<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Preparation]-->
<tool id="Ligand3DGenerator" name="Ligand3DGenerator" version="1.1.0">
  <description>generate 3D coordinates for small molecules</description>
  <macros>
    <token name="@EXECUTABLE@">Ligand3DGenerator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>Ligand3DGenerator

#if $param_i:
  -i $param_i
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_ph:
  -ph $param_ph
#end if
#if $param_ff:
  -ff     "$param_ff"
#end if
#if $param_rm:
  -rm $param_rm
#end if
#if $param_k:
  -k $param_k
#end if
#if $param_kp:
  -kp $param_kp
#end if
</command>
  <inputs>
    <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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
    <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/>
    <param name="param_ff" type="text" size="30" value="MMFF94" label="Forcefield to use for optimization (any available OpenBabel plugin)" help="(-ff) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
    <param name="param_k" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates (flag precedes '-kp')" help="(-k) "/>
    <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) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" metadata_source="param_i" format="input"/>
  </outputs>
  <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
containing valid topologies and conistent bond order assignements. 2D coordinates in the input file are overwritten, 3D coordinates can be kept ('-k' or '-kp').

  '-k':   3D coordinates are tried to be kept. Molecules with non-zero coordinates in all three dimensions are passed through without modifications. 
          However, if a molecule is not ready for docking (i.e. unusual bond leghts, unusual charges), the molecule will be rebuild and new 
          3D coordinates are assigned. If only hydrogens are missing, the coordinates of non-hydrogen atoms are kept but the molecule gets newly protonated.
  '-kp':  3D coordinates are tried to be kept as for the '-k' flag but the molecule will be newly protonated.

Please note that the main purpose of this tool is to generate valid starting conformations for docking or other optimization procedures.
Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) 
different fragments might still overlap with each other.

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.

</help>
</tool>