1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
|
#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
# 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)
|
