Mercurial > repos > bgruening > prepare_ligands_for_docking

annotate ob_spectrophore_search.py @ 7:fac2c28b4c55 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:04:16 +0000
parents a5f4b80e6769
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
2 """
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
3 Input: tabular format file with one column storing the unique id for the compounds and any other with the Spectrophores(TM) descriptors.
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
4 Output: parse the target file using the same protocol used to generate the databases in our servers. Physico-chemical properties are computed and stored as metadata in the sdf output file.
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
5 Copyright 2012, Bjoern Gruening and Xavier Lucas
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
6 """
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
7 import argparse
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
8
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
9 import numpy as np
4
de4c80d17527 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 0
diff changeset
10 from openbabel import openbabel, pybel
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
11
4
de4c80d17527 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 0
diff changeset
12 openbabel.obErrorLog.StopLogging()
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
13 # TODO get rid of eval()
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
14
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
15 global spectrophore
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
16 spectrophore = pybel.ob.OBSpectrophore()
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
17
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
18
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
19 def parse_command_line():
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
20 parser = argparse.ArgumentParser()
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
21 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
22 "--target",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
23 required=True,
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
24 help="target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
25 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
26 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
27 "--library",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
28 required=True,
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
29 help="library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
30 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
31 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
32 "-c",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
33 "--column",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
34 required=True,
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
35 type=int,
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
36 help="#column containing the Spectrophores(TM) descriptors in the library file",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
37 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
38 parser.add_argument("-o", "--output", required=True, help="output file name")
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
39 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
40 "-n",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
41 "--normalization",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
42 default="ZeroMeanAndUnitStd",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
43 choices=["No", "ZeroMean", "UnitStd", "ZeroMeanAndUnitStd"],
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
44 help="Normalization method",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
45 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
46 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
47 "-a",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
48 "--accuracy",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
49 default="20",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
50 choices=["1", "2", "5", "10", "15", "20", "30", "36", "45", "60"],
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
51 help="Accuracy expressed as angular stepsize",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
52 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
53 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
54 "-s",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
55 "--stereo",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
56 default="No",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
57 choices=["No", "Unique", "Mirror", "All"],
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
58 help="Stereospecificity of the cage",
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
59 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
60 parser.add_argument(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
61 "-r", "--resolution", type=float, default="3.0", help="Resolution"
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
62 )
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
63 return parser.parse_args()
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
64
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
65
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
66 def set_parameters(args):
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
67 if args.normalization == "No":
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
68 spectrophore.SetNormalization(spectrophore.NoNormalization)
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
69 else:
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
70 spectrophore.SetNormalization(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
71 eval("spectrophore.NormalizationTowards" + args.normalization)
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
72 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
73 spectrophore.SetAccuracy(eval("spectrophore.AngStepSize" + args.accuracy))
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
74 spectrophore.SetStereo(eval("spectrophore." + args.stereo + "StereoSpecificProbes"))
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
75 spectrophore.SetResolution(args.resolution)
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
76 return True
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
77
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
78
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
79 def Compute_Spectrophores_distance(target_spectrophore, args):
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
80 outfile = open(args.output, "w")
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
81 for mol in open(args.library, "r"):
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
82 try:
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
83 distance = (
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
84 (
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
85 np.asarray(target_spectrophore, dtype=float)
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
86 - np.asarray(
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
87 mol.split("\t")[args.column - 1].strip().split(", "),
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
88 dtype=float,
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
89 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
90 )
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
91 ** 2
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
92 ).sum()
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
93 except ValueError:
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
94 distance = 0
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
95 outfile.write("%s\t%f\n" % (mol.strip(), distance))
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
96 outfile.close()
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
97
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
98
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
99 def __main__():
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
100 """
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
101 Computation of Spectrophores(TM) distances to a target molecule.
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
102 """
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
103 args = parse_command_line()
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
104 # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
105 set_parameters(args)
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
106
7
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
107 mol = next(pybel.readfile("sdf", args.target))
fac2c28b4c55 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
parents: 5
diff changeset
108 target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(", ")
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
109 # Compute the paired-distance between every molecule in the library and the target
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
110 Compute_Spectrophores_distance(target_spectrophore, args)
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
111
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
112
5
a5f4b80e6769 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
parents: 4
diff changeset
113 if __name__ == "__main__":
0
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
bgruening
parents:
diff changeset
114 __main__()