annotate prepare_ligand.xml @ 0:965badb456d4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472

<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>