| Previous changeset 2:4fb73be7f4cb (2020-07-28) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9" |
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modified:
fpocket.xml test-data/2brc.pdb test-data/2brc_info.txt test-data/custom_pockets.pqr test-data/pocket1_atm.pdb test-data/pocket2_vert.pqr |
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added:
dpocket.xml macros.xml test-data/1L83.pdb test-data/ligs.txt test-data/ligs2.txt |
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| diff -r 4fb73be7f4cb -r 4cc9d85c3bae dpocket.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dpocket.xml Fri Sep 10 08:20:08 2021 +0000 |
| [ |
| b'@@ -0,0 +1,183 @@\n+<tool id="dpocket" name="dpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n+ <description>to calculate descriptors for protein pockets</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <token name="@GALAXY_VERSION@">0</token>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ ## create config file\n+ #for i in $input:\n+ ln -s \'$i\' $i.name.replace(\' \', \'_\') &&\n+ echo $i.name.replace(\' \', \'_\') >> pdbs.txt &&\n+ #end for\n+ paste pdbs.txt \'$ligs\' > dp_conf.txt &&\n+\n+ ## run dpocket\n+ dpocket\n+ -f dp_conf.txt\n+\n+ ## pocket definition params common with fpocket\n+ #if $inp.pocket_type == \'channel\':\n+ --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30\n+ #elif $inp.pocket_type == \'external\':\n+ --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30\n+ #elif $inp.pocket_type == \'custom\':\n+ --min_alpha_size \'$inp.min\'\n+ --max_alpha_size \'$inp.max\'\n+ --min_spheres_per_pocket \'$inp.i\'\n+ --clustering_distance \'$inp.D\'\n+ --clustering_method \'$inp.C\'\n+ ##--clustering_measure $inp.e\n+ #end if\n+\n+ ## specific params for explicit pocket definition\n+ #if $explicit_output.output == "true":\n+ $explicit_output.interface_definition\n+ -d $explicit_output.dist\n+ #end if\n+\n+ &&\n+ ## reformat output files to match Galaxy tabular\n+ sed -e "s/\\s\\+/\\t/g" dpout_fpocketp.txt > $fpocketp &&\n+ sed -e "s/\\s\\+/\\t/g" dpout_fpocketnp.txt > $fpocketnp\n+ #if $explicit_output.output:\n+ &&\n+ sed -e "s/\\s\\+/\\t/g" dpout_explicitp.txt > $explicitp\n+ #end if\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="pdb" multiple="true" label="Input file" help="Protein structure file(s) (PDB) to search."/>\n+ <param name="ligs" type="data" format="txt" label="Ligand codes" help="List of ligand codes (as provided in the PDB files), one per line. The number of codes must match the number of input PDB files."/>\n+ <expand macro="inputs" />\n+ <!-- <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">\n+ <option value="fpocketp" selected="true">Pockets which match the ligand position</option>\n+ <option value="fpocketnp">Pockets which do NOT match the ligand position</option>\n+ <option value="explicitp">Define pocket explicitly as all vertices/atoms within a given distance from the ligand, regardless of what fpocket found. </option>\n+ </param> -->\n+ <conditional name="explicit_output">\n+ <param name="output" type="select" label="Calculate explicit pocket?" help="Define pocket explicitly as all vertices/atoms within a given distance from the ligand, regardless of what fpocket found.">\n+ <option value="true" selected="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\n+ <when value="false" />\n+ <when value="true">\n+ <param name="interface_definition" type="select" label="Definition of the explicit pocket" help="Protein-ligand explicit interface definition">\n+ <option value="-e" selected="true">All atoms in contact with alpha spheres within a distance threshold from any ligand atom</option>\n+ <option value="-E">All atoms within a distance threshold from any ligand atom</option>\n+ </param>\n+ <param name="dist" type="float" value="4.0" min="0" label="Distance threshold for explicit pocket definition (angstroms)" />\n+ </when>\n+\n+ </conditional>\n+ </inputs>\n+\n'..b's+0.77\\s+1.00\\s+1\\s+1.54"/>\n+ <has_text_matching expression="6.50\\s+0.96\\s+0.44\\s+14.39\\s+23.64\\s+12.20\\s+42.27\\s+15.29\\s+2\\s+1\\s+0\\s+2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="fpocketnp" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="57" />\n+ <has_n_lines n="2" />\n+ <has_text_matching expression="2brc.pdb\\s+CT5\\s+0.00\\s+0\\s+17.62\\s+0.00\\s+0.00\\s+0\\s+-1.25"/>\n+ <has_text_matching expression="4.36\\s+0.69\\s+0.00\\s+4.37\\s+31.43\\s+42.10\\s+33.81\\s+17.20\\s+5\\s+0\\s+1\\s+1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="explicitp" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="57" />\n+ <has_n_lines n="2" />\n+ <has_text_matching expression="2brc.pdb\\s+CT5\\s+100.00\\s+1\\s+0.00\\s+1.00\\s+1.00\\s+1\\s+2.00"/>\n+ <has_text_matching expression="11.97\\s+0.00\\s+0.00\\s+107.35\\s+56.94\\s+61.01\\s+57.97\\s+34.40\\s+3\\s+2\\s+0\\s+2"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="input" ftype="pdb" value="2brc.pdb,1L83.pdb"/>\n+ <param name="ligs" ftype="txt" value="ligs2.txt"/>\n+ <param name=\'pocket_type\' value=\'small_mol\' />\n+ <param name=\'explicit_output\' value=\'false\' />\n+ <output name="fpocketp" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="57" />\n+ <has_n_lines n="3" />\n+ <has_text_matching expression="2brc.pdb\\s+CT5\\s+38.60\\s+1\\s+0.54\\s+0.46\\s+0.80\\s+0\\s+0.67"/>\n+ <has_text_matching expression="1L83.pdb\\s+BNZ\\s+100.00\\s+1\\s+0.83\\s+1.00\\s+0.85\\s+1\\s+1.81"/>\n+ </assert_contents>\n+ </output>\n+ <output name="fpocketnp" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="57" />\n+ <has_n_lines n="19" />\n+ <has_text_matching expression="2brc.pdb\\s+CT5\\s+0.00\\s+0\\s+17.15\\s+0.00\\s+0.00\\s+0\\s+-1.25"/>\n+ <has_text_matching expression="29.17\\s+4.03\\s+0.65\\s+11.05\\s+0.65\\s+0.14\\s+13.17\\s+29.13\\s+19.24"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+Calculate descriptors (i.e. featurize) \'pockets\' in a protein structure, using the\n+dpocket module of the fpocket software.\n+\n+To use, upload one or more protein structures in PDB format and select the type of pocket to \n+detect. \'Custom options\' can also be selected - this exposes all internal fpocket \n+parameters. Using this option requires some knowledge of the fpocket prediction \n+algorithm. Please consult the cited publications for more details.\n+\n+In addition, a list of ligand identifiers should be provided as a text file, one per line and\n+one for each of the protein structures.\n+\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+- One or more protein structures in PDB format. If using multiple structures, submitting them as a dataset collection is recommended to ensure ordering is preserved.\n+- Text file with ligand identifiers, matching the ligand code in the PDB files. One identifier should be listed per line and one per PDB file. \n+\n+-----\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+- Tabular file with descriptors of pockets matching the positions of the input ligands.\n+- Tabular file with descriptors of pockets which do NOT match the positions of the input ligands.\n+- (Optional) Tabular file with descriptors of pockets which are explicitly defined by the positions of the input ligands.\n+\n+Each tabular file contains 57 columns (55 descriptors, plus protein and ligand names), a header line, and\n+one row per pocket found.\n+\n+]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 4fb73be7f4cb -r 4cc9d85c3bae fpocket.xml --- a/fpocket.xml Tue Jul 28 08:29:23 2020 -0400 +++ b/fpocket.xml Fri Sep 10 08:20:08 2021 +0000 |
| [ |
| @@ -1,55 +1,32 @@ <tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>- find potential binding sites in protein structures</description> <macros> - <token name="@TOOL_VERSION@">3.1.4.2</token> + <import>macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> - <description>- find potential binding sites in protein structures</description> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement> - </requirements> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$input' ./input.pdb && fpocket -f ./input.pdb #if $inp.pocket_type == 'channel': - -m 2.8 -M 5.5 -i 30 + --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30 #elif $inp.pocket_type == 'external': - -m 3.5 -M 10 -i 30 + --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30 #elif $inp.pocket_type == 'custom': - -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $inp.e + --min_alpha_size $inp.min + --max_alpha_size $inp.max + --min_spheres_per_pocket $inp.i + --clustering_distance $inp.D + --clustering_method $inp.C + --clustering_measure $inp.e #end if ]]></command> <inputs> <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/> - <conditional name="inp"> - <param name="pocket_type" type="select" label="Type of pocket to detect" help="Search for different kinds of pockets - or select 'custom' for more fine-grained control"> - <option value="small_mol">Small molecule binding sites</option> - <option value="channel">Putative channels and small cavities</option> - <option value="external">Large, external pockets</option> - <option value="custom">Custom options (advanced)</option> - </param> - <when value="custom"> - <param name="min" type="float" value="3" min="0" max="10" label="Minimum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/> - <param name="max" type="float" value="6" min="0" max="10" label="Maximum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/> - <param name="i" type="integer" value="35" min="20" max="50" label="Minimum number of alpha spheres a pocket must contain" help="Below this threshold pockets will not be listed in results"/> - <param name="D" type="float" value="2.4" min="0" max="10" label="Distance threshold for clustering algorithm (angstroms)" help="Alpha spheres may be clustered if they are separated by less than this distance"/> - <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres"> - <option value="s">Single linkage clustering</option> - <option value="m">Complete linkage clustering</option> - <option value="a">Average linkage clustering</option> - <option value="c">Centroid linkage clustering</option> - </param> - <param name="e" type="select" value="e" label="Distance measure for clustering"> - <option value="e">Euclidean distance</option> - <option value="b">Manhattan distance</option> - </param> - </when> - <when value="small_mol"/> - <when value="channel"/> - <when value="external"/> - </conditional> + <expand macro="inputs" /> <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files"> <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option> <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option> @@ -84,8 +61,8 @@ <test> <param name="input" ftype="pdb" value="2brc.pdb"/> <param name='pocket_type' value='custom' /> - <param name="min" value="4.0"/> - <param name="max" value="7.0"/> + <param name="min" value="1.0"/> + <param name="max" value="3.0"/> <param name="i" value="20" /> <param name="D" value="2.0"/> <param name="C" value="c" /> @@ -145,8 +122,5 @@ - A text file listing properties of all pockets detected. ]]></help> - <citations> - <citation type="doi">10.1186/1471-2105-10-168</citation> - <citation type="doi">10.1093/nar/gkq383</citation> - </citations> + <expand macro="citations" /> </tool> |
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| diff -r 4fb73be7f4cb -r 4cc9d85c3bae macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 10 08:20:08 2021 +0000 |
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| @@ -0,0 +1,43 @@ +<macros> + <token name="@TOOL_VERSION@">4.0.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement> + </requirements> + </xml> + <xml name="inputs"> + <conditional name="inp"> + <param name="pocket_type" type="select" label="Type of pocket to detect" help="Search for different kinds of pockets - or select 'custom' for more fine-grained control"> + <option value="small_mol">Small molecule binding sites</option> + <option value="channel">Putative channels and small cavities</option> + <option value="external">Large, external pockets</option> + <option value="custom">Custom options (advanced)</option> + </param> + <when value="custom"> + <param name="min" type="float" value="3" min="0" max="10" label="Minimum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/> + <param name="max" type="float" value="6" min="0" max="10" label="Maximum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/> + <param name="i" type="integer" value="35" min="20" max="50" label="Minimum number of alpha spheres a pocket must contain" help="Below this threshold pockets will not be listed in results"/> + <param name="D" type="float" value="2.4" min="0" max="10" label="Distance threshold for clustering algorithm (angstroms)" help="Alpha spheres may be clustered if they are separated by less than this distance"/> + <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres"> + <option value="s">Single linkage clustering</option> + <option value="m">Complete linkage clustering</option> + <option value="a">Average linkage clustering</option> + <option value="c">Centroid linkage clustering</option> + </param> + <param name="e" type="select" value="e" label="Distance measure for clustering"> + <option value="e">Euclidean distance</option> + <option value="b">Manhattan distance</option> + </param> + </when> + <when value="small_mol"/> + <when value="channel"/> + <when value="external"/> + </conditional> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/1471-2105-10-168</citation> + <citation type="doi">10.1093/nar/gkq383</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/1L83.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1L83.pdb Fri Sep 10 08:20:08 2021 +0000 |
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| b'@@ -0,0 +1,1693 @@\n+HEADER HYDROLASE(O-GLYCOSYL) 21-JAN-92 1L83 \n+TITLE A CAVITY-CONTAINING MUTANT OF T4 LYSOZYME IS STABILIZED BY BURIED \n+TITLE 2 BENZENE \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: T4 LYSOZYME; \n+COMPND 3 CHAIN: A; \n+COMPND 4 EC: 3.2.1.17; \n+COMPND 5 ENGINEERED: YES \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; \n+SOURCE 3 ORGANISM_TAXID: 10665; \n+SOURCE 4 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \n+SOURCE 5 EXPRESSION_SYSTEM_PLASMID: M13 \n+KEYWDS HYDROLASE(O-GLYCOSYL) \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR A.E.ERIKSSON,B.W.MATTHEWS \n+REVDAT 3 29-NOV-17 1L83 1 HELIX \n+REVDAT 2 24-FEB-09 1L83 1 VERSN \n+REVDAT 1 31-OCT-93 1L83 0 \n+JRNL AUTH A.E.ERIKSSON,W.A.BAASE,J.A.WOZNIAK,B.W.MATTHEWS \n+JRNL TITL A CAVITY-CONTAINING MUTANT OF T4 LYSOZYME IS STABILIZED BY \n+JRNL TITL 2 BURIED BENZENE. \n+JRNL REF NATURE V. 355 371 1992 \n+JRNL REFN ISSN 0028-0836 \n+JRNL PMID 1731252 \n+JRNL DOI 10.1038/355371A0 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.70 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 PROGRAM : TNT \n+REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS \n+REMARK 3 \n+REMARK 3 DATA USED IN REFINEMENT. \n+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 \n+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL \n+REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL \n+REMARK 3 COMPLETENESS FOR RANGE (%) : NULL \n+REMARK 3 NUMBER OF REFLECTIONS : NULL \n+REMARK 3 \n+REMARK 3 USING DATA ABOVE SIGMA CUTOFF. \n+REMARK 3 CROSS-VALIDATION METHOD : NULL \n+REMARK 3 FREE R VALUE TEST SET SELECTION : NULL \n+REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 \n+REMARK 3 R VALUE (WORKING SET) : NULL \n+REMARK 3 FREE R VALUE : NULL \n+REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL \n+REMARK 3 FREE R VALUE TEST SET COUNT : NULL \n+REMARK 3 '..b'YR A 161 43.666 4.258 4.401 1.00 20.08 C \n+ATOM 1275 CD1 TYR A 161 42.570 4.167 3.539 1.00 14.73 C \n+ATOM 1276 CD2 TYR A 161 43.793 5.361 5.247 1.00 12.95 C \n+ATOM 1277 CE1 TYR A 161 41.564 5.135 3.529 1.00 15.18 C \n+ATOM 1278 CE2 TYR A 161 42.799 6.349 5.243 1.00 14.08 C \n+ATOM 1279 CZ TYR A 161 41.693 6.228 4.385 1.00 22.69 C \n+ATOM 1280 OH TYR A 161 40.695 7.181 4.365 1.00 17.31 O \n+ATOM 1281 N LYS A 162 47.309 1.888 2.400 1.00 44.48 N \n+ATOM 1282 CA LYS A 162 48.526 1.128 2.555 1.00 55.19 C \n+ATOM 1283 C LYS A 162 49.627 1.743 1.731 1.00 41.34 C \n+ATOM 1284 O LYS A 162 50.630 2.186 2.281 1.00 72.96 O \n+ATOM 1285 CB LYS A 162 48.381 -0.346 2.323 1.00 40.17 C \n+ATOM 1286 CG LYS A 162 47.496 -0.965 3.387 1.00 41.10 C \n+ATOM 1287 CD LYS A 162 46.714 -2.161 2.865 1.00100.00 C \n+ATOM 1288 CE LYS A 162 46.774 -2.284 1.346 1.00100.00 C \n+ATOM 1289 NZ LYS A 162 45.730 -3.169 0.796 1.00 75.54 N \n+TER 1290 LYS A 162 \n+HETATM 1291 CL CL A 173 43.105 16.437 1.838 1.00 31.25 CL \n+HETATM 1292 CL CL A 178 31.797 15.637 23.970 0.50 36.01 CL \n+HETATM 1293 C1 BME A 901 31.762 -0.871 15.008 1.00 59.34 C \n+HETATM 1294 C2 BME A 901 31.892 -0.606 13.524 1.00 42.69 C \n+HETATM 1295 O1 BME A 901 33.090 -0.817 15.520 1.00 86.60 O \n+HETATM 1296 S2 BME A 901 33.378 -1.464 12.974 1.00 66.76 S \n+HETATM 1297 C1 BME A 902 34.058 -3.174 9.669 1.00 83.63 C \n+HETATM 1298 C2 BME A 902 32.984 -2.119 10.002 1.00 42.57 C \n+HETATM 1299 O1 BME A 902 35.190 -2.535 9.107 1.00 60.57 O \n+HETATM 1300 S2 BME A 902 33.624 -0.782 11.042 1.00100.00 S \n+HETATM 1301 C1 BNZ A 400 26.408 5.086 3.512 1.00 21.10 C \n+HETATM 1302 C2 BNZ A 400 27.385 5.881 2.928 1.00 23.87 C \n+HETATM 1303 C3 BNZ A 400 27.891 6.973 3.620 1.00 21.16 C \n+HETATM 1304 C4 BNZ A 400 27.441 7.240 4.913 1.00 24.84 C \n+HETATM 1305 C5 BNZ A 400 26.490 6.418 5.520 1.00 23.50 C \n+HETATM 1306 C6 BNZ A 400 25.957 5.352 4.805 1.00 18.26 C \n+CONECT 1293 1294 1295 \n+CONECT 1294 1293 1296 \n+CONECT 1295 1293 \n+CONECT 1296 1294 1300 \n+CONECT 1297 1298 1299 \n+CONECT 1298 1297 1300 \n+CONECT 1299 1297 \n+CONECT 1300 1296 1298 \n+CONECT 1301 1302 1306 \n+CONECT 1302 1301 1303 \n+CONECT 1303 1302 1304 \n+CONECT 1304 1303 1305 \n+CONECT 1305 1304 1306 \n+CONECT 1306 1301 1305 \n+MASTER 292 0 5 10 4 0 7 6 1447 1 14 13 \n+END \n' |
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| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/2brc.pdb --- a/test-data/2brc.pdb Tue Jul 28 08:29:23 2020 -0400 +++ b/test-data/2brc.pdb Fri Sep 10 08:20:08 2021 +0000 |
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| @@ -2136,6 +2136,32 @@ ATOM 1663 O GLU A 214 50.269 -25.321 5.741 1.00 39.17 O ATOM 1664 CB GLU A 214 47.235 -26.118 7.659 1.00 36.52 C TER 1665 GLU A 214 +HETATM 1666 C15 CT5 A1215 15.832 -3.998 -6.208 1.00 25.67 C +HETATM 1667 C12 CT5 A1215 14.587 -4.452 -5.763 1.00 28.05 C +HETATM 1668 O17 CT5 A1215 14.301 -5.791 -5.677 1.00 30.93 O +HETATM 1669 O18 CT5 A1215 12.319 -3.924 -4.962 1.00 29.97 O +HETATM 1670 C16 CT5 A1215 13.552 -3.469 -5.403 1.00 28.80 C +HETATM 1671 C22 CT5 A1215 13.860 -2.115 -5.505 1.00 27.01 C +HETATM 1672 C20 CT5 A1215 15.121 -1.683 -5.940 1.00 25.07 C +HETATM 1673 C8 CT5 A1215 16.106 -2.626 -6.272 1.00 22.65 C +HETATM 1674 C4 CT5 A1215 17.463 -2.201 -6.740 1.00 20.99 C +HETATM 1675 C1 CT5 A1215 17.793 -1.365 -7.889 1.00 20.01 C +HETATM 1676 C7 CT5 A1215 16.898 -0.697 -8.883 1.00 20.86 C +HETATM 1677 N5 CT5 A1215 19.135 -1.325 -7.892 1.00 20.33 N +HETATM 1678 C2 CT5 A1215 18.765 -2.576 -6.126 1.00 20.47 C +HETATM 1679 N3 CT5 A1215 19.722 -2.059 -6.829 1.00 17.62 N +HETATM 1680 C6 CT5 A1215 18.777 -3.426 -4.926 1.00 18.05 C +HETATM 1681 C10 CT5 A1215 17.894 -3.156 -3.904 1.00 20.49 C +HETATM 1682 C14 CT5 A1215 17.913 -3.976 -2.805 1.00 20.25 C +HETATM 1683 C26 CT5 A1215 16.971 -3.760 -1.648 1.00 22.59 C +HETATM 1684 C27 CT5 A1215 15.676 -3.093 -2.071 1.00 23.73 C +HETATM 1685 C13 CT5 A1215 18.858 -5.086 -2.726 1.00 18.94 C +HETATM 1686 C17 CT5 A1215 12.914 -6.160 -5.760 1.00 31.68 C +HETATM 1687 O25 CT5 A1215 18.763 -5.850 -1.608 1.00 19.94 O +HETATM 1688 C11 CT5 A1215 19.738 -5.362 -3.766 1.00 18.56 C +HETATM 1689 C18 CT5 A1215 12.153 -5.328 -4.722 1.00 31.36 C +HETATM 1690 C9 CT5 A1215 19.743 -4.525 -4.868 1.00 16.40 C +HETATM 1691 O24 CT5 A1215 20.591 -4.693 -5.899 1.00 16.05 O HETATM 1692 O HOH A2001 33.747 10.121 4.457 1.00 32.57 O HETATM 1693 O HOH A2002 33.709 14.705 5.205 1.00 49.78 O HETATM 1694 O HOH A2003 33.271 8.020 7.785 1.00 58.21 O |
| b |
| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/2brc_info.txt --- a/test-data/2brc_info.txt Tue Jul 28 08:29:23 2020 -0400 +++ b/test-data/2brc_info.txt Fri Sep 10 08:20:08 2021 +0000 |
| b |
| @@ -1,11 +1,32 @@ Pocket 1 : + Score : 0.673 + Druggability Score : 0.079 + Number of Alpha Spheres : 30 + Total SASA : 11.395 + Polar SASA : 5.357 + Apolar SASA : 6.038 + Volume : 250.565 + Mean local hydrophobic density : 14.875 + Mean alpha sphere radius : 3.824 + Mean alp. sph. solvent access : 0.418 + Apolar alpha sphere proportion : 0.533 + Hydrophobicity score: 54.333 + Volume score: 4.000 + Polarity score: 3 + Charge score : -1 + Proportion of polar atoms: 31.818 + Alpha sphere density : 3.241 + Cent. of mass - Alpha Sphere max dist: 7.463 + Flexibility : 0.061 + +Pocket 2 : Score : 0.408 Druggability Score : 0.180 Number of Alpha Spheres : 32 Total SASA : 96.965 Polar SASA : 25.715 Apolar SASA : 71.250 - Volume : 382.870 + Volume : 381.420 Mean local hydrophobic density : 25.556 Mean alpha sphere radius : 3.999 Mean alp. sph. solvent access : 0.537 @@ -19,27 +40,6 @@ Cent. of mass - Alpha Sphere max dist: 8.155 Flexibility : 0.497 -Pocket 2 : - Score : 0.369 - Druggability Score : 0.054 - Number of Alpha Spheres : 30 - Total SASA : 86.527 - Polar SASA : 22.523 - Apolar SASA : 64.004 - Volume : 253.729 - Mean local hydrophobic density : 14.875 - Mean alpha sphere radius : 3.824 - Mean alp. sph. solvent access : 0.418 - Apolar alpha sphere proportion : 0.533 - Hydrophobicity score: 54.333 - Volume score: 4.000 - Polarity score: 3 - Charge score : -1 - Proportion of polar atoms: 31.818 - Alpha sphere density : 3.241 - Cent. of mass - Alpha Sphere max dist: 7.463 - Flexibility : 0.061 - Pocket 3 : Score : 0.324 Druggability Score : 0.026 @@ -47,7 +47,7 @@ Total SASA : 84.602 Polar SASA : 21.805 Apolar SASA : 62.797 - Volume : 303.063 + Volume : 306.764 Mean local hydrophobic density : 13.500 Mean alpha sphere radius : 3.858 Mean alp. sph. solvent access : 0.517 @@ -68,7 +68,7 @@ Total SASA : 131.017 Polar SASA : 37.634 Apolar SASA : 93.383 - Volume : 454.302 + Volume : 450.836 Mean local hydrophobic density : 11.143 Mean alpha sphere radius : 4.002 Mean alp. sph. solvent access : 0.676 @@ -83,13 +83,34 @@ Flexibility : 0.430 Pocket 5 : + Score : 0.292 + Druggability Score : 0.000 + Number of Alpha Spheres : 15 + Total SASA : 41.160 + Polar SASA : 18.215 + Apolar SASA : 22.945 + Volume : 231.631 + Mean local hydrophobic density : 2.000 + Mean alpha sphere radius : 3.730 + Mean alp. sph. solvent access : 0.433 + Apolar alpha sphere proportion : 0.200 + Hydrophobicity score: 46.667 + Volume score: 4.000 + Polarity score: 3 + Charge score : 0 + Proportion of polar atoms: 40.000 + Alpha sphere density : 2.986 + Cent. of mass - Alpha Sphere max dist: 6.120 + Flexibility : 0.447 + +Pocket 6 : Score : 0.242 Druggability Score : 0.000 Number of Alpha Spheres : 25 Total SASA : 71.098 Polar SASA : 32.454 Apolar SASA : 38.644 - Volume : 248.857 + Volume : 246.831 Mean local hydrophobic density : 6.000 Mean alpha sphere radius : 4.116 Mean alp. sph. solvent access : 0.593 @@ -103,27 +124,6 @@ Cent. of mass - Alpha Sphere max dist: 4.963 Flexibility : 0.458 -Pocket 6 : - Score : 0.214 - Druggability Score : 0.000 - Number of Alpha Spheres : 15 - Total SASA : 60.464 - Polar SASA : 27.858 - Apolar SASA : 32.606 - Volume : 227.733 - Mean local hydrophobic density : 2.000 - Mean alpha sphere radius : 3.730 - Mean alp. sph. solvent access : 0.433 - Apolar alpha sphere proportion : 0.200 - Hydrophobicity score: 46.667 - Volume score: 4.000 - Polarity score: 3 - Charge score : 0 - Proportion of polar atoms: 40.000 - Alpha sphere density : 2.986 - Cent. of mass - Alpha Sphere max dist: 6.120 - Flexibility : 0.447 - Pocket 7 : Score : 0.173 Druggability Score : 0.000 @@ -131,7 +131,7 @@ Total SASA : 66.915 Polar SASA : 34.309 Apolar SASA : 32.606 - Volume : 236.449 + Volume : 234.533 Mean local hydrophobic density : 3.000 Mean alpha sphere radius : 4.040 Mean alp. sph. solvent access : 0.553 @@ -152,7 +152,7 @@ Total SASA : 67.693 Polar SASA : 33.879 Apolar SASA : 33.814 - Volume : 222.256 + Volume : 228.901 Mean local hydrophobic density : 7.000 Mean alpha sphere radius : 3.970 Mean alp. sph. solvent access : 0.559 @@ -173,7 +173,7 @@ Total SASA : 54.304 Polar SASA : 20.490 Apolar SASA : 33.814 - Volume : 183.135 + Volume : 184.196 Mean local hydrophobic density : 2.000 Mean alpha sphere radius : 4.035 Mean alp. sph. solvent access : 0.729 @@ -194,7 +194,7 @@ Total SASA : 86.620 Polar SASA : 32.277 Apolar SASA : 54.343 - Volume : 190.741 + Volume : 190.350 Mean local hydrophobic density : 6.000 Mean alpha sphere radius : 3.840 Mean alp. sph. solvent access : 0.424 |
| b |
| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/custom_pockets.pqr --- a/test-data/custom_pockets.pqr Tue Jul 28 08:29:23 2020 -0400 +++ b/test-data/custom_pockets.pqr Fri Sep 10 08:20:08 2021 +0000 |
| b |
| b'@@ -1,60 +1,111 @@\n HEADER\n HEADER This is a pqr format file writen by the programm fpocket. \n HEADER It contains all the pocket vertices found by fpocket. \n-ATOM 1 O STP 1 22.235 5.785 11.829 0.00 4.54\n-ATOM 2 O STP 1 24.944 5.482 14.095 0.00 5.40\n-ATOM 3 O STP 1 23.325 6.121 12.557 0.00 4.91\n-ATOM 4 C STP 1 23.075 5.982 12.334 0.00 4.79\n-ATOM 5 C STP 1 23.220 6.029 11.947 0.00 4.51\n-ATOM 6 C STP 1 23.185 4.250 12.539 0.00 4.13\n-ATOM 7 O STP 1 24.015 4.397 13.299 0.00 4.47\n-ATOM 8 O STP 1 21.392 6.291 11.964 0.00 4.39\n-ATOM 9 O STP 1 21.439 6.103 11.763 0.00 4.37\n-ATOM 10 O STP 1 22.473 5.862 11.169 0.00 4.07\n-ATOM 11 O STP 1 23.267 6.052 11.527 0.00 4.22\n-ATOM 12 O STP 1 21.784 5.960 11.813 0.00 4.44\n-ATOM 13 O STP 1 21.539 6.105 11.851 0.00 4.41\n-ATOM 14 O STP 1 21.552 6.052 11.794 0.00 4.40\n-ATOM 15 O STP 1 22.174 5.648 11.802 0.00 4.47\n-ATOM 16 O STP 1 21.898 4.956 11.553 0.00 4.04\n-ATOM 17 C STP 1 22.737 4.444 12.246 0.00 4.04\n-ATOM 18 C STP 1 23.607 3.963 12.947 0.00 4.20\n-ATOM 19 O STP 1 23.654 3.917 12.908 0.00 4.14\n-ATOM 20 O STP 1 21.171 6.959 12.487 0.00 4.46\n-ATOM 21 O STP 2 15.143 -2.441 -4.373 0.00 4.87\n-ATOM 22 O STP 2 13.315 -2.689 -5.008 0.00 5.31\n-ATOM 23 O STP 2 15.522 -2.882 -5.276 0.00 5.08\n-ATOM 24 C STP 2 15.995 -2.955 -4.856 0.00 4.82\n-ATOM 25 O STP 2 13.095 -2.490 -4.004 0.00 5.03\n-ATOM 26 C STP 2 13.183 -1.721 -5.144 0.00 4.48\n-ATOM 27 O STP 2 12.781 -3.134 -5.440 0.00 5.47\n-ATOM 28 O STP 2 12.861 -2.571 -3.836 0.00 4.99\n-ATOM 29 O STP 2 12.884 -2.675 -2.474 0.00 4.53\n-ATOM 30 O STP 2 12.590 -3.183 -5.255 0.00 5.41\n-ATOM 31 O STP 2 13.360 -2.540 -2.472 0.00 4.44\n-ATOM 32 O STP 2 13.700 -2.356 -3.546 0.00 4.77\n-ATOM 33 C STP 2 15.868 -2.633 -3.988 0.00 4.59\n-ATOM 34 C STP 2 15.151 -2.431 -4.329 0.00 4.85\n-ATOM 35 C STP 2 14.118 -2.694 -7.846 0.00 5.29\n-ATOM 36 O STP 2 13.022 -3.130 -6.128 0.00 5.74\n-ATOM 37 O STP 2 15.554 -2.894 -5.340 0.00 5.08\n-ATOM 38 C STP 2 16.099 -3.003 -5.155 0.00 4.86\n-ATOM 39 O STP 2 14.105 -3.171 -6.160 0.00 5.44\n-ATOM 40 O STP 2 15.257 -2.955 -5.446 0.00 5.12\n-ATOM 41 O STP 2 15.188 -2.969 -5.479 0.00 5.13\n-ATOM 42 O STP 2 15.213 -2.988 -5.463 0.00 5.11\n-ATOM 43 C STP 2 15.550 -2.204 -8.230 0.00 4.87\n-ATOM 44 C STP 2 14.802 -2.746 -7.776 0.00 5.21\n-ATOM 45 C STP 2 14.991 -3.351 -8.348 0.00 4.52\n-ATOM 46 C STP 2 16.789 -1.762 -7.588 0.00 4.46\n-ATOM 47 C STP 2 15.635 -2.200 -8.169 0.00 4.85\n-ATOM 48 C STP 2 17.600 -2.165 -6.557 0.00 4.14\n-ATOM 49 C STP 2 16.541 -2.876 -5.796 0.00 4.72\n-ATOM 50 C STP 2 16.721 -2.043 -6.937 0.00 4.51\n-ATOM 51 O STP 2 16.042 -2.737 -6.112 0.00 4.93\n-ATOM 52 O STP 2 15.126 -3.117 -7.369 0.00 4.96\n-ATOM 5'..b'3 15.556 9.232 5.752 0.00 2.14\n+ATOM 53 O STP 3 17.021 8.685 6.655 0.00 2.14\n+ATOM 54 C STP 3 17.850 9.519 4.848 0.00 2.23\n+ATOM 55 C STP 3 16.679 9.036 5.879 0.00 2.31\n+ATOM 56 C STP 3 16.062 9.075 5.784 0.00 2.19\n+ATOM 57 C STP 3 16.661 8.938 5.398 0.00 2.22\n+ATOM 58 C STP 3 16.627 8.928 5.334 0.00 2.21\n+ATOM 59 O STP 3 16.664 8.465 6.728 0.00 2.06\n+ATOM 60 O STP 3 17.542 8.226 6.792 0.00 1.85\n+ATOM 61 C STP 3 18.220 8.243 6.024 0.00 1.79\n+ATOM 62 C STP 3 17.703 8.162 6.715 0.00 1.79\n+ATOM 63 O STP 3 17.905 8.304 7.371 0.00 1.47\n+ATOM 64 C STP 3 18.193 7.629 6.517 0.00 1.54\n+ATOM 65 C STP 3 17.197 7.387 7.056 0.00 1.53\n+ATOM 66 C STP 3 16.575 6.932 7.205 0.00 1.70\n+ATOM 67 O STP 4 16.837 -11.608 -2.363 0.00 1.89\n+ATOM 68 O STP 4 17.705 -12.568 -2.964 0.00 1.38\n+ATOM 69 O STP 4 17.418 -13.762 -2.519 0.00 1.98\n+ATOM 70 O STP 4 17.457 -13.824 -2.476 0.00 1.99\n+ATOM 71 O STP 4 17.424 -13.838 -2.562 0.00 1.99\n+ATOM 72 O STP 4 15.754 -12.761 -0.806 0.00 1.51\n+ATOM 73 O STP 4 16.201 -12.208 -2.193 0.00 1.91\n+ATOM 74 O STP 4 16.643 -12.006 -2.129 0.00 1.94\n+ATOM 75 O STP 4 16.590 -12.276 -2.039 0.00 1.97\n+ATOM 76 O STP 4 16.861 -11.658 -1.910 0.00 1.80\n+ATOM 77 O STP 4 15.896 -12.779 -0.765 0.00 1.53\n+ATOM 78 O STP 4 17.696 -14.140 -1.718 0.00 2.08\n+ATOM 79 O STP 4 16.339 -12.781 -0.519 0.00 1.66\n+ATOM 80 O STP 4 16.973 -11.684 -1.640 0.00 1.71\n+ATOM 81 O STP 4 16.962 -11.055 -1.527 0.00 1.57\n+ATOM 82 O STP 4 16.943 -11.182 -1.569 0.00 1.59\n+ATOM 83 O STP 4 16.802 -12.554 -1.355 0.00 1.87\n+ATOM 84 O STP 4 16.468 -12.791 -0.754 0.00 1.73\n+ATOM 85 O STP 4 17.133 -13.055 -0.806 0.00 1.97\n+ATOM 86 O STP 4 17.133 -13.055 -0.806 0.00 1.97\n+ATOM 87 O STP 5 17.482 -9.427 13.398 0.00 2.22\n+ATOM 88 O STP 5 18.125 -8.454 13.111 0.00 2.31\n+ATOM 89 O STP 5 20.339 -8.658 13.555 0.00 2.09\n+ATOM 90 O STP 5 17.511 -9.506 13.446 0.00 2.20\n+ATOM 91 O STP 5 16.828 -9.624 13.441 0.00 1.97\n+ATOM 92 C STP 5 20.013 -8.402 13.599 0.00 2.11\n+ATOM 93 O STP 5 19.032 -8.268 13.563 0.00 2.23\n+ATOM 94 C STP 5 19.260 -8.347 13.688 0.00 2.26\n+ATOM 95 C STP 5 19.272 -8.349 13.690 0.00 2.26\n+ATOM 96 O STP 5 17.667 -9.985 14.018 0.00 2.01\n+ATOM 97 C STP 5 18.156 -9.578 13.296 0.00 2.38\n+ATOM 98 O STP 5 17.974 -9.211 13.100 0.00 2.40\n+ATOM 99 C STP 5 19.824 -9.610 13.853 0.00 1.95\n+ATOM 100 C STP 5 19.528 -8.921 13.649 0.00 2.11\n+ATOM 101 C STP 5 18.416 -9.297 13.335 0.00 2.29\n+ATOM 102 O STP 5 18.144 -9.407 13.205 0.00 2.39\n+ATOM 103 C STP 5 18.163 -9.572 13.293 0.00 2.38\n+ATOM 104 C STP 5 18.370 -9.984 13.425 0.00 2.24\n+ATOM 105 C STP 5 18.182 -9.654 13.312 0.00 2.36\n+ATOM 106 C STP 5 18.175 -9.630 13.306 0.00 2.36\n TER\n END\n' |
| b |
| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/ligs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligs.txt Fri Sep 10 08:20:08 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +CT5 |
| b |
| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/ligs2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligs2.txt Fri Sep 10 08:20:08 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +CT5 +BNZ |
| b |
| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/pocket1_atm.pdb --- a/test-data/pocket1_atm.pdb Tue Jul 28 08:29:23 2020 -0400 +++ b/test-data/pocket1_atm.pdb Fri Sep 10 08:20:08 2021 +0000 |
| b |
| @@ -3,42 +3,42 @@ HEADER It represents the atoms contacted by the voronoi vertices of the pocket. HEADER HEADER Information about the pocket 1: -HEADER 0 - Pocket Score : 0.4077 -HEADER 1 - Drug Score : 0.1805 -HEADER 2 - Number of alpha spheres : 32 -HEADER 3 - Mean alpha-sphere radius : 3.9986 -HEADER 4 - Mean alpha-sphere Solvent Acc. : 0.5373 -HEADER 5 - Mean B-factor of pocket residues : 0.4975 -HEADER 6 - Hydrophobicity Score : 61.5000 -HEADER 7 - Polarity Score : 2 -HEADER 8 - Amino Acid based volume Score : 3.8750 -HEADER 9 - Pocket volume (Monte Carlo) : 382.8695 -HEADER 10 -Pocket volume (convex hull) : 30.1615 -HEADER 11 - Charge Score : 0 -HEADER 12 - Local hydrophobic density Score : 25.5556 -HEADER 13 - Number of apolar alpha sphere : 27 -HEADER 14 - Proportion of apolar alpha sphere : 0.8438 -ATOM 824 C LEU A 108 -0.296 -10.140 11.088 0.00 0.00 C 0 -ATOM 830 N SER A 109 -1.070 -9.074 11.216 0.00 0.00 N 0 -ATOM 831 CA SER A 109 -2.043 -8.976 12.305 0.00 0.00 C 0 -ATOM 826 CB LEU A 108 1.927 -9.300 10.337 0.00 0.00 C 0 -ATOM 825 O LEU A 108 -0.379 -11.116 11.836 0.00 0.00 O 0 -ATOM 140 CD2 LEU A 18 5.097 -5.086 15.037 0.00 0.00 C 0 -ATOM 803 O MET A 105 -0.195 -6.553 10.014 0.46 2.14 O 0 -ATOM 835 OG SER A 109 -2.353 -6.599 12.613 0.00 0.00 O 0 -ATOM 135 C LEU A 18 8.999 -6.439 13.809 0.00 0.00 C 0 -ATOM 828 CD1 LEU A 108 4.257 -8.547 9.875 0.00 0.00 C 0 -ATOM 146 CG1 ILE A 19 9.936 -7.046 9.942 0.00 0.00 C 0 -ATOM 136 O LEU A 18 9.127 -7.436 14.524 0.62 2.14 O 0 -ATOM 137 CB LEU A 18 6.757 -5.487 13.252 0.00 0.00 C 0 -ATOM 169 CB THR A 22 9.130 -10.655 15.002 0.00 0.00 C 0 -ATOM 829 CD2 LEU A 108 3.635 -10.934 9.401 0.00 0.00 C 0 -ATOM 170 OG1 THR A 22 8.375 -11.870 15.047 0.00 0.00 O 0 -ATOM 864 CG2 VAL A 114 6.941 -12.860 10.496 0.00 0.00 C 0 -ATOM 863 CG1 VAL A 114 8.697 -12.396 8.764 0.00 0.00 C 0 -ATOM 171 CG2 THR A 22 10.194 -10.923 13.921 0.00 0.00 C 0 -ATOM 848 O ALA A 112 2.150 -14.097 9.345 0.00 0.00 O 0 -ATOM 139 CD1 LEU A 18 4.408 -4.815 12.618 0.00 0.00 C 0 -ATOM 142 CA ILE A 19 10.680 -7.277 12.291 0.00 0.00 C 0 +HEADER 0 - Pocket Score : 0.6733 +HEADER 1 - Drug Score : 0.0789 +HEADER 2 - Number of alpha spheres : 30 +HEADER 3 - Mean alpha-sphere radius : 3.8238 +HEADER 4 - Mean alpha-sphere Solvent Acc. : 0.4181 +HEADER 5 - Mean B-factor of pocket residues : 0.0614 +HEADER 6 - Hydrophobicity Score : 54.3333 +HEADER 7 - Polarity Score : 3 +HEADER 8 - Amino Acid based volume Score : 4.0000 +HEADER 9 - Pocket volume (Monte Carlo) : 250.5648 +HEADER 10 -Pocket volume (convex hull) : 21.6759 +HEADER 11 - Charge Score : -1 +HEADER 12 - Local hydrophobic density Score : 14.8750 +HEADER 13 - Number of apolar alpha sphere : 16 +HEADER 14 - Proportion of apolar alpha sphere : 0.5333 +ATOM 661 CE MET A 84 19.571 0.058 -3.679 0.00 0.00 C 0 +ATOM 1034 CG1 VAL A 136 21.855 -0.304 -0.316 0.00 0.00 C 0 +ATOM 934 CE1 PHE A 124 17.881 -3.184 2.290 0.00 0.00 C 0 +ATOM 1323 CD1 LEU A 173 21.559 -4.418 -0.201 0.00 0.00 C 0 +ATOM 1324 CD2 LEU A 173 20.321 -5.971 1.309 0.00 0.00 C 0 +ATOM 608 O ILE A 77 24.977 -7.461 -1.093 0.47 3.21 O 0 +ATOM 611 CG2 ILE A 77 23.364 -10.499 -1.037 0.00 0.00 C 0 +ATOM 932 CD1 PHE A 124 16.873 -3.983 1.732 0.00 0.00 C 0 +ATOM 293 OD1 ASN A 37 15.033 -6.613 -1.866 0.61 1.07 O 0 +ATOM 291 CB ASN A 37 16.388 -7.582 -3.559 0.00 0.00 C 0 +ATOM 1308 CG2 THR A 171 22.878 -2.566 -3.082 0.00 0.00 C 0 +ATOM 630 OD1 ASP A 79 22.421 -6.453 -5.650 0.62 1.07 O 0 +ATOM 268 O LEU A 34 18.916 -10.154 -2.649 0.00 0.00 O 0 +ATOM 299 CB ALA A 38 20.902 -9.742 -5.476 0.00 0.00 C 0 +ATOM 295 N ALA A 38 18.584 -8.907 -5.326 0.00 0.00 N 0 +ATOM 1307 OG1 THR A 171 22.816 -1.800 -5.313 0.00 0.00 O 0 +ATOM 1306 CB THR A 171 23.393 -2.853 -4.494 0.00 0.00 C 0 +ATOM 289 C ASN A 37 17.497 -8.223 -5.690 0.00 0.00 C 0 +ATOM 930 CB PHE A 124 14.441 -4.551 1.341 0.00 0.00 C 0 +ATOM 731 CD2 LEU A 93 16.203 0.130 -0.341 0.00 0.00 C 0 +ATOM 290 O ASN A 37 17.456 -7.431 -6.621 0.00 0.00 O 0 +ATOM 318 CB ALA A 41 19.432 -5.156 -8.748 0.00 0.00 C 0 TER END |
| b |
| diff -r 4fb73be7f4cb -r 4cc9d85c3bae test-data/pocket2_vert.pqr --- a/test-data/pocket2_vert.pqr Tue Jul 28 08:29:23 2020 -0400 +++ b/test-data/pocket2_vert.pqr Fri Sep 10 08:20:08 2021 +0000 |
| b |
| @@ -4,54 +4,42 @@ HEADER algorithm. HEADER HEADER Information about the pocket 2: -HEADER 0 - Pocket Score : 0.0437 -HEADER 1 - Drug Score : 0.0843 -HEADER 2 - Number of V. Vertices : 35 -HEADER 3 - Mean alpha-sphere radius : 4.9417 -HEADER 4 - Mean alpha-sphere SA : 0.5173 -HEADER 5 - Mean B-factor : 0.3317 -HEADER 6 - Hydrophobicity Score : 34.1818 -HEADER 7 - Polarity Score : 4 -HEADER 8 - Volume Score : 4.0000 -HEADER 9 - Real volume (approximation) : 557.1453 +HEADER 0 - Pocket Score : 0.6121 +HEADER 1 - Drug Score : 0.0003 +HEADER 2 - Number of V. Vertices : 23 +HEADER 3 - Mean alpha-sphere radius : 1.7590 +HEADER 4 - Mean alpha-sphere SA : 0.3239 +HEADER 5 - Mean B-factor : 0.1741 +HEADER 6 - Hydrophobicity Score : 33.1667 +HEADER 7 - Polarity Score : 3 +HEADER 8 - Volume Score : 3.1667 +HEADER 9 - Real volume (approximation) : 1.6145 HEADER 10 - Charge Score : 0 -HEADER 11 - Local hydrophobic density Score : 15.0000 -HEADER 12 - Number of apolar alpha sphere : 16 -HEADER 13 - Proportion of apolar alpha sphere : 0.4571 -ATOM 1 O STP 2 15.143 -2.441 -4.373 0.00 4.87 -ATOM 2 O STP 2 13.315 -2.689 -5.008 0.00 5.31 -ATOM 3 O STP 2 15.522 -2.882 -5.276 0.00 5.08 -ATOM 4 C STP 2 15.995 -2.955 -4.856 0.00 4.82 -ATOM 5 O STP 2 13.095 -2.490 -4.004 0.00 5.03 -ATOM 6 C STP 2 13.183 -1.721 -5.144 0.00 4.48 -ATOM 7 O STP 2 12.781 -3.134 -5.440 0.00 5.47 -ATOM 8 O STP 2 12.861 -2.571 -3.836 0.00 4.99 -ATOM 9 O STP 2 12.884 -2.675 -2.474 0.00 4.53 -ATOM 10 O STP 2 12.590 -3.183 -5.255 0.00 5.41 -ATOM 11 O STP 2 13.360 -2.540 -2.472 0.00 4.44 -ATOM 12 O STP 2 13.700 -2.356 -3.546 0.00 4.77 -ATOM 13 C STP 2 15.868 -2.633 -3.988 0.00 4.59 -ATOM 14 C STP 2 15.151 -2.431 -4.329 0.00 4.85 -ATOM 15 C STP 2 14.118 -2.694 -7.846 0.00 5.29 -ATOM 16 O STP 2 13.022 -3.130 -6.128 0.00 5.74 -ATOM 17 O STP 2 15.554 -2.894 -5.340 0.00 5.08 -ATOM 18 C STP 2 16.099 -3.003 -5.155 0.00 4.86 -ATOM 19 O STP 2 14.105 -3.171 -6.160 0.00 5.44 -ATOM 20 O STP 2 15.257 -2.955 -5.446 0.00 5.12 -ATOM 21 O STP 2 15.188 -2.969 -5.479 0.00 5.13 -ATOM 22 O STP 2 15.213 -2.988 -5.463 0.00 5.11 -ATOM 23 C STP 2 15.550 -2.204 -8.230 0.00 4.87 -ATOM 24 C STP 2 14.802 -2.746 -7.776 0.00 5.21 -ATOM 25 C STP 2 14.991 -3.351 -8.348 0.00 4.52 -ATOM 26 C STP 2 16.789 -1.762 -7.588 0.00 4.46 -ATOM 27 C STP 2 15.635 -2.200 -8.169 0.00 4.85 -ATOM 28 C STP 2 17.600 -2.165 -6.557 0.00 4.14 -ATOM 29 C STP 2 16.541 -2.876 -5.796 0.00 4.72 -ATOM 30 C STP 2 16.721 -2.043 -6.937 0.00 4.51 -ATOM 31 O STP 2 16.042 -2.737 -6.112 0.00 4.93 -ATOM 32 O STP 2 15.126 -3.117 -7.369 0.00 4.96 -ATOM 33 C STP 2 15.094 -3.059 -7.417 0.00 5.00 -ATOM 34 O STP 2 14.998 -2.901 -7.258 0.00 5.19 -ATOM 35 C STP 2 14.975 -2.857 -7.412 0.00 5.19 +HEADER 11 - Local hydrophobic density Score : 0.0000 +HEADER 12 - Number of apolar alpha sphere : 1 +HEADER 13 - Proportion of apolar alpha sphere : 0.0435 +ATOM 1 O STP 2 17.955 -10.537 -4.347 0.00 1.99 +ATOM 2 O STP 2 17.960 -10.528 -4.354 0.00 1.99 +ATOM 3 O STP 2 19.277 -10.570 -5.672 0.00 1.83 +ATOM 4 O STP 2 19.338 -10.601 -4.559 0.00 2.01 +ATOM 5 C STP 2 19.848 -10.431 -6.443 0.00 1.59 +ATOM 6 O STP 2 19.347 -10.649 -5.895 0.00 1.85 +ATOM 7 O STP 2 18.746 -9.722 -6.457 0.00 1.40 +ATOM 8 O STP 2 19.153 -10.558 -5.862 0.00 1.83 +ATOM 9 O STP 2 17.080 -11.566 -5.016 0.00 1.50 +ATOM 10 O STP 2 17.675 -10.493 -5.103 0.00 1.84 +ATOM 11 O STP 2 17.679 -10.469 -6.073 0.00 1.95 +ATOM 12 O STP 2 17.441 -10.922 -4.644 0.00 1.74 +ATOM 13 O STP 2 17.230 -11.067 -4.458 0.00 1.67 +ATOM 14 O STP 2 17.131 -11.474 -4.929 0.00 1.52 +ATOM 15 O STP 2 19.921 -11.196 -4.236 0.00 2.15 +ATOM 16 O STP 2 17.328 -9.376 -4.902 0.00 1.41 +ATOM 17 O STP 2 17.256 -9.863 -5.605 0.00 1.66 +ATOM 18 O STP 2 17.667 -10.452 -6.086 0.00 1.95 +ATOM 19 O STP 2 17.535 -9.883 -6.475 0.00 1.84 +ATOM 20 O STP 2 17.314 -9.938 -5.917 0.00 1.74 +ATOM 21 O STP 2 17.662 -10.499 -6.098 0.00 1.94 +ATOM 22 O STP 2 16.737 -9.546 -5.775 0.00 1.53 +ATOM 23 O STP 2 16.765 -9.569 -5.773 0.00 1.53 TER END |