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Commit message:
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty |
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modified:
apoc.xml lisica.xml psovina.xml rdock.xml smina.xml |
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added:
acpc.xml test-data/acpc/database.mol2 test-data/acpc/output test-data/acpc/output_mol2reader test-data/acpc/query.mol2 |
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| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 acpc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/acpc.xml Tue Sep 20 09:57:24 2016 -0400 |
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| b'@@ -0,0 +1,282 @@\n+<tool id="acpc" name="ACPC" version="1.0">\n+ <description>Chemoinformatics tool for ligand-based virtual screening</description>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ <![CDATA[ \n+ #if $program_chose.program=="acpc" #\n+ if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then \n+ cat $program_chose.q > query.mol2;\n+ cat $program_chose.db > database.mol2 ;\n+ else\n+ if cat $program_chose.q | grep "BEGIN" > /dev/null; then \n+ cat $program_chose.q > query.pl;\n+ cat $program_chose.db > database.pl ;\n+ else\n+ cat $program_chose.q > query.pqr;\n+ cat $program_chose.db > database.pqr ;\n+ fi;\n+ fi;\n+ acpc \n+ -q query.*\n+ -db database.*\n+ #if $program_chose.top_mol.top_scoring_mol=="true"\n+ -top $program_chose.top_mol.top\n+ -o mol_output\n+ #end if\n+ #if $program_chose.a\n+ -a $program_chose.a\n+ #end if\n+ #if $program_chose.nopp=="true"\n+ -nopp\n+ #end if\n+ #if $program_chose.er\n+ -er $program_chose.er\n+ #end if\n+ #if $program_chose.scan=="true"\n+ -scan scan_out\n+ #end if\n+ -v\n+ ;\n+ cat *.scores > $score_output_acpc;\n+ #if $program_chose.top_mol.top_scoring_mol=="true" #\n+ cat mol_output > $mol_output_acpc;\n+ #end if #\n+ #if $program_chose.scan=="true" #\n+ cat scan_out > $scan_output_acpc;\n+ cat query.mol2.bld > $bld_output_acpc;\n+ #end if #\n+ #end if #\n+ #if $program_chose.program=="acpc_mol2tool" #\n+ cat $program_chose.i > query.mol2;\n+ acpc_mol2tool -i query.mol2;\n+ mkdir results;\n+ mv query_*/* results/. ;\n+ #end if #\n+ #if $program_chose.program=="acpc_par" #\n+ if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then \n+ cat $program_chose.q > query.mol2;\n+ cat $program_chose.db > database.mol2 ;\n+ else\n+ if cat $program_chose.q | grep "BEGIN" > /dev/null; then \n+ cat $program_chose.q > query.pl;\n+ cat $program_chose.db > database.pl ;\n+ else\n+ cat $program_chose.q > query.pqr;\n+ cat $program_chose.db > database.pqr ;\n+ fi;\n+ fi;\n+ acpc_par \n+ -q query.*\n+ -db database.*\n+ -o score\n+ #if $program_chose.a\n+ -a $a\n+ #end if\n+ #if $program_chose.np\n+ -np $np\n+ #end if\n+ ;\n+ cat score > $output_acpc_par;\n+ #end if #\n+ #if $program_chose.program=="acpc_pqrtool" #\n+ cat $program_chose.pqrfile > pqrfile.pqr;\n+ acpc_pqrtool pqrfile.pqr > $output_acpc_pqrtool;\n+ #end if # \n+ #if $program_chose.program=="acpc_mol2reader" #\n+ cat $program_chose.mol2file > mol2file.mol2;\n+ acpc_mol2reader mol2file.mol2 > $output_acpc_mol2reader;\n+ #end if # \n+ #if $program_chose.program=="acpc_auctool" #\n+ cat $program_chose.i > score.scores;\n+ acpc_auctool -i score.scores -p $program_chose.p > $output_acpc_auctool;\n+ #end if #\n+ #if $program_chose.program=="acpc_pltool" #\n+ cat $program_chose.plfile > plfile.pl;\n+ acpc_pltool plfile.pl > $output_acpc_pltool;\n+ #end if #\n+\n+ ]]>\n+ </command>\n+ <inputs>\n+ '..b' <filter>program_chose["scan"]=="true"</filter>\n+ </data>\n+ <data format="txt" name="report">\n+ <filter>program_chose["program"]=="acpc_mol2tool"</filter>\n+ <discover_datasets pattern="([0123456789]*)\\.mol2" directory="results" visible="true" />\n+ </data>\n+ <data name="output_acpc_par" format="txt" label="ACPC: score file">\n+ <filter>program_chose["program"]=="acpc_par" </filter>\n+ </data> \n+ <data name="output_acpc_mol2reader" format="txt" label="ACPC mol2reader output">\n+ <filter>program_chose["program"]=="acpc_mol2reader" </filter>\n+ </data> \n+ <data name="output_acpc_pltool" format="txt" label="ACPC pltool output">\n+ <filter>program_chose["program"]=="acpc_pltool" </filter>\n+ </data> \n+ <data name="output_acpc_auctool" format="txt" label="ACPC auctool output">\n+ <filter>program_chose["program"]=="acpc_auctool" </filter>\n+ </data> \n+ <data name="output_acpc_pqrtool" format="txt" label="ACPC pqrtool output">\n+ <filter>program_chose["program"]=="acpc_pqrtool" </filter>\n+ </data> \n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="program" value="acpc" />\n+ <param name="top_scoring_mol" value="true" />\n+ <param name="q" value="acpc/query.mol2" />\n+ <param name="db" value="acpc/database.mol2" />\n+ <output name="mol_output_acpc" file="acpc/output"/>\n+ </test> \n+ <test>\n+ <param name="program" value="acpc_mol2reader" />\n+ <param name="mol2file" value="acpc/query.mol2" />\n+ <output name="output_acpc_mol2reader" file="acpc/output_mol2reader"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+************\n+Description\n+************\n+ACPC is a ligand-based virtual screening tool using AutoCorrelation of Partial Charges. \n+\n+*******\n+Help\n+*******\n+ \n+ acpc \n+ \n+ --a float kernel parameter (default depends on considered feature space and was optimized on DUD-E)\n+ --db db database in .mol2, .pl or .pqr format\n+ --er x enrichment rate parameter; e.g. 0.01 --> ER_1%\n+ --nopp don\'t rm duplicate molecules (based on names)\n+ --q query query in .mol2, .pl or .pqr format\n+ --scan out_file scan delta AUC per atom in the query and create a new query molecule\n+ --top int number of top scoring molecules to output (only works for MOL2 files)\n+ \n+ \n+ acpc_mol2tool\n+ \n+ --i in input mol2 file\n+ \n+ acpc_auctool\n+ \n+ -i in input scores file\n+ -p x a float such that 0.0 < x <= 1.0 \n+ \n+ \n+ \n+ acpc_par\n+ \n+ --a float kernel parameter (default was optimized on DUD-E and depends on considered feature space)\n+ --db db molecules database in .mol2, .pl or .pqr format\n+ --q query molecule in .mol2, .pl or .pqr format\n+ --np int max number of cores to use\n+ \n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @article{Berenger2014,\n+ doi = {10.1186/1758-2946-6-23},\n+ url = {http://dx.doi.org/10.1186/1758-2946-6-23},\n+ year = {2014},\n+ publisher = {Springer Nature},\n+ volume = {6},\n+ number = {1},\n+ pages = {23},\n+ author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},\n+ title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},\n+ journal = {Journal of Cheminformatics}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 apoc.xml --- a/apoc.xml Wed Sep 14 09:47:48 2016 -0400 +++ b/apoc.xml Tue Sep 20 09:57:24 2016 -0400 |
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| @@ -75,7 +75,7 @@ <when value="list"> <param name="lt" type="data" format="data" label="List of templates to compare in a file" help="(-lt)" /> <repeat name="template" title="pdb file from list of templates"> - <param name="input" type="data" format="pdb" label="pdbfile" help="load all pdb files in the same order as in the list of templates" /> + <param name="input" type="data" format="pdb" label="pdbfile" help="Load all pdb files in the same order as in the list of templates" /> </repeat> </when> </conditional> @@ -91,7 +91,7 @@ <when value="list"> <param name="lq" type="data" format="data" label="List of queries (targets) to compare in a file." help="(-lq)" /> <repeat name="query" title="pdb file from list of queries"> - <param name="input" type="data" format="pdb" label="pdbfile" help="load all pdb files in the same order as in the list of queries" /> + <param name="input" type="data" format="pdb" label="pdbfile" help="Load all pdb files in the same order as in the list of queries" /> </repeat> </when> </conditional> |
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| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 lisica.xml --- a/lisica.xml Wed Sep 14 09:47:48 2016 -0400 +++ b/lisica.xml Tue Sep 20 09:57:24 2016 -0400 |
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| @@ -26,23 +26,23 @@ ]]> </command> <inputs> - <param name="R" type="data" format="mol2" label="reference molecule" help="(-R)" /> - <param name="T" type="data" format="mol2" label="target molecules" help="(-T)" /> - <param name="n" type="integer" label="the number of CPUs to use" help="(-n)" optional="true" /> + <param name="R" type="data" format="mol2" label="Reference molecule" help="(-R)" /> + <param name="T" type="data" format="mol2" label="Target molecules" help="(-T)" /> + <param name="n" type="integer" label="The number of CPUs to use" help="(-n)" optional="true" /> <conditional name="graph_dimension"> - <param name="d" type="select" label="product graph dimension" help="(-d)" > + <param name="d" type="select" label="Product graph dimension" help="(-d)" > <option value="2" selected="true">2</option> <option value="3">3</option> </param> <when value="2"> - <param name="s" type="float" value="1" label="maximum allowed shortest path size for 2D product graph" help="(-s)" /> + <param name="s" type="float" value="1" label="Maximum allowed shortest path size for 2D product graph" help="(-s)" /> </when> <when value="3"> - <param name="m" type="float" value="1" label="maximum allowed atom spatial distance for 3D product graph" help="(-m)" /> + <param name="m" type="float" value="1" label="Maximum allowed atom spatial distance for 3D product graph" help="(-m)" /> </when> </conditional> <!-- <param name="w" type="integer" label="number of highest ranked molecules to write to output" optional="true" help="(-w)" /> --> - <param name="h" type="select" label="consider hydrogens" help="(-h)" > + <param name="h" type="select" label="Consider hydrogens" help="(-h)" > <option value="true" > Use this option </option> @@ -71,7 +71,7 @@ ****** Help ****** - Use: ./lisica -R <path to reference molecule> -T <path to target molecules> [parameters] + Use: ./lisica -R <reference molecule> -T <target molecules> [parameters] **Parameters** |
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| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 psovina.xml --- a/psovina.xml Wed Sep 14 09:47:48 2016 -0400 +++ b/psovina.xml Tue Sep 20 09:57:24 2016 -0400 |
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| @@ -65,17 +65,17 @@ </command> <inputs> <section name="input" title="Input" expanded="True"> - <param name="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/> - <param name="ligand" type="data" format="pdbqt" label="ligand(s)" help="(--ligand)"/> - <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex)"/> + <param name="receptor" type="data" format="pdbqt" label="Rigid part of the receptore" help="(--receptor)"/> + <param name="ligand" type="data" format="pdbqt" label="Ligand(s)" help="(--ligand)"/> + <param name="flex" type="data" format="pdbqt" label="Flexible side chains, if any" optional="true" help="(--flex)"/> </section> <section name="search_space" title="Search space" expanded="True"> <param name="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/> <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/> <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/> - <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/> - <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/> - <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/> + <param name="size_x" type="integer" value="1" label="Size in the X dimension" help="(--size_x)"/> + <param name="size_y" type="integer" value="1" label="Size in the Y dimension" help="(--size_y)"/> + <param name="size_z" type="integer" value="1" label="Size in the Z dimension" help="(--size_z)"/> </section> <section name="pso_parameters" title="PSO parameters" > <param name="num_particles" type="integer" value="8" label="Number of particles of each thread" help="(--num_particles)"/> @@ -90,33 +90,33 @@ </param> </section> <section name="advanced_options" title="Advanced option"> - <param name="score_only" type="select" label="score only - search space can be omitted" help="(--score_only)"> + <param name="score_only" type="select" label="Score only - search space can be omitted" help="(--score_only)"> <option value="false" selected="true">Do not use this option</option> <option value="true">Use this option</option> </param> - <param name="local_only" type="select" label="do local search only" help="(--local_only)"> + <param name="local_only" type="select" label="Do local search only" help="(--local_only)"> <option value="false" selected="true">Do not use this option</option> <option value="true">Use this option</option> </param> - <param name="randomize_only" type="select" label="randomize input, attempting to avoid clashes" help="(--randomize_only)"> + <param name="randomize_only" type="select" label="Randomize input, attempting to avoid clashes" help="(--randomize_only)"> <option value="false" selected="true">Do not use this option</option> <option value="true">Use this option</option> </param> <param name="weight_gauss1" type="float" value="-0.035579" label="gauss_1 weight" help="(--weight_gauss1)"/> <param name="weight_gauss2" type="float" value="-0.005156" label="gauss_2 weight" help="(--weight_gauss2)"/> - <param name="weight_repulsion" type="float" value="0.84024500000000002" label="repulsion weight" help="(--weight_repulsion)"/> - <param name="weight_hydrophobic" type="float" value="-0.035069000000000003" label="hydrophobic weight" help="(--weight_hydrophobic)"/> + <param name="weight_repulsion" type="float" value="0.84024500000000002" label="Repulsion weight" help="(--weight_repulsion)"/> + <param name="weight_hydrophobic" type="float" value="-0.035069000000000003" label="Hydrophobic weight" help="(--weight_hydrophobic)"/> <param name="weight_hydrogen" type="float" value="-0.58743900000000004" label="Hydrogen bond weight" help="(--weight_hydrogen)"/> <param name="weight_rot" type="float" value="0.058459999999999998" label="N_rot weight" help="(--weight_rot)"/> </section> <section name="misc" title="Misc"> - <param name="cpu" type="integer" label="the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)" optional="true" help="(--cpu)"/> - <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/> - <param name="exhaustiveness" type="integer" value="8" label="exhaustiveness of the global search (roughly proportional to time)" help="(--exhaustiveness)"/> - <param name="num_modes" type="integer" value="9" label="exhaustiveness of the global search (roughly proportional to time)" help="(--num_modes)"> + <param name="cpu" type="integer" label="The number of CPUs to use " optional="true" help="(--cpu)"/> + <param name="seed" type="float" label="Explicit random seed" optional="true" help="(--seed)"/> + <param name="exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" help="(--exhaustiveness)"/> + <param name="num_modes" type="integer" value="9" label="Maximum number of binding modes to generate" help="(--num_modes)"> <validator type="in_range" min="1"/> </param> - <param name="energy_range" type="float" value="3" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/> + <param name="energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/> </section> </inputs> <outputs> @@ -180,10 +180,10 @@ --size_z arg size in the Z dimension (Angstroms) **PSO parameters (optional):** - --num_particles arg Number of particles of each thread - --w arg Inertia weight - --c1 arg Cognitive weight - --c2 arg Social weight + --num_particles arg number of particles of each thread + --w arg inertia weight + --c1 arg cognitive weight + --c2 arg social weight **Output (optional):** --log optionally, write log file |
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| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 rdock.xml --- a/rdock.xml Wed Sep 14 09:47:48 2016 -0400 +++ b/rdock.xml Tue Sep 20 09:57:24 2016 -0400 |
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| @@ -13,9 +13,9 @@ ]]> </command> <inputs> - <param name="inputprm" format="prm" type="data" label="receptor param file (contains active site params)" help="(-r)"/> - <param name="inputmol2" format="mol2" type="data" label="input MOL2 file" /> - <param name="inputsd" format="sd" type="data" label="input ligand SD file" help="(-i)"/> + <param name="inputprm" format="prm" type="data" label="Receptor param file (contains active site params)" help="(-r)"/> + <param name="inputmol2" format="mol2" type="data" label="Input MOL2 file" /> + <param name="inputsd" format="sd" type="data" label="Input ligand SD file" help="(-i)"/> </inputs> <outputs> <data name="output_rdock" format="data" /> @@ -53,6 +53,21 @@ ]]> </help> <citations> - <citation type="doi">doi:10.1371/journal.pcbi.1003571</citation> + <citation type="bibtex"> + @article{RuizCarmona2014, + doi = {10.1371/journal.pcbi.1003571}, + url = {http://dx.doi.org/10.1371/journal.pcbi.1003571}, + year = {2014}, + month = {apr}, + publisher = {Public Library of Science ({PLoS})}, + volume = {10}, + number = {4}, + pages = {e1003571}, + author = {Sergio Ruiz-Carmona and Daniel Alvarez-Garcia and Nicolas Foloppe and A. Beatriz Garmendia-Doval and Szilveszter Juhos and Peter Schmidtke and Xavier Barril and Roderick E. Hubbard and S. David Morley}, + editor = {Andreas Prlic}, + title = {{rDock}: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids}, + journal = {{PLoS} Comput Biol} + } + </citation> </citations> </tool> |
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| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 smina.xml --- a/smina.xml Wed Sep 14 09:47:48 2016 -0400 +++ b/smina.xml Tue Sep 20 09:57:24 2016 -0400 |
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| b'@@ -130,24 +130,24 @@\n </command>\n <inputs>\n <section name="input" title="Input" expanded="True">\n- <param name="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/>\n- <param name="ligand" type="data" format="data" label="ligand(s)" help="(--ligand)"/>\n- <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex)"/>\n- <param name="flexres" type="text" label="flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/>\n+ <param name="receptor" type="data" format="pdbqt" label="Rigid part of the receptore" help="(--receptor)"/>\n+ <param name="ligand" type="data" format="data" label="Ligand(s)" help="(--ligand)"/>\n+ <param name="flex" type="data" format="pdbqt" label="Flexible side chains, if any" optional="true" help="(--flex)"/>\n+ <param name="flexres" type="text" label="Flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/>\n <param name="flexdist_ligand" type="data" format="data" label="Ligand to use for flexdist" optional="true" help="(--flexdist_ligand)"/>\n- <param name="flexdist" type="float" label="set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(--flexdist)"/>\n+ <param name="flexdist" type="float" label="Set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(--flexdist)"/>\n </section>\n <section name="search_space" title="Search space" expanded="True">\n <param name="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/>\n <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/>\n <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/>\n- <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/>\n- <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/>\n- <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/>\n+ <param name="size_x" type="integer" value="1" label="Size in the X dimension" help="(--size_x)"/>\n+ <param name="size_y" type="integer" value="1" label="Size in the Y dimension" help="(--size_y)"/>\n+ <param name="size_z" type="integer" value="1" label="Size in the Z dimension" help="(--size_z)"/>\n \n <param name="autobox_ligand" type="data" format="data" label="Ligand to use for autobox" optional="true" help="(--autobox_ligand)"/>\n- <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" help="(--autobox_add)"/>\n- <param name="no_lig" type="select" label="no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" help="(--no_lig)">\n+ <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text" optional="true" help="(--autobox_add)"/>\n+ <param name="no_lig" type="select" label="No ligand; for sampling/minimizing flexible residues " help="(--no_lig)">\n <option value="false" selected="true">Do not use this option</option>\n <option value="true">Use this option</option>\n </param>\n@@ -165,13 +165,13 @@\n <option value="false" selected="true" >No </option>\n <option value="true" >Yes </option>\n </param>\n- <param name="atom_term_data" type="select" label="embedded per-atom interaction terms in output sd data" help="(--atom_term_d'..b"tructures\n- --user_grid arg Autodock map file for user grid data based calculations\n- --user_grid_lambda arg Scales user_grid and functional scoring\n- --print_terms Print all available terms with default parameterizations\n- --print_atom_types Print all available atom types \n-\n- **Output**\n-\n- --out arg output file name, format taken from file extension\n- --out_flex arg output file for flexible receptor residues\n- --atom_terms arg optionally write per-atom interaction term values\n- --atom_term_data embedded per-atom \n- interaction terms in output sd data\n-\n- **Misc**\n-\n- --seed arg explicit random seed\n- --exhaustiveness arg exhaustiveness of the global search (roughly proportional to time)\n- --num_modes arg maximum number of binding modes to generate\n- --energy_range arg maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)\n- --min_rmsd_filter arg rmsd value used to filter final poses to remove redundancy\n- --addH arg automatically add hydrogens \n- in ligands (on by default)\n+ **Scoring and minimization options:**\n+ --scoring arg specify alternative builtin scoring function\n+ --custom_scoring arg custom scoring function file\n+ --custom_atoms arg custom atom type parameters file\n+ --score_only score provided ligand pose\n+ --local_only local search only using autobox (you probably \n+ want to use --minimize)\n+ --minimize energy minimization\n+ --randomize_only generate random poses, attempting to avoid \n+ clashes\n+ --minimize_iters arg number iterations of steepest descent; default \n+ scales with rotors and usually isn't sufficient \n+ for convergence\n+ --accurate_line use accurate line search\n+ --minimize_early_term stop minimization before convergence conditions \n+ are fully met\n+ --approximation arg approximation (linear, spline, or exact) to use\n+ --factor arg approximation factor: higher results in a \n+ finer-grained approximation\n+ --force_cap arg max allowed force; lower values more gently \n+ minimize clashing structures\n+ --user_grid arg Autodock map file for user grid data based \n+ calculations\n+ --user_grid_lambda arg scales user_grid and functional scoring\n+ --print_terms print all available terms with default \n+ parameterizations\n+ --print_atom_types print all available atom types\n+ \n+ **Misc (optional):**\n+ --cpu arg the number of CPUs to use (the default is to try \n+ to detect the number of CPUs or, failing that, use\n+ 1)\n+ --seed arg explicit random seed\n+ --exhaustiveness arg exhaustiveness of the global search (roughly \n+ proportional to time)\n+ --num_modes arg maximum number of binding modes to generate\n+ --energy_range arg maximum energy difference between the best binding\n+ mode and the worst one displayed (kcal/mol)\n+ --min_rmsd_filter arg rmsd value used to filter final poses to remove \n+ redundancy\n+ --addH arg automatically add hydrogens in ligands (on by \n+ default)\n \n ]]>\n </help>\n" |
| b |
| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 test-data/acpc/database.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/acpc/database.mol2 Tue Sep 20 09:57:24 2016 -0400 |
| b |
| b'@@ -0,0 +1,3470729 @@\n+@<TRIPOS>MOLECULE\n+active_ZINC02046793\n+ 49 52 0 0 0\n+SMALL\n+USER_CHARGES\n+\n+@<TRIPOS>ATOM\n+ 1 C1 -1.8261 -7.4561 -3.8870 C.ar 1 <0> -0.1201\n+ 2 C2 -1.7068 -6.5751 -4.9617 C.ar 1 <0> -0.1125\n+ 3 C3 -1.4053 -7.0662 -2.6155 C.ar 1 <0> -0.1112\n+ 4 C4 -1.1666 -5.3042 -4.7651 C.ar 1 <0> -0.1097\n+ 5 C5 -0.8651 -5.7953 -2.4189 C.ar 1 <0> -0.1032\n+ 6 C6 5.7285 -8.7355 -0.5523 C.ar 1 <0> -0.1150\n+ 7 C7 5.9431 -9.0669 0.7886 C.ar 1 <0> -0.0830\n+ 8 C8 4.4094 -7.3331 1.5226 C.ar 1 <0> -0.0493\n+ 9 C9 3.3683 -6.0029 -0.4651 C.2 1 <0> -0.1029\n+ 10 C10 4.1773 -6.9810 0.1781 C.ar 1 <0> -0.1082\n+ 11 C11 -0.7458 -4.9143 -3.4937 C.ar 1 <0> -0.0652\n+ 12 C12 4.8409 -7.6889 -0.8263 C.ar 1 <0> 0.1151\n+ 13 C13 5.2948 -8.3778 1.8116 C.ar 1 <0> -0.0616\n+ 14 C14 3.5532 -6.1333 -1.8223 C.2 1 <0> 0.0308\n+ 15 C15 2.9564 -5.3743 -2.8753 C.2 1 <0> 0.5835\n+ 16 C16 2.8342 0.3789 -6.9868 C.2 1 <0> 0.4750\n+ 17 C17 1.8963 -2.1307 -3.2071 C.2 1 <0> 0.5363\n+ 18 C18 2.4815 0.0118 -4.4865 C.3 1 <0> 0.1180\n+ 19 C19 1.7793 -1.5779 -5.7345 C.3 1 <0> 0.1228\n+ 20 C20 1.9079 -0.0595 -5.9067 C.3 1 <0> -0.1629\n+ 21 C21 -0.1611 -3.5397 -3.2803 C.3 1 <0> -0.0921\n+ 22 C22 1.3546 -3.5105 -3.4688 C.3 1 <0> 0.1432\n+ 23 N1 4.4429 -7.1529 -2.0303 N.pl3 1 <0> -0.5743\n+ 24 N2 2.0145 -1.3502 -4.3231 N.am 1 <0> -0.6374\n+ 25 N3 2.0542 -4.3480 -2.5212 N.am 1 <0> -0.7098\n+ 26 O1 2.7950 -0.3106 -8.0434 O.co2 1 <0> -0.7582\n+ 27 O2 3.2044 -5.6185 -4.0832 O.2 1 <0> -0.4955\n+ 28 O3 3.5401 1.3869 -6.7025 O.co2 1 <0> -0.6306\n+ 29 O4 2.1947 -1.7632 -2.0718 O.2 1 <0> -0.5509\n+ 30 Cl1 5.5839 -8.8166 3.4525 Cl 1 <0> -0.0744\n+ 31 H1 -2.2480 -8.4452 -4.0400 H 1 <0> 0.1150\n+ 32 H2 -2.0354 -6.8781 -5.9516 H 1 <0> 0.1135\n+ 33 H3 -1.4991 -7.7515 -1.7783 H 1 <0> 0.1179\n+ 34 H4 -1.0773 -4.6245 -5.6085 H 1 <0> 0.1072\n+ 35 H5 -0.5398 -5.5003 -1.4248 H 1 <0> 0.1197\n+ 36 H6 6.2345 -9.2723 -1.3479 H 1 <0> 0.1333\n+ 37 H7 6.6305 -9.8777 1.0204 H 1 <0> 0.1378\n+ 38 H8 3.9034 -6.7944 2.3195 H 1 <0> 0.1365\n+ 39 H9 2.7211 -5.2825 0.0173 H 1 <0> 0.1593\n+ 40 H10 3.5691 0.0934 -4.4016 H 1 <0> 0.0793\n+ 41 H11 1.9931 0.7303 -3.8234 H 1 <0> 0.0912\n+ 42 H12 0.7914 -1.9854 -5.9640 H 1 <0> 0.1001\n+ 43 H13 2.5604 -2.1896 -6.1959 H 1 <0> 0.0721\n+ 44 H14 0.9341 0.4391 -5.9940 H 1 <0> 0.1029\n+ 45 H15 -0.6398 -2.8443 -3.9830 H 1 <0> 0.0800\n+ 46 H16 -0.4339 -3.1741 -2.2808 H 1 <0> 0.0939\n+ 47 H17 1.6531 -3.8196 -4.4755 H 1 <0> 0.1191\n+ 48 H18 4.7636 -7.4691 -2.9353 H 1 <0> 0.4214\n+ 49 H19 1.8298 -4.2214 -1.5397 H 1 <0> 0.40'..b'<0> 0.1048\n+ 25 H8 3.8814 -0.1681 -0.6921 H 1 <0> 0.1057\n+ 26 H9 5.3921 1.1188 -5.8677 H 1 <0> 0.1283\n+ 27 H10 4.5563 -0.2052 -5.0266 H 1 <0> 0.1240\n+ 28 H11 -1.1056 -0.5800 0.0958 H 1 <0> 0.2790\n+ 29 H12 -0.6090 0.3195 -1.2998 H 1 <0> 0.2282\n+@<TRIPOS>BOND\n+ 1 1 8 1\n+ 2 1 9 3\n+ 3 2 8 1\n+ 4 2 11 am\n+ 5 2 16 2\n+ 6 3 10 2\n+ 7 3 12 1\n+ 8 3 13 1\n+ 9 4 6 1\n+ 10 4 11 1\n+ 11 5 7 1\n+ 12 5 11 1\n+ 13 6 12 1\n+ 14 7 12 1\n+ 15 10 14 1\n+ 16 14 15 1\n+ 17 14 17 2\n+ 18 4 18 1\n+ 19 4 19 1\n+ 20 5 20 1\n+ 21 5 21 1\n+ 22 6 22 1\n+ 23 6 23 1\n+ 24 7 24 1\n+ 25 7 25 1\n+ 26 8 26 1\n+ 27 8 27 1\n+ 28 13 28 1\n+ 29 13 29 1\n+@<TRIPOS>MOLECULE\n+ZINC04402625\n+ 29 29 0 0 0\n+SMALL\n+USER_CHARGES\n+\n+@<TRIPOS>ATOM\n+ 1 C1 -4.4762 3.8455 -5.5906 C.1 1 <0> -0.1344\n+ 2 C2 -3.2397 1.9533 -4.7230 C.2 1 <0> 0.3074\n+ 3 C3 0.3527 0.6437 -0.8128 C.2 1 <0> 0.3429\n+ 4 C4 -2.8212 1.0984 -2.4364 C.3 1 <0> -0.0276\n+ 5 C5 -1.1328 2.5939 -3.4452 C.3 1 <0> -0.0319\n+ 6 C6 -1.7223 0.1239 -2.0249 C.3 1 <0> -0.0269\n+ 7 C7 -0.0262 1.6256 -3.0350 C.3 1 <0> -0.0353\n+ 8 C8 -3.1625 3.2171 -5.5415 C.3 1 <0> -0.0889\n+ 9 N1 -5.5158 4.3587 -5.6395 N.1 1 <0> -0.0069\n+ 10 N2 1.1860 1.5058 -0.2851 N.2 1 <0> -0.3821\n+ 11 N3 -2.4102 1.8831 -3.6052 N.am 1 <0> -0.3573\n+ 12 N4 -0.4433 0.8139 -1.8968 N.pl3 1 <0> -0.2842\n+ 13 N5 0.2075 -0.6082 -0.2620 N.pl3 1 <0> -0.4109\n+ 14 N6 1.8676 1.0853 0.8033 N.pl3 1 <0> 0.6256\n+ 15 O1 2.9626 0.5252 0.6386 O.3 1 <0> -0.3533\n+ 16 O2 -4.0118 1.0557 -5.0694 O.2 1 <0> -0.3335\n+ 17 O3 1.3855 1.3017 1.9261 O.2 1 <0> -0.4832\n+ 18 H1 -3.7498 0.5543 -2.6339 H 1 <0> 0.1439\n+ 19 H2 -3.0206 1.8120 -1.6278 H 1 <0> 0.1024\n+ 20 H3 -1.2876 3.3462 -2.6624 H 1 <0> 0.1037\n+ 21 H4 -0.8388 3.1233 -4.3531 H 1 <0> 0.1028\n+ 22 H5 -2.0082 -0.3623 -1.0851 H 1 <0> 0.1557\n+ 23 H6 -1.6209 -0.6650 -2.7801 H 1 <0> 0.1021\n+ 24 H7 0.2140 0.9585 -3.8719 H 1 <0> 0.1048\n+ 25 H8 0.8811 2.1962 -2.8049 H 1 <0> 0.1057\n+ 26 H9 -2.4283 3.8666 -5.0689 H 1 <0> 0.1283\n+ 27 H10 -2.8165 2.9405 -6.5354 H 1 <0> 0.1240\n+ 28 H11 0.7389 -0.8852 0.5563 H 1 <0> 0.2790\n+ 29 H12 -0.4318 -1.2897 -0.6558 H 1 <0> 0.2282\n+@<TRIPOS>BOND\n+ 1 1 8 1\n+ 2 1 9 3\n+ 3 2 8 1\n+ 4 2 11 am\n+ 5 2 16 2\n+ 6 3 10 2\n+ 7 3 12 1\n+ 8 3 13 1\n+ 9 4 6 1\n+ 10 4 11 1\n+ 11 5 7 1\n+ 12 5 11 1\n+ 13 6 12 1\n+ 14 7 12 1\n+ 15 10 14 1\n+ 16 14 15 1\n+ 17 14 17 2\n+ 18 4 18 1\n+ 19 4 19 1\n+ 20 5 20 1\n+ 21 5 21 1\n+ 22 6 22 1\n+ 23 6 23 1\n+ 24 7 24 1\n+ 25 7 25 1\n+ 26 8 26 1\n+ 27 8 27 1\n+ 28 13 28 1\n+ 29 13 29 1\n' |
| b |
| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 test-data/acpc/output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/acpc/output Tue Sep 20 09:57:24 2016 -0400 |
| b |
| @@ -0,0 +1,81 @@ +@<TRIPOS>MOLECULE +ZINC01061693 + 36 37 0 0 0 +SMALL +USER_CHARGES + +@<TRIPOS>ATOM + 1 C1 -6.6174 -0.3366 -0.5185 C.ar 1 <0> -0.1734 + 2 C2 -5.9327 -1.7841 1.2906 C.ar 1 <0> -0.2498 + 3 C3 -5.2939 -0.2503 -0.9505 C.ar 1 <0> 0.0056 + 4 C4 -4.6092 -1.6980 0.8586 C.ar 1 <0> 0.0108 + 5 C5 -6.9367 -1.1034 0.6020 C.ar 1 <0> 0.1473 + 6 C6 -4.2898 -0.9310 -0.2620 C.ar 1 <0> -0.8000 + 7 C7 -9.6333 0.3738 -0.1361 C.2 1 <0> 0.3013 + 8 C8 -2.8453 1.8064 -0.1748 C.3 1 <0> -0.0347 + 9 C9 -1.9196 0.3199 1.5529 C.3 1 <0> -0.0345 + 10 C10 -2.1110 2.9584 0.4965 C.3 1 <0> -0.0308 + 11 C11 -1.2245 1.5346 2.1518 C.3 1 <0> -0.0304 + 12 C12 -9.2445 -1.0765 0.0281 C.3 1 <0> -0.0412 + 13 N1 -2.0965 0.5426 0.0880 N.pl3 1 <0> -0.8414 + 14 N2 -10.6107 0.5501 -1.0909 N.am 1 <0> -0.4309 + 15 O1 -9.1318 1.2895 0.5096 O.2 1 <0> -0.3284 + 16 O2 -1.9156 -1.9949 -0.3294 O.2 1 <0> -0.9157 + 17 O3 -2.6261 -0.4828 -2.2153 O.2 1 <0> -0.9133 + 18 O4 -1.9868 2.7171 1.8998 O.3 1 <0> -0.2701 + 19 O5 -8.2283 -1.1880 1.0234 O.3 1 <0> -0.1715 + 20 S1 -2.6145 -0.8213 -0.8081 S.o2 1 <0> 2.7667 + 21 H1 -7.3954 0.1954 -1.0594 H 1 <0> 0.1566 + 22 H2 -6.1753 -2.3830 2.1641 H 1 <0> 0.1354 + 23 H3 -5.0563 0.3499 -1.8245 H 1 <0> 0.1540 + 24 H4 -3.8346 -2.2319 1.4024 H 1 <0> 0.1483 + 25 H5 -3.8589 1.7103 0.2314 H 1 <0> 0.1027 + 26 H6 -2.9049 1.9859 -1.2529 H 1 <0> 0.1097 + 27 H7 -1.3105 -0.5736 1.7223 H 1 <0> 0.1077 + 28 H8 -2.9045 0.1776 2.0125 H 1 <0> 0.1026 + 29 H9 -1.1140 3.1068 0.0645 H 1 <0> 0.0711 + 30 H10 -2.6737 3.8880 0.3655 H 1 <0> 0.1156 + 31 H11 -1.1367 1.4184 3.2365 H 1 <0> 0.0692 + 32 H12 -0.2139 1.6614 1.7456 H 1 <0> 0.1145 + 33 H13 -8.8621 -1.4621 -0.9219 H 1 <0> 0.0976 + 34 H14 -10.1191 -1.6557 0.3398 H 1 <0> 0.0949 + 35 H15 -10.9936 -0.2408 -1.5983 H 1 <0> 0.2141 + 36 H16 -10.9844 1.4651 -1.3226 H 1 <0> 0.2404 +@<TRIPOS>BOND + 1 1 3 ar + 2 1 5 ar + 3 2 4 ar + 4 2 5 ar + 5 3 6 ar + 6 4 6 ar + 7 5 19 1 + 8 6 20 1 + 9 7 12 1 + 10 7 14 am + 11 7 15 2 + 12 8 10 1 + 13 8 13 1 + 14 9 11 1 + 15 9 13 1 + 16 10 18 1 + 17 11 18 1 + 18 12 19 1 + 19 13 20 1 + 20 16 20 2 + 21 17 20 2 + 22 1 21 1 + 23 2 22 1 + 24 3 23 1 + 25 4 24 1 + 26 8 25 1 + 27 8 26 1 + 28 9 27 1 + 29 9 28 1 + 30 10 29 1 + 31 10 30 1 + 32 11 31 1 + 33 11 32 1 + 34 12 33 1 + 35 12 34 1 + 36 14 35 1 + 37 14 36 1 |
| b |
| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 test-data/acpc/output_mol2reader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/acpc/output_mol2reader Tue Sep 20 09:57:24 2016 -0400 |
| b |
| @@ -0,0 +1,37 @@ +ZINC01061693 0 +-6.617400 -0.336600 -0.518500 -0.173400 +-5.932700 -1.784100 1.290600 -0.249800 +-5.293900 -0.250300 -0.950500 0.005600 +-4.609200 -1.698000 0.858600 0.010800 +-6.936700 -1.103400 0.602000 0.147300 +-4.289800 -0.931000 -0.262000 -0.800000 +-9.633300 0.373800 -0.136100 0.301300 +-2.845300 1.806400 -0.174800 -0.034700 +-1.919600 0.319900 1.552900 -0.034500 +-2.111000 2.958400 0.496500 -0.030800 +-1.224500 1.534600 2.151800 -0.030400 +-9.244500 -1.076500 0.028100 -0.041200 +-2.096500 0.542600 0.088000 -0.841400 +-10.610700 0.550100 -1.090900 -0.430900 +-9.131800 1.289500 0.509600 -0.328400 +-1.915600 -1.994900 -0.329400 -0.915700 +-2.626100 -0.482800 -2.215300 -0.913300 +-1.986800 2.717100 1.899800 -0.270100 +-8.228300 -1.188000 1.023400 -0.171500 +-2.614500 -0.821300 -0.808100 2.766700 +-7.395400 0.195400 -1.059400 0.156600 +-6.175300 -2.383000 2.164100 0.135400 +-5.056300 0.349900 -1.824500 0.154000 +-3.834600 -2.231900 1.402400 0.148300 +-3.858900 1.710300 0.231400 0.102700 +-2.904900 1.985900 -1.252900 0.109700 +-1.310500 -0.573600 1.722300 0.107700 +-2.904500 0.177600 2.012500 0.102600 +-1.114000 3.106800 0.064500 0.071100 +-2.673700 3.888000 0.365500 0.115600 +-1.136700 1.418400 3.236500 0.069200 +-0.213900 1.661400 1.745600 0.114500 +-8.862100 -1.462100 -0.921900 0.097600 +-10.119100 -1.655700 0.339800 0.094900 +-10.993600 -0.240800 -1.598300 0.214100 +-10.984400 1.465100 -1.322600 0.240400 |
| b |
| diff -r 958fa7ba4715 -r 8c2e85bb2ce9 test-data/acpc/query.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/acpc/query.mol2 Tue Sep 20 09:57:24 2016 -0400 |
| b |
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