Mercurial > repos > bgruening > openbabel_remove_protonation_state

comparison distance_finder.py @ 13:b578d0c101cd draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:43:40 +0000
parents bf4e668b6690
children 22a866858b81
comparison
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12:bf4e668b6690 13:b578d0c101cd
9 # That would encode 3 points. 9 # That would encode 3 points.
10 # Each record in the SDF input is read and the closest heavy atom to each of the reference points is recorded as 10 # Each record in the SDF input is read and the closest heavy atom to each of the reference points is recorded as
11 # a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example 11 # a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example
12 # there would be properties for distance1, distance2 and distance3. 12 # there would be properties for distance1, distance2 and distance3.
13 13
14 import argparse, os, sys, math 14 import argparse
15 import math
16 import sys
15 17
16 from openbabel import pybel 18 from openbabel import pybel
17 19
18 20
19 def log(*args, **kwargs): 21 def log(*args, **kwargs):
28 :param points_file: A file with the points to consider. 30 :param points_file: A file with the points to consider.
29 :param outfile: The name of the file for the SDF output 31 :param outfile: The name of the file for the SDF output
30 :return: 32 :return:
31 """ 33 """
32 34
33
34 points = [] 35 points = []
35 36
36 # read the points 37 # read the points
37 with open(points_file, 'r') as f: 38 with open(points_file, 'r') as f:
38 for line in f.readlines(): 39 for line in f.readlines():
39 line.strip() 40 line.strip()
40 if line: 41 if line:
41 p = line.split() 42 p = line.split()
42 if len(p) == 3: 43 if len(p) == 3:
43 points.append((float(p[0]), float(p[1]), float(p[2]))) 44 points.append((float(p[0]), float(p[1]), float(p[2])))
44 log("Read points",p) 45 log("Read points", p)
45 continue 46 continue
46 log("Failed to read line:", line) 47 log("Failed to read line:", line)
47 log('Found', len(points), 'atom points') 48 log('Found', len(points), 'atom points')
48 49
49 sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True) 50 sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True)
54 if count % 50000 == 0: 55 if count % 50000 == 0:
55 log('Processed', count) 56 log('Processed', count)
56 57
57 try: 58 try:
58 # print("Processing mol", mol.title) 59 # print("Processing mol", mol.title)
59
60 clone = pybel.Molecule(mol) 60 clone = pybel.Molecule(mol)
61 clone.removeh() 61 clone.removeh()
62 62
63 coords = [] 63 coords = []
64 for atom in clone.atoms: 64 for atom in clone.atoms:
80 mol.data['distance' + str(p)] = min_distance 80 mol.data['distance' + str(p)] = min_distance
81 81
82 sdf_writer.write(mol) 82 sdf_writer.write(mol)
83 83
84 except Exception as e: 84 except Exception as e:
85 log('Failed to handle molecule: '+ str(e)) 85 log('Failed to handle molecule: ' + str(e))
86 continue 86 continue
87 87
88 sdf_writer.close() 88 sdf_writer.close()
89 log('Wrote', count, 'molecules') 89 log('Wrote', count, 'molecules')
90 90
91 91
92 def main(): 92 def main():
93 global work_dir 93 global work_dir
94 94
95 parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points') 95 parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points')
96
97 parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)") 96 parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)")
98 parser.add_argument('-p', '--points', help="PDB format file with atoms") 97 parser.add_argument('-p', '--points', help="PDB format file with atoms")
99 parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results") 98 parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results")
100
101 99
102 args = parser.parse_args() 100 args = parser.parse_args()
103 log("XChem distances args: ", args) 101 log("XChem distances args: ", args)
104 102
105 execute(args.input, args.points, args.outfile) 103 execute(args.input, args.points, args.outfile)