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#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 __future__ import print_function
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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