2
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
|
|
3 <!--Proposed Tool Section: [Preparation]-->
|
|
4 <tool id="Ligand3DGenerator" name="Ligand3DGenerator" version="1.1.0">
|
|
5 <description>generate 3D coordinates for small molecules</description>
|
|
6 <macros>
|
|
7 <token name="@EXECUTABLE@">Ligand3DGenerator</token>
|
|
8 <import>macros.xml</import>
|
|
9 </macros>
|
|
10 <expand macro="stdio"/>
|
|
11 <expand macro="requirements"/>
|
|
12 <command>Ligand3DGenerator
|
|
13
|
|
14 #if $param_i:
|
|
15 -i $param_i
|
|
16 #end if
|
|
17 #if $param_o:
|
|
18 -o $param_o
|
|
19 #end if
|
|
20 #if $param_ph:
|
|
21 -ph $param_ph
|
|
22 #end if
|
|
23 #if $param_ff:
|
|
24 -ff "$param_ff"
|
|
25 #end if
|
|
26 #if $param_rm:
|
|
27 -rm $param_rm
|
|
28 #end if
|
|
29 #if $param_k:
|
|
30 -k $param_k
|
|
31 #end if
|
|
32 #if $param_kp:
|
|
33 -kp $param_kp
|
|
34 #end if
|
|
35 </command>
|
|
36 <inputs>
|
|
37 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/>
|
|
38 <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/>
|
|
39 <param name="param_ff" type="text" size="30" value="MMFF94" label="Forcefield to use for optimization (any available OpenBabel plugin)" help="(-ff) ">
|
|
40 <sanitizer>
|
|
41 <valid initial="string.printable">
|
|
42 <remove value="'"/>
|
|
43 <remove value="""/>
|
|
44 </valid>
|
|
45 </sanitizer>
|
|
46 </param>
|
|
47 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
|
|
48 <param name="param_k" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates (flag precedes '-kp')" help="(-k) "/>
|
|
49 <param name="param_kp" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates but re-protonate compound in a pH dependent manner (flag is preceded by '-k')" help="(-kp) "/>
|
|
50 </inputs>
|
|
51 <expand macro="advanced_options"/>
|
|
52 <outputs>
|
|
53 <data name="param_o" metadata_source="param_i" format="input"/>
|
|
54 </outputs>
|
|
55 <help>This tool takes input molecules and generates a single 3D conformation which is ready for docking. The input has to be a chemical file
|
|
56 containing valid topologies and conistent bond order assignements. 2D coordinates in the input file are overwritten, 3D coordinates can be kept ('-k' or '-kp').
|
|
57
|
|
58 '-k': 3D coordinates are tried to be kept. Molecules with non-zero coordinates in all three dimensions are passed through without modifications.
|
|
59 However, if a molecule is not ready for docking (i.e. unusual bond leghts, unusual charges), the molecule will be rebuild and new
|
|
60 3D coordinates are assigned. If only hydrogens are missing, the coordinates of non-hydrogen atoms are kept but the molecule gets newly protonated.
|
|
61 '-kp': 3D coordinates are tried to be kept as for the '-k' flag but the molecule will be newly protonated.
|
|
62
|
|
63 Please note that the main purpose of this tool is to generate valid starting conformations for docking or other optimization procedures.
|
|
64 Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules)
|
|
65 different fragments might still overlap with each other.
|
|
66
|
|
67 Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz.
|
|
68
|
|
69 </help>
|
|
70 </tool>
|