Mercurial > repos > bgruening > prepare_ligands_for_docking
changeset 4:de4c80d17527 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
| author | bgruening |
|---|---|
| date | Tue, 28 Jul 2020 08:40:43 -0400 |
| parents | 015ccbd1ad68 |
| children | a5f4b80e6769 |
| files | change_title_to_metadata_value.py cheminfolib.py distance_finder.py macros.xml multi_obgrep.py ob_addh.py ob_filter.py ob_genProp.py ob_prepare_ligands.xml ob_remIons.py ob_spectrophore_search.py remove_protonation_state.py subsearch.py test-data/ob_convert_on_CID2244.cml test-data/ob_convert_on_CID2244.pdb test-data/ob_depiction_svg_on_8_mol.svg test-data/ob_prepare_ligands1.pdbqt test-data/ob_prepare_ligands2.pdbqt test-data/split1.pdbqt test-data/split2.pdbqt |
| diffstat | 20 files changed, 595 insertions(+), 626 deletions(-) [+] |
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--- a/change_title_to_metadata_value.py Thu Apr 09 10:10:31 2020 -0400 +++ b/change_title_to_metadata_value.py Tue Jul 28 08:40:43 2020 -0400 @@ -9,13 +9,13 @@ import os import sys import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import random import string +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() + def main(): parser = argparse.ArgumentParser( description="Change the title from a molecule file to metadata \
--- a/cheminfolib.py Thu Apr 09 10:10:31 2020 -0400 +++ b/cheminfolib.py Tue Jul 28 08:40:43 2020 -0400 @@ -13,8 +13,8 @@ print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB') try: - import pybel - import openbabel + from openbabel import openbabel, pybel + openbabel.obErrorLog.StopLogging() except: print('OpenBabel could not be found. A few functions are not available without OpenBabel.')
--- a/distance_finder.py Thu Apr 09 10:10:31 2020 -0400 +++ b/distance_finder.py Tue Jul 28 08:40:43 2020 -0400 @@ -12,10 +12,10 @@ # there would be properties for distance1, distance2 and distance3. import argparse, os, sys, math + from openbabel import pybel - def log(*args, **kwargs): """Log output to STDERR """
--- a/macros.xml Thu Apr 09 10:10:31 2020 -0400 +++ b/macros.xml Tue Jul 28 08:40:43 2020 -0400 @@ -1,9 +1,9 @@ <macros> - <token name="@VERSION@">2.4.2.2</token> + <token name="@TOOL_VERSION@">3.1.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.4.1">openbabel</requirement> + <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement> <requirement type="package" version="3">python</requirement> <yield /> </requirements>
--- a/multi_obgrep.py Thu Apr 09 10:10:31 2020 -0400 +++ b/multi_obgrep.py Tue Jul 28 08:40:43 2020 -0400 @@ -6,15 +6,14 @@ """ import sys, os import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import multiprocessing import tempfile import subprocess import shutil import shlex +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
--- a/ob_addh.py Thu Apr 09 10:10:31 2020 -0400 +++ b/ob_addh.py Tue Jul 28 08:40:43 2020 -0400 @@ -5,9 +5,9 @@ """ import sys, os import argparse -import openbabel + +from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -import pybel def parse_command_line(argv): parser = argparse.ArgumentParser()
--- a/ob_filter.py Thu Apr 09 10:10:31 2020 -0400 +++ b/ob_filter.py Tue Jul 28 08:40:43 2020 -0400 @@ -10,9 +10,9 @@ import argparse import cheminfolib import json -import pybel import shlex, subprocess +from openbabel import pybel cheminfolib.pybel_stop_logging() def parse_command_line():
--- a/ob_genProp.py Thu Apr 09 10:10:31 2020 -0400 +++ b/ob_genProp.py Tue Jul 28 08:40:43 2020 -0400 @@ -8,9 +8,9 @@ import argparse import openbabel openbabel.obErrorLog.StopLogging() -import pybel import cheminfolib +from openbabel import pybel def parse_command_line(argv): parser = argparse.ArgumentParser()
--- a/ob_prepare_ligands.xml Thu Apr 09 10:10:31 2020 -0400 +++ b/ob_prepare_ligands.xml Tue Jul 28 08:40:43 2020 -0400 @@ -1,7 +1,8 @@ -<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@VERSION@.0"> +<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>Tool to prepare ligands for docking with tools like Autodock Vina</description> <macros> <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[
--- a/ob_remIons.py Thu Apr 09 10:10:31 2020 -0400 +++ b/ob_remIons.py Tue Jul 28 08:40:43 2020 -0400 @@ -6,9 +6,9 @@ """ import sys, os import argparse -import openbabel + +from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -import pybel def parse_command_line(): parser = argparse.ArgumentParser()
--- a/ob_spectrophore_search.py Thu Apr 09 10:10:31 2020 -0400 +++ b/ob_spectrophore_search.py Tue Jul 28 08:40:43 2020 -0400 @@ -6,12 +6,11 @@ """ import sys, os import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import math import numpy as np +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() #TODO get rid of eval() global spectrophore
--- a/remove_protonation_state.py Thu Apr 09 10:10:31 2020 -0400 +++ b/remove_protonation_state.py Tue Jul 28 08:40:43 2020 -0400 @@ -6,9 +6,9 @@ """ import sys, os import argparse -import openbabel + +from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -import pybel def parse_command_line(): parser = argparse.ArgumentParser()
--- a/subsearch.py Thu Apr 09 10:10:31 2020 -0400 +++ b/subsearch.py Tue Jul 28 08:40:43 2020 -0400 @@ -6,14 +6,14 @@ """ import sys, os import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import multiprocessing import tempfile import subprocess import shutil +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() + def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
--- a/test-data/ob_convert_on_CID2244.cml Thu Apr 09 10:10:31 2020 -0400 +++ b/test-data/ob_convert_on_CID2244.cml Tue Jul 28 08:40:43 2020 -0400 @@ -1,27 +1,27 @@ <?xml version="1.0"?> <molecule id="id2244" xmlns="http://www.xml-cml.org/schema"> <atomArray> - <atom id="a1" elementType="O" x2="3.732000" y2="-0.060000"/> - <atom id="a2" elementType="O" x2="6.330100" y2="1.440000"/> - <atom id="a3" elementType="O" x2="4.598100" y2="1.440000"/> - <atom id="a4" elementType="O" x2="2.866000" y2="-1.560000"/> - <atom id="a5" elementType="C" x2="4.598100" y2="-0.560000"/> - <atom id="a6" elementType="C" x2="5.464100" y2="-0.060000"/> - <atom id="a7" elementType="C" x2="4.598100" y2="-1.560000"/> - <atom id="a8" elementType="C" x2="6.330100" y2="-0.560000"/> - <atom id="a9" elementType="C" x2="5.464100" y2="-2.060000"/> - <atom id="a10" elementType="C" x2="6.330100" y2="-1.560000"/> - <atom id="a11" elementType="C" x2="5.464100" y2="0.940000"/> - <atom id="a12" elementType="C" x2="2.866000" y2="-0.560000"/> - <atom id="a13" elementType="C" x2="2.000000" y2="-0.060000"/> - <atom id="a14" elementType="H" x2="4.061100" y2="-1.870000"/> - <atom id="a15" elementType="H" x2="6.867100" y2="-0.250000"/> - <atom id="a16" elementType="H" x2="5.464100" y2="-2.680000"/> - <atom id="a17" elementType="H" x2="6.867100" y2="-1.870000"/> - <atom id="a18" elementType="H" x2="2.310000" y2="0.476900"/> - <atom id="a19" elementType="H" x2="1.463100" y2="0.250000"/> - <atom id="a20" elementType="H" x2="1.690000" y2="-0.596900"/> - <atom id="a21" elementType="H" x2="6.330100" y2="2.060000"/> + <atom id="a1" elementType="O" hydrogenCount="0" x2="3.732000" y2="-0.060000"/> + <atom id="a2" elementType="O" hydrogenCount="1" x2="6.330100" y2="1.440000"/> + <atom id="a3" elementType="O" hydrogenCount="0" x2="4.598100" y2="1.440000"/> + <atom id="a4" elementType="O" hydrogenCount="0" x2="2.866000" y2="-1.560000"/> + <atom id="a5" elementType="C" hydrogenCount="0" x2="4.598100" y2="-0.560000"/> + <atom id="a6" elementType="C" hydrogenCount="0" x2="5.464100" y2="-0.060000"/> + <atom id="a7" elementType="C" hydrogenCount="1" x2="4.598100" y2="-1.560000"/> + <atom id="a8" elementType="C" hydrogenCount="1" x2="6.330100" y2="-0.560000"/> + <atom id="a9" elementType="C" hydrogenCount="1" x2="5.464100" y2="-2.060000"/> + <atom id="a10" elementType="C" hydrogenCount="1" x2="6.330100" y2="-1.560000"/> + <atom id="a11" elementType="C" hydrogenCount="0" x2="5.464100" y2="0.940000"/> + <atom id="a12" elementType="C" hydrogenCount="0" x2="2.866000" y2="-0.560000"/> + <atom id="a13" elementType="C" hydrogenCount="3" x2="2.000000" y2="-0.060000"/> + <atom id="a14" elementType="H" hydrogenCount="0" x2="4.061100" y2="-1.870000"/> + <atom id="a15" elementType="H" hydrogenCount="0" x2="6.867100" y2="-0.250000"/> + <atom id="a16" elementType="H" hydrogenCount="0" x2="5.464100" y2="-2.680000"/> + <atom id="a17" elementType="H" hydrogenCount="0" x2="6.867100" y2="-1.870000"/> + <atom id="a18" elementType="H" hydrogenCount="0" x2="2.310000" y2="0.476900"/> + <atom id="a19" elementType="H" hydrogenCount="0" x2="1.463100" y2="0.250000"/> + <atom id="a20" elementType="H" hydrogenCount="0" x2="1.690000" y2="-0.596900"/> + <atom id="a21" elementType="H" hydrogenCount="0" x2="6.330100" y2="2.060000"/> </atomArray> <bondArray> <bond atomRefs2="a1 a5" order="1"/>
--- a/test-data/ob_convert_on_CID2244.pdb Thu Apr 09 10:10:31 2020 -0400 +++ b/test-data/ob_convert_on_CID2244.pdb Tue Jul 28 08:40:43 2020 -0400 @@ -1,5 +1,5 @@ COMPND 2244 -AUTHOR GENERATED BY OPEN BABEL 2.3.90 +AUTHOR GENERATED BY OPEN BABEL 3.1.0 HETATM 1 O UNL 1 3.732 -0.060 0.000 1.00 0.00 O HETATM 2 O UNL 1 6.330 1.440 0.000 1.00 0.00 O HETATM 3 O UNL 1 4.598 1.440 0.000 1.00 0.00 O @@ -23,16 +23,16 @@ HETATM 21 H UNL 1 6.330 2.060 0.000 1.00 0.00 H CONECT 1 5 12 CONECT 2 11 21 -CONECT 3 11 -CONECT 4 12 -CONECT 5 1 6 7 -CONECT 6 5 8 11 -CONECT 7 5 9 14 -CONECT 8 6 10 15 -CONECT 9 7 10 16 -CONECT 10 8 9 17 -CONECT 11 2 3 6 -CONECT 12 1 4 13 +CONECT 3 11 11 +CONECT 4 12 12 +CONECT 5 1 6 7 7 +CONECT 6 5 8 8 11 +CONECT 7 5 5 9 14 +CONECT 8 6 6 10 15 +CONECT 9 7 10 10 16 +CONECT 10 8 9 9 17 +CONECT 11 2 3 3 6 +CONECT 12 1 4 4 13 CONECT 13 12 18 19 20 CONECT 14 7 CONECT 15 8
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+0.132 C -BRANCH 34 37 -ATOM 37 C UNL 1 -4.794 6.118 0.000 0.00 0.00 +0.037 A -ATOM 38 C UNL 1 -4.033 7.411 0.000 0.00 0.00 +0.013 A -ATOM 39 C UNL 1 -4.772 8.716 0.000 0.00 0.00 +0.001 A +BRANCH 2 33 +ATOM 33 N UNL 1 -2.551 4.803 0.000 0.00 0.00 +0.000 N +ATOM 34 C UNL 1 -1.944 5.838 0.000 0.00 0.00 +0.000 C +ATOM 35 C UNL 1 -4.052 4.814 0.000 0.00 0.00 +0.000 C +ATOM 36 O UNL 1 -4.659 3.778 0.000 0.00 0.00 +0.000 OA +BRANCH 35 37 +ATOM 37 C UNL 1 -4.794 6.118 0.000 0.00 0.00 +0.000 A +ATOM 38 C UNL 1 -6.294 6.131 0.000 0.00 0.00 +0.000 A +ATOM 39 C UNL 1 -7.033 7.436 0.000 0.00 0.00 +0.000 A ATOM 40 C UNL 1 -6.272 8.729 0.000 0.00 0.00 +0.000 A -ATOM 41 C UNL 1 -7.033 7.436 0.000 0.00 0.00 +0.001 A -ATOM 42 C UNL 1 -6.294 6.131 0.000 0.00 0.00 +0.013 A -ENDBRANCH 34 37 -ENDBRANCH 32 33 +ATOM 41 C UNL 1 -4.772 8.716 0.000 0.00 0.00 +0.000 A +ATOM 42 C UNL 1 -4.033 7.411 0.000 0.00 0.00 +0.000 A +ENDBRANCH 35 37 +ENDBRANCH 2 33 BRANCH 1 44 -ATOM 43 C UNL 1 -4.720 3.343 0.000 0.00 0.00 +0.194 C -ATOM 44 O UNL 1 -4.147 2.289 0.000 0.00 0.00 -0.373 OA +ATOM 43 C UNL 1 -4.720 3.343 0.000 0.00 0.00 +0.000 C +ATOM 44 O UNL 1 -4.147 2.289 0.000 0.00 0.00 +0.000 OA ENDBRANCH 1 44 TORSDOF 3
--- a/test-data/split1.pdbqt Thu Apr 09 10:10:31 2020 -0400 +++ b/test-data/split1.pdbqt Tue Jul 28 08:40:43 2020 -0400 @@ -7,24 +7,24 @@ REMARK x y z vdW Elec q Type REMARK _______ _______ _______ _____ _____ ______ ____ ROOT -ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.149 A -ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.038 A -ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.003 A +ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A ATOM 4 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A -ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.004 A -ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.049 A +ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A ENDROOT BRANCH 6 7 -ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.076 C -ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA -ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 C +ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA +ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA ENDBRANCH 6 7 BRANCH 1 10 -ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.424 OA +ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA BRANCH 10 12 -ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.122 C -ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.322 C -ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.250 OA +ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 C +ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 C +ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA ENDBRANCH 10 12 ENDBRANCH 1 10 TORSDOF 3
--- a/test-data/split2.pdbqt Thu Apr 09 10:10:31 2020 -0400 +++ b/test-data/split2.pdbqt Tue Jul 28 08:40:43 2020 -0400 @@ -7,24 +7,24 @@ REMARK x y z vdW Elec q Type REMARK _______ _______ _______ _____ _____ ______ ____ ROOT -ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.149 A -ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.038 A -ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.003 A +ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A ATOM 4 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A -ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.004 A -ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.049 A +ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A ENDROOT BRANCH 6 7 -ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.076 C -ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA -ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 C +ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA +ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA ENDBRANCH 6 7 BRANCH 1 10 -ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.424 OA +ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA BRANCH 10 12 -ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.122 C -ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.322 C -ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.250 OA +ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 C +ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 C +ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 OA ENDBRANCH 10 12 ENDBRANCH 1 10 TORSDOF 3