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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e |
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modified:
butina_clustering.xml mol2fps.xml nxn_clustering.py nxn_clustering.xml sdf2fps.xml test-data/CID_2244_FP2.fps test-data/CID_2244_FP3.fps test-data/CID_2244_FP4.fps test-data/CID_2244_MACCS.fps test-data/NxN_Clustering_on_q.svg |
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added:
test-data/CID_2244_torsions.fps test-data/NxN_Clustering_on_q.txt |
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| diff -r e3a7d6cc87af -r 0d88631bb7de butina_clustering.xml --- a/butina_clustering.xml Fri Mar 23 03:26:33 2018 -0400 +++ b/butina_clustering.xml Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.2"> +<tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina clustering" version="1.5"> <description>of molecular fingerprints</description> <requirements> - <requirement type="package" version="1.1p1">chemfp</requirement> + <requirement type="package" version="1.5">chemfp</requirement> <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> <command detect_errors="exit_code"> @@ -14,8 +14,8 @@ ]]> </command> <inputs> - <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> - <param name='threshold' type='float' value='0.8'/> + <param name="infile" type="data" format="fps" label="Fingerprint dataset" help="Dataset missing? See TIP below"/> + <param name='threshold' type='float' label='Threshold' value='0.8'/> </inputs> <outputs> <data format="tabular" name="outfile"/> @@ -35,7 +35,7 @@ **What this tool does** -Unsupervised non-hierarchical clustering method based on the Taylor-Butina algorithm, which guarantees that every cluster contains molecules which are within a distance cutoff of the central molecule. This tool is based on the chemfp_ project. +Unsupervised non-hierarchical clustering of molecular fingerprints, based on the Taylor-Butina algorithm, which guarantees that every cluster contains molecules which are within a distance cutoff of the central molecule. This tool is based on the chemfp_ project. .. _chemfp: http://chemfp.com/ @@ -89,5 +89,6 @@ </help> <citations> <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> + <citation type="doi">10.1021/ci9803381</citation> </citations> </tool> |
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| diff -r e3a7d6cc87af -r 0d88631bb7de mol2fps.xml --- a/mol2fps.xml Fri Mar 23 03:26:33 2018 -0400 +++ b/mol2fps.xml Tue May 07 13:32:50 2019 -0400 |
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| b'@@ -1,21 +1,20 @@\n-<tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0">\n- <description>with different fingerprint types</description>\n+<tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="1.5">\n+ <description>conversion to several different fingerprint formats</description>\n <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->\n <requirements>\n- <requirement type="package" version="1.1p1">chemfp</requirement>\n- <requirement type="package" version="2016.03.3">rdkit</requirement>\n+ <requirement type="package" version="1.5">chemfp</requirement>\n+ <requirement type="package" version="2018.09.3">rdkit</requirement>\n <requirement type="package" version="2.4.1">openbabel</requirement>\n </requirements>\n <command>\n <![CDATA[\n- #set $fptype = $fp_opts.fp_opts_selector\n \n- #if $fptype in [\'--FP2\', \'--FP3\', \'--FP4\', \'--MACCS\']:\n+ #if $fp_opts.fp_opts_selector in [\'--FP2\', \'--FP3\', \'--FP4\', \'--MACCS\']:\n ## Open Babel fingerprints\n- ob2fps $fptype --in \'${infile.ext}\' \'${infile}\' -o \'${outfile}\'\n+ ob2fps $fp_opts.fp_opts_selector --in \'${infile.ext}\' \'${infile}\' -o \'${outfile}\' --out \'fps\'\n #else:\n ## RDKit fingerprints\n- rdkit2fps --in \'${infile.ext}\' \'${infile}\' -o \'${outfile}\'\n+ rdkit2fps --in \'${infile.ext}\' \'${infile}\' -o \'${outfile}\' --out \'fps\'\n #if $fp_opts.fp_opts_selector == "--RDK":\n --RDK\n --fpSize $fp_opts.fpSize\n@@ -35,7 +34,7 @@\n $fp_opts.useChirality\n $fp_opts.useBondTypes\n #elif $fp_opts.fp_opts_selector == "--pairs":\n- --paris\n+ --pairs\n --fpSize $fp_opts.fpSize\n --minLength $fp_opts.minLength\n --maxLength $fp_opts.maxLength\n@@ -49,7 +48,7 @@\n ]]>\n </command>\n <inputs>\n- <param name="infile" type=\'data\' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>\n+ <param name="infile" type=\'data\' format="sdf,smi,mol,mol2,cml,inchi" label="Molecule file"/>\n <conditional name="fp_opts">\n <param name="fp_opts_selector" type="select" label="Type of fingerprint">\n <option value=\'--FP2\' selected="True">Open Babel FP2 fingerprints</option>\n@@ -68,51 +67,51 @@\n <when value="--FP4" />\n <when value="--MACCS" />\n <when value="--RDK">\n- <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">\n+ <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">\n <validator type="in_range" min="1" />\n </param>\n- <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">\n+ <param name="minPath" type="integer" value="1" label="Minimum number of bonds to include in the subgraph" help="">\n <validator type="in_range" min="1" />\n </param>\n- <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">\n+ <param name="maxPath" type="integer" value="7" label="Maximum number of bonds to include in the subgraph" help="">\n <validator type="in_range" min="1" />\n </param>\n- <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">\n+ <param name="nBitsPerHash" type="integer" value="4" label="Number of bits to set per path" help="">\n <validator type="in_range" min="1" />\n </param>\n <param name="useHs" type="boolean" truevalue'..b' </conditional>\n <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>\n </test>\n <test>\n <param name="infile" value="CID_2244.smi" ftype="smi" />\n- <param name="fp_opts.fp_opts_selector" value="--FP2" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--FP2" />\n+ </conditional>\n <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>\n </test>\n <!-- FP3 -->\n <test>\n <param name="infile" value="CID_2244.sdf" ftype="sdf" />\n- <param name="fp_opts.fp_opts_selector" value="--FP3" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--FP3" />\n+ </conditional>\n <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>\n </test>\n <test>\n <param name="infile" value="CID_2244.smi" ftype="smi" />\n- <param name="fp_opts.fp_opts_selector" value="--FP3" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--FP3" />\n+ </conditional>\n <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>\n </test>\n <!-- FP4 -->\n <test>\n <param name="infile" value="CID_2244.sdf" ftype="sdf" />\n- <param name="fp_opts.fp_opts_selector" value="--FP4" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--FP4" />\n+ </conditional>\n <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>\n </test>\n <test>\n <param name="infile" value="CID_2244.smi" ftype="smi" />\n- <param name="fp_opts.fp_opts_selector" value="--FP4" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--FP4" />\n+ </conditional>\n <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>\n </test>\n <!-- MACCS -->\n <test>\n <param name="infile" value="CID_2244.sdf" ftype="sdf" />\n- <param name="fp_opts.fp_opts_selector" value="--MACCS" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--MACCS" />\n+ </conditional>\n <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>\n </test>\n <test>\n <param name="infile" value="CID_2244.smi" ftype="smi" />\n- <param name="fp_opts.fp_opts_selector" value="--MACCS" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--MACCS" />\n+ </conditional>\n <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>\n </test>\n+ <!-- RDKit2fps -->\n+ <test>\n+ <param name="infile" value="CID_2244.smi" ftype="smi" />\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" value="--torsions" />\n+ </conditional>\n+ <param name="fp_opts.fpSize" value="2048" />\n+ <param name="fp_opts.targetSize" value="4" />\n+ <output name="outfile" file="CID_2244_torsions.fps" ftype="fps" lines_diff="4"/>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n@@ -177,7 +202,7 @@\n \n **What this tool does**\n \n-This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_.\n+This tool uses chemfp to calculate molecular fingerprints, supporting a number of common file formats. Chemfp uses OpenBabel, OpenEye and RDKit.\n \n For more information check the websites listed below::\n \n@@ -194,7 +219,7 @@\n \n * Example::\n \n-\t - SDF File\n+\t - SD-File\n \n \t\t28434379\n \t\t -OEChem-02031205132D\n' |
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| diff -r e3a7d6cc87af -r 0d88631bb7de nxn_clustering.py --- a/nxn_clustering.py Fri Mar 23 03:26:33 2018 -0400 +++ b/nxn_clustering.py Tue May 07 13:32:50 2019 -0400 |
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| @@ -69,12 +69,10 @@ distances = distance_matrix( arena, args.tanimoto_threshold ) if args.similarity_matrix: - distances.tofile( args.similarity_matrix ) + numpy.savetxt(args.similarity_matrix, distances) if args.cluster_image: - linkage = hcluster.linkage( distances, method="single", metric="euclidean" ) + linkage = hcluster.linkage(distances, method="single", metric="euclidean") + hcluster.dendrogram(linkage, labels=arena.ids, leaf_rotation=90.) + pylab.savefig(args.cluster_image, format=args.oformat) - hcluster.dendrogram(linkage, labels=arena.ids) - - pylab.savefig( args.cluster_image, format=args.oformat ) - |
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| diff -r e3a7d6cc87af -r 0d88631bb7de nxn_clustering.xml --- a/nxn_clustering.xml Fri Mar 23 03:26:33 2018 -0400 +++ b/nxn_clustering.xml Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,10 +1,9 @@ -<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.4"> +<tool id="ctb_chemfp_nxn_clustering" name="NxN clustering" version="1.5"> <description>of molecular fingerprints</description> <requirements> - <requirement type="package" version="1.1p1">chemfp</requirement> - <requirement type="package" version="2">python</requirement> - <requirement type="package" version="2.0.2">matplotlib</requirement> - <requirement type="package" version="0.19.0">scipy</requirement> + <requirement type="package" version="1.5">chemfp</requirement> + <requirement type="package" version="2.2.3">matplotlib</requirement> + <requirement type="package" version="1.2.1">scipy</requirement> <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> <command detect_errors="exit_code"> @@ -16,43 +15,44 @@ --cluster '$image' #end if #if str($output_files) in ['both', 'matrix']: - --smatrix '$smilarity_matrix' + --smatrix '$similarity_matrix' #end if --oformat '$oformat' ]]> </command> <inputs> - <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> - <param name='threshold' type='float' value='0.0' /> + <param name="infile" type="data" format="fps" label="Fingerprint dataset" help="Dataset missing? See TIP below"/> + <param name='threshold' label='Threshold' type='float' value='0.0' /> <param name='oformat' type='select' format='text' label="Format of the resulting picture"> <option value='png'>PNG</option> <option value='svg'>SVG</option> </param> <param name='output_files' type='select' format='text' label="Output options"> - <option value='both'>NxN matrix and Image</option> + <option value='both'>NxN matrix and image</option> <option value='image'>Image</option> - <option value='matrix'>NxN Matrix</option> + <option value='matrix'>NxN ḿatrix</option> </param> </inputs> <outputs> - <data name="image" format="svg" label="${tool.name} on ${on_string} - Cluster Image"> + <data name="image" format="svg" label="${tool.name} on ${on_string} - Dendrogram Image"> <filter>output_files == "both" or output_files == "image"</filter> <change_format> <when input="oformat" value="png" format="png"/> </change_format> </data> - <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix"> + <data name="similarity_matrix" format="txt" label="${tool.name} on ${on_string} - Similarity Matrix"> <filter>output_files == "both" or output_files == "matrix"</filter> </data> </outputs> <tests> <test> <param name="infile" ftype="fps" value="targets.fps" /> - <param name='treshold' value='0.75' /> + <param name='threshold' value='0.75' /> <param name='oformat' value='svg' /> - <param name='output_files' value='image' /> - <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg" compare="sim_size"/> + <param name='output_files' value='both' /> + <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg"/> + <output name="similarity_matrix" file='NxN_Clustering_on_q.txt' ftype="txt"/> </test> </tests> <help> @@ -62,8 +62,7 @@ **What this tool does** -Generating hierarchical clusters and visualizing clusters with dendrograms. -For the clustering and the fingerprint handling the chemfp_ project is used. +Based on a set of fingerprints, generates a square self-similarity (NxN) matrix, as well as a dendrogram visualizing the clusters derived from it using hierarchical clustering. For the clustering and the fingerprint handling the chemfp_ project is used. .. _chemfp: http://chemfp.com/ @@ -73,7 +72,7 @@ **Hint** -The plotting of the cluster image is sensible only with a small dataset. +The plotting of the dendrogram is sensible only with a small dataset - if more than around 20 fingerprints are used the plot will be unreadable. ----- |
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| diff -r e3a7d6cc87af -r 0d88631bb7de sdf2fps.xml --- a/sdf2fps.xml Fri Mar 23 03:26:33 2018 -0400 +++ b/sdf2fps.xml Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,8 +1,8 @@ -<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.2"> - <description>extract fingerprints from sdf files metadata</description> +<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="1.5"> + <description>- extract fingerprints from sdf file metadata</description> <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> <requirements> - <requirement type="package" version="1.1p1">chemfp</requirement> + <requirement type="package" version="1.5">chemfp</requirement> <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> <command> @@ -11,7 +11,7 @@ ]]> </command> <inputs> - <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/> + <param name="infile" type='data' format="sdf" label="SD-file with fingerprints as metadata"/> </inputs> <outputs> <data name="outfile" format="fps"/> @@ -37,7 +37,7 @@ **Input** -`SD-Format`_ +`SD-Format`_, storing the atom types, together with the Cartesian coordinates. .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file @@ -93,6 +93,8 @@ **Output** +After the first few lines, starting with a hash symbol, which contain generic information, the fingerprints are listed as hexadecimal strings. + * Example:: #FPS1 |
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| diff -r e3a7d6cc87af -r 0d88631bb7de test-data/CID_2244_FP2.fps --- a/test-data/CID_2244_FP2.fps Fri Mar 23 03:26:33 2018 -0400 +++ b/test-data/CID_2244_FP2.fps Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,7 +1,7 @@ #FPS1 #num_bits=1021 #type=OpenBabel-FP2/1 -#software=OpenBabel/2.4.1 -#source=/tmp/tmptaAke4/files/000/dataset_3.dat -#date=2017-05-19T13:52:59 +#software=OpenBabel/2.4.1 chemfp/1.5 +#source=CID_2244.sdf +#date=2019-05-03T12:39:13 00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004 2244 |
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| diff -r e3a7d6cc87af -r 0d88631bb7de test-data/CID_2244_FP3.fps --- a/test-data/CID_2244_FP3.fps Fri Mar 23 03:26:33 2018 -0400 +++ b/test-data/CID_2244_FP3.fps Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,7 +1,7 @@ #FPS1 -#num_bits=1021 -#type=OpenBabel-FP2/1 -#software=OpenBabel/2.4.1 -#source=/tmp/tmptaAke4/files/000/dataset_7.dat -#date=2017-05-19T13:53:45 -00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004 2244 +#num_bits=55 +#type=OpenBabel-FP3/1 +#software=OpenBabel/2.4.1 chemfp/1.5 +#source=CID_2244.sdf +#date=2019-05-03T12:39:21 +0400000c50b007 2244 |
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| diff -r e3a7d6cc87af -r 0d88631bb7de test-data/CID_2244_FP4.fps --- a/test-data/CID_2244_FP4.fps Fri Mar 23 03:26:33 2018 -0400 +++ b/test-data/CID_2244_FP4.fps Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,7 +1,7 @@ #FPS1 -#num_bits=1021 -#type=OpenBabel-FP2/1 -#software=OpenBabel/2.4.1 -#source=/tmp/tmptaAke4/files/000/dataset_11.dat -#date=2017-05-19T13:54:39 -00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004 2244 +#num_bits=307 +#type=OpenBabel-FP4/1 +#software=OpenBabel/2.4.1 chemfp/1.5 +#source=CID_2244.sdf +#date=2019-05-03T12:39:27 +010000000000000000009800000000004001000000000000000000000000000000000240402801 2244 |
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| diff -r e3a7d6cc87af -r 0d88631bb7de test-data/CID_2244_MACCS.fps --- a/test-data/CID_2244_MACCS.fps Fri Mar 23 03:26:33 2018 -0400 +++ b/test-data/CID_2244_MACCS.fps Tue May 07 13:32:50 2019 -0400 |
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| @@ -1,7 +1,7 @@ #FPS1 -#num_bits=1021 -#type=OpenBabel-FP2/1 -#software=OpenBabel/2.4.1 -#source=/tmp/tmptaAke4/files/000/dataset_15.dat -#date=2017-05-19T13:55:30 -00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004 2244 +#num_bits=166 +#type=OpenBabel-MACCS/2 +#software=OpenBabel/2.4.1 chemfp/1.5 +#source=CID_2244.sdf +#date=2019-05-03T12:39:49 +0000000000000000000000010000016480cca2d21e 2244 |
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| diff -r e3a7d6cc87af -r 0d88631bb7de test-data/CID_2244_torsions.fps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244_torsions.fps Tue May 07 13:32:50 2019 -0400 |
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| @@ -0,0 +1,7 @@ +#FPS1 +#num_bits=2048 +#type=RDKit-Torsion/2 fpSize=2048 targetSize=4 +#software=RDKit/2018.09.3 chemfp/1.5 +#source=test-data/CID_2244.smi +#date=2019-04-25T15:11:02 +00100010000003000000000000000000000000000000000000000000000000000000000000000000000000000000000300000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000000100000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000010000001000000000000110000000000000000000000000000000000001001000000000000000000001000000000000000000000 2244 |
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| diff -r e3a7d6cc87af -r 0d88631bb7de test-data/NxN_Clustering_on_q.svg --- a/test-data/NxN_Clustering_on_q.svg Fri Mar 23 03:26:33 2018 -0400 +++ b/test-data/NxN_Clustering_on_q.svg Tue May 07 13:32:50 2019 -0400 |
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