-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbuild3Dmodel_aln_rsr.py
291 lines (271 loc) · 14.6 KB
/
build3Dmodel_aln_rsr.py
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
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
#############################################################################################################################################
# File Name : build3Dmodel_aln_rsr.py #
# Developed By : Rahmatullah Roche #
# Creation Date : [2020-11-23 18:12] #
# Last Modified : [2020-11-23 18:12] #
# Description : model building with additional restraints from predicted distances, orientations, and secondary structures #
# Credit : https://salilab.org/modeller/ #
#############################################################################################################################################
from modeller import *
from modeller.automodel import *
import os,sys,optparse
import math
parser=optparse.OptionParser()
parser.add_option('-f', dest='alignment_file',
default= '', #default empty!'
help= 'alignment file in MODELLER format')
parser.add_option('--ss', dest='ss',
default= '', #default empty!'
help= 'secondary structure file')
parser.add_option('--rr', dest='rr',
default= '', #default empty!'
help= 'contact map in standard rr format (the output of trRosetta9classrr_ss5.py)')
parser.add_option('--target', dest='target',
default= '', #default empty!'
help= 'name of target')
parser.add_option('--template', dest='template',
default= '', #default empty!
help= 'name of template')
parser.add_option('--phi', dest='phi',
default= '', #default empty!
help= 'phi orientation (the output of trRosetta_phi_upper_lower.py)')
parser.add_option('--theta', dest='theta',
default= '', #default empty!
help= 'theta orientation (the output of trRosetta_theta_upper_lower.py)')
parser.add_option('--omega', dest='omega',
default= '', #default empty!
help= 'omega orientation (the output of trRosetta_omega_upper_lower.py)')
(options,args) = parser.parse_args()
alignment_file = options.alignment_file
target = options.target
template = options.template
ss = options.ss
rr = options.rr
ctype = "CB"
phi = options.phi
theta = options.theta
omega = options.omega
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
class MyModel(automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
cutoff = 0.85
fss = open(ss, 'r')
self.secondary = fss.read()
self.secondary = self.secondary.split() #secondary structure is now in self.secondary[0]
fss.close()
print (self.secondary[0])
frr = open(rr, 'r')
rrlines = frr.readlines()
faln = open(alignment_file, 'r')
alnlines = faln.readlines()
n = len(rrlines[0].strip())
pair_u = {}
pair_l = {}
self.CM = [[0 for x in range(n)] for y in range(n)]
max_upper = 0
for line in rrlines[1:]:
line = line.strip().split()
self.CM[int(line[0]) - 1][int(line[1]) - 1] = self.CM[int(line[1]) - 1][int(line[0]) - 1] = 1
if (float(line[4]) <= cutoff):
self.CM[int(line[0]) - 1][int(line[1]) - 1] = self.CM[int(line[1]) - 1][int(line[0]) - 1] = -1
pair_l[(int(line[0]) - 1, int(line[1]) - 1)] = pair_l[(int(line[1]) - 1, int(line[0]) - 1)] = float(line[2])
pair_u[(int(line[0]) - 1, int(line[1]) - 1)] = pair_u[(int(line[1]) - 1, int(line[0]) - 1)] = float(line[3])
if (max_upper < float(line[3])):
max_upper = float(line[3])
#mdl = template + '.B99990001.pdb'
#if os.path.exists(mdl):
# print ('changing')
# os.system('mv ' + template + '.B99990001.pdb ' + template + '.pdb')
fpdb = open(template + '.pdb', 'r')
fpdblines = fpdb.readlines()
pos = []
if(ctype == 'cb' or ctype == 'CB'):
ct = "CB"
else:
ct = "CA"
for line in fpdblines:
if(line[:4] == "ATOM" and line[12:16].strip() == ct):
x = float(line[30:38].strip())
y = float(line[38:46].strip())
z = float(line[46:54].strip())
pos.append([x, y, z])
for i in range(n):
for j in range(i+6, n):
if (abs(i - j) < 6):
continue
#d = math.sqrt((pos[i][0] - pos[j][0]) ** 2 + (pos[i][1] - pos[j][1]) ** 2 + (pos[i][2] - pos[j][2]) ** 2)
if (self.CM[i][j] == 1): # and d > pair_u[(i,j)]):
firstres = ct + ':' + str(i+1)
secondres = ct + ':' + str(j+1)
if(rrlines[0][i] == 'G'):
firstres = 'CA:' + str(i+1)
if(rrlines[0][j] == 'G'):
secondres = 'CA:' + str(i+1)
rsr.add(forms.lower_bound(group=physical.xy_distance,
feature=features.distance(at[firstres],
at[secondres]),
mean=3.6, stdev=.1))
rsr.add(forms.upper_bound(group=physical.xy_distance,
feature=features.distance(at[firstres],
at[secondres]),
mean=pair_u[(i,j)], stdev=0.1))
elif (self.CM[i][j] == 0): # and d < 14):
firstres = ct + ':' + str(i+1)
secondres = ct + ':' + str(j+1)
if(rrlines[0][i] == 'G'):
firstres = 'CA:' + str(i+1)
if(rrlines[0][j] == 'G'):
secondres = 'CA:' + str(i+1)
rsr.add(forms.lower_bound(group=physical.xy_distance,
feature=features.distance(at[firstres],
at[secondres]),
mean=max_upper, stdev=0.1))
fphi = open(phi, 'r')
ftheta = open(theta, 'r')
fomega = open(omega, 'r')
philines = fphi.readlines()
thetalines = ftheta.readlines()
omegalines = fomega.readlines()
for line in philines[1:]:
line = line.strip().split()
res1 = line[0]
res2 = line[1]
prob = float(line[4])
lb = float(line[2])
ub = float(line[3])
l_u_mean = (lb + ub) / 2
atm1 = 'CA:' + res1
atm2 = 'CB:' + res1
atm3 = 'CB:' + res2
if(rrlines[0][int(res1)-1] == 'G' or rrlines[0][int(res2)-1] == 'G'):
continue
if(abs(int(res1) - int(res2)) <= 5):
continue
if(prob <= 0.85):
break
#lb = max(0, lb-(30*3.1416/180))
#ub = min(180, ub + (30*3.1416/180))
rsr.add(forms.upper_bound(group=physical.angle,
feature=features.angle(at[atm1],
at[atm2],
at[atm3]),
mean=ub, stdev=0.1))
rsr.add(forms.lower_bound(group=physical.angle,
feature=features.angle(at[atm1],
at[atm2],
at[atm3]),
mean=lb, stdev=0.1))
for line in thetalines[1:]:
line = line.strip().split()
res1 = line[0]
res2 = line[1]
prob = float(line[4])
lb = float(line[2])
ub = float(line[3])
l_u_mean = (lb + ub) / 2
atm1 = 'N:' + res1
atm2 = 'CA:' + res1
atm3 = 'CB:' + res1
atm4 = 'CB:' + res2
if(rrlines[0][int(res1)-1] == 'G' or rrlines[0][int(res2)-1] == 'G'):
continue
if(abs(int(res1) - int(res2)) <= 5):
continue
if(prob <= 0.85):
break
#lb = max(-180, lb-(15*3.1416/180))
#ub = min(180, ub + (15*3.1416/180))
rsr.add(forms.upper_bound(group=physical.dihedral,
feature=features.dihedral(at[atm1],
at[atm2],
at[atm3],
at[atm4]),
mean=ub, stdev=0.1))
rsr.add(forms.lower_bound(group=physical.dihedral,
feature=features.dihedral(at[atm1],
at[atm2],
at[atm3],
at[atm4]),
mean=lb, stdev=0.1))
for line in omegalines[1:]:
line = line.strip().split()
res1 = line[0]
res2 = line[1]
prob = float(line[4])
lb = float(line[2])
ub = float(line[3])
l_u_mean = (lb + ub) / 2
atm1 = 'CA:' + res1
atm2 = 'CB:' + res1
atm3 = 'CB:' + res2
atm4 = 'CA:' + res2
if(rrlines[0][int(res1)-1] == 'G' or rrlines[0][int(res2)-1] == 'G'):
continue
if(abs(int(res1) - int(res2)) <= 5):
continue
if(prob <= 0.85):
break
#lb = max(-180, lb-(15*3.1416/180))
#ub = min(180, ub + (15*3.1416/180))
rsr.add(forms.gauss(group=physical.dihedral,
feature=features.dihedral(at[atm1],
at[atm2],
at[atm3],
at[atm4]),
mean=ub, stdev=0.1))
rsr.add(forms.gauss(group=physical.dihedral,
feature=features.dihedral(at[atm1],
at[atm2],
at[atm3],
at[atm4]),
mean=lb, stdev=0.1))
self.helices = []
self.sheets = []
i = 1
while(i < len(self.secondary[0])):
if self.secondary[0][i] == 'H':
j = i
while (self.secondary[0][j] == 'H' and j < len(self.secondary[0]) - 1):
j = j + 1
if (j - i >= 3):
self.helices.append((i, j))
i = j
i = i + 1
i = 1
while(i < len(self.secondary[0])):
if self.secondary[0][i] == 'E':
j = i
while (self.secondary[0][j] == 'E' and j < len(self.secondary[0]) - 1):
j = j + 1
if (j - i >= 3):
self.sheets.append((i, j-1))
i = j
i = i + 1
for (i,j) in self.helices:
start = str(i) + ':'
end = str(j) + ':'
rsr.add(secondary_structure.alpha(self.residue_range(start, end)))
print (start)
print (end)
for (i,j) in self.sheets:
start = str(i) + ':'
end = str(j) + ':'
rsr.add(secondary_structure.strand(self.residue_range(start, end)))
print (start)
print (end)
log.verbose()
env = environ() #consistant models each time
a = MyModel(env,alnfile=alignment_file,
knowns=template,sequence=target,
assess_methods=(assess.DOPE))
a.starting_model= 1
a.ending_model = 1
a.make()
#mdl = template + '.B99990001.pdb'
#if not os.path.exists(mdl):
# os.system('mv ' + template + '.pdb ' + template + '.B99990001.pdb')