annotate prepare_ligand.xml @ 1:1b4a6ebd9898 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787

<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>