/
generate_leads.py
executable file
·150 lines (130 loc) · 6.05 KB
/
generate_leads.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
#!/dls/science/groups/i04-1/software/pandda-update/ccp4-linux64-2016-10-22-0115/libexec/python2.7
import sys, getopt, os, subprocess, re
import sqlite3
from Bio.PDB import NeighborSearch, PDBParser, Atom, Residue, PDBIO
import pandas as pd
import numpy as np
def get_id_string(out):
"""
Regex function for finding proasis strucid
"""
try:
strucidstr = re.search(r"strucid='.....'", out)
strucidstr = strucidstr.group()
strucidstr = strucidstr.replace('strucid=', '')
strucidstr = strucidstr.replace("'", '')
except:
strucidstr = ''
return strucidstr
def main(argv):
reference_structure = ''
pandda_analyse_centroids = ''
name = ''
processing_directory=''
database_file = 'database/soakDBDataFile.sqlite'
try:
opts, args = getopt.getopt(argv,"hr:p:n:d:",["rfile=","pfile=","name="])
except getopt.GetoptError:
print 'usage: generate_leads.py -r <reference_pdb.pdb> -p <pandda_analyse_sites.csv> -n <name>'
sys.exit(2)
except:
print 'usage: generate_leads.py -r <reference_pdb.pdb> -p <pandda_analyse_sites.csv> -n <name>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'usage: generate_leads.py -r <reference_pdb.pdb> -p <pandda_analyse_sites.csv> -n <name>'
sys.exit()
elif opt in ("-r", "--rfile"):
reference_structure = arg
elif opt in ("-p", "--pfile"):
pandda_analyse_centroids = arg
elif opt in ("-n", "--name"):
name = arg
elif opt in ("-d", "--dir"):
processing_directory = arg
print('\n The apo structure ' + str(name) + ' in ' + str(reference_structure) +
' will be searched for leads defined by the site centroids in ' + str(pandda_analyse_centroids) + '\n')
# read structure from reference file with BioPy PDBParser
structure = PDBParser(PERMISSIVE=0).get_structure(str(name), str(reference_structure))
# read centroids from pandda analyse sites list (native)
site_list = pd.read_csv(str(pandda_analyse_centroids))['native_centroid']
print(' Searching for residue atoms for ' + str(len(site_list)) + ' site centroids \n')
print(' NOTE: 3 residue atoms are required for each site centroid \n')
print site_list
no = 0
for centroid in site_list:
print('next centroid')
structure = PDBParser(PERMISSIVE=0).get_structure(str(name), str(reference_structure))
no += 1
res_list = []
# initial distance for nearest neighbor (NN) search is 2A
neighbor_distance = 20
centroid_coordinates = centroid.replace('(', '[')
centroid_coordinates = centroid_coordinates.replace(')', ']')
centroid_coordinates = eval(str(centroid_coordinates))
# define centroid as an atom object for NN search
centroid_atom = Atom.Atom('CEN', centroid_coordinates, 0, 0, 0, 0, 9999, 'C')
atoms = list(structure.get_atoms())
center = np.array(centroid_atom.get_coord())
ns = NeighborSearch(atoms)
# calculate NN list
neighbors = ns.search(center, neighbor_distance)
res_list = []
# for each atom in the NN list
for neighbor in neighbors:
try:
# get the residue that the neighbor belongs to
parent = Atom.Atom.get_parent(neighbor)
# if the residue is not a water etc. (amino acids have blank)
if parent.get_id()[0] == ' ':
# get the chain that the residue belongs to
chain = Residue.Residue.get_parent(parent)
# if statements for fussy proasis formatting
if len(str(parent.get_id()[1]))==3:
# residue string = 'RES CHAIN NUMBER :...'
res = (str(parent.get_resname()) + ' ' + str(chain.get_id()) + ' ' + str(parent.get_id()[1]))
res_list.append(res)
if len(str(parent.get_id()[1]))==2:
res = (str(parent.get_resname()) + ' ' + str(chain.get_id()) + ' ' + str(parent.get_id()[1]))
res_list.append(res)
except:
break
res_list = (list(set(res_list)))
print res_list
lig1 = str("'" + str(res_list[0]) + ' :' + str(res_list[1]) + ' :'
+ str(res_list[2]) + " ' ")
print lig1
res_string = "-o '"
for i in range(3,len(res_list)-1):
res_string += str(res_list[i] + ' ,')
res_string += str(res_list[i+1] + ' ')
#print str(res_string[i+1])
submit_to_proasis = str('/usr/local/Proasis2/utils/submitStructure.py -p ' + str(name) + ' -t ' + str(name + '_lead -d admin -f '+ str(reference_structure) + ' -l ' + str(lig1)) + str(res_string) + "' -x XRAY -n")
process = subprocess.Popen(submit_to_proasis, stdout=subprocess.PIPE, shell=True)
out, err = process.communicate()
print out
strucidstr = re.search(r"strucid='.....'", out)
strucidstr = strucidstr.group()
strucidstr = strucidstr.replace('strucid=','')
strucidstr = strucidstr.replace("'",'')
add_lead = str('/usr/local/Proasis2/utils/addnewlead.py -p ' + str(name) + ' -s ' + str(strucidstr))
os.system(add_lead)
#process = subprocess.Popen(add_lead, stdout=subprocess.PIPE, shell=True)
#out, err = process.communicate()
#strucidstr = get_id_string(out)
if strucidstr != '':
print('Success... ' + name + ' submitted. ProasisID: ' + str(strucidstr))
conn = sqlite3.connect(os.path.join(processing_directory, database_file))
c = conn.cursor()
c.execute("CREATE TABLE IF NOT EXISTS 'proasisLead' ('protein' TEXT, "
"'leadDir' TEXT, 'proasisID');")
c.execute(str("INSERT INTO proasisLead (protein, leadDir, proasisID) VALUES ('"
+ str(name) + "','" +
str(reference_structure) + "','" +
str(strucidstr) + "');"))
conn.commit()
c.close()
else:
print('Error: ' + str(err))
if __name__ == "__main__":
main(sys.argv[1:])