Mercurial > repos > bgruening > autodock_vina_prepare_ligand
changeset 0:965badb456d4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
| author | bgruening |
|---|---|
| date | Sat, 04 Jun 2016 12:37:34 -0400 |
| parents | |
| children | 1b4a6ebd9898 |
| files | prepare_ligand.xml test-data/NuBBE_1_obabel_3D.mol2 test-data/NuBBE_1_obabel_3D.pdbqt |
| diffstat | 3 files changed, 253 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_ligand.xml Sat Jun 04 12:37:34 2016 -0400 @@ -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="The ligand which needs to be prepared" help="In MOL2 format." /> + </inputs> + <outputs> + <data name="file_output" format="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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NuBBE_1_obabel_3D.mol2 Sat Jun 04 12:37:34 2016 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NuBBE_1_obabel_3D.pdbqt Sat Jun 04 12:37:34 2016 -0400 @@ -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