefix+".dat")
      
      f = open(self.prefix+".com",'w')
      # get home-relative path
#      pth = os.getcwd()
#      pth = re.sub(r".*\/"+getpass.getuser()+"\/",'',pth)
      # provide io filenames
#      f.write("%s\n%s\n"%(pth+"/"+self.prefix+".dat",
#                          pth+"/"+self.prefix+".out"))
      f.write("%s\n%s\n"%(self.prefix+".dat",
                          self.prefix+".out"))
      f.write(" MMOD       0      1      0      0     0.0000     0.0000     0.0000     0.0000\n")
      # select forcefield treatments
      if not solvation: # no solvent, constant dielectric
         f.write(" FFLD      10      1      0      1     1.0000     0.0000     0.0000     0.0000\n")
      else: 
         f.write(''' FFLD      10      1      0      1     1.0000     0.0000     0.0000     0.0000
 SOLV       3      1      0      0     0.0000     0.0000     0.0000     0.0000
 EXNB       0      0      0      0     0.0000     0.0000     0.0000     0.0000
''')
      # read files
      f.write(" READ       0      0      0      0     0.0000     0.0000     0.0000     0.0000\n")
      # fix/restrain atoms according to flags provided
      if fix_flag!=None: # are we fixing any atoms?
         c = 0
         mask= 2 ** fix_flag
         for a in self.model.atom:
            c = c + 1
            if mask&a.flags:
               f.write(" FXAT  %6d      0      0      0    -1.0000     0.0000     0.0000     0.0000\n"%
                       c)
      if rest_flag!=None: # are we restraining any atoms?
         c = 0
         mask= 2 ** rest_flag
         for a in self.model.atom:
            c = c + 1
            if mask&a.flags:
               f.write(" FXAT  %6d      0      0      0 %10.4f     0.0000     0.0000     0.0000\n"%
                       (c,rest_coeff))
      f.write(
''' CONV       2      0      0      0     0.0500     0.0000     0.0000     0.0000
 MINI       1      0 %6d      0     0.0000     0.0000     0.0000     0.0000
 DEBG 6
 '''%(max_iter))
      f.close()
      
      bmin.do(self.prefix)
      io.mmd.updateFromFile(self.model,self.prefix+".out")
      if hasattr(self.model.molecule,'energy'):
         self.model.molecule.title = "%1.3f"%self.model.molecule.energy
   def load_model(self,a):
      if feedback['verbose']:
         print ' '+str(self.__class__)+': new model loaded.'
      self.model = a






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