# HG changeset patch
# User bgruening
# Date 1465058254 14400
# Node ID 965badb456d4a32068e79d87053dc71a4fa72437

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

diff -r 000000000000 -r 965badb456d4 prepare_ligand.xml
--- /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>
diff -r 000000000000 -r 965badb456d4 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	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
diff -r 000000000000 -r 965badb456d4 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	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