| Previous changeset 6:0ae768a0e5c0 (2019-06-19) Next changeset 8:7a871df65202 (2020-07-28) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645" |
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modified:
docking.xml |
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added:
test-data/box.txt test-data/input_ligand.pdbqt test-data/input_ligands.sdf test-data/ligand1_docked.sdf test-data/ligand2_docked.sdf test-data/ligand3_docked.sdf test-data/ligand4_docked.sdf test-data/ligand5_docked.sdf test-data/ligand_params.sdf test-data/protein.pdbqt |
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removed:
test-data/3u1i_for_DM.pdbqt test-data/NuBBE_1_obabel_3D.pdbqt test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.log test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.sdf test-data/config_complexo_dm.txt |
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| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 docking.xml --- a/docking.xml Wed Jun 19 06:43:41 2019 -0400 +++ b/docking.xml Wed Oct 02 12:49:30 2019 -0400 |
| [ |
| b'@@ -1,56 +1,50 @@\n-<tool id="docking" name="Docking" version="0.2.1">\n+<tool id="docking" name="VINA Docking" version="0.3.0">\n <description>tool to perform protein-ligand docking with Autodock Vina</description>\n <requirements>\n <requirement type="package" version="1.1.2">autodock-vina</requirement>\n <requirement type="package" version="2.4.1">openbabel</requirement>\n+ <requirement type="package" version="20190722">parallel</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1" />\n- </stdio>\n- <command><![CDATA[\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $ligands.is_of_type("sdf")\n+ obabel -isdf \'$ligands\' -O ligand.pdbqt -m -p $ph_value &&\n+ #else\n+ ln -s \'$ligands\' ligand1.pdbqt &&\n+ #end if\n+ mkdir output &&\n+ ls ligand*.pdbqt | parallel --will-cite -j \\${GALAXY_SLOTS:-1} $\'OUTNAME={.}_docked && vina\n+ --receptor \\\'$receptor\\\'\n+ --ligand {}\n+ --out ./\\${OUTNAME}.pdbqt\n+ --log ./\\${OUTNAME}.log\n+ --cpu 1\n #if $config_params.config_params == \'vals\':\n- vina\n- --center_x \'$config_params.center_x\' \n- --center_y \'$config_params.center_y\' \n- --center_z \'$config_params.center_z\' \n- --size_x \'$config_params.size_x\' \n- --size_y \'$config_params.size_y\' \n- --size_z \'$config_params.size_z\' \n- --exhaustiveness \'$config_params.exh\' \n- --num_modes 9999 \n- --energy_range 9999 \n- --receptor \'$receptor\' \n- --ligand \'$ligand\' \n- --out \'./output1.dat\' \n- --log \'./output2.dat\' \n- --cpu \\${GALAXY_SLOTS:-1}\n- #if $config_params.seed.seed == \'true\':\n- --seed \'$config_params.seed.seed_value\'\n- #end if\n- #end if\n- #if $config_params.config_params == \'file\':\n- vina \n- --config \'$config_params.box\' \n- --receptor \'$receptor\' \n- --ligand \'$ligand\' \n- --out \'./output1.dat\' \n- --log \'./output2.dat\'\n- --cpu \\${GALAXY_SLOTS:-1}\n+ --center_x $config_params.center_x\n+ --center_y $config_params.center_y\n+ --center_z $config_params.center_z\n+ --size_x $config_params.size_x\n+ --size_y $config_params.size_y\n+ --size_z $config_params.size_z\n #if $config_params.exh != "":\n --exhaustiveness $config_params.exh\n #end if\n+ #if $config_params.seed.seed == \'true\':\n+ --seed $config_params.seed.seed_value\n+ #end if\n+ #else if $config_params.config_params == \'file\':\n+ --config $config_params.box\n+ #if $config_params.exh != "":\n+ --exhaustiveness $config_params.exh\n+ #end if\n #end if\n- #if $output_format == \'sdf\':\n- && python \'$__tool_directory__/convert_pdbqt_to_sdf.py\' \'./output1.dat\' \'$sdf_output\' \n- #else\n- && mv ./output1.dat \'$file_output1\'\n- && mv ./output2.dat \'$file_output2\'\n- #end if\n+ && python \\\'$__tool_directory__/convert_pdbqt_to_sdf.py\\\' ./\\${OUTNAME}.pdbqt output/\\${OUTNAME}.sdf\'\n \n ]]></command>\n <inputs>\n <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." />\n- <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand (PDBQT format). This can be prepared using the ligand preparation tool." />\n+ <param type="data" name="ligands" format="sdf,pdbqt" label="Ligands" help="Select ligands (SDF format with'..b'.037 C \n- BRANCH 8 9\n- ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C \n- BRANCH 9 10\n- ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C \n- ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C \n- ATOM 12 C LIG d 1 75.833 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 second output is a log file containing the binding affinity scores, like the following::\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' |
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| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/3u1i_for_DM.pdbqt --- a/test-data/3u1i_for_DM.pdbqt Wed Jun 19 06:43:41 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1983 +0,0 @@\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 0ae768a0e5c0 -r 7b2f205b3f68 test-data/NuBBE_1_obabel_3D.pdbqt --- a/test-data/NuBBE_1_obabel_3D.pdbqt Wed Jun 19 06:43:41 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,55 +0,0 @@ -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 |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.log --- a/test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.log Wed Jun 19 06:43:41 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ -################################################################# -# 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 0ae768a0e5c0 -r 7b2f205b3f68 test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt --- a/test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt Wed Jun 19 06:43:41 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,1160 +0,0 @@\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 0ae768a0e5c0 -r 7b2f205b3f68 test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.sdf --- a/test-data/NuBBE_1_obabel_3D_-_3u1i_for_DM.sdf Wed Jun 19 06:43:41 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,1620 +0,0 @@\n-./output1.dat\n- OpenBabel06171915303D\n-\n- 23 23 0 0 0 0 0 0 0 0999 V2000\n- 66.9030 73.3450 36.0040 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.8190 73.2170 37.2120 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.0490 72.3370 37.8940 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.2290 70.9500 37.5970 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.2070 70.4140 38.6010 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 68.5140 70.1440 38.3980 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.2150 70.3400 37.0800 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.3810 69.5970 39.5210 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 68.7730 69.8280 40.9100 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.3750 71.0120 41.6220 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 68.7550 72.1570 41.9760 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.3280 72.4970 41.6430 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.4770 73.2270 42.7560 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.5570 74.0540 38.1920 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.9010 75.0480 38.9340 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.6300 75.8170 39.8300 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 68.9950 75.5990 39.9980 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.6510 74.6060 39.2850 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 68.9300 73.8240 38.3800 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.0450 76.8040 40.5760 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.5560 77.4980 40.9760 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.7010 76.3670 40.8780 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.2520 76.7930 41.5990 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 2 0 0 0 0\n- 2 3 1 0 0 0 0\n- 2 14 1 0 0 0 0\n- 4 3 1 0 0 0 0\n- 4 5 1 0 0 0 0\n- 6 5 2 0 0 0 0\n- 6 8 1 0 0 0 0\n- 7 6 1 0 0 0 0\n- 8 9 1 0 0 0 0\n- 9 10 1 0 0 0 0\n- 10 11 2 0 0 0 0\n- 11 13 1 0 0 0 0\n- 12 11 1 0 0 0 0\n- 14 19 2 0 0 0 0\n- 14 15 1 0 0 0 0\n- 15 16 2 0 0 0 0\n- 16 17 1 0 0 0 0\n- 16 20 1 0 0 0 0\n- 17 22 1 0 0 0 0\n- 18 17 2 0 0 0 0\n- 19 18 1 0 0 0 0\n- 20 21 1 0 0 0 0\n- 22 23 1 0 0 0 0\n-M END\n-> <MODEL>\n-1\n-\n-> <REMARK>\n- VINA RESULT: 0.0 0.000 0.000\n- 9 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_2 and O_3 \n- 2 A between atoms: C_2 and C_14 \n- 3 A between atoms: O_3 and C_4 \n- 4 A between atoms: C_4 and C_5 \n- 5 A between atoms: C_6 and C_8 \n- 6 A between atoms: C_8 and C_9 \n- 7 A between atoms: C_9 and C_10 \n- 8 A between atoms: C_16 and O_17 \n- 9 A between atoms: C_19 and O_20 \n-\n-> <TORSDO>\n-F 9\n-\n-> <SCORE>\n-0.0\n-\n-> <RMSD_LB>\n-0.000\n-\n-> <RMSD_UB>\n-0.000\n-\n-$$$$\n-./output1.dat\n- OpenBabel06171915303D\n-\n- 23 23 0 0 0 0 0 0 0 0999 V2000\n- 66.6610 72.1980 38.7380 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.7310 71.5290 37.7240 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.8850 70.1860 37.6330 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 65.9100 69.3760 38.2940 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 64.8700 69.0260 37.2700 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 63.6420 69.5710 37.1410 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 63.1050 70.6500 38.0430 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 62.6920 69.1050 36.0480 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 63.4080 68.3600 34.9150 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 63.6580 69.2300 33.7100 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 64.8520 69.6150 33.2110 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.1830 69.2970 33.8330 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 64.9420 70.4310 31.9460 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.6870 72.0910 36.3500 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.8460 72.1740"..b" 1 0 0 0 0\n- 5 4 1 0 0 0 0\n- 5 6 2 0 0 0 0\n- 6 7 1 0 0 0 0\n- 8 6 1 0 0 0 0\n- 9 8 1 0 0 0 0\n- 10 9 1 0 0 0 0\n- 11 10 2 0 0 0 0\n- 12 11 1 0 0 0 0\n- 13 11 1 0 0 0 0\n- 14 2 1 0 0 0 0\n- 14 19 2 0 0 0 0\n- 15 14 1 0 0 0 0\n- 16 15 2 0 0 0 0\n- 16 17 1 0 0 0 0\n- 17 18 2 0 0 0 0\n- 18 19 1 0 0 0 0\n- 20 16 1 0 0 0 0\n- 21 20 1 0 0 0 0\n- 22 17 1 0 0 0 0\n- 23 22 1 0 0 0 0\n-M END\n-> <MODEL>\n-19\n-\n-> <REMARK>\n- VINA RESULT: 0.0 5.737 8.627\n- 9 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_2 and O_3 \n- 2 A between atoms: C_2 and C_14 \n- 3 A between atoms: O_3 and C_4 \n- 4 A between atoms: C_4 and C_5 \n- 5 A between atoms: C_6 and C_8 \n- 6 A between atoms: C_8 and C_9 \n- 7 A between atoms: C_9 and C_10 \n- 8 A between atoms: C_16 and O_17 \n- 9 A between atoms: C_19 and O_20 \n-\n-> <TORSDO>\n-F 9\n-\n-> <SCORE>\n-0.0\n-\n-> <RMSD_LB>\n-5.737\n-\n-> <RMSD_UB>\n-8.627\n-\n-$$$$\n-./output1.dat\n- OpenBabel06171915303D\n-\n- 23 23 0 0 0 0 0 0 0 0999 V2000\n- 66.6420 67.4990 40.1730 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.8380 68.6440 40.5360 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.8530 69.1000 41.3080 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.1820 68.8470 40.8480 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.6150 70.0630 40.0810 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.6800 70.1970 38.7400 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 69.3200 69.1030 37.7690 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 70.1450 71.5000 38.1080 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 70.0730 72.6890 39.0730 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 68.8480 73.5420 38.8600 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.8250 73.7350 39.7180 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 67.6850 73.0530 41.0510 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 66.7000 74.6830 39.3890 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 65.9480 69.7870 40.2070 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 65.0990 70.3450 41.1740 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 64.2740 71.4040 40.8210 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 64.2960 71.9130 39.5250 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 65.1460 71.3820 38.5650 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 65.9820 70.3160 38.9060 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 63.4210 71.9850 41.7190 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 62.7920 72.6460 41.4570 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 63.4750 72.9500 39.1890 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 62.7330 72.7990 38.6140 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 2 0 0 0 0\n- 2 3 1 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 4 1 0 0 0 0\n- 6 5 2 0 0 0 0\n- 7 6 1 0 0 0 0\n- 8 6 1 0 0 0 0\n- 8 9 1 0 0 0 0\n- 10 9 1 0 0 0 0\n- 10 11 2 0 0 0 0\n- 11 12 1 0 0 0 0\n- 13 11 1 0 0 0 0\n- 14 2 1 0 0 0 0\n- 14 15 2 0 0 0 0\n- 16 15 1 0 0 0 0\n- 16 20 1 0 0 0 0\n- 17 16 2 0 0 0 0\n- 18 19 2 0 0 0 0\n- 18 17 1 0 0 0 0\n- 19 14 1 0 0 0 0\n- 21 20 1 0 0 0 0\n- 22 17 1 0 0 0 0\n- 23 22 1 0 0 0 0\n-M END\n-> <MODEL>\n-20\n-\n-> <REMARK>\n- VINA RESULT: 0.0 2.715 4.755\n- 9 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_2 and O_3 \n- 2 A between atoms: C_2 and C_14 \n- 3 A between atoms: O_3 and C_4 \n- 4 A between atoms: C_4 and C_5 \n- 5 A between atoms: C_6 and C_8 \n- 6 A between atoms: C_8 and C_9 \n- 7 A between atoms: C_9 and C_10 \n- 8 A between atoms: C_16 and O_17 \n- 9 A between atoms: C_19 and O_20 \n-\n-> <TORSDO>\n-F 9\n-\n-> <SCORE>\n-0.0\n-\n-> <RMSD_LB>\n-2.715\n-\n-> <RMSD_UB>\n-4.755\n-\n-$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/box.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/box.txt Wed Oct 02 12:49:30 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ + +size_x = 18.768 +size_y = 10.205999999999996 +size_z = 15.521999999999991 +center_x = 36.454 +center_y = -43.608000000000004 +center_z = 75.176 |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/config_complexo_dm.txt --- a/test-data/config_complexo_dm.txt Wed Jun 19 06:43:41 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -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 |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/input_ligand.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_ligand.pdbqt Wed Oct 02 12:49:30 2019 -0400 |
| b |
| @@ -0,0 +1,39 @@ +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_8 +REMARK 2 A between atoms: C_2 and C_13 +REMARK 3 A between atoms: C_8 and C_9 +REMARK 4 A between atoms: C_8 and O_18 +REMARK 5 A between atoms: C_10 and O_18 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 32.005 -44.916 74.336 0.00 0.00 +0.121 A +ATOM 2 C UNL 1 32.549 -44.128 75.349 0.00 0.00 +0.046 A +ATOM 3 C UNL 1 33.923 -44.093 75.533 0.00 0.00 +0.012 A +ATOM 4 C UNL 1 34.786 -44.839 74.720 0.00 0.00 -0.018 A +ATOM 5 C UNL 1 34.208 -45.623 73.711 0.00 0.00 +0.012 A +ATOM 6 C UNL 1 32.837 -45.668 73.510 0.00 0.00 +0.046 A +ENDROOT +BRANCH 4 7 +ATOM 7 C UNL 1 36.265 -44.807 74.914 0.00 0.00 -0.018 A +ATOM 8 C UNL 1 36.840 -44.968 76.179 0.00 0.00 +0.008 A +ATOM 9 C UNL 1 38.220 -44.942 76.345 0.00 0.00 +0.001 A +ATOM 10 C UNL 1 39.053 -44.765 75.258 0.00 0.00 +0.000 A +ATOM 11 C UNL 1 38.505 -44.603 73.996 0.00 0.00 +0.001 A +ATOM 12 C UNL 1 37.126 -44.628 73.827 0.00 0.00 +0.008 A +ENDBRANCH 4 7 +BRANCH 1 13 +ATOM 13 O UNL 1 30.638 -44.943 74.167 0.00 0.00 -0.483 OA +BRANCH 13 15 +ATOM 14 C UNL 1 29.070 -43.224 73.766 0.00 0.00 +0.058 C +ATOM 15 C UNL 1 30.063 -44.175 73.116 0.00 0.00 +0.216 C +BRANCH 15 16 +ATOM 16 C UNL 1 29.431 -45.148 72.125 0.00 0.00 +0.082 C +ATOM 17 O UNL 1 28.191 -45.276 72.149 0.00 0.00 -0.546 OA +ATOM 18 O UNL 1 30.205 -45.764 71.367 0.00 0.00 -0.546 OA +ENDBRANCH 15 16 +ENDBRANCH 13 15 +ENDBRANCH 1 13 +TORSDOF 4 |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/input_ligands.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_ligands.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| @@ -0,0 +1,190 @@ + + OpenBabel06051719483D + + 18 19 0 0 0 0 2 V2000 + 29.0700 -43.2240 73.7660 C 0 0 0 0 0 + 36.2650 -44.8070 74.9140 C 0 0 0 0 0 + 37.1260 -44.6280 73.8270 C 0 0 0 0 0 + 38.5050 -44.6030 73.9960 C 0 0 0 0 0 + 39.0530 -44.7650 75.2580 C 0 0 0 0 0 + 38.2200 -44.9420 76.3450 C 0 0 0 0 0 + 36.8400 -44.9680 76.1790 C 0 0 0 0 0 + 30.0630 -44.1750 73.1160 C 0 0 0 0 0 + 29.4310 -45.1480 72.1250 C 0 0 0 0 0 + 32.0050 -44.9160 74.3360 C 0 0 0 0 0 + 32.8370 -45.6680 73.5100 C 0 0 0 0 0 + 34.2080 -45.6230 73.7110 C 0 0 0 0 0 + 34.7860 -44.8390 74.7200 C 0 0 0 0 0 + 33.9230 -44.0930 75.5330 C 0 0 0 0 0 + 32.5490 -44.1280 75.3490 C 0 0 0 0 0 + 30.2050 -45.7640 71.3670 O 0 0 0 0 0 + 28.1910 -45.2760 72.1490 O 0 0 0 0 0 + 30.6380 -44.9430 74.1670 O 0 0 0 0 0 + 1 8 1 0 0 0 + 2 3 2 0 0 0 + 2 7 1 0 0 0 + 2 13 1 0 0 0 + 3 4 1 0 0 0 + 4 5 2 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 16 2 0 0 0 + 9 17 1 0 0 0 + 10 11 2 0 0 0 + 10 15 1 0 0 0 + 10 18 1 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 + 13 14 1 0 0 0 + 14 15 2 0 0 0 +M CHG 1 17 -1 +M END +$$$$ + + OpenBabel06051719493D + + 15 15 0 0 0 0 0 0 0 0999 V2000 + 43.8380 -40.5050 75.5450 C 0 0 0 0 0 + 37.8220 -44.0850 71.6600 C 0 0 0 0 0 + 37.5780 -43.4290 69.4150 C 0 0 0 0 0 + 40.3050 -44.0100 74.8240 C 0 0 0 0 0 + 42.7750 -41.1180 74.6630 C 0 0 0 0 0 + 42.0430 -42.2190 75.0860 C 0 0 0 0 0 + 41.0610 -42.8130 74.2970 C 0 0 0 0 0 + 40.8220 -42.2590 73.0290 C 0 0 0 0 0 + 41.5460 -41.1500 72.5640 C 0 0 0 0 0 + 42.5160 -40.6050 73.4010 C 0 0 0 0 0 + 41.3160 -40.5470 71.2050 C 0 0 0 0 0 + 38.5590 -43.1100 72.5360 C 0 0 0 0 0 + 39.8270 -42.8380 72.1770 N 0 0 0 0 0 + 37.9900 -42.6530 73.5190 O 0 0 0 0 0 + 38.3500 -44.1660 70.3600 O 0 0 0 0 0 + 1 5 1 0 0 0 + 2 12 1 0 0 0 + 2 15 1 0 0 0 + 3 15 1 0 0 0 + 4 7 1 0 0 0 + 5 6 2 0 0 0 + 5 10 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 8 13 1 0 0 0 + 9 10 2 0 0 0 + 9 11 1 0 0 0 + 12 13 1 0 0 0 + 12 14 2 0 0 0 +M END +$$$$ + + OpenBabel06051719503D + + 15 15 0 0 0 0 2 V2000 + 30.4200 -44.6760 75.3810 C 0 0 0 0 0 + 34.1940 -44.4600 79.0210 C 0 0 0 0 0 + 32.8220 -44.8070 75.5180 C 0 0 0 0 0 + 32.9030 -44.5470 76.8690 C 0 0 0 0 0 + 34.1120 -44.7350 77.5380 C 0 0 0 0 0 + 35.2440 -45.1700 76.8480 C 0 0 0 0 0 + 35.1680 -45.4350 75.4980 C 0 0 0 0 0 + 33.9580 -45.2430 74.8220 C 0 0 0 0 0 + 33.3100 -46.7470 73.1260 C 0 0 0 0 0 + 37.3690 -46.4220 75.2800 C 0 0 0 0 0 + 31.6970 -44.6680 74.7450 O 0 0 0 0 0 + 33.8850 -45.4900 73.4700 O 0 0 0 0 0 + 36.2050 -45.8370 74.6970 O 0 0 0 0 0 + 35.2420 -43.9560 79.4700 O 0 0 0 0 0 + 33.2140 -44.7540 79.7160 O 0 0 0 0 0 + 1 11 1 0 0 0 + 2 5 1 0 0 0 + 2 14 2 0 0 0 + 2 15 1 0 0 0 + 3 4 2 0 0 0 + 3 8 1 0 0 0 + 3 11 1 0 0 0 + 4 5 1 0 0 0 + 5 6 2 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 7 13 1 0 0 0 + 8 12 1 0 0 0 + 9 12 1 0 0 0 + 10 13 1 0 0 0 +M CHG 1 15 -1 +M END +$$$$ + + OpenBabel06051719513D + + 14 14 0 0 0 0 2 V2000 + 38.2930 -46.7110 80.9370 C 0 0 0 0 0 + 36.9850 -45.5210 75.2940 C 0 0 0 0 0 + 38.8660 -45.6010 80.0750 C 0 0 0 0 0 + 37.8540 -45.1340 79.0500 C 0 0 0 0 0 + 38.3500 -44.0300 76.8380 C 0 0 0 0 0 + 37.0480 -44.5100 76.2540 C 0 0 0 0 0 + 35.8360 -43.9670 76.6710 C 0 0 0 0 0 + 34.6180 -44.3960 76.1610 C 0 0 0 0 0 + 34.6010 -45.3970 75.2120 C 0 0 0 0 0 + 35.7770 -45.9630 74.7700 C 0 0 0 0 0 + 38.2970 -43.9040 78.3260 N 0 0 0 0 0 + 39.3030 -44.5290 80.9000 O 0 0 0 0 0 + 38.4490 -46.2630 74.7020 Cl 0 0 0 0 0 + 35.8410 -42.7060 77.8780 Cl 0 0 0 0 0 + 1 3 1 0 0 0 + 2 6 2 0 0 0 + 2 10 1 0 0 0 + 2 13 1 0 0 0 + 3 4 1 0 0 0 + 3 12 1 0 0 0 + 4 11 1 0 0 0 + 5 6 1 0 0 0 + 5 11 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 7 14 1 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 +M CHG 1 11 1 +M END +$$$$ + + OpenBabel06051719513D + + 15 17 0 0 0 0 0 0 0 0999 V2000 + 29.2630 -45.1730 73.8460 C 0 0 0 0 0 + 37.5430 -46.6210 74.5090 C 0 0 0 0 0 + 38.7930 -46.0820 74.2450 C 0 0 0 0 0 + 30.3800 -44.8860 74.6890 C 0 0 0 0 0 + 31.5430 -45.3560 74.1430 C 0 0 0 0 0 + 29.5870 -45.8960 72.7630 C 0 0 0 0 0 + 32.8720 -45.3610 74.7260 C 0 0 0 0 0 + 33.2370 -45.1090 76.0240 C 0 0 0 0 0 + 34.5780 -45.4470 76.2870 C 0 0 0 0 0 + 35.3120 -45.5650 75.1170 C 0 0 0 0 0 + 36.7240 -45.5570 74.8040 C 0 0 0 0 0 + 38.7610 -44.7530 74.3540 N 0 0 0 0 0 + 37.4840 -44.4410 74.6930 N 0 0 0 0 0 + 31.2660 -45.9980 72.5700 S 0 0 0 0 0 + 34.2600 -45.7390 73.7630 S 0 0 0 0 0 + 1 4 1 0 0 0 + 1 6 2 0 0 0 + 2 3 1 0 0 0 + 2 11 2 0 0 0 + 3 12 2 0 0 0 + 4 5 2 0 0 0 + 5 7 1 0 0 0 + 5 14 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 15 1 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 13 1 0 0 0 + 12 13 1 0 0 0 +M END +$$$$ |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/ligand1_docked.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand1_docked.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b"@@ -0,0 +1,639 @@\n+=\n+ OpenBabel09021916083D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.9000 -44.6750 75.3700 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6880 -44.2080 75.8770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5200 -44.3960 75.1540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5270 -45.0480 73.9140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7620 -45.5050 73.4310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9390 -45.3290 74.1410 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2740 -45.2520 73.1310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2120 -46.1670 72.0750 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.0360 -46.3510 71.3570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.8990 -45.6380 71.6800 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9370 -44.7260 72.7230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1110 -44.5390 73.4420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.0530 -44.4790 76.0980 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.3930 -44.6860 76.3330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.2720 -44.2530 75.4010 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.3200 -42.7760 75.0190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7140 -42.4870 73.8720 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9750 -41.9560 75.8920 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 9 10 2 0 0 0 0\n+ 9 8 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -6.3 0.000 0.000\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-6.3\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel09021916083D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.9890 -44.7290 75.3400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7740 -44.3230 75.8900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5980 -44.5060 75.1780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6020 -45.0920 73.9050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8400 -45.4880 73.3780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0250 -45.3160 74.0770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.3410 -45.2900 73.1330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1700 -44.5940 73.4530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.0040 -44.7840 72.7210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9810 -45.6590 71.6540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1290 -46.3590 71.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2960 -46.1720 72.0490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1480 -44.5380 76.0590 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.4940 -44.7080 76.2650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.3560 -44.2790 75.3520 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.3740 -42.7950 74.9960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0060 -41.9850 75.8700 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7410 -42.4950 73.8440 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 9 8 2 0 "..b" 0 0 0 0 0 0 0 0 0\n+ 34.8520 -40.2490 79.9850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.1250 -45.2010 75.8320 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6370 -45.8600 73.6180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.4770 -44.9310 74.4800 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 35.9810 -45.1500 74.3420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.4560 -46.2100 74.7950 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.6360 -44.2400 73.7980 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 2 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 5 2 0 0 0 0\n+ 7 8 2 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 11 2 0 0 0 0\n+ 13 1 1 0 0 0 0\n+ 15 14 1 6 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 18 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -5.1 4.107 6.896\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-5.1\n+\n+> <RMSD_LB>\n+4.107\n+\n+> <RMSD_UB>\n+6.896\n+\n+$$$$\n+=\n+ OpenBabel09021916083D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 35.8450 -42.2310 77.0780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0840 -42.9180 78.0230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5460 -42.2360 79.1040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.7510 -40.8600 79.2720 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.5220 -40.1980 78.3060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.0650 -40.8630 77.2170 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.1760 -40.1210 80.4330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8090 -40.1720 80.7280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2870 -39.4820 81.8170 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.1130 -38.7390 82.6370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.4700 -38.6740 82.3630 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9940 -39.3620 81.2750 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.3760 -42.9230 76.0120 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.2250 -44.3750 76.2200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.7070 -44.2960 76.1830 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 36.0740 -45.0710 75.0320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.5290 -46.2040 74.7760 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.1520 -44.5080 74.4110 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 6 2 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 8 2 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 11 2 0 0 0 0\n+ 13 15 1 0 0 0 0\n+ 13 1 1 0 0 0 0\n+ 15 14 1 6 0 0 0\n+ 16 15 1 0 0 0 0\n+ 17 16 1 0 0 0 0\n+ 18 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -5.1 4.937 7.596\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-5.1\n+\n+> <RMSD_LB>\n+4.937\n+\n+> <RMSD_UB>\n+7.596\n+\n+$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/ligand2_docked.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand2_docked.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b"@@ -0,0 +1,612 @@\n+=\n+ OpenBabel09021916093D\n+\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 30.7270 -43.7450 76.1540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2320 -43.8770 76.1820 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9030 -44.5770 75.1900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.2880 -44.7130 75.1870 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9550 -45.4820 74.0800 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0120 -44.1090 76.2270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.3700 -43.3850 77.2450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.1200 -42.7180 78.3740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9820 -43.2890 77.1920 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.4390 -44.2310 76.2340 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8300 -44.9440 76.7890 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.2890 -43.4500 75.5420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0090 -42.3660 75.0480 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.6760 -43.9990 75.3480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.7980 -44.7930 74.1950 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.6010 -46.1780 74.4680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 9 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 4 6 1 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 10 1 0 0 0 0\n+ 6 7 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 7 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 12 10 1 0 0 0 0\n+ 13 12 2 0 0 0 0\n+ 14 12 1 0 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 14 1 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -4.9 0.000 0.000\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_5\n+ 2 A between atoms: C_2 and C_12\n+ 3 A between atoms: C_2 and O_15\n+ 4 A between atoms: C_3 and O_15\n+ 5 A between atoms: C_4 and C_7\n+ 6 A between atoms: C_8 and N_13\n+ 7 A between atoms: C_9 and C_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 3\n+\n+> <SCORE>\n+-4.9\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel09021916093D\n+\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 30.7330 -43.6060 76.3350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2340 -43.7750 76.2880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.0410 -43.2270 77.2740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.4260 -43.3690 77.2600 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.2450 -42.7520 78.3610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0040 -44.0990 76.2100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.2200 -44.6770 75.1980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.8090 -45.4740 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8400 -44.4960 75.2690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.4270 -44.2630 76.1860 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8070 -45.0000 76.7160 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.2860 -43.4900 75.4970 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0290 -42.3860 75.0350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.6520 -44.0730 75.2620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.7120 -44.8940 74.1230 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.5590 -46.2750 74.4420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 6 4 2 0 0 0 0\n+ 7 9 2 0 0 0 0\n+ 7 6 1 0 0 0 0\n+ 8 7 1 0 0 0 0\n+ 9 2 1 0 0 0 0\n+ 10 6 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 12 10 1 0 0 0 0\n+ 13 12 2 0 0 0 0\n+ 14 12 1 0 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 14 1 0 0 0 0\n+M END\n+> <MODEL>\n+2\n+\n+> <REMARK>\n+ VINA RESULT: -4.9 0.118 2.246\n+ Name = \n+ 7 active torsions:\n+ s"..b"29.3330 -42.9960 74.1500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.4010 -44.8100 72.4170 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.0440 -43.8770 74.8450 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6940 -43.1840 74.5860 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.8900 -44.1170 76.1600 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.3600 -45.1120 76.6390 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.3840 -43.0420 77.0880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.0560 -41.7460 76.6550 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.0630 -40.8000 77.7210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 2 9 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 4 6 2 0 0 0 0\n+ 6 10 1 0 0 0 0\n+ 7 6 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 7 2 0 0 0 0\n+ 10 12 1 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 12 14 1 0 0 0 0\n+ 15 14 1 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -4.3 3.964 5.892\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_5\n+ 2 A between atoms: C_2 and C_12\n+ 3 A between atoms: C_2 and O_15\n+ 4 A between atoms: C_3 and O_15\n+ 5 A between atoms: C_4 and C_7\n+ 6 A between atoms: C_8 and N_13\n+ 7 A between atoms: C_9 and C_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 3\n+\n+> <SCORE>\n+-4.3\n+\n+> <RMSD_LB>\n+3.964\n+\n+> <RMSD_UB>\n+5.892\n+\n+$$$$\n+=\n+ OpenBabel09021916093D\n+\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 36.2810 -45.5880 74.7420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.7970 -45.3090 74.6830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.0060 -45.8780 73.6960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6360 -45.6430 73.6170 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.8340 -46.2940 72.5230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.0540 -44.8050 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8200 -44.2170 75.6010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2240 -43.3170 76.6570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.1850 -44.4900 75.6220 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.6450 -44.5600 74.5200 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.0630 -45.1230 75.0810 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.0510 -43.6230 73.7590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.5710 -43.0480 72.8120 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.6490 -43.2470 74.1530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.7000 -44.2290 73.8180 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.2950 -44.1460 72.4540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 2 9 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 4 6 1 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 7 2 0 0 0 0\n+ 7 9 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 10 6 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 12 14 1 0 0 0 0\n+ 12 10 1 0 0 0 0\n+ 13 12 2 0 0 0 0\n+ 15 14 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -4.3 3.971 6.363\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_5\n+ 2 A between atoms: C_2 and C_12\n+ 3 A between atoms: C_2 and O_15\n+ 4 A between atoms: C_3 and O_15\n+ 5 A between atoms: C_4 and C_7\n+ 6 A between atoms: C_8 and N_13\n+ 7 A between atoms: C_9 and C_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 3\n+\n+> <SCORE>\n+-4.3\n+\n+> <RMSD_LB>\n+3.971\n+\n+> <RMSD_UB>\n+6.363\n+\n+$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/ligand3_docked.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand3_docked.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b"@@ -0,0 +1,594 @@\n+=\n+ OpenBabel09021916093D\n+\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 35.5160 -44.1770 76.5970 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5400 -44.3480 75.6050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.8770 -44.9300 74.3780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1800 -45.3120 74.1400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.1490 -45.1400 75.1290 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8160 -44.5650 76.3550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.5720 -45.5740 74.8710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.4810 -44.8440 75.2860 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.7610 -46.6440 74.2600 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.3170 -42.2230 77.9920 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0570 -43.6050 77.7570 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.2440 -43.9490 75.8370 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.4200 -44.9350 76.4520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8380 -45.0140 73.4880 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.1260 -46.2430 73.3400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 11 1 0 0 0 0\n+ 2 12 1 0 0 0 0\n+ 2 1 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 6 1 1 0 0 0 0\n+ 7 5 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 7 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 14 3 1 0 0 0 0\n+ 15 14 1 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -4.7 0.000 0.000\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and O_11\n+ 2 A between atoms: C_2 and C_5\n+ 3 A between atoms: C_3 and O_11\n+ 4 A between atoms: C_7 and O_13\n+ 5 A between atoms: C_8 and O_12\n+ 6 A between atoms: C_9 and O_12\n+ 7 A between atoms: C_10 and O_13\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-4.7\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel09021916093D\n+\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 34.4290 -45.2520 74.5550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.1990 -44.7310 75.8360 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.2630 -44.2340 76.5960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.5440 -44.2810 76.0890 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.7700 -44.8010 74.8140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.7120 -45.2930 74.0520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.1730 -44.8380 74.2550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.6020 -43.8130 73.7110 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.8260 -45.8920 74.3700 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8550 -44.9990 72.7490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.3040 -45.6970 73.9090 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9220 -44.7010 76.3480 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2040 -43.5000 76.0850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9060 -43.7790 77.8380 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.2090 -42.4370 78.2190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 12 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 3 14 1 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 9 1 0 0 0 0\n+ 7 5 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 11 1 1 0 0 0 0\n+ 13 12 1 0 0 0 0\n+ 14 15 1 0 0 0 0\n+M END\n+> <MODEL>\n+2\n+\n+> <REMARK>\n+ VINA RESULT: -4.5 0.957 3.283\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and O_11\n+ 2 A between atoms: C_2 and C_5\n+ 3 A between atoms: C_3 and O_11\n+ 4 A bet"..b" 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5520 -39.7420 79.5360 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.4610 -40.9870 77.5540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.6930 -42.1710 77.2810 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.0820 -40.0230 77.0640 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5580 -38.7910 82.5190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6150 -38.5740 81.4700 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.3180 -39.9000 81.2450 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.4360 -38.8530 80.8500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.8920 -41.7040 79.3540 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.4610 -42.4730 78.2320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 11 1 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 2 12 1 0 0 0 0\n+ 3 14 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 4 5 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 7 5 1 0 0 0 0\n+ 8 7 1 0 0 0 0\n+ 9 7 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 13 12 1 0 0 0 0\n+ 15 14 1 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -3.7 4.675 6.625\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and O_11\n+ 2 A between atoms: C_2 and C_5\n+ 3 A between atoms: C_3 and O_11\n+ 4 A between atoms: C_7 and O_13\n+ 5 A between atoms: C_8 and O_12\n+ 6 A between atoms: C_9 and O_12\n+ 7 A between atoms: C_10 and O_13\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-3.7\n+\n+> <RMSD_LB>\n+4.675\n+\n+> <RMSD_UB>\n+6.625\n+\n+$$$$\n+=\n+ OpenBabel09021916093D\n+\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 34.1480 -43.6220 77.0860 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8810 -43.8000 76.5150 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.7470 -44.4510 75.2840 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8720 -44.8960 74.6230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.1320 -44.7170 75.1930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.2690 -44.0730 76.4230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.3620 -45.2200 74.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8640 -44.4890 73.6130 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8100 -46.3410 74.7860 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.8100 -41.7230 78.4140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.1440 -42.9800 78.2990 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.7600 -43.3380 77.1680 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.3800 -42.0080 76.8280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.4580 -44.5350 74.8260 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.1740 -44.2830 73.4500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 11 1 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 2 12 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 4 5 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 7 9 1 0 0 0 0\n+ 7 5 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 13 12 1 0 0 0 0\n+ 14 3 1 0 0 0 0\n+ 15 14 1 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -3.7 1.807 2.240\n+ Name = \n+ 7 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and O_11\n+ 2 A between atoms: C_2 and C_5\n+ 3 A between atoms: C_3 and O_11\n+ 4 A between atoms: C_7 and O_13\n+ 5 A between atoms: C_8 and O_12\n+ 6 A between atoms: C_9 and O_12\n+ 7 A between atoms: C_10 and O_13\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-3.7\n+\n+> <RMSD_LB>\n+1.807\n+\n+> <RMSD_UB>\n+2.240\n+\n+$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/ligand4_docked.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand4_docked.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b"@@ -0,0 +1,621 @@\n+=\n+ OpenBabel09021916103D\n+\n+ 17 17 0 0 1 0 0 0 0 0999 V2000\n+ 33.6530 -43.4110 76.9560 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.5760 -44.3910 75.8160 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.3800 -45.0310 75.5040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.9550 -44.6740 76.4480 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2790 -45.9490 74.4680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.3990 -46.2450 73.7200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.6040 -45.6350 73.9920 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.6850 -44.7210 75.0350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.2300 -43.9700 75.3420 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.3670 -43.9700 78.1430 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0650 -44.6170 77.7760 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6770 -44.4160 78.7460 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.1170 -42.9680 78.9600 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.2970 -40.4860 78.7440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.3820 -41.6490 79.0800 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 33.8390 -41.4730 80.3820 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5070 -41.7050 81.0450 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 10 1 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 5 3 2 0 0 0 0\n+ 6 7 2 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 8 2 2 0 0 0 0\n+ 10 12 1 0 0 0 0\n+ 10 13 1 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 13 15 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 16 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -4.7 0.000 0.000\n+ Name = \n+ 6 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_3\n+ 2 A between atoms: C_3 and C_4\n+ 3 A between atoms: C_3 and O_12\n+ 4 A between atoms: C_4 and N_11\n+ 5 A between atoms: C_5 and C_6\n+ 6 A between atoms: C_5 and N_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 5\n+\n+> <SCORE>\n+-4.7\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel09021916103D\n+\n+ 17 17 0 0 1 0 0 0 0 0999 V2000\n+ 33.7330 -43.3710 76.9460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6010 -44.3820 75.8380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.6940 -44.7140 75.0420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.2330 -43.9510 75.3500 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.6020 -45.6330 74.0050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.3890 -46.2380 73.7470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.2810 -45.9390 74.5100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.3930 -45.0150 75.5410 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.9660 -44.6710 76.4840 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.3590 -43.9470 78.1740 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0640 -44.6080 77.8500 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6220 -44.3800 78.7300 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0770 -42.9630 79.0400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.2850 -40.4890 78.7630 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.3570 -41.6340 79.1280 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 33.8170 -41.4200 80.4250 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9040 -41.7450 80.4530 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 10 1 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 5 3 1 0 0 0 0\n+ 6 5 2 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 2 0 0 0 0\n+ 8 2 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 10 12 1 0 0 0 0\n+ 10 13 1 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 13 15 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 16 1 0 0 0 0\n+"..b"l 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1420 -45.8880 71.7040 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.2370 -45.6460 72.1060 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.4900 -46.7980 72.0060 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.9400 -45.9370 70.2240 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.6540 -44.9350 70.1160 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.4930 -46.1700 69.8420 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 27.9460 -47.2850 70.5340 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.6250 -47.9690 70.6330 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 2 8 1 0 0 0 0\n+ 3 5 1 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 7 6 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 9 8 1 0 0 0 0\n+ 10 12 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 1 1 0 0 0 0\n+ 13 10 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 13 1 0 0 0 0\n+ 15 16 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -4.0 5.260 7.358\n+ Name = \n+ 6 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_3\n+ 2 A between atoms: C_3 and C_4\n+ 3 A between atoms: C_3 and O_12\n+ 4 A between atoms: C_4 and N_11\n+ 5 A between atoms: C_5 and C_6\n+ 6 A between atoms: C_5 and N_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 5\n+\n+> <SCORE>\n+-4.0\n+\n+> <RMSD_LB>\n+5.260\n+\n+> <RMSD_UB>\n+7.358\n+\n+$$$$\n+=\n+ OpenBabel09021916103D\n+\n+ 17 17 0 0 1 0 0 0 0 0999 V2000\n+ 34.5130 -42.2860 79.2430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8220 -40.9820 79.5390 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5300 -39.9010 80.0590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.2420 -40.0700 80.3530 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.9200 -38.6890 80.3540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5660 -38.5460 80.1320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.8260 -39.5890 79.6190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.4550 -40.7940 79.3320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.4800 -42.0860 78.6800 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.7760 -42.4750 77.7840 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0570 -41.5630 77.4250 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.9240 -42.8340 77.3540 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.8910 -43.4140 77.4580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.4060 -45.3030 75.9060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.8430 -43.8980 76.0240 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 36.5490 -43.0220 75.1550 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.9180 -42.5470 74.5930 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 3 5 2 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 6 2 0 0 0 0\n+ 8 2 2 0 0 0 0\n+ 8 7 1 0 0 0 0\n+ 9 8 1 0 0 0 0\n+ 10 1 1 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 10 1 0 0 0 0\n+ 13 10 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n+ 17 16 1 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -3.9 3.392 6.457\n+ Name = \n+ 6 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_3\n+ 2 A between atoms: C_3 and C_4\n+ 3 A between atoms: C_3 and O_12\n+ 4 A between atoms: C_4 and N_11\n+ 5 A between atoms: C_5 and C_6\n+ 6 A between atoms: C_5 and N_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 5\n+\n+> <SCORE>\n+-3.9\n+\n+> <RMSD_LB>\n+3.392\n+\n+> <RMSD_UB>\n+6.457\n+\n+$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/ligand5_docked.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand5_docked.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b"@@ -0,0 +1,585 @@\n+=\n+ OpenBabel09021916103D\n+\n+ 16 18 0 0 1 0 0 0 0 0999 V2000\n+ 35.0590 -45.0990 74.7630 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 34.0860 -44.5170 76.0710 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6340 -44.9860 75.2690 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 32.9250 -45.7580 74.1550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.2710 -45.6170 73.7660 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.4120 -44.4980 75.8690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.0250 -44.7450 77.1440 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.5510 -45.2630 77.7960 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.8160 -44.1840 77.4030 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.4430 -43.5860 76.2710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.4050 -43.7650 75.2880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.7470 -45.5580 74.8960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.7940 -44.2900 75.3300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.2940 -43.5240 75.1590 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.5060 -45.0170 74.8210 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 37.4200 -46.0180 74.6370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 1 0 0 0\n+ 1 15 1 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 3 6 1 6 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 9 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 10 9 2 0 0 0 0\n+ 11 6 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 14 13 1 0 0 0 0\n+ 15 16 1 1 0 0 0\n+ 15 14 1 0 0 0 0\n+ 16 12 1 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -5.2 0.000 0.000\n+ Name = \n+ 2 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_5 and C_7\n+ 2 A between atoms: C_10 and C_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 2\n+\n+> <SCORE>\n+-5.2\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel09021916103D\n+\n+ 16 18 0 0 1 0 0 0 0 0999 V2000\n+ 33.8500 -44.7820 74.9490 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 35.4480 -44.9340 74.3020 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1510 -44.3520 75.7640 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 35.1930 -44.2700 76.7620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8900 -44.2950 76.2310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.5630 -44.0470 75.6910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0840 -42.9300 75.1270 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.5490 -42.2030 74.7340 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.4400 -42.9460 75.1780 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.7680 -44.0930 75.7740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.6290 -44.8130 76.1020 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2980 -46.1930 72.6390 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.5800 -45.0930 72.9130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2460 -44.2290 74.2080 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6910 -45.1630 74.1630 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 32.5530 -46.2320 73.3200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 1 0 0 0\n+ 2 1 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 6 1 6 0 0 0\n+ 3 4 1 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 11 2 0 0 0 0\n+ 7 9 1 0 0 0 0\n+ 7 6 1 0 0 0 0\n+ 8 7 1 0 0 0 0\n+ 9 10 2 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 12 16 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 15 16 1 6 0 0 0\n+ 15 14 1 0 0 0 0\n+ 15 1 1 0 0 0 0\n+M END\n+> <MODEL>\n+2\n+\n+> <REMARK>\n+ VINA RESULT: -5.1 3.519 6.461\n+ Name = \n+ 2 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_5 and C_7\n+ 2 A between atoms: C_10 and"..b"0.7220 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 38.1600 -42.6100 70.5790 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.6960 -43.4000 71.6480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 40.5350 -41.8360 69.8210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 41.8320 -42.2250 69.8670 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 42.1950 -42.8820 70.5040 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 42.5650 -41.5890 68.9170 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 41.7130 -40.7870 68.2780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 40.4400 -40.9040 68.8150 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0960 -45.1840 75.9490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.3050 -44.1650 76.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.4170 -42.8720 75.2310 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.2710 -43.8340 74.0870 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 38.6330 -45.0340 74.6340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 1 0 0 0\n+ 1 15 1 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 3 6 1 6 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 7 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 9 2 0 0 0 0\n+ 11 6 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 14 13 1 0 0 0 0\n+ 15 16 1 6 0 0 0\n+ 15 14 1 0 0 0 0\n+ 16 12 1 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -4.6 6.586 8.750\n+ Name = \n+ 2 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_5 and C_7\n+ 2 A between atoms: C_10 and C_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 2\n+\n+> <SCORE>\n+-4.6\n+\n+> <RMSD_LB>\n+6.586\n+\n+> <RMSD_UB>\n+8.750\n+\n+$$$$\n+=\n+ OpenBabel09021916103D\n+\n+ 16 18 0 0 1 0 0 0 0 0999 V2000\n+ 37.7170 -43.6430 74.0280 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.8920 -43.5790 72.3070 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.4300 -42.8130 72.4390 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 39.8650 -42.8270 73.7550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.8060 -43.0840 74.6470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.9700 -42.2960 71.2010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 41.2160 -42.5530 70.7350 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 41.8690 -43.1380 71.1830 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 41.4450 -41.8960 69.5690 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 40.3280 -41.2160 69.3100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.3870 -41.4300 70.3060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.5520 -45.3650 74.9520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.6300 -44.6830 76.1060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1360 -43.9290 76.2750 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.5430 -44.2440 74.6330 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 35.6320 -45.0890 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 15 1 0 0 0 0\n+ 1 5 1 1 0 0 0\n+ 2 3 1 0 0 0 0\n+ 2 1 1 0 0 0 0\n+ 3 6 1 1 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 7 6 1 0 0 0 0\n+ 9 7 1 0 0 0 0\n+ 10 9 2 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 11 6 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 15 16 1 6 0 0 0\n+ 15 14 1 0 0 0 0\n+ 16 12 1 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -4.6 5.569 8.005\n+ Name = \n+ 2 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_5 and C_7\n+ 2 A between atoms: C_10 and C_11\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 2\n+\n+> <SCORE>\n+-4.6\n+\n+> <RMSD_LB>\n+5.569\n+\n+> <RMSD_UB>\n+8.005\n+\n+$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/ligand_params.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand_params.sdf Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b"@@ -0,0 +1,639 @@\n+=\n+ OpenBabel09251908563D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.9280 -44.6820 75.3750 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7190 -44.2180 75.8910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5470 -44.4040 75.1740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5480 -45.0510 73.9310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7800 -45.5040 73.4390 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9620 -45.3300 74.1420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2900 -45.2520 73.1550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1270 -44.5310 73.4460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9630 -44.7240 72.7110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9360 -45.6290 71.6680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.0760 -46.3550 71.3620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2400 -46.1640 72.0960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.0850 -44.4870 76.0970 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.4290 -44.6740 76.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.2990 -44.2490 75.3930 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.3310 -42.7720 75.0140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7150 -42.4760 73.8650 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9860 -41.9560 75.8910 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 9 8 2 0 0 0 0\n+ 10 9 1 0 0 0 0\n+ 11 10 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 7 2 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -6.3 0.000 0.000\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-6.3\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel09251908563D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 31.9300 -45.2520 74.0180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.3420 -44.4800 75.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6900 -44.4000 75.4200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.6560 -45.0850 74.6710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.2090 -45.8540 73.5870 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8670 -45.9430 73.2530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1070 -45.0040 75.0080 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9740 -46.0760 74.7690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.3250 -45.9860 75.0820 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.8420 -44.8280 75.6300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0010 -43.7540 75.8750 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.6500 -43.8410 75.5640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.5870 -45.3240 73.7170 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.0480 -43.9840 72.5310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1640 -45.0070 72.3960 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 29.7340 -46.3080 71.7240 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.6180 -46.7750 72.0260 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.5400 -46.8260 70.9270 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 5 2 0 0 0 0\n+ 6 1 1 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 8 9 1 0 "..b" 0 0 0 0 0 0 0 0 0\n+ 35.5820 -40.2040 79.8470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8280 -44.3780 75.0110 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.8510 -44.0720 72.9050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0660 -44.0170 74.4100 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 39.1280 -44.9860 74.9200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.0420 -46.1790 74.5660 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 40.0040 -44.5190 75.6740 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 2 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 5 2 0 0 0 0\n+ 7 8 2 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 11 2 0 0 0 0\n+ 13 1 1 0 0 0 0\n+ 15 14 1 6 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -5.0 4.650 6.732\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-5.0\n+\n+> <RMSD_LB>\n+4.650\n+\n+> <RMSD_UB>\n+6.732\n+\n+$$$$\n+=\n+ OpenBabel09251908563D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.6100 -44.4120 75.7940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7490 -43.8540 76.7380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.3970 -43.7370 76.4540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.8700 -44.1680 75.2300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.7610 -44.7240 74.3010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.1160 -44.8510 74.5680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.4160 -44.0440 74.9180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.9370 -44.1560 73.6080 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.5790 -44.0440 73.3320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.6730 -43.8270 74.3510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.1250 -43.7120 75.6550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.4820 -43.8230 75.9340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.9510 -44.5190 76.0890 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.8190 -45.6060 75.1370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.8960 -44.4020 75.0310 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.6070 -43.0610 75.1920 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9690 -42.1260 75.7140 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.7780 -42.9890 74.7720 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 1 2 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 1 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 7 12 2 0 0 0 0\n+ 8 7 1 0 0 0 0\n+ 9 8 2 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 18 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -4.9 1.456 2.281\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-4.9\n+\n+> <RMSD_LB>\n+1.456\n+\n+> <RMSD_UB>\n+2.281\n+\n+$$$$\n" |
| b |
| diff -r 0ae768a0e5c0 -r 7b2f205b3f68 test-data/protein.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein.pdbqt Wed Oct 02 12:49:30 2019 -0400 |
| b |
| b'@@ -0,0 +1,1933 @@\n+ATOM 1 N SER A 15 59.869 -59.274 94.881 1.00 76.84 -0.064 N \n+ATOM 2 HN1 SER A 15 59.189 -59.537 95.594 1.00 0.00 0.275 HD\n+ATOM 3 HN2 SER A 15 60.772 -59.726 95.024 1.00 0.00 0.275 HD\n+ATOM 4 HN3 SER A 15 59.647 -59.676 93.970 1.00 0.00 0.275 HD\n+ATOM 5 CA SER A 15 59.985 -57.783 94.828 1.00 71.13 0.297 C \n+ATOM 6 C SER A 15 58.610 -57.164 94.540 1.00 67.52 0.251 C \n+ATOM 7 O SER A 15 57.643 -57.893 94.314 1.00 65.98 -0.271 OA\n+ATOM 8 CB SER A 15 61.002 -57.390 93.761 1.00 66.24 0.206 C \n+ATOM 9 OG SER A 15 60.570 -57.811 92.472 1.00 67.23 -0.398 OA\n+ATOM 10 HG SER A 15 61.203 -57.566 91.808 1.00 0.00 0.209 HD\n+ATOM 11 N MET A 16 58.539 -55.834 94.563 1.00 58.08 -0.346 N \n+ATOM 12 HN MET A 16 59.391 -55.306 94.754 1.00 0.00 0.163 HD\n+ATOM 13 CA MET A 16 57.293 -55.088 94.326 1.00 59.05 0.177 C \n+ATOM 14 C MET A 16 56.683 -55.346 92.933 1.00 60.19 0.241 C \n+ATOM 15 O MET A 16 55.452 -55.432 92.802 1.00 57.04 -0.271 OA\n+ATOM 16 CB MET A 16 57.515 -53.574 94.563 1.00 55.78 0.045 C \n+ATOM 17 CG MET A 16 56.673 -52.616 93.735 1.00 58.54 0.076 C \n+ATOM 18 SD MET A 16 56.941 -50.885 94.202 1.00 67.90 -0.173 SA\n+ATOM 19 CE MET A 16 58.554 -50.592 93.508 1.00 63.96 0.089 C \n+ATOM 20 N LEU A 17 57.526 -55.468 91.912 1.00 53.59 -0.346 N \n+ATOM 21 HN LEU A 17 58.531 -55.493 92.086 1.00 0.00 0.163 HD\n+ATOM 22 CA LEU A 17 57.027 -55.566 90.550 1.00 55.31 0.177 C \n+ATOM 23 C LEU A 17 56.583 -56.984 90.257 1.00 55.34 0.241 C \n+ATOM 24 O LEU A 17 55.576 -57.195 89.583 1.00 50.16 -0.271 OA\n+ATOM 25 CB LEU A 17 58.079 -55.116 89.534 1.00 53.94 0.038 C \n+ATOM 26 CG LEU A 17 58.257 -53.602 89.470 1.00 56.21 -0.020 C \n+ATOM 27 CD1 LEU A 17 59.299 -53.272 88.406 1.00 54.07 0.009 C \n+ATOM 28 CD2 LEU A 17 56.947 -52.872 89.190 1.00 55.51 0.009 C \n+ATOM 29 N ASP A 18 57.343 -57.937 90.783 1.00 53.67 -0.346 N \n+ATOM 30 HN ASP A 18 58.158 -57.664 91.332 1.00 0.00 0.163 HD\n+ATOM 31 CA ASP A 18 57.063 -59.355 90.610 1.00 55.96 0.186 C \n+ATOM 32 C ASP A 18 55.817 -59.777 91.346 1.00 54.31 0.241 C \n+ATOM 33 O ASP A 18 55.071 -60.644 90.851 1.00 51.31 -0.271 OA\n+ATOM 34 CB ASP A 18 58.244 -60.213 91.111 1.00 63.00 0.147 C \n+ATOM 35 CG ASP A 18 59.374 -60.344 90.084 1.00 68.30 0.175 C \n+ATOM 36 OD1 ASP A 18 59.406 -59.615 89.060 1.00 65.22 -0.648 OA\n+ATOM 37 OD2 ASP A 18 60.238 -61.215 90.313 1.00 75.83 -0.648 OA\n+ATOM 38 N ASP A 19 55.625 -59.203 92.540 1.00 51.81 -0.345 N \n+ATOM 39 HN ASP A 19 56.363 -58.612 92.924 1.00 0.00 0.163 HD\n+ATOM 40 CA ASP A 19 54.401 -59.389 93.315 1.00 54.58 0.186 C \n+ATOM 41 C ASP A 19 53.161 -58.848 92.558 1.00 48.17 0.241 C \n+ATOM 42 O ASP A 19 52.182 -59.582 92.412 1.00 43.63 -0.271 OA\n+ATOM 43 CB ASP A 19 54.528 -58.761 94.712 1.00 64.34 0.147 C \n+ATOM 44 CG ASP A 19 55.601 -59.459 95.597 1.00 73.54 0.175 C \n+ATOM 45 OD1 ASP A 19 56.010 -60.625 95.311 1.00 69.01 -0.648 OA\n+ATOM 46 OD2 ASP A 19 56.047 -58.812 96.580 1.00 74.57 -0.648 OA\n+ATOM 47 N ALA A 20 53.250 -57.621 92.027 1.00 39.46 -0.346 N \n+ATOM 48 HN ALA A 20 54.104 -57.084 92.177 1.00 0.00 0.163 HD\n+ATOM 49 CA ALA A 20 52.188 -57.028 91.253 1.00 39.99 0.172 C \n+ATOM 5'..b'1.00 53.99 0.000 OA\n+HETATM 1882 O HOH B 152 36.679 -51.241 100.506 1.00 57.57 0.000 OA\n+HETATM 1883 O HOH B 153 52.191 -61.314 94.961 1.00 58.41 0.000 OA\n+HETATM 1884 O HOH B 154 43.934 -26.726 90.863 1.00 59.30 0.000 OA\n+HETATM 1885 O HOH B 155 53.659 -36.279 85.569 1.00 52.56 0.000 OA\n+HETATM 1886 O HOH B 158 42.200 -33.494 96.714 1.00 56.16 0.000 OA\n+HETATM 1887 O HOH B 159 55.504 -39.201 82.113 1.00 59.28 0.000 OA\n+HETATM 1888 O HOH B 160 30.376 -55.240 82.444 1.00 63.54 0.000 OA\n+HETATM 1889 O HOH B 161 51.795 -59.031 96.828 1.00 67.98 0.000 OA\n+HETATM 1890 O HOH B 162 22.526 -46.703 74.926 1.00 57.40 0.000 OA\n+HETATM 1891 O HOH B 164 50.733 -57.148 73.024 1.00 56.47 0.000 OA\n+HETATM 1892 O HOH B 165 48.104 -47.994 59.942 1.00 45.95 0.000 OA\n+HETATM 1893 O HOH B 166 54.973 -56.153 97.297 1.00 64.13 0.000 OA\n+HETATM 1894 O HOH B 167 39.253 -43.161 103.576 1.00 54.76 0.000 OA\n+HETATM 1895 O HOH B 170 51.981 -48.990 95.987 1.00 43.41 0.000 OA\n+HETATM 1896 O HOH B 171 51.448 -48.354 56.783 1.00 56.00 0.000 OA\n+HETATM 1897 O HOH B 172 60.277 -51.573 96.315 1.00 57.45 0.000 OA\n+HETATM 1898 O HOH B 174 51.577 -54.024 69.020 1.00 60.28 0.000 OA\n+HETATM 1899 O HOH B 175 35.389 -59.160 66.962 1.00 73.86 0.000 OA\n+HETATM 1900 O HOH B 176 54.325 -40.404 94.788 1.00 71.31 0.000 OA\n+HETATM 1901 O HOH B 178 30.495 -40.155 85.802 1.00 63.37 0.000 OA\n+HETATM 1902 O HOH B 179 50.958 -37.034 91.471 1.00 53.17 0.000 OA\n+HETATM 1903 O HOH B 180 53.453 -52.474 96.288 1.00 57.62 0.000 OA\n+HETATM 1904 O HOH B 182 54.933 -49.346 66.605 1.00 65.59 0.000 OA\n+HETATM 1905 O HOH B 184 52.755 -38.706 96.230 1.00 60.20 0.000 OA\n+HETATM 1906 O HOH B 188 48.197 -39.939 97.526 1.00 38.94 0.000 OA\n+HETATM 1907 O HOH B 190 47.525 -59.982 77.805 1.00 58.12 0.000 OA\n+HETATM 1908 O HOH B 191 51.832 -50.237 67.773 1.00 58.72 0.000 OA\n+HETATM 1909 O HOH B 192 49.087 -42.082 98.262 1.00 50.34 0.000 OA\n+HETATM 1910 O HOH B 193 60.481 -55.025 91.931 1.00 49.74 0.000 OA\n+HETATM 1911 O HOH B 194 26.866 -55.431 67.876 1.00 55.14 0.000 OA\n+HETATM 1912 O HOH B 196 42.244 -39.591 71.487 1.00 60.09 0.000 OA\n+HETATM 1913 O HOH B 199 61.339 -56.770 90.212 1.00 59.65 0.000 OA\n+TER 1914 HOH B 199 \n+HETATM 1914 C ACT D 1 39.632 -32.467 85.009 1.00 92.90 0.168 C \n+HETATM 1915 O ACT D 1 39.508 -32.058 86.187 1.00 93.19 -0.648 OA\n+HETATM 1916 CH3 ACT D 1 38.386 -32.806 84.223 1.00 84.58 0.129 C \n+HETATM 1917 OXT ACT D 1 40.773 -32.594 84.493 1.00 90.66 -0.648 OA\n+HETATM 1918 C ACT D 2 58.453 -56.204 76.997 1.00 88.70 0.168 C \n+HETATM 1919 O ACT D 2 57.709 -56.233 75.983 1.00 85.04 -0.648 OA\n+HETATM 1920 CH3 ACT D 2 58.693 -57.480 77.774 1.00 83.03 0.129 C \n+HETATM 1921 OXT ACT D 2 58.996 -55.131 77.372 1.00 85.86 -0.648 OA\n+TER 1922 ACT D 2 \n+HETATM 1922 O DMS C 1 60.177 -42.366 76.499 1.00 68.99 -0.259 OA\n+HETATM 1923 C1 DMS C 1 60.547 -42.644 73.915 1.00 91.27 0.126 C \n+HETATM 1924 C2 DMS C 1 58.286 -41.770 74.686 1.00 93.07 0.126 C \n+HETATM 1925 S DMS C 1 59.919 -41.707 75.193 1.00 96.08 0.006 S \n+HETATM 1926 O DMS C 2 62.131 -50.369 84.252 1.00100.77 -0.259 OA\n+HETATM 1927 C1 DMS C 2 63.293 -52.714 84.253 1.00108.09 0.126 C \n+HETATM 1928 C2 DMS C 2 60.654 -52.426 84.716 1.00115.63 0.126 C \n+HETATM 1929 S DMS C 2 61.947 -51.761 83.804 1.00116.45 0.006 S \n+TER 1930 DMS C 2 \n' |