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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:
prepare_ligand.xml test-data/NuBBE_1_obabel_3D.mol2 test-data/NuBBE_1_obabel_3D.pdbqt |
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removed:
prepare_receptor.xml test-data/3u1i_for_DM.pdb test-data/3u1i_for_DM.pdbqt |
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| diff -r 8bc060fcf41a -r d9ee79230d31 prepare_ligand.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_ligand.xml Fri Jun 03 16:49:02 2016 -0400 |
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| @@ -0,0 +1,148 @@ +<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 8bc060fcf41a -r d9ee79230d31 prepare_receptor.xml --- a/prepare_receptor.xml Fri Jun 03 16:48:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,92 +0,0 @@ -<tool id="prepare_receptor" name="Prepare receptor" version="0.1.0"> - <description>- Tool to prepare receptor 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 $receptor ./receptor.pdb && prepare_receptor4.py -r ./receptor.pdb -o "$file_output" -v -U nphs_lps -A hydrogens - ]]></command> - <inputs> - <param type="data" name="receptor" format="pdb" help="Select a pdb file." /> - </inputs> - <outputs> - <data name="file_output" format="pdbqt" label="#echo os.path.splitext (str($receptor.name))[0]#.pdbqt" /> - </outputs> - <tests> - <test> - <param name="receptor" value="3u1i_for_DM.pdb"/> - <output name="file_output" file="3u1i_for_DM.pdbqt"/> - </test> - </tests> - <help><![CDATA[ - ** What it does? ** - - This tool uses the MGLTools programming packages to convert a pdb molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. - - ** input ** - - It's required at least one pdb dataset in history, what is informed in ligand field, for use the tool. The pdb molecule file looks like the following example: - - ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C - ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O - ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C - ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H - ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H - ATOM 6 3HH3 ACE A 49 5.518 -4.686 7.568 1.00 0.00 H - ATOM 7 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 N - ATOM 8 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 C - ATOM 9 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 C - ATOM 10 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 O - ATOM 11 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 C - ATOM 12 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 C - ATOM 13 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 O - ATOM 14 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 O1- - ATOM 15 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 N - ATOM 16 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 C - ATOM 17 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 C - ATOM 18 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 O - ATOM 19 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 C - ATOM 20 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 C - ATOM 21 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 C - ATOM 22 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 C - ATOM 23 N THR A 52 10.527 -5.061 16.117 1.00 55.68 N - ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C - ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C - ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O - ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C - - ** output ** - - The output is a pdbqt molecule file converted from a pdb molecule file. The pdbqt molecule file looks like the following example: - - ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C - ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA - ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C - ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N - ATOM 5 HN ASP A 50 6.246 -5.360 11.009 1.00 0.00 0.163 HD - ATOM 6 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 0.186 C - ATOM 7 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 0.241 C - ATOM 8 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 -0.271 OA - ATOM 9 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 0.147 C - ATOM 10 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 0.175 C - ATOM 11 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 -0.648 OA - ATOM 12 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 -0.648 OA - ATOM 13 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 -0.346 N - ATOM 14 HN LEU A 51 10.177 -3.384 12.264 1.00 0.00 0.163 HD - ATOM 15 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 0.177 C - ATOM 16 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 0.241 C - ATOM 17 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 -0.271 OA - ATOM 18 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 0.038 C - ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C - ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C - ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C - ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N - ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD - ]]></help> - <citations> - <citation type="doi">10.1002/jcc.21334</citation> - </citations> -</tool> \ No newline at end of file |
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| diff -r 8bc060fcf41a -r d9ee79230d31 test-data/3u1i_for_DM.pdb --- a/test-data/3u1i_for_DM.pdb Fri Jun 03 16:48:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1627 +0,0 @@\n-ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C \n-ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O \n-ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C \n-ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H \n-ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H \n-ATOM 6 3HH3 ACE A 49 5.518 -4.686 7.568 1.00 0.00 H \n-ATOM 7 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 N \n-ATOM 8 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 C \n-ATOM 9 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 C \n-ATOM 10 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 O \n-ATOM 11 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 C \n-ATOM 12 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 C \n-ATOM 13 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 O \n-ATOM 14 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 O1-\n-ATOM 15 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 N \n-ATOM 16 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 C \n-ATOM 17 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 C \n-ATOM 18 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 O \n-ATOM 19 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 C \n-ATOM 20 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 C \n-ATOM 21 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 C \n-ATOM 22 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 C \n-ATOM 23 N THR A 52 10.527 -5.061 16.117 1.00 55.68 N \n-ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C \n-ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C \n-ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O \n-ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C \n-ATOM 28 CG2 THR A 52 9.344 -5.211 19.697 1.00 57.60 C \n-ATOM 29 OG1 THR A 52 8.263 -3.881 18.000 1.00 59.52 O \n-ATOM 30 N VAL A 53 11.995 -4.605 19.433 1.00 52.78 N \n-ATOM 31 CA VAL A 53 13.184 -4.932 20.191 1.00 50.89 C \n-ATOM 32 C VAL A 53 12.790 -5.088 21.663 1.00 51.45 C \n-ATOM 33 O VAL A 53 12.137 -4.217 22.224 1.00 52.72 O \n-ATOM 34 CB VAL A 53 14.252 -3.824 19.943 1.00 50.64 C \n-ATOM 35 CG1 VAL A 53 15.024 -3.484 21.172 1.00 51.07 C \n-ATOM 36 CG2 VAL A 53 15.176 -4.211 18.809 1.00 48.66 C \n-ATOM 37 N GLU A 54 13.149 -6.211 22.281 1.00 50.29 N \n-ATOM 38 CA GLU A 54 12.846 -6.399 23.696 1.00 50.84 C \n-ATOM 39 C GLU A 54 14.024 -6.935 24.512 1.00 49.31 C \n-ATOM 40 O GLU A 54 14.646 -7.934 24.159 1.00 47.75 O \n-ATOM 41 CB GLU A 54 11.551 -7.200 23.896 1.00 51.87 C \n-ATOM 42 CG GLU A 54 11.689 -8.703 23.982 1.00 53.50 C \n-ATOM 43 CD GLU A 54 10.417 -9.381 24.495 1.00 58.29 C \n-ATOM 44 OE1 GLU A 54 10.519 -10.418 25.200 1.00 59.29 O \n-ATOM 45 OE2 GLU A 54 9.313 -8.875 24.194 1.00 60.50 O1-\n-ATOM 46 N LYS A 55 14.318 -6.231 25.596 1.00 49.81 N \n-ATOM 47 CA LYS A 55 15.435 -6.521 26.496 1.00 49.61 C \n-ATOM 48 C LYS A 55 15.433 -7.962 27.023 1.00 49.10 C \n-ATOM 49 O LYS A 55 14.388 -8.'..b'66 31.761 -12.886 14.194 1.00 0.00 N \n-ATOM 1580 CA ALA B 166 31.563 -11.731 13.318 1.00 0.00 C \n-ATOM 1581 C ALA B 166 31.911 -10.421 14.039 1.00 0.00 C \n-ATOM 1582 O ALA B 166 31.257 -10.037 15.004 1.00 0.00 O \n-ATOM 1583 CB ALA B 166 30.143 -11.702 12.741 1.00 0.00 C \n-ATOM 1584 N GLN B 167 32.973 -9.770 13.581 1.00 0.00 N \n-ATOM 1585 CA GLN B 167 33.446 -8.519 14.183 1.00 0.00 C \n-ATOM 1586 C GLN B 167 34.026 -7.589 13.104 1.00 0.00 C \n-ATOM 1587 O GLN B 167 34.456 -8.043 12.045 1.00 0.00 O \n-ATOM 1588 CB GLN B 167 34.484 -8.808 15.290 1.00 0.00 C \n-ATOM 1589 CG GLN B 167 35.004 -7.601 16.100 1.00 0.00 C \n-ATOM 1590 CD GLN B 167 33.909 -6.792 16.790 1.00 0.00 C \n-ATOM 1591 NE2 GLN B 167 33.973 -6.703 18.110 1.00 0.00 N \n-ATOM 1592 OE1 GLN B 167 33.040 -6.225 16.133 1.00 0.00 O \n-ATOM 1593 N THR B 168 34.015 -6.290 13.364 1.00 0.00 N \n-ATOM 1594 CA THR B 168 34.654 -5.359 12.444 1.00 0.00 C \n-ATOM 1595 C THR B 168 35.857 -4.704 13.134 1.00 0.00 C \n-ATOM 1596 O THR B 168 36.723 -5.414 13.684 1.00 0.00 O \n-ATOM 1597 CB THR B 168 33.629 -4.361 11.810 1.00 0.00 C \n-ATOM 1598 CG2 THR B 168 33.078 -3.401 12.818 1.00 0.00 C \n-ATOM 1599 OG1 THR B 168 34.256 -3.632 10.746 1.00 0.00 O \n-ATOM 1600 N ASN B 169 35.919 -3.372 13.074 1.00 0.00 N \n-ATOM 1601 CA ASN B 169 36.844 -2.529 13.854 1.00 0.00 C \n-ATOM 1602 C ASN B 169 36.139 -1.192 14.133 1.00 0.00 C \n-ATOM 1603 O ASN B 169 35.816 -0.463 13.194 1.00 0.00 O \n-ATOM 1604 CB ASN B 169 38.168 -2.317 13.105 1.00 0.00 C \n-ATOM 1605 CG ASN B 169 38.987 -3.594 13.003 1.00 0.00 C \n-ATOM 1606 ND2 ASN B 169 38.679 -4.424 12.011 1.00 0.00 N \n-ATOM 1607 OD1 ASN B 169 39.864 -3.844 13.828 1.00 0.00 O \n-ATOM 1608 N ALA B 170 35.899 -0.889 15.413 1.00 0.00 N \n-ATOM 1609 CA ALA B 170 34.911 0.134 15.837 1.00 0.00 C \n-ATOM 1610 C ALA B 170 35.224 1.605 15.513 1.00 0.00 C \n-ATOM 1611 O ALA B 170 36.387 2.020 15.549 1.00 0.00 O \n-ATOM 1612 CB ALA B 170 34.616 -0.011 17.325 1.00 0.00 C \n-ATOM 1613 N GLU B 171 34.163 2.374 15.226 1.00 0.00 N \n-ATOM 1614 CA GLU B 171 34.214 3.825 14.927 1.00 0.00 C \n-ATOM 1615 C GLU B 171 34.565 4.100 13.458 1.00 0.00 C \n-ATOM 1616 O GLU B 171 35.734 4.246 13.088 1.00 0.00 O \n-ATOM 1617 CB GLU B 171 35.138 4.591 15.908 1.00 0.00 C \n-ATOM 1618 CG GLU B 171 35.404 6.082 15.578 1.00 0.00 C \n-ATOM 1619 CD GLU B 171 34.361 7.046 16.155 1.00 0.00 C \n-ATOM 1620 OE1 GLU B 171 33.447 6.594 16.887 1.00 0.00 O \n-ATOM 1621 OE2 GLU B 171 34.463 8.263 15.878 1.00 0.00 O1- \n-ATOM 1623 N NME B 172 33.642 3.039 13.031 1.00 0.00 N \n-ATOM 1624 CH3 NME B 172 33.700 2.990 11.580 1.00 0.00 C \n-ATOM 1625 H NME B 172 33.064 2.445 13.643 1.00 0.00 H \n-ATOM 1626 1HH3 NME B 172 34.021 3.944 11.191 1.00 0.00 H \n-ATOM 1627 2HH3 NME B 172 34.400 2.229 11.264 1.00 0.00 H \n-ATOM 1628 3HH3 NME B 172 32.724 2.757 11.179 1.00 0.00 H \n-END\n' |
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| diff -r 8bc060fcf41a -r d9ee79230d31 test-data/3u1i_for_DM.pdbqt --- a/test-data/3u1i_for_DM.pdbqt Fri Jun 03 16:48:38 2016 -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 8bc060fcf41a -r d9ee79230d31 test-data/NuBBE_1_obabel_3D.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NuBBE_1_obabel_3D.mol2 Fri Jun 03 16:49:02 2016 -0400 |
| b |
| @@ -0,0 +1,50 @@ +@<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 8bc060fcf41a -r d9ee79230d31 test-data/NuBBE_1_obabel_3D.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NuBBE_1_obabel_3D.pdbqt Fri Jun 03 16:49:02 2016 -0400 |
| b |
| @@ -0,0 +1,55 @@ +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 |