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Commit message:
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9 |
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added:
docking.xml test-data/3u1i_for_DM.pdbqt test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.log test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt test-data/config_complexo_dm.txt |
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removed:
prepare_ligand.xml test-data/NuBBE_1_obabel_3D.mol2 |
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| diff -r d9ee79230d31 -r 18dec59e29ae docking.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docking.xml Fri Jun 03 16:49:49 2016 -0400 |
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| b'@@ -0,0 +1,171 @@\n+<tool id="docking" name="Docking" version="0.1.0">\n+ <description>- Tool to running molecular docking with Autodock Vina</description>\n+ <requirements>\n+ <requirement type="package" version="1.1.2">autodock-vina</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1" />\n+ </stdio>\n+ <command><![CDATA[\n+ vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2"\n+ ]]></command>\n+ <inputs>\n+ <param type="data" name="box" format="txt" label="Box configuration: " help="Select a text file with the box configurations" />\n+ <param type="data" name="receptor" format="pdbqt" label="Receptor: " help="Select a receptor pdbqt file" />\n+ <param type="data" name="ligand" format="pdbqt" label="Ligand: " help="Select a ligand pdbqt file" />\n+ </inputs>\n+ <outputs>\n+ <data name="file_output1" format="pdbqt" label="#echo (os.path.splitext (str($ligand.name))[0]) + \'_-_\' + (os.path.splitext (str($receptor.name))[0])#.pdbqt" />\n+ <data name="file_output2" format="txt" label="#echo (os.path.splitext (str($ligand.name))[0]) + \'_-_\' + (os.path.splitext (str($receptor.name))[0])#.log" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="box" value="config_complexo_dm.txt"/>\n+ <param name="receptor" value="3u1i_for_DM.pdbqt"/>\n+ <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>\n+ <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>\n+ <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ ** What it does? **\n+\n+ This tool performs molecular docking with Autodock Vina program.\n+\n+ ** inputs **\n+\n+ Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example:\n+\n+ size_x = 20.00\n+ size_y = 18.40\n+ size_z = 23.60\n+ center_x = 70.92\n+ center_y = 70.57\n+ center_z = 36.86\n+ num_modes = 9999\n+ energy_range = 9999\n+ exhaustiveness = 10\n+ cpu = 4\n+ seed = 1\n+\n+ Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. \n+ The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.\n+\n+ The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.\n+ The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.\n+\n+ ** outputs **\n+\n+ Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example:\n+\n+ MODEL 1\n+ REMARK VINA RESULT: -0.0 0.000 0.000\n+ REMARK 9 active torsions:\n+ REMARK status: (\'A\' for Active; \'I\' for Inactive)\n+ REMARK 1 A between atoms: C_2 and O_3 \n+ REMARK 2 A between atoms: C_2 and C_14 \n+ REMARK 3 A between atoms: O_3 and C_4 \n+ REMARK 4 A between atoms: C_4 and C_5 \n+ REMARK 5 A between atoms: C_6 and C_8 \n+ REMARK 6 A between atoms: C_8 and C_9 \n+ REMARK 7 A between atoms: C_9 and C_10 \n+ REMARK 8 A between atoms: C_16 and O_17 \n+ REMARK 9 A between atoms: C_19 and O_20 \n+ ROOT\n+ ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA\n+ ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C \n+ ENDROOT\n+ BRANCH 2 3\n+ ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA\n+ BRANCH 3 4\n+ ATOM '..b'833 75.151 40.104 0.00 0.00 0.042 C \n+ ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C \n+ ENDBRANCH 9 10\n+ ENDBRANCH 8 9\n+ ENDBRANCH 6 8\n+ ENDBRANCH 4 5\n+ ENDBRANCH 3 4\n+ ENDBRANCH 2 3\n+ BRANCH 2 14\n+ ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A \n+ ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A \n+ ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A \n+ ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A \n+ ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A \n+ ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A \n+ BRANCH 16 20\n+ ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA\n+ ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD\n+ ENDBRANCH 16 20\n+ BRANCH 17 22\n+ ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA\n+ ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD\n+ ENDBRANCH 17 22\n+ ENDBRANCH 2 14\n+ TORSDOF 9\n+ ENDMDL \n+\n+ The last is a log file with the binding affinity scores, this file looks like the following example:\n+\n+ -----------------------------------------------------------------\n+ If you used AutoDock Vina in your work, please cite: \n+ \n+ O. Trott, A. J. Olson, \n+ AutoDock Vina: improving the speed and accuracy of docking \n+ with a new scoring function, efficient optimization and \n+ multithreading, Journal of Computational Chemistry 31 (2010) \n+ 455-461 \n+ \n+ DOI 10.1002/jcc.21334 \n+ \n+ Please see http://vina.scripps.edu for more information. \n+ ------------------------------------------------------------------\n+\n+ Reading input ... done.\n+ Setting up the scoring function ... done.\n+ Analyzing the binding site ... done.\n+ Using random seed: 1899908181\n+ Performing search ... done.\n+ Refining results ... done.\n+\n+ mode | affinity | dist from best mode\n+ | (kcal/mol) | rmsd l.b.| rmsd u.b.\n+ -----+------------+----------+----------\n+ 1 -0.0 0.000 0.000\n+ 2 -0.0 2.046 2.443\n+ 3 -0.0 5.896 7.949\n+ 4 -0.0 2.518 3.100\n+ 5 -0.0 2.417 4.527\n+ 6 -0.0 5.686 7.689\n+ 7 -0.0 2.828 4.792\n+ 8 -0.0 5.547 7.086\n+ 9 -0.0 7.388 9.966\n+ 10 -0.0 7.877 11.352\n+ 11 -0.0 8.203 10.157\n+ 12 -0.0 5.163 7.653\n+ 13 -0.0 3.093 6.011\n+ 14 -0.0 7.998 11.146\n+ 15 -0.0 7.015 10.108\n+ 16 -0.0 8.795 11.682\n+ 17 -0.0 7.317 10.367\n+ 18 0.0 3.274 4.160\n+ 19 0.0 10.286 12.001\n+ 20 0.0 3.566 5.349\n+ Writing output ... done.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1002/jcc.21334</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r d9ee79230d31 -r 18dec59e29ae prepare_ligand.xml --- a/prepare_ligand.xml Fri Jun 03 16:49:02 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,148 +0,0 @@ -<tool id="prepare_ligand" name="Prepare ligand" version="0.1.0"> - <description>- Tool to prepare ligand for Autodock Vina</description> - <requirements> - <requirement type="package" version="1.5.6">mgltools</requirement> - </requirements> - <stdio> - <exit_code range="1" /> - </stdio> - <command><![CDATA[ - ln -s $ligand ./ligand.mol2 && prepare_ligand4.py -l ./ligand.mol2 -v -o "$file_output" -U nphs_lps -A hydrogens - ]]></command> - <inputs> - <param type="data" name="ligand" format="mol2" label="Ligand: " help="Select a mol2 file." /> - </inputs> - <outputs> - <data name="file_output" format="pdbqt" label="#echo os.path.splitext (str($ligand.name))[0]#.pdbqt" /> - </outputs> - <tests> - <test> - <param name="ligand" value="NuBBE_1_obabel_3D.mol2"/> - <output name="file_output" file="NuBBE_1_obabel_3D.pdbqt"/> - </test> - </tests> - <help><![CDATA[ - ** What it does? ** - - This tool uses the MGLTools programming packages to convert a mol2 molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. - - ** input ** - - It's required at least one mol2 dataset in history, what is informed in ligand field, for use the tool. The mol2 molecule file looks like the following example: - - @<TRIPOS>MOLECULE - NuBBE_1 - 21 21 0 0 0 - SMALL - GASTEIGER - - @<TRIPOS>ATOM - 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449 - 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396 - 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570 - 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113 - 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480 - 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731 - 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437 - 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285 - 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308 - 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850 - 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796 - 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440 - 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440 - 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627 - 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026 - 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590 - 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033 - 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583 - 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033 - 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158 - 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441 - @<TRIPOS>BOND - 1 1 2 2 - 2 2 3 1 - 3 3 4 1 - 4 4 5 1 - 5 5 6 2 - 6 6 7 1 - 7 6 8 1 - 8 8 9 1 - 9 9 10 1 - 10 10 11 2 - 11 11 12 1 - 12 11 13 1 - 13 2 14 1 - 14 14 15 ar - 15 15 16 ar - 16 16 17 1 - 17 16 18 ar - 18 18 19 1 - 19 18 20 ar - 20 20 21 ar - 21 14 21 ar - - ** output ** - - The output is a pdbqt molecule file converted from a mol2 molecule file. The pdbqt molecule file looks like the following example: - - REMARK 9 active torsions: - REMARK status: ('A' for Active; 'I' for Inactive) - REMARK 1 A between atoms: C_2 and O_3 - REMARK 2 A between atoms: C_2 and C_14 - REMARK 3 A between atoms: O_3 and C_4 - REMARK 4 A between atoms: C_4 and C_5 - REMARK 5 A between atoms: C_6 and C_8 - REMARK 6 A between atoms: C_8 and C_9 - REMARK 7 A between atoms: C_9 and C_10 - REMARK 8 A between atoms: C_16 and O_17 - REMARK 9 A between atoms: C_19 and O_20 - ROOT - ATOM 1 O LIG d 1 -0.947 -0.436 -3.210 0.00 0.00 -0.259 OA - ATOM 2 C LIG d 1 -1.207 0.245 -2.235 0.00 0.00 0.293 C - ENDROOT - BRANCH 2 3 - ATOM 3 O LIG d 1 -1.935 -0.114 -1.151 0.00 0.00 -0.314 OA - BRANCH 3 4 - ATOM 4 C LIG d 1 -2.338 -1.483 -1.065 0.00 0.00 0.206 C - BRANCH 4 5 - ATOM 5 C LIG d 1 -1.745 -2.032 0.200 0.00 0.00 0.002 C - ATOM 6 C LIG d 1 -0.550 -2.644 0.338 0.00 0.00 -0.085 C - ATOM 7 C LIG d 1 0.405 -2.885 -0.801 0.00 0.00 0.043 C - BRANCH 6 8 - ATOM 8 C LIG d 1 -0.086 -3.153 1.694 0.00 0.00 0.037 C - BRANCH 8 9 - ATOM 9 C LIG d 1 0.730 -2.114 2.473 0.00 0.00 0.031 C - BRANCH 9 10 - ATOM 10 C LIG d 1 1.187 -2.618 3.818 0.00 0.00 -0.024 C - ATOM 11 C LIG d 1 2.352 -3.233 4.110 0.00 0.00 -0.091 C - ATOM 12 C LIG d 1 3.401 -3.605 3.099 0.00 0.00 0.042 C - ATOM 13 C LIG d 1 2.699 -3.614 5.527 0.00 0.00 0.042 C - ENDBRANCH 9 10 - ENDBRANCH 8 9 - ENDBRANCH 6 8 - ENDBRANCH 4 5 - ENDBRANCH 3 4 - ENDBRANCH 2 3 - BRANCH 2 14 - ATOM 14 C LIG d 1 -0.778 1.657 -2.066 0.00 0.00 0.042 A - ATOM 15 C LIG d 1 -0.640 2.224 -0.790 0.00 0.00 0.057 A - ATOM 16 C LIG d 1 -0.249 3.551 -0.677 0.00 0.00 0.099 A - ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A - ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A - ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A - BRANCH 16 20 - ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA - ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD - ENDBRANCH 16 20 - BRANCH 17 22 - ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA - ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD - ENDBRANCH 17 22 - ENDBRANCH 2 14 - TORSDOF 9 - - ]]></help> - <citations> - <citation type="doi">10.1002/jcc.21334</citation> - </citations> -</tool> \ No newline at end of file |
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| diff -r d9ee79230d31 -r 18dec59e29ae test-data/3u1i_for_DM.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3u1i_for_DM.pdbqt Fri Jun 03 16:49:49 2016 -0400 |
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| b'@@ -0,0 +1,1983 @@\n+ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C \n+ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA\n+ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C \n+ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N \n+ATOM 5 HN ASP A 50 6.246 -5.360 11.009 1.00 0.00 0.163 HD\n+ATOM 6 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 0.186 C \n+ATOM 7 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 0.241 C \n+ATOM 8 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 -0.271 OA\n+ATOM 9 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 0.147 C \n+ATOM 10 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 0.175 C \n+ATOM 11 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 -0.648 OA\n+ATOM 12 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 -0.648 OA\n+ATOM 13 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 -0.346 N \n+ATOM 14 HN LEU A 51 10.177 -3.384 12.264 1.00 0.00 0.163 HD\n+ATOM 15 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 0.177 C \n+ATOM 16 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 0.241 C \n+ATOM 17 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 -0.271 OA\n+ATOM 18 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 0.038 C \n+ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C \n+ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C \n+ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C \n+ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N \n+ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD\n+ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 0.205 C \n+ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 0.243 C \n+ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 -0.271 OA\n+ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 0.146 C \n+ATOM 28 CG2 THR A 52 9.344 -5.211 19.697 1.00 57.60 0.042 C \n+ATOM 29 OG1 THR A 52 8.263 -3.881 18.000 1.00 59.52 -0.393 OA\n+ATOM 30 HG1 THR A 52 7.441 -4.100 18.422 1.00 0.00 0.210 HD\n+ATOM 31 N VAL A 53 11.995 -4.605 19.433 1.00 52.78 -0.346 N \n+ATOM 32 HN VAL A 53 11.340 -3.921 19.813 1.00 0.00 0.163 HD\n+ATOM 33 CA VAL A 53 13.184 -4.932 20.191 1.00 50.89 0.180 C \n+ATOM 34 C VAL A 53 12.790 -5.088 21.663 1.00 51.45 0.241 C \n+ATOM 35 O VAL A 53 12.137 -4.217 22.224 1.00 52.72 -0.271 OA\n+ATOM 36 CB VAL A 53 14.252 -3.824 19.943 1.00 50.64 0.009 C \n+ATOM 37 CG1 VAL A 53 15.024 -3.484 21.172 1.00 51.07 0.012 C \n+ATOM 38 CG2 VAL A 53 15.176 -4.211 18.809 1.00 48.66 0.012 C \n+ATOM 39 N GLU A 54 13.149 -6.211 22.281 1.00 50.29 -0.346 N \n+ATOM 40 HN GLU A 54 13.637 -6.942 21.764 1.00 0.00 0.163 HD\n+ATOM 41 CA GLU A 54 12.846 -6.399 23.696 1.00 50.84 0.177 C \n+ATOM 42 C GLU A 54 14.024 -6.935 24.512 1.00 49.31 0.241 C \n+ATOM 43 O GLU A 54 14.646 -7.934 24.159 1.00 47.75 -0.271 OA\n+ATOM 44 CB GLU A 54 11.551 -7.200 23.896 1.00 51.87 0.045 C \n+ATOM 45 CG GLU A 54 11.689 -8.703 23.982 1.00 53.50 0.116 C \n+ATOM 46 CD GLU A 54 10.417 -9.381 24.495 1.00 58.29 0.172 C \n+ATOM 47 OE1 GLU A 54 10.519 -10.418 25.200 1.00 59.29 -0.648 OA\n+ATOM 48 OE2 GLU A 54 9.313 -8.875 24.194 1.00 60.50 -0.648 OA\n+ATOM 49 N LYS A 55 14.318 -6.231 25.596 1.00 49.81 -0.346 N \n+ATOM 5'..b'\n+ATOM 1933 CA GLN B 167 33.446 -8.519 14.183 1.00 0.00 0.177 C \n+ATOM 1934 C GLN B 167 34.026 -7.589 13.104 1.00 0.00 0.241 C \n+ATOM 1935 O GLN B 167 34.456 -8.043 12.045 1.00 0.00 -0.271 OA\n+ATOM 1936 CB GLN B 167 34.484 -8.808 15.290 1.00 0.00 0.044 C \n+ATOM 1937 CG GLN B 167 35.004 -7.601 16.100 1.00 0.00 0.105 C \n+ATOM 1938 CD GLN B 167 33.909 -6.792 16.790 1.00 0.00 0.215 C \n+ATOM 1939 NE2 GLN B 167 33.973 -6.703 18.110 1.00 0.00 -0.370 N \n+ATOM 1940 1HE2 GLN B 167 33.241 -6.162 18.571 1.00 0.00 0.159 HD\n+ATOM 1941 2HE2 GLN B 167 34.695 -7.174 18.656 1.00 0.00 0.159 HD\n+ATOM 1942 OE1 GLN B 167 33.040 -6.225 16.133 1.00 0.00 -0.274 OA\n+ATOM 1943 N THR B 168 34.015 -6.290 13.364 1.00 0.00 -0.344 N \n+ATOM 1944 HN THR B 168 33.559 -5.942 14.208 1.00 0.00 0.163 HD\n+ATOM 1945 CA THR B 168 34.654 -5.359 12.444 1.00 0.00 0.205 C \n+ATOM 1946 C THR B 168 35.857 -4.704 13.134 1.00 0.00 0.243 C \n+ATOM 1947 O THR B 168 36.723 -5.414 13.684 1.00 0.00 -0.271 OA\n+ATOM 1948 CB THR B 168 33.629 -4.361 11.810 1.00 0.00 0.146 C \n+ATOM 1949 CG2 THR B 168 33.078 -3.401 12.818 1.00 0.00 0.042 C \n+ATOM 1950 OG1 THR B 168 34.256 -3.632 10.746 1.00 0.00 -0.393 OA\n+ATOM 1951 HG1 THR B 168 33.634 -3.026 10.361 1.00 0.00 0.210 HD\n+ATOM 1952 N ASN B 169 35.919 -3.372 13.074 1.00 0.00 -0.345 N \n+ATOM 1953 HN ASN B 169 35.276 -2.900 12.438 1.00 0.00 0.163 HD\n+ATOM 1954 CA ASN B 169 36.844 -2.529 13.854 1.00 0.00 0.185 C \n+ATOM 1955 C ASN B 169 36.139 -1.192 14.133 1.00 0.00 0.241 C \n+ATOM 1956 O ASN B 169 35.816 -0.463 13.194 1.00 0.00 -0.271 OA\n+ATOM 1957 CB ASN B 169 38.168 -2.317 13.105 1.00 0.00 0.137 C \n+ATOM 1958 CG ASN B 169 38.987 -3.594 13.003 1.00 0.00 0.217 C \n+ATOM 1959 ND2 ASN B 169 38.679 -4.424 12.011 1.00 0.00 -0.370 N \n+ATOM 1960 1HD2 ASN B 169 37.952 -4.217 11.327 1.00 0.00 0.159 HD\n+ATOM 1961 2HD2 ASN B 169 39.228 -5.281 11.943 1.00 0.00 0.159 HD\n+ATOM 1962 OD1 ASN B 169 39.864 -3.844 13.828 1.00 0.00 -0.274 OA\n+ATOM 1963 N ALA B 170 35.899 -0.889 15.413 1.00 0.00 -0.346 N \n+ATOM 1964 HN ALA B 170 36.421 -1.386 16.134 1.00 0.00 0.163 HD\n+ATOM 1965 CA ALA B 170 34.911 0.134 15.837 1.00 0.00 0.172 C \n+ATOM 1966 C ALA B 170 35.224 1.605 15.513 1.00 0.00 0.240 C \n+ATOM 1967 O ALA B 170 36.387 2.020 15.549 1.00 0.00 -0.271 OA\n+ATOM 1968 CB ALA B 170 34.616 -0.011 17.325 1.00 0.00 0.042 C \n+ATOM 1969 N GLU B 171 34.163 2.374 15.226 1.00 0.00 -0.346 N \n+ATOM 1970 HN GLU B 171 33.248 1.924 15.212 1.00 0.00 0.163 HD\n+ATOM 1971 CA GLU B 171 34.214 3.825 14.927 1.00 0.00 0.177 C \n+ATOM 1972 C GLU B 171 34.565 4.100 13.458 1.00 0.00 0.240 C \n+ATOM 1973 O GLU B 171 35.734 4.246 13.088 1.00 0.00 -0.271 OA\n+ATOM 1974 CB GLU B 171 35.138 4.591 15.908 1.00 0.00 0.045 C \n+ATOM 1975 CG GLU B 171 35.404 6.082 15.578 1.00 0.00 0.116 C \n+ATOM 1976 CD GLU B 171 34.361 7.046 16.155 1.00 0.00 0.172 C \n+ATOM 1977 OE1 GLU B 171 33.447 6.594 16.887 1.00 0.00 -0.648 OA\n+ATOM 1978 OE2 GLU B 171 34.463 8.263 15.878 1.00 0.00 -0.648 OA\n+ATOM 1979 N NME B 172 33.642 3.039 13.031 1.00 0.00 -0.364 N \n+ATOM 1980 CH3 NME B 172 33.700 2.990 11.580 1.00 0.00 0.149 C \n+ATOM 1981 H NME B 172 33.064 2.445 13.643 1.00 0.00 0.161 HD\n+TER 1982 NME B 172 \n' |
| b |
| diff -r d9ee79230d31 -r 18dec59e29ae test-data/NuBBE_1_obabel_3D.mol2 --- a/test-data/NuBBE_1_obabel_3D.mol2 Fri Jun 03 16:49:02 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,50 +0,0 @@ -@<TRIPOS>MOLECULE -NuBBE_1 - 21 21 0 0 0 -SMALL -GASTEIGER - -@<TRIPOS>ATOM - 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449 - 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396 - 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570 - 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113 - 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480 - 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731 - 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437 - 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285 - 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308 - 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850 - 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796 - 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440 - 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440 - 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627 - 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026 - 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590 - 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033 - 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583 - 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033 - 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158 - 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441 -@<TRIPOS>BOND - 1 1 2 2 - 2 2 3 1 - 3 3 4 1 - 4 4 5 1 - 5 5 6 2 - 6 6 7 1 - 7 6 8 1 - 8 8 9 1 - 9 9 10 1 - 10 10 11 2 - 11 11 12 1 - 12 11 13 1 - 13 2 14 1 - 14 14 15 ar - 15 15 16 ar - 16 16 17 1 - 17 16 18 ar - 18 18 19 1 - 19 18 20 ar - 20 20 21 ar - 21 14 21 ar |
| b |
| diff -r d9ee79230d31 -r 18dec59e29ae test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.log Fri Jun 03 16:49:49 2016 -0400 |
| b |
| @@ -0,0 +1,45 @@ +################################################################# +# If you used AutoDock Vina in your work, please cite: # +# # +# O. Trott, A. J. Olson, # +# AutoDock Vina: improving the speed and accuracy of docking # +# with a new scoring function, efficient optimization and # +# multithreading, Journal of Computational Chemistry 31 (2010) # +# 455-461 # +# # +# DOI 10.1002/jcc.21334 # +# # +# Please see http://vina.scripps.edu for more information. # +################################################################# + +Reading input ... done. +Setting up the scoring function ... done. +Analyzing the binding site ... done. +Using random seed: 1 +Performing search ... done. +Refining results ... done. + +mode | affinity | dist from best mode + | (kcal/mol) | rmsd l.b.| rmsd u.b. +-----+------------+----------+---------- + 1 0.0 0.000 0.000 + 2 0.0 3.859 6.800 + 3 0.0 2.967 4.947 + 4 0.0 7.373 9.992 + 5 0.0 10.065 12.509 + 6 0.0 9.552 11.270 + 7 0.0 4.758 7.761 + 8 0.0 8.908 10.819 + 9 0.0 4.989 6.808 + 10 0.0 6.560 9.146 + 11 0.0 4.373 7.846 + 12 0.0 5.905 8.469 + 13 0.0 12.324 14.703 + 14 0.0 5.481 8.276 + 15 0.0 4.529 7.709 + 16 0.0 2.548 5.281 + 17 0.0 7.043 9.534 + 18 0.0 5.414 7.921 + 19 0.0 5.737 8.627 + 20 0.0 2.715 4.755 +Writing output ... done. |
| b |
| diff -r d9ee79230d31 -r 18dec59e29ae test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt Fri Jun 03 16:49:49 2016 -0400 |
| b |
| b"@@ -0,0 +1,1160 @@\n+MODEL 1\n+REMARK VINA RESULT: 0.0 0.000 0.000\n+REMARK 9 active torsions:\n+REMARK status: ('A' for Active; 'I' for Inactive)\n+REMARK 1 A between atoms: C_2 and O_3 \n+REMARK 2 A between atoms: C_2 and C_14 \n+REMARK 3 A between atoms: O_3 and C_4 \n+REMARK 4 A between atoms: C_4 and C_5 \n+REMARK 5 A between atoms: C_6 and C_8 \n+REMARK 6 A between atoms: C_8 and C_9 \n+REMARK 7 A between atoms: C_9 and C_10 \n+REMARK 8 A between atoms: C_16 and O_17 \n+REMARK 9 A between atoms: C_19 and O_20 \n+ROOT\n+ATOM 1 O LIG d 1 66.903 73.345 36.004 0.00 0.00 -0.259 OA\n+ATOM 2 C LIG d 1 66.819 73.217 37.212 0.00 0.00 0.293 C \n+ENDROOT\n+BRANCH 2 3\n+ATOM 3 O LIG d 1 66.049 72.337 37.894 0.00 0.00 -0.314 OA\n+BRANCH 3 4\n+ATOM 4 C LIG d 1 66.229 70.950 37.597 0.00 0.00 0.206 C \n+BRANCH 4 5\n+ATOM 5 C LIG d 1 67.207 70.414 38.601 0.00 0.00 0.002 C \n+ATOM 6 C LIG d 1 68.514 70.144 38.398 0.00 0.00 -0.085 C \n+ATOM 7 C LIG d 1 69.215 70.340 37.080 0.00 0.00 0.043 C \n+BRANCH 6 8\n+ATOM 8 C LIG d 1 69.381 69.597 39.521 0.00 0.00 0.037 C \n+BRANCH 8 9\n+ATOM 9 C LIG d 1 68.773 69.828 40.910 0.00 0.00 0.031 C \n+BRANCH 9 10\n+ATOM 10 C LIG d 1 69.375 71.012 41.622 0.00 0.00 -0.024 C \n+ATOM 11 C LIG d 1 68.755 72.157 41.976 0.00 0.00 -0.091 C \n+ATOM 12 C LIG d 1 67.328 72.497 41.643 0.00 0.00 0.042 C \n+ATOM 13 C LIG d 1 69.477 73.227 42.756 0.00 0.00 0.042 C \n+ENDBRANCH 9 10\n+ENDBRANCH 8 9\n+ENDBRANCH 6 8\n+ENDBRANCH 4 5\n+ENDBRANCH 3 4\n+ENDBRANCH 2 3\n+BRANCH 2 14\n+ATOM 14 C LIG d 1 67.557 74.054 38.192 0.00 0.00 0.042 A \n+ATOM 15 C LIG d 1 66.901 75.048 38.934 0.00 0.00 0.057 A \n+ATOM 16 C LIG d 1 67.630 75.817 39.830 0.00 0.00 0.099 A \n+ATOM 17 C LIG d 1 68.995 75.599 39.998 0.00 0.00 0.098 A \n+ATOM 18 C LIG d 1 69.651 74.606 39.285 0.00 0.00 0.040 A \n+ATOM 19 C LIG d 1 68.930 73.824 38.380 0.00 0.00 0.020 A \n+BRANCH 16 20\n+ATOM 20 O LIG d 1 67.045 76.804 40.576 0.00 0.00 -0.358 OA\n+ATOM 21 HO LIG d 1 67.556 77.498 40.976 1.00 0.00 0.217 HD\n+ENDBRANCH 16 20\n+BRANCH 17 22\n+ATOM 22 O LIG d 1 69.701 76.367 40.878 0.00 0.00 -0.358 OA\n+ATOM 23 HO LIG d 1 69.252 76.793 41.599 1.00 0.00 0.217 HD\n+ENDBRANCH 17 22\n+ENDBRANCH 2 14\n+TORSDOF 9\n+ENDMDL\n+MODEL 2\n+REMARK VINA RESULT: 0.0 3.859 6.800\n+REMARK 9 active torsions:\n+REMARK status: ('A' for Active; 'I' for Inactive)\n+REMARK 1 A between atoms: C_2 and O_3 \n+REMARK 2 A between atoms: C_2 and C_14 \n+REMARK 3 A between atoms: O_3 and C_4 \n+REMARK 4 A between atoms: C_4 and C_5 \n+REMARK 5 A between atoms: C_6 and C_8 \n+REMARK 6 A between atoms: C_8 and C_9 \n+REMARK 7 A between atoms: C_9 and C_10 \n+REMARK 8 A between atoms: C_16 and O_17 \n+REMARK 9 A between atoms: C_19 and O_20 \n+ROOT\n+ATOM 1 O LIG d 1 66.661 72.198 38.738 0.00 0.00 -0.259 OA\n+ATOM 2 C LIG d 1 66.731 71.529 37.724 0.00 0.00 0.293 C \n+ENDROOT\n+BRANCH 2 3\n+ATOM 3 O LIG d 1 66.885 70.186 37.633 0.00 0.00 -0.314 OA\n+BRANCH 3 4\n+ATOM 4 C LIG d 1 65.910 69.376 38.294 0.00 0.00 0.206 C \n+BRANCH 4 5\n+ATOM 5 C LIG d 1 64.870 69.026 37.270 0.00 0.00 0.002 C \n+ATOM 6 C LIG d 1 63.642 69.571 37.141 0.00 0.00 -0.085 C \n+ATOM 7 C LIG d 1 63.105 "..b" C LIG d 1 70.427 64.875 39.479 0.00 0.00 0.042 C \n+ATOM 13 C LIG d 1 67.950 64.380 39.535 0.00 0.00 0.042 C \n+ENDBRANCH 9 10\n+ENDBRANCH 8 9\n+ENDBRANCH 6 8\n+ENDBRANCH 4 5\n+ENDBRANCH 3 4\n+ENDBRANCH 2 3\n+BRANCH 2 14\n+ATOM 14 C LIG d 1 70.790 67.792 41.877 0.00 0.00 0.042 A \n+ATOM 15 C LIG d 1 70.578 68.432 40.646 0.00 0.00 0.057 A \n+ATOM 16 C LIG d 1 69.302 68.446 40.101 0.00 0.00 0.099 A \n+ATOM 17 C LIG d 1 68.246 67.825 40.763 0.00 0.00 0.098 A \n+ATOM 18 C LIG d 1 68.447 67.172 41.971 0.00 0.00 0.040 A \n+ATOM 19 C LIG d 1 69.726 67.149 42.532 0.00 0.00 0.020 A \n+BRANCH 16 20\n+ATOM 20 O LIG d 1 69.034 69.059 38.908 0.00 0.00 -0.358 OA\n+ATOM 21 HO LIG d 1 69.686 69.123 38.221 1.00 0.00 0.217 HD\n+ENDBRANCH 16 20\n+BRANCH 17 22\n+ATOM 22 O LIG d 1 66.994 67.852 40.219 0.00 0.00 -0.358 OA\n+ATOM 23 HO LIG d 1 66.597 68.684 39.988 1.00 0.00 0.217 HD\n+ENDBRANCH 17 22\n+ENDBRANCH 2 14\n+TORSDOF 9\n+ENDMDL\n+MODEL 20\n+REMARK VINA RESULT: 0.0 2.715 4.755\n+REMARK 9 active torsions:\n+REMARK status: ('A' for Active; 'I' for Inactive)\n+REMARK 1 A between atoms: C_2 and O_3 \n+REMARK 2 A between atoms: C_2 and C_14 \n+REMARK 3 A between atoms: O_3 and C_4 \n+REMARK 4 A between atoms: C_4 and C_5 \n+REMARK 5 A between atoms: C_6 and C_8 \n+REMARK 6 A between atoms: C_8 and C_9 \n+REMARK 7 A between atoms: C_9 and C_10 \n+REMARK 8 A between atoms: C_16 and O_17 \n+REMARK 9 A between atoms: C_19 and O_20 \n+ROOT\n+ATOM 1 O LIG d 1 66.642 67.499 40.173 0.00 0.00 -0.259 OA\n+ATOM 2 C LIG d 1 66.838 68.644 40.536 0.00 0.00 0.293 C \n+ENDROOT\n+BRANCH 2 3\n+ATOM 3 O LIG d 1 67.853 69.100 41.308 0.00 0.00 -0.314 OA\n+BRANCH 3 4\n+ATOM 4 C LIG d 1 69.182 68.847 40.848 0.00 0.00 0.206 C \n+BRANCH 4 5\n+ATOM 5 C LIG d 1 69.615 70.063 40.081 0.00 0.00 0.002 C \n+ATOM 6 C LIG d 1 69.680 70.197 38.740 0.00 0.00 -0.085 C \n+ATOM 7 C LIG d 1 69.320 69.103 37.769 0.00 0.00 0.043 C \n+BRANCH 6 8\n+ATOM 8 C LIG d 1 70.145 71.500 38.108 0.00 0.00 0.037 C \n+BRANCH 8 9\n+ATOM 9 C LIG d 1 70.073 72.689 39.073 0.00 0.00 0.031 C \n+BRANCH 9 10\n+ATOM 10 C LIG d 1 68.848 73.542 38.860 0.00 0.00 -0.024 C \n+ATOM 11 C LIG d 1 67.825 73.735 39.718 0.00 0.00 -0.091 C \n+ATOM 12 C LIG d 1 67.685 73.053 41.051 0.00 0.00 0.042 C \n+ATOM 13 C LIG d 1 66.700 74.683 39.389 0.00 0.00 0.042 C \n+ENDBRANCH 9 10\n+ENDBRANCH 8 9\n+ENDBRANCH 6 8\n+ENDBRANCH 4 5\n+ENDBRANCH 3 4\n+ENDBRANCH 2 3\n+BRANCH 2 14\n+ATOM 14 C LIG d 1 65.948 69.787 40.207 0.00 0.00 0.042 A \n+ATOM 15 C LIG d 1 65.099 70.345 41.174 0.00 0.00 0.057 A \n+ATOM 16 C LIG d 1 64.274 71.404 40.821 0.00 0.00 0.099 A \n+ATOM 17 C LIG d 1 64.296 71.913 39.525 0.00 0.00 0.098 A \n+ATOM 18 C LIG d 1 65.146 71.382 38.565 0.00 0.00 0.040 A \n+ATOM 19 C LIG d 1 65.982 70.316 38.906 0.00 0.00 0.020 A \n+BRANCH 16 20\n+ATOM 20 O LIG d 1 63.421 71.985 41.719 0.00 0.00 -0.358 OA\n+ATOM 21 HO LIG d 1 62.792 72.646 41.457 1.00 0.00 0.217 HD\n+ENDBRANCH 16 20\n+BRANCH 17 22\n+ATOM 22 O LIG d 1 63.475 72.950 39.189 0.00 0.00 -0.358 OA\n+ATOM 23 HO LIG d 1 62.733 72.799 38.614 1.00 0.00 0.217 HD\n+ENDBRANCH 17 22\n+ENDBRANCH 2 14\n+TORSDOF 9\n+ENDMDL\n" |
| b |
| diff -r d9ee79230d31 -r 18dec59e29ae test-data/config_complexo_dm.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config_complexo_dm.txt Fri Jun 03 16:49:49 2016 -0400 |
| b |
| @@ -0,0 +1,11 @@ +size_x = 20.00 +size_y = 18.40 +size_z = 23.60 +center_x = 70.92 +center_y = 70.57 +center_z = 36.86 +num_modes = 9999 +energy_range = 9999 +exhaustiveness = 10 +cpu = 4 +seed = 1 \ No newline at end of file |