# HG changeset patch # User bgruening # Date 1368306754 14400 # Node ID 18617b9fc70ee4a50ef4a36b403fe7132a74fdb6 # Parent d241ff83e485497312a927a3bef42b69ff2ac3e5 Uploaded diff -r d241ff83e485 -r 18617b9fc70e chemfp_mol2fps/mol2fps.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chemfp_mol2fps/mol2fps.xml Sat May 11 17:12:34 2013 -0400 @@ -0,0 +1,239 @@ + + with different fingerprint types + + + chemfp + rdkit + + + #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']: + ## Open Babel fingerprints + ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1 + #else: + ## RDKit fingerprints + rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}" + #if $fp_opts.fp_opts_selector=="--RDK": + --RDK + --fpSize $fp_opts.fpSize + --minPath $fp_opts.minPath + --maxPath $fp_opts.maxPath + --nBitsPerHash $fp_opts.nBitsPerHash + $fp_opts.useHs + #elif $fp_opts.fp_opts_selector=="--torsions": + --torsions + --fpSize $fp_opts.fpSize + --targetSize $fp_opts.targetSize + #elif $fp_opts.fp_opts_selector=="--morgan": + --morgan + --fpSize $fp_opts.fpSize + --radius $fp_opts.radius + $fp_opts.useFeatures + $fp_opts.useChirality + $fp_opts.useBondTypes + #elif $fp_opts.fp_opts_selector=="--pairs": + --paris + --fpSize $fp_opts.fpSize + --minLength $fp_opts.minLength + --maxLength $fp_opts.maxLength + #elif $fp_opts.fp_opts_selector=="--maccs166": + --maccs166 + #elif $fp_opts.fp_opts_selector=="--substruct": + --substruct + #endif + --errors report 2>&1 + #endif + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Generate fingerprints using OpenBabel + +----- + +**Example** + +* input:: + + - SDF File + + 28434379 + -OEChem-02031205132D + + 37 39 0 0 0 0 0 0 0999 V2000 + 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3704 0.9433 0.0000 C 0 0 0 0 + ...... + 1 15 1 0 0 0 0 + 1 35 1 0 0 0 0 + 2 5 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 12 1 0 0 0 0 + 3 12 2 0 0 0 0 + 3 13 1 0 0 0 0 + 4 18 1 0 0 0 0 + ...... + + >PUBCHEM_COMPOUND_CID< + 28434379 + + > <PUBCHEM_COMPOUND_CANONICALIZED> + 1 + + > <PUBCHEM_CACTVS_COMPLEXITY> + 280 + + > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> + 2 + + > <PUBCHEM_CACTVS_HBOND_DONOR> + 2 + + > <PUBCHEM_CACTVS_ROTATABLE_BOND> + 2 + + > <PUBCHEM_CACTVS_SUBSKEYS> + AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== + + > + + - type : FP2 + +* output:: + + #FPS1 + #num_bits=1021 + #type=OpenBabel-FP2/1 + #software=OpenBabel/2.3.0 + #source=/tmp/dataset_409.dat.sdf + #date=2012-02-03T11:13:39 + c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c + 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300 + 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379 + + + + diff -r d241ff83e485 -r 18617b9fc70e chemfp_mol2fps/ob2fps.xml --- a/chemfp_mol2fps/ob2fps.xml Fri Apr 26 11:07:08 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,239 +0,0 @@ - - with different fingerprint types - - - chemfp - rdkit - - - #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']: - ## Open Babel fingerprints - ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1 - #else: - ## RDKit fingerprints - rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}" - #if $fp_opts.fp_opts_selector=="--RDK": - --RDK - --fpSize $fp_opts.fpSize - --minPath $fp_opts.minPath - --maxPath $fp_opts.maxPath - --nBitsPerHash $fp_opts.nBitsPerHash - $fp_opts.useHs - #elif $fp_opts.fp_opts_selector=="--torsions": - --torsions - --fpSize $fp_opts.fpSize - --targetSize $fp_opts.targetSize - #elif $fp_opts.fp_opts_selector=="--morgan": - --morgan - --fpSize $fp_opts.fpSize - --radius $fp_opts.radius - $fp_opts.useFeatures - $fp_opts.useChirality - $fp_opts.useBondTypes - #elif $fp_opts.fp_opts_selector=="--pairs": - --paris - --fpSize $fp_opts.fpSize - --minLength $fp_opts.minLength - --maxLength $fp_opts.maxLength - #elif $fp_opts.fp_opts_selector=="--maccs166": - --maccs166 - #elif $fp_opts.fp_opts_selector=="--substruct": - --substruct - #endif - --errors report 2>&1 - #endif - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -Generate fingerprints using OpenBabel - ------ - -**Example** - -* input:: - - - SDF File - - 28434379 - -OEChem-02031205132D - - 37 39 0 0 0 0 0 0 0999 V2000 - 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.3704 0.9433 0.0000 C 0 0 0 0 - ...... - 1 15 1 0 0 0 0 - 1 35 1 0 0 0 0 - 2 5 1 0 0 0 0 - 2 11 1 0 0 0 0 - 2 12 1 0 0 0 0 - 3 12 2 0 0 0 0 - 3 13 1 0 0 0 0 - 4 18 1 0 0 0 0 - ...... - - >PUBCHEM_COMPOUND_CID< - 28434379 - - > <PUBCHEM_COMPOUND_CANONICALIZED> - 1 - - > <PUBCHEM_CACTVS_COMPLEXITY> - 280 - - > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> - 2 - - > <PUBCHEM_CACTVS_HBOND_DONOR> - 2 - - > <PUBCHEM_CACTVS_ROTATABLE_BOND> - 2 - - > <PUBCHEM_CACTVS_SUBSKEYS> - AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== - - > - - - type : FP2 - -* output:: - - #FPS1 - #num_bits=1021 - #type=OpenBabel-FP2/1 - #software=OpenBabel/2.3.0 - #source=/tmp/dataset_409.dat.sdf - #date=2012-02-03T11:13:39 - c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c - 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300 - 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379 - - - - diff -r d241ff83e485 -r 18617b9fc70e repository_dependencies.xml --- a/repository_dependencies.xml Fri Apr 26 11:07:08 2013 -0400 +++ b/repository_dependencies.xml Sat May 11 17:12:34 2013 -0400 @@ -1,5 +1,5 @@ - - + + diff -r d241ff83e485 -r 18617b9fc70e tool_dependencies.xml --- a/tool_dependencies.xml Fri Apr 26 11:07:08 2013 -0400 +++ b/tool_dependencies.xml Sat May 11 17:12:34 2013 -0400 @@ -1,12 +1,12 @@ - + - + - +