| Next changeset 1:909c8763f127 (2020-03-17) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51" |
|
added:
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 |
| b |
| diff -r 000000000000 -r 2063e965531c fpocket.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fpocket.xml Mon Aug 12 13:27:10 2019 -0400 |
| [ |
| @@ -0,0 +1,138 @@ +<tool id="fpocket" name="fpocket" version="0.1.0"> + <description>- find potential binding sites in protein structures</description> + <requirements> + <requirement type="package" version="3.1.3">fpocket</requirement> + </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 + #elif $inp.pocket_type == 'external': + -m 3.5 -M 10 -i 30 + #elif $inp.pocket_type == 'custom': + -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $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> + <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> + <option value="all_verts">PQR file containing all Voronoi vertices found</option> + <option value="info" selected="true">Log file containing pocket properties</option> + </param> + </inputs> + + <outputs> + <collection type="list" name="atoms_output" label="Atoms in contact with each pocket"> + <discover_datasets pattern="(?P<designation>^pocket\d+)_atm\.pdb$" directory="input_out/pockets" ext="pdb"/> + <filter>"atoms" in outputs</filter> + </collection> + <collection type="list" name="pock_verts_output" label="Voronoi vertices of each pocket"> + <discover_datasets pattern="(?P<designation>^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/> + <filter>"pock_verts" in outputs</filter> + </collection> + <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr"> + <filter>"all_verts" in outputs</filter> + </data> + <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt"> + <filter>"info" in outputs</filter> + </data> + </outputs> + + <tests> + <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run --> + <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="i" value="20" /> + <param name="D" value="2.0"/> + <param name="C" value="c" /> + <param name="e" value="b" /> + <param name='outputs' value='pock_verts,all_verts' /> + <output_collection name="pock_verts_output" type="list"> + <element name="pocket2" ftype="pqr" file="pocket2_vert.pqr" lines_diff="2"/> + </output_collection> + <output name="all_verts_output" ftype="pqr" file='custom_pockets.pqr'/> + </test> + <test> + <param name="input" ftype="pdb" value="2brc.pdb"/> + <param name='pocket_type' value='small_mol' /> + <output_collection name="atoms_output" type="list"> + <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/> + </output_collection> + <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/> + </test> + </tests> + <help><![CDATA[ + +Detect 'pockets' in a protein structure using the fpocket software. A potential use +of this tool is locating potential binding sites in a protein prior to performing +protein-ligand docking. + +To use, upload a protein structure in PDB format and select the type of pocket to +detect. 'Custom options' can also be selected - this exposes all internal fpocket +parameters. Using this option requires some knowledge of the fpocket prediction +algorithm. Please consult the cited publications for more details. + + +----- + +.. class:: infomark + +**Input** + +A protein structure in PDB format. + +----- + +.. class:: infomark + +**Output** + +Some or all of the following files: + +- A collection of PDB files, one for each pocket, each containing the atoms bordering the pocket. +- A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket. +- A single PQR file containing all Voronoi vertices for all pockets. +- 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> +</tool> |
| b |
| diff -r 000000000000 -r 2063e965531c test-data/2brc.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2brc.pdb Mon Aug 12 13:27:10 2019 -0400 |
| b |
| b"@@ -0,0 +1,2424 @@\n+HEADER CHAPERONE 04-MAY-05 2BRC \n+TITLE STRUCTURE OF A HSP90 INHIBITOR BOUND TO THE N-TERMINUS OF YEAST HSP90.\n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82; \n+COMPND 3 CHAIN: A; \n+COMPND 4 FRAGMENT: N-TERMINUS, RESIDUES 1-214; \n+COMPND 5 SYNONYM: HSP90,HEAT SHOCK PROTEIN HSP90,82 KDA HEAT SHOCK PROTEIN; \n+COMPND 6 ENGINEERED: YES \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; \n+SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; \n+SOURCE 4 ORGANISM_TAXID: 4932; \n+SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \n+SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 \n+KEYWDS ATP-BINDING, CHAPERONE, HEAT SHOCK, INHIBITOR, MULTIGENE FAMILY, \n+KEYWDS 2 CHAPERONE-COMPLEX \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR S.M.ROE,L.H.PEARL,C.PRODROMOU \n+REVDAT 3 28-FEB-18 2BRC 1 JRNL \n+REVDAT 2 24-FEB-09 2BRC 1 VERSN \n+REVDAT 1 29-SEP-05 2BRC 0 \n+JRNL AUTH K.M.CHEUNG,T.P.MATTHEWS,K.JAMES,M.G.ROWLANDS,K.J.BOXALL, \n+JRNL AUTH 2 S.Y.SHARP,A.MALONEY,S.M.ROE,C.PRODROMOU,L.H.PEARL, \n+JRNL AUTH 3 G.W.AHERNE,E.MCDONALD,P.WORKMAN \n+JRNL TITL THE IDENTIFICATION, SYNTHESIS, PROTEIN CRYSTAL STRUCTURE AND \n+JRNL TITL 2 IN VITRO BIOCHEMICAL EVALUATION OF A NEW 3,4-DIARYLPYRAZOLE \n+JRNL TITL 3 CLASS OF HSP90 INHIBITORS. \n+JRNL REF BIOORG. MED. CHEM. LETT. V. 15 3338 2005 \n+JRNL REFN ISSN 0960-894X \n+JRNL PMID 15955698 \n+JRNL DOI 10.1016/J.BMCL.2005.05.046 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.60 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 PROGRAM : REFMAC 5.0 \n+REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON \n+REMARK 3 \n+REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD \n+REMARK 3 \n+REMARK 3 DATA USED IN REFINEMENT. \n+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 \n+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.54 \n+REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL \n+REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 \n+REMARK 3 NUMBER OF REFLECTIONS : 39187 \n+REMARK 3 \n+REMARK 3 FIT TO DATA USED IN REFINEMENT. \n+REMARK 3 CROSS-VALIDATION METHOD "..b'OH A2238 19.988 -27.212 2.120 1.00 39.11 O \n+HETATM 1930 O HOH A2239 18.327 -26.462 -5.000 1.00 63.36 O \n+HETATM 1931 O HOH A2240 13.601 -21.438 5.691 1.00 74.16 O \n+HETATM 1932 O HOH A2241 16.123 -16.122 -3.584 1.00 22.16 O \n+HETATM 1933 O HOH A2242 18.009 -18.650 0.335 1.00 23.06 O \n+HETATM 1934 O HOH A2243 19.825 -21.212 -7.504 1.00 45.98 O \n+HETATM 1935 O HOH A2244 14.921 -16.420 -11.269 1.00 25.34 O \n+HETATM 1936 O HOH A2245 15.055 -20.293 -6.721 1.00 52.72 O \n+HETATM 1937 O HOH A2246 21.697 -19.022 -16.150 1.00 45.59 O \n+HETATM 1938 O HOH A2247 24.798 -18.394 -14.646 1.00 43.45 O \n+HETATM 1939 O HOH A2248 22.656 -19.813 -9.663 1.00 30.78 O \n+HETATM 1940 O HOH A2249 31.014 -17.921 -10.745 1.00 42.17 O \n+HETATM 1941 O HOH A2250 31.584 -13.848 -12.033 1.00 55.19 O \n+HETATM 1942 O HOH A2251 34.869 -14.722 3.970 1.00 25.72 O \n+HETATM 1943 O HOH A2252 35.003 -17.198 5.681 1.00 38.13 O \n+HETATM 1944 O HOH A2253 37.393 -12.101 4.512 1.00 52.80 O \n+HETATM 1945 O HOH A2254 39.159 -20.600 1.562 1.00 41.31 O \n+HETATM 1946 O HOH A2255 48.702 -20.387 8.539 1.00 30.44 O \n+HETATM 1947 O HOH A2256 45.978 -25.641 3.122 1.00 39.05 O \n+HETATM 1948 O HOH A2257 47.493 -26.980 4.869 1.00 60.05 O \n+HETATM 1949 O HOH A2258 20.380 -7.911 -1.824 1.00 15.88 O \n+CONECT 1666 1667 1673 \n+CONECT 1667 1666 1668 1670 \n+CONECT 1668 1667 1686 \n+CONECT 1669 1670 1689 \n+CONECT 1670 1667 1669 1671 \n+CONECT 1671 1670 1672 \n+CONECT 1672 1671 1673 \n+CONECT 1673 1666 1672 1674 \n+CONECT 1674 1673 1675 1678 \n+CONECT 1675 1674 1676 1677 \n+CONECT 1676 1675 \n+CONECT 1677 1675 1679 \n+CONECT 1678 1674 1679 1680 \n+CONECT 1679 1677 1678 \n+CONECT 1680 1678 1681 1690 \n+CONECT 1681 1680 1682 \n+CONECT 1682 1681 1683 1685 \n+CONECT 1683 1682 1684 \n+CONECT 1684 1683 \n+CONECT 1685 1682 1687 1688 \n+CONECT 1686 1668 1689 \n+CONECT 1687 1685 \n+CONECT 1688 1685 1690 \n+CONECT 1689 1669 1686 \n+CONECT 1690 1680 1688 1691 \n+CONECT 1691 1690 \n+MASTER 390 0 1 10 8 0 4 6 1948 1 26 17 \n+END \n' |
| b |
| diff -r 000000000000 -r 2063e965531c test-data/2brc_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2brc_info.txt Mon Aug 12 13:27:10 2019 -0400 |
| b |
| @@ -0,0 +1,210 @@ +Pocket 1 : + 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 + Mean local hydrophobic density : 25.556 + Mean alpha sphere radius : 3.999 + Mean alp. sph. solvent access : 0.537 + Apolar alpha sphere proportion : 0.844 + Hydrophobicity score: 61.500 + Volume score: 3.875 + Polarity score: 2 + Charge score : 0 + Proportion of polar atoms: 31.818 + Alpha sphere density : 3.752 + 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 + Number of Alpha Spheres : 24 + Total SASA : 84.602 + Polar SASA : 21.805 + Apolar SASA : 62.797 + Volume : 303.063 + Mean local hydrophobic density : 13.500 + Mean alpha sphere radius : 3.858 + Mean alp. sph. solvent access : 0.517 + Apolar alpha sphere proportion : 0.667 + Hydrophobicity score: 13.600 + Volume score: 5.600 + Polarity score: 4 + Charge score : 1 + Proportion of polar atoms: 33.333 + Alpha sphere density : 3.743 + Cent. of mass - Alpha Sphere max dist: 8.961 + Flexibility : 0.624 + +Pocket 4 : + Score : 0.304 + Druggability Score : 0.023 + Number of Alpha Spheres : 24 + Total SASA : 131.017 + Polar SASA : 37.634 + Apolar SASA : 93.383 + Volume : 454.302 + Mean local hydrophobic density : 11.143 + Mean alpha sphere radius : 4.002 + Mean alp. sph. solvent access : 0.676 + Apolar alpha sphere proportion : 0.583 + Hydrophobicity score: 31.000 + Volume score: 3.556 + Polarity score: 4 + Charge score : -1 + Proportion of polar atoms: 45.833 + Alpha sphere density : 5.452 + Cent. of mass - Alpha Sphere max dist: 12.168 + Flexibility : 0.430 + +Pocket 5 : + 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 + Mean local hydrophobic density : 6.000 + Mean alpha sphere radius : 4.116 + Mean alp. sph. solvent access : 0.593 + Apolar alpha sphere proportion : 0.280 + Hydrophobicity score: 4.286 + Volume score: 3.857 + Polarity score: 6 + Charge score : 0 + Proportion of polar atoms: 55.556 + Alpha sphere density : 2.064 + 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 + Number of Alpha Spheres : 19 + Total SASA : 66.915 + Polar SASA : 34.309 + Apolar SASA : 32.606 + Volume : 236.449 + Mean local hydrophobic density : 3.000 + Mean alpha sphere radius : 4.040 + Mean alp. sph. solvent access : 0.553 + Apolar alpha sphere proportion : 0.211 + Hydrophobicity score: 22.111 + Volume score: 3.889 + Polarity score: 6 + Charge score : 1 + Proportion of polar atoms: 56.250 + Alpha sphere density : 2.154 + Cent. of mass - Alpha Sphere max dist: 5.576 + Flexibility : 0.571 + +Pocket 8 : + Score : 0.140 + Druggability Score : 0.001 + Number of Alpha Spheres : 18 + Total SASA : 67.693 + Polar SASA : 33.879 + Apolar SASA : 33.814 + Volume : 222.256 + Mean local hydrophobic density : 7.000 + Mean alpha sphere radius : 3.970 + Mean alp. sph. solvent access : 0.559 + Apolar alpha sphere proportion : 0.444 + Hydrophobicity score: 19.833 + Volume score: 5.167 + Polarity score: 4 + Charge score : 2 + Proportion of polar atoms: 43.750 + Alpha sphere density : 2.012 + Cent. of mass - Alpha Sphere max dist: 4.964 + Flexibility : 0.333 + +Pocket 9 : + Score : 0.133 + Druggability Score : 0.000 + Number of Alpha Spheres : 17 + Total SASA : 54.304 + Polar SASA : 20.490 + Apolar SASA : 33.814 + Volume : 183.135 + Mean local hydrophobic density : 2.000 + Mean alpha sphere radius : 4.035 + Mean alp. sph. solvent access : 0.729 + Apolar alpha sphere proportion : 0.176 + Hydrophobicity score: -26.333 + Volume score: 3.667 + Polarity score: 6 + Charge score : -1 + Proportion of polar atoms: 50.000 + Alpha sphere density : 1.532 + Cent. of mass - Alpha Sphere max dist: 3.484 + Flexibility : 0.621 + +Pocket 10 : + Score : 0.114 + Druggability Score : 0.001 + Number of Alpha Spheres : 19 + Total SASA : 86.620 + Polar SASA : 32.277 + Apolar SASA : 54.343 + Volume : 190.741 + Mean local hydrophobic density : 6.000 + Mean alpha sphere radius : 3.840 + Mean alp. sph. solvent access : 0.424 + Apolar alpha sphere proportion : 0.368 + Hydrophobicity score: 22.857 + Volume score: 3.857 + Polarity score: 2 + Charge score : -1 + Proportion of polar atoms: 37.500 + Alpha sphere density : 2.412 + Cent. of mass - Alpha Sphere max dist: 5.289 + Flexibility : 0.728 + |
| b |
| diff -r 000000000000 -r 2063e965531c test-data/custom_pockets.pqr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_pockets.pqr Mon Aug 12 13:27:10 2019 -0400 |
| b |
| @@ -0,0 +1,60 @@ +HEADER +HEADER This is a pqr format file writen by the programm fpocket. +HEADER It contains all the pocket vertices found by fpocket. +ATOM 1 O STP 1 22.235 5.785 11.829 0.00 4.54 +ATOM 2 O STP 1 24.944 5.482 14.095 0.00 5.40 +ATOM 3 O STP 1 23.325 6.121 12.557 0.00 4.91 +ATOM 4 C STP 1 23.075 5.982 12.334 0.00 4.79 +ATOM 5 C STP 1 23.220 6.029 11.947 0.00 4.51 +ATOM 6 C STP 1 23.185 4.250 12.539 0.00 4.13 +ATOM 7 O STP 1 24.015 4.397 13.299 0.00 4.47 +ATOM 8 O STP 1 21.392 6.291 11.964 0.00 4.39 +ATOM 9 O STP 1 21.439 6.103 11.763 0.00 4.37 +ATOM 10 O STP 1 22.473 5.862 11.169 0.00 4.07 +ATOM 11 O STP 1 23.267 6.052 11.527 0.00 4.22 +ATOM 12 O STP 1 21.784 5.960 11.813 0.00 4.44 +ATOM 13 O STP 1 21.539 6.105 11.851 0.00 4.41 +ATOM 14 O STP 1 21.552 6.052 11.794 0.00 4.40 +ATOM 15 O STP 1 22.174 5.648 11.802 0.00 4.47 +ATOM 16 O STP 1 21.898 4.956 11.553 0.00 4.04 +ATOM 17 C STP 1 22.737 4.444 12.246 0.00 4.04 +ATOM 18 C STP 1 23.607 3.963 12.947 0.00 4.20 +ATOM 19 O STP 1 23.654 3.917 12.908 0.00 4.14 +ATOM 20 O STP 1 21.171 6.959 12.487 0.00 4.46 +ATOM 21 O STP 2 15.143 -2.441 -4.373 0.00 4.87 +ATOM 22 O STP 2 13.315 -2.689 -5.008 0.00 5.31 +ATOM 23 O STP 2 15.522 -2.882 -5.276 0.00 5.08 +ATOM 24 C STP 2 15.995 -2.955 -4.856 0.00 4.82 +ATOM 25 O STP 2 13.095 -2.490 -4.004 0.00 5.03 +ATOM 26 C STP 2 13.183 -1.721 -5.144 0.00 4.48 +ATOM 27 O STP 2 12.781 -3.134 -5.440 0.00 5.47 +ATOM 28 O STP 2 12.861 -2.571 -3.836 0.00 4.99 +ATOM 29 O STP 2 12.884 -2.675 -2.474 0.00 4.53 +ATOM 30 O STP 2 12.590 -3.183 -5.255 0.00 5.41 +ATOM 31 O STP 2 13.360 -2.540 -2.472 0.00 4.44 +ATOM 32 O STP 2 13.700 -2.356 -3.546 0.00 4.77 +ATOM 33 C STP 2 15.868 -2.633 -3.988 0.00 4.59 +ATOM 34 C STP 2 15.151 -2.431 -4.329 0.00 4.85 +ATOM 35 C STP 2 14.118 -2.694 -7.846 0.00 5.29 +ATOM 36 O STP 2 13.022 -3.130 -6.128 0.00 5.74 +ATOM 37 O STP 2 15.554 -2.894 -5.340 0.00 5.08 +ATOM 38 C STP 2 16.099 -3.003 -5.155 0.00 4.86 +ATOM 39 O STP 2 14.105 -3.171 -6.160 0.00 5.44 +ATOM 40 O STP 2 15.257 -2.955 -5.446 0.00 5.12 +ATOM 41 O STP 2 15.188 -2.969 -5.479 0.00 5.13 +ATOM 42 O STP 2 15.213 -2.988 -5.463 0.00 5.11 +ATOM 43 C STP 2 15.550 -2.204 -8.230 0.00 4.87 +ATOM 44 C STP 2 14.802 -2.746 -7.776 0.00 5.21 +ATOM 45 C STP 2 14.991 -3.351 -8.348 0.00 4.52 +ATOM 46 C STP 2 16.789 -1.762 -7.588 0.00 4.46 +ATOM 47 C STP 2 15.635 -2.200 -8.169 0.00 4.85 +ATOM 48 C STP 2 17.600 -2.165 -6.557 0.00 4.14 +ATOM 49 C STP 2 16.541 -2.876 -5.796 0.00 4.72 +ATOM 50 C STP 2 16.721 -2.043 -6.937 0.00 4.51 +ATOM 51 O STP 2 16.042 -2.737 -6.112 0.00 4.93 +ATOM 52 O STP 2 15.126 -3.117 -7.369 0.00 4.96 +ATOM 53 C STP 2 15.094 -3.059 -7.417 0.00 5.00 +ATOM 54 O STP 2 14.998 -2.901 -7.258 0.00 5.19 +ATOM 55 C STP 2 14.975 -2.857 -7.412 0.00 5.19 +TER +END |
| b |
| diff -r 000000000000 -r 2063e965531c test-data/pocket1_atm.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pocket1_atm.pdb Mon Aug 12 13:27:10 2019 -0400 |
| b |
| @@ -0,0 +1,44 @@ +HEADER +HEADER This is a pdb format file writen by the programm fpocket. +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 +TER +END |
| b |
| diff -r 000000000000 -r 2063e965531c test-data/pocket2_vert.pqr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pocket2_vert.pqr Mon Aug 12 13:27:10 2019 -0400 |
| b |
| @@ -0,0 +1,57 @@ +HEADER +HEADER This is a pqr format file writen by the programm fpocket. +HEADER It represent the voronoi vertices of a single pocket found by the +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 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 +TER +END |