Mercurial > repos > bgruening > openbabel_compound_convert

annotate cheminfolib.py @ 4:56080bd1eb86 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c84729ec58f7f52d594066158afed175208d3d66
author bgruening
date Wed, 24 May 2017 10:02:09 -0400
parents edb576416262
children 1c66bf08f687
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edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 Small library with cheminformatic functions based on openbabel and pgchem.
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 Copyright 2012, Bjoern Gruening and Xavier Lucas
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 """
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 import os, sys
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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8
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9 try:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 from galaxy import eggs
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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11 eggs.require('psycopg2')
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 except:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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13 print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB')
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 try:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 import pybel
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 import openbabel
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18 except:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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19 print('OpenBabel could not be found. A few functions are not available without OpenBabel.')
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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20
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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21 from multiprocessing import Pool
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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22 import glob, tempfile, re
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 import subprocess
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24
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25 def CountLines( path ):
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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26 out = subprocess.Popen(['wc', '-l', path],
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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27 stdout=subprocess.PIPE,
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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28 stderr=subprocess.STDOUT
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 ).communicate()[0]
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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30 return int(out.partition(b' ')[0])
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31
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32 def grep(pattern, file_obj):
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33 grepper = re.compile(pattern)
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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34 for line in file_obj:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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35 if grepper.search(line):
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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36 return True
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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37 return False
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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38
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39 def check_filetype(filepath):
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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40 mol = False
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 possible_inchi = True
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 for line_counter, line in enumerate(open(filepath)):
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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43 if line_counter > 10000:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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44 break
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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45 if line.find('$$$$') != -1:
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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46 return 'sdf'
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47 elif line.find('@<TRIPOS>MOLECULE') != -1:
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48 return 'mol2'
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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49 elif line.find('ligand id') != -1:
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50 return 'drf'
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51 elif possible_inchi and re.findall('^InChI=', line):
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52 return 'inchi'
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53 elif re.findall('^M\s+END', line):
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54 mol = True
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55 # first line is not an InChI, so it can't be an InChI file
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56 possible_inchi = False
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57
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58 if mol:
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59 # END can occures before $$$$, so and SDF file will
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60 # be recognised as mol, if you not using this hack'
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61 return 'mol'
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62 return 'smi'
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63
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64 def db_connect(args):
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65 try:
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66 db_conn = psycopg2.connect("dbname=%s user=%s host=%s password=%s" % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd));
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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67 return db_conn
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68 except:
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69 sys.exit('Unable to connect to the db')
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70
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71 ColumnNames = {
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72 'can_smiles' : 'Canonical SMILES',
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73 'can' : 'Canonical SMILES',
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74 'inchi' : 'InChI',
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75 'inchi_key' : 'InChI key',
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76 'inchi_key_first' : 'InChI key first',
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77 'inchi_key_last' : 'InChI key last',
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78 'molwt' : 'Molecular weight',
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79 'hbd' : 'Hydrogen-bond donors',
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80 'donors' : 'Hydrogen-bond donors',
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81 'hba' : 'Hydrogen-bond acceptors',
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82 'acceptors' : 'Hydrogen-bond acceptors',
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83 'rotbonds' : 'Rotatable bonds',
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84 'logp' : 'logP',
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85 'psa' : 'Polar surface area',
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86 'mr' : 'Molecular refractivity',
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87 'atoms' : 'Number of heavy atoms',
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88 'rings' : 'Number of rings',
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89 'set_bits' : 'FP2 bits',
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90 'id' : 'Internal identifier',
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91 'tani' : 'Tanimoto coefficient',
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92 'spectrophore' : 'Spectrophores(TM)',
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93 'dist_spectrophore' : 'Spectrophores(TM) distance to target',
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94 'synonym' : 'Entry id',
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95 }
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96
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97 OBDescriptor = {
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98 'atoms': ["atoms","Number of atoms"],
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99 'hatoms': ["hatoms","Number of heavy atoms"], # self defined tag hatoms in plugindefines.txt
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100 'can_smiles' : ["cansmi","Canonical SMILES"],
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101 'can_smilesNS' : ["cansmiNS","Canonical SMILES without isotopes or stereo"],
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102 #["abonds","Number of aromatic bonds"],
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103 #["bonds","Number of bonds"],
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104 #["dbonds","Number of double bonds"],
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105 #["formula","Chemical formula"],
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106 'hba': ["HBA1","Number of Hydrogen Bond Acceptors 1 (JoelLib)"],
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107 'hba2': ["HBA2","Number of Hydrogen Bond Acceptors 2 (JoelLib)"],
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108 'hbd': ["HBD","Number of Hydrogen Bond Donors (JoelLib)"],
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109 'inchi': ["InChI","IUPAC InChI identifier"],
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110 'inchi_key': ["InChIKey","InChIKey"],
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111 #["L5","Lipinski Rule of Five"],
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112 'logp': ["logP","octanol/water partition coefficient"],
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113 'mr': ["MR","molar refractivity"],
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114 'molwt': ["MW","Molecular Weight filter"],
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115 #["nF","Number of Fluorine Atoms"],
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116 #["s","SMARTS filter"],
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117 #["sbonds","Number of single bonds"],
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118 #["smarts","SMARTS filter"],
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119 #["tbonds","Number of triple bonds"],
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120 #["title","For comparing a molecule's title"],
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121 'psa': ["TPSA","topological polar surface area"],
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122 'rotbonds' : ['ROTATABLE_BOND', 'rotatable bonds'],
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123 }
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124
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125
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126 def print_output(args, rows):
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127 if args.oformat == 'table':
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128 outfile = open(args.output, 'w')
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129 requested_fields = (filter(lambda x: x not in ["[", "]", "'"], args.fetch)).split(', ')
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130 if args.header:
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131 outfile.write( 'Identifier\t' + '\t'.join( [ColumnNames[key] for key in requested_fields] ) + '\n' )
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132 for row in rows:
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133 outfile.write( row['synonym'] + '\t' + '\t'.join( [str(row[key]) for key in requested_fields] ) + '\n' )
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134
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135 elif args.oformat in ['sdf', 'mol2']:
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136 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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137 for row in rows:
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138 try:
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139 mol = pybel.readstring('sdf', row['mol'])
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140 if args.oformat == 'sdf':
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141 keys = filter(lambda x: x not in ["[", "]", "'"], args.fetch).split(', ')
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142 mol.data.update( { ColumnNames['synonym'] : row['synonym'] } )
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143 if 'inchi_key' in keys:
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144 keys = (', '.join(keys).replace( "inchi_key", "inchi_key_first, inchi_key_last" )).split(', ')
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145 [ mol.data.update( { ColumnNames[key] : row[key] } ) for key in keys if key]
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146 outfile.write(mol)
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147 except:
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148 pass
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149 else:
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150 outfile = open(args.output, 'w')
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151 outfile.write( '\n'.join( [ '%s\t%s' % (row[args.oformat], row['synonym'] ) for row in rows ] ) )
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152 outfile.close()
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153
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154 def pybel_stop_logging():
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155 openbabel.obErrorLog.StopLogging()
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156
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157 def get_properties_ext(mol):
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158
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159 HBD = pybel.Smarts("[!#6;!H0]")
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160 HBA = pybel.Smarts("[$([$([#8,#16]);!$(*=N~O);" +
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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161 "!$(*~N=O);X1,X2]),$([#7;v3;" +
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162 "!$([nH]);!$(*(-a)-a)])]"
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163 )
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164 calc_desc_dict = mol.calcdesc()
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165
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166 try:
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167 logp = calc_desc_dict['logP']
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168 except:
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169 logp = calc_desc_dict['LogP']
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170
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171 return {"molwt": mol.molwt,
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172 "logp": logp,
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173 "donors": len(HBD.findall(mol)),
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174 "acceptors": len(HBA.findall(mol)),
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175 "psa": calc_desc_dict['TPSA'],
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176 "mr": calc_desc_dict['MR'],
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177 "rotbonds": mol.OBMol.NumRotors(),
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178 "can": mol.write("can").split()[0].strip(), ### tthis one works fine for both zinc and chembl (no ZINC code added after can descriptor string)
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179 "inchi": mol.write("inchi").strip(),
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180 "inchi_key": get_inchikey(mol).strip(),
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181 "rings": len(mol.sssr),
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182 "atoms": mol.OBMol.NumHvyAtoms(),
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183 "spectrophore" : OBspectrophore(mol),
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184 }
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185
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186 def get_inchikey(mol):
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187 conv = openbabel.OBConversion()
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188 conv.SetInAndOutFormats("mol", "inchi")
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189 conv.SetOptions("K", conv.OUTOPTIONS)
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190 inchikey = conv.WriteString( mol.OBMol )
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191 return inchikey
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192
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193 def OBspectrophore(mol):
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194 spectrophore = pybel.ob.OBSpectrophore()
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195 # Parameters: rotation angle = 20, normalization for mean and sd, accuracy = 3.0 A and non-stereospecific cages.
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196 spectrophore.SetNormalization( spectrophore.NormalizationTowardsZeroMeanAndUnitStd )
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197 return ', '.join( [ "%.3f" % value for value in spectrophore.GetSpectrophore( mol.OBMol ) ] )
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198
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199 def squared_euclidean_distance(a, b):
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200 try:
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201 return ((np.asarray( a ) - np.asarray( b ))**2).sum()
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202 except ValueError:
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203 return 0
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204
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205 def split_library( lib_path, lib_format = 'sdf', package_size = None ):
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206 """
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207 Split a library of compounds. Usage: split_library( lib_path, lib_format, package_size )
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208 IT currently ONLY WORKS FOR SD-Files
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209 """
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210 pack = 1
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211 mol_counter = 0
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212
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213 outfile = open('/%s/%s_pack_%i.%s' % ( '/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w' )
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214
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215 for line in open(lib_path, 'r'):
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216 outfile.write( line )
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217 if line.strip() == '$$$$':
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218 mol_counter += 1
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219 if mol_counter % package_size == 0:
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220 outfile.close()
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221 pack += 1
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222 outfile = open('/%s/%s_pack_%i.%s' % ( '/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w' )
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223 if mol_counter*10 % package_size == 0:
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224 print('%i molecules parsed, starting pack nr. %i' % ( mol_counter, pack - 1 ))
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225 outfile.close()
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226
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227 return True
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228
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229 def split_smi_library( smiles_file, structures_in_one_file ):
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230 """
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231 Split a file with SMILES to several files for multiprocessing usage.
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232 Usage: split_smi_library( smiles_file, 10 )
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233 """
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234 output_files = []
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235 tfile = tempfile.NamedTemporaryFile(delete=False)
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236
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237 smiles_handle = open(smiles_file, 'r')
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238 for count, line in enumerate( smiles_handle ):
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239 if count % structures_in_one_file == 0 and count != 0:
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240 tfile.close()
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241 output_files.append(tfile.name)
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242 tfile = tempfile.NamedTemporaryFile(delete=False)
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243 tfile.write(line)
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244 tfile.close()
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245 output_files.append(tfile.name)
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246 smiles_handle.close()
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247 return output_files
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248
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249
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250 def mp_run(input_path, regex, PROCESSES, function_to_call ):
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251 paths = []
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252 [ paths.append(compound_file) for compound_file in glob.glob(str(input_path) + str(regex)) ]
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253 paths.sort()
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254
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255 pool = Pool(processes=PROCESSES)
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256 print('Process initialized with', PROCESSES, 'processors')
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257 result = pool.map_async(function_to_call, paths)
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258 result.get()
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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260 return paths
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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262 if __name__ == '__main__':
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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263 print(check_filetype(sys.argv[1]))
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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264