annotate tleap.xml @ 0:3de1359b86cc draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"

<tool id="tleap" name="Build tLEaP" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <description>interactively build and run tLEaP files to set up systems with AmberTools</description>
     <macros>
          <import>macros.xml</import>
          <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements" />
     <version_command>tleap -h</version_command>
     <command detect_errors="exit_code"><![CDATA[
        cp '${tleap_in}' '${output_tleap_in}' && mkdir out && tleap -f '${tleap_in}' > '${output_tleap}'
    ]]>     </command>
     <configfiles>
          <configfile name="tleap_in"><![CDATA[#for $i, $cmd in $enumerate($tleap_cmds):
#if $cmd.tleap_cond.tleap_cmd == "add":
add ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b}
#elif $cmd.tleap_cond.tleap_cmd == "addAtomTypes":
addAtomTypes {
#for $atmvars in $cmd.tleap_cond.atomtypevars:
             { "${atmvars.arg_addAtomTypes_var1}" "${atmvars.arg_addAtomTypes_var2}" "${atmvars.arg_addAtomTypes_var3}" }
#end for
             }
#elif $cmd.tleap_cond.tleap_cmd == "addH":
addH ${cmd.tleap_cond.arg_obj}
#elif $cmd.tleap_cond.tleap_cmd == "addIons":
addIons ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion1} ${cmd.tleap_cond.arg__ion1}
addIons ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion2} ${cmd.tleap_cond.arg__ion2}
#elif $cmd.tleap_cond.tleap_cmd == "addIons2":
addIons2 ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion1} ${cmd.tleap_cond.arg__ion1} ${cmd.tleap_cond.arg_ion2} ${cmd.tleap_cond.arg__ion2}
#elif $cmd.tleap_cond.tleap_cmd == "addIonsRand":
addIonsRand ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion1} ${cmd.tleap_cond.arg__ion1} ${cmd.tleap_cond.arg_ion2} ${cmd.tleap_cond.arg__ion2} ${cmd.tleap_cond.arg_separation}
#elif $cmd.tleap_cond.tleap_cmd == "addPath":
addPath ${cmd.tleap_cond.arg_path}
#elif $cmd.tleap_cond.tleap_cmd == "addPdbAtomMap":
addPdbAtomMap {
#for $atmmapvars in $cmd.tleap_cond.AtomMapList:
             {$atmmapvars.oddpdbname $atmmapvars.libpdbname}
#end for
             }
#elif $cmd.tleap_cond.tleap_cmd == "addPdbResMap":
addPdbResMap {
#for $atmresmapvars in $cmd.tleap_cond.resmap:
             {$atmresmapvars.terminalflag "$atmresmapvars.pdbname" "$atmresmapvars.leapvar"}
#end for
             }
#elif $cmd.tleap_cond.tleap_cmd == "alignAxes":
alignAxes ${cmd.tleap_cond.arg_unit}
#elif $cmd.tleap_cond.tleap_cmd == "bond":
bond ${cmd.tleap_cond.arg_atom1} ${cmd.tleap_cond.arg_atom2} ${cmd.tleap_cond.arg_order}
#elif $cmd.tleap_cond.tleap_cmd == "bondByDistance":
bondByDistance ${cmd.tleap_cond.arg_container} ${cmd.tleap_cond.arg_maxBond}
#elif $cmd.tleap_cond.tleap_cmd == "center":
center ${cmd.tleap_cond.arg_container}
#elif $cmd.tleap_cond.tleap_cmd == "charge":
charge ${cmd.tleap_cond.arg_container}
#elif $cmd.tleap_cond.tleap_cmd == "check":
check ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_parmset} 
#elif $cmd.tleap_cond.tleap_cmd == "clearPdbAtomMap":
clearPdbAtomMap
#elif $cmd.tleap_cond.tleap_cmd == "clearPdbResMap":
clearPdbResMap
#elif $cmd.tleap_cond.tleap_cmd == "clearVariables":
clearVariables { ${cmd.tleap_cond.arg_list} }
#elif $cmd.tleap_cond.tleap_cmd == "combine":
#if $cmd.tleap_cond.combine_assign:
${cmd.tleap_cond.combine_assign} = combine { ${cmd.tleap_cond.arg_list} }h
#else:
combine ${cmd.tleap_cond.arg_list}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "copy":
#if $cmd.tleap_cond.copy_assign:
${cmd.tleap_cond.copy_assign} = copy ${cmd.tleap_cond.arg_variable}
#else:
copy ${cmd.tleap_cond.arg_variable}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "createAtom":
#if $cmd.tleap_cond.createVar_assign:
${cmd.tleap_cond.createVar_assign} = createAtom ${cmd.tleap_cond.arg_name} ${cmd.tleap_cond.arg_type} ${cmd.tleap_cond.arg_charge}
#else:
createAtom ${cmd.tleap_cond.arg_name} ${cmd.tleap_cond.arg_type} ${cmd.tleap_cond.arg_charge}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "createParmset":
#if $cmd.tleap_cond.createVar_assign:
${cmd.tleap_cond.createVar_assign} = createParmset ${cmd.tleap_cond.arg_name}
#else:
createParmset ${cmd.tleap_cond.arg_name}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "createResidue":
#if $cmd.tleap_cond.createVar_assign:
${cmd.tleap_cond.createVar_assign} = createResidue ${cmd.tleap_cond.arg_name}
#else:
createResidue ${cmd.tleap_cond.arg_name}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "createUnit":
#if $cmd.tleap_cond.createVar_assign:
${cmd.tleap_cond.createVar_assign} = createUnit ${cmd.tleap_cond.arg_name}
#else:
createUnit ${cmd.tleap_cond.arg_name}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "crossLink":
crossLink ${cmd.tleap_cond.arg_res1} ${cmd.tleap_cond.arg_conn1} ${cmd.tleap_cond.arg_res2} ${cmd.tleap_cond.arg_conn2}
#elif $cmd.tleap_cond.tleap_cmd == "debugOff":
debugOff ${cmd.tleap_cond.arg_filename}
#elif $cmd.tleap_cond.tleap_cmd == "debugOn":
debugOn ${cmd.tleap_cond.arg_filename}
#elif $cmd.tleap_cond.tleap_cmd == "debugStatus":
debugStatus
#elif $cmd.tleap_cond.tleap_cmd == "deleteBond":
deleteBond ${cmd.tleap_cond.arg_atom1} ${cmd.tleap_cond.arg_atom2}
#elif $cmd.tleap_cond.tleap_cmd == "deleteOffLibEntry":
deleteOffLibEntry ${cmd.tleap_cond.arg_library} ${cmd.tleap_cond.arg_entry}
#elif $cmd.tleap_cond.tleap_cmd == "deleteRestraint":
deleteRestraint ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b} ${cmd.tleap_cond.arg_c} ${cmd.tleap_cond.arg_d}
#elif $cmd.tleap_cond.tleap_cmd == "desc":
desc ${cmd.tleap_cond.arg_unit}
#elif $cmd.tleap_cond.tleap_cmd == "deSelect":
deSelect ${cmd.tleap_cond.arg_obj}
#elif $cmd.tleap_cond.tleap_cmd == "displayPdbAtomMap":
displayPdbAtomMap
#elif $cmd.tleap_cond.tleap_cmd == "displayPdbResMap":
displayPdbResMap
#elif $cmd.tleap_cond.tleap_cmd == "edit":
edit ${cmd.tleap_cond.arg_unit_parmset}
#elif $cmd.tleap_cond.tleap_cmd == "flip":
flip ${cmd.tleap_cond.arg_obj}
#elif $cmd.tleap_cond.tleap_cmd == "groupSelectedAtoms":
groupSelectedAtoms ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_name}
#elif $cmd.tleap_cond.tleap_cmd == "help":
help ${cmd.tleap_cond.arg_string}
#elif $cmd.tleap_cond.tleap_cmd == "impose":
impose ${cmd.tleap_cond.arg_unit} { ${cmd.tleap_cond.arg_seqlist} } { { "$cmd.tleap_cond.arg_internals_atom1" "$cmd.tleap_cond.arg_internals_atom2" $cmd.tleap_cond.arg_internals_displacement} }
#elif $cmd.tleap_cond.tleap_cmd == "list":
list
#elif $cmd.tleap_cond.tleap_cmd == "listOff":
listOff ${cmd.tleap_cond.arg_library}
#elif $cmd.tleap_cond.tleap_cmd == "loadAmberParams":
#if $cmd.tleap_cond.loadAmberParams_assign:
${cmd.tleap_cond.loadAmberParams_assign} = loadAmberParams ${cmd.tleap_cond.file_source.arg_filename}
#else:
loadAmberParams ${cmd.tleap_cond.file_source.arg_filename}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "loadAmberPrep":
loadAmberPrep ${cmd.tleap_cond.file_source.arg_filename} ${cmd.tleap_cond.arg_prefix}
#elif $cmd.tleap_cond.tleap_cmd == "loadMol2":
#if $cmd.tleap_cond.loadMol2_assign:
${cmd.tleap_cond.loadMol2_assign} = loadMol2 ${cmd.tleap_cond.arg_filename}
#else:
loadMol2 ${cmd.tleap_cond.arg_filename}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "loadMol3":
#if $cmd.tleap_cond.loadMol3_assign:
${cmd.tleap_cond.loadMol3_assign} = loadMol3 ${cmd.tleap_cond.arg_filename}
#else:
loadMol3 ${cmd.tleap_cond.arg_filename}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "loadOff":
loadOff ${cmd.tleap_cond.arg_filename}
#elif $cmd.tleap_cond.tleap_cmd == "loadPdb":
#if $cmd.tleap_cond.loadPdb_assign:
${cmd.tleap_cond.loadPdb_assign} = loadPdb ${cmd.tleap_cond.arg_filename}
#else:
loadPdb ${cmd.tleap_cond.arg_filename}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "loadPdbUsingSeq":
loadPdbUsingSeq ${cmd.tleap_cond.arg_filename} { ${cmd.tleap_cond.arg_unitlist} }
#elif $cmd.tleap_cond.tleap_cmd == "logFile":
logFile ${cmd.tleap_cond.arg_filename}
#elif $cmd.tleap_cond.tleap_cmd == "matchVariables":
#if $cmd.tleap_cond.matchVariables_assign:
${cmd.tleap_cond.matchVariables_assign} = matchVariables ${cmd.tleap_cond.arg_string}
#else:
matchVariables ${cmd.tleap_cond.arg_string}
#end if
#elif $cmd.tleap_cond.tleap_cmd == "measureGeom":
measureGeom ${cmd.tleap_cond.arg_atom1} ${cmd.tleap_cond.arg_atom2} ${cmd.tleap_cond.arg_atom3} ${cmd.tleap_cond.arg_atom4} 
#elif $cmd.tleap_cond.tleap_cmd == "relax":
relax ${cmd.tleap_cond.arg_obj}
#elif $cmd.tleap_cond.tleap_cmd == "remove":
remove ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b}
#elif $cmd.tleap_cond.tleap_cmd == "restrainAngle":
restrainAngle ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b} ${cmd.tleap_cond.arg_c} ${cmd.tleap_cond.arg_force} ${cmd.tleap_cond.arg_angle}
#elif $cmd.tleap_cond.tleap_cmd == "restrainBond":
restrainBond ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b} ${cmd.tleap_cond.arg_force} ${cmd.tleap_cond.arg_length}
#elif $cmd.tleap_cond.tleap_cmd == "restrainTorsion":
restrainTorsion ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b} ${cmd.tleap_cond.arg_c} ${cmd.tleap_cond.arg_d} ${cmd.tleap_cond.arg_force} ${cmd.tleap_cond.arg_phi} ${cmd.tleap_cond.arg_multiplicity}
#elif $cmd.tleap_cond.tleap_cmd == "saveAmberParm":
saveAmberParm ${cmd.tleap_cond.arg_unit} out/saveAmberParm_topologyfilename_${i}_1.prmtop out/saveAmberParm_coordinatefilename_${i}_2.inpcrd
#elif $cmd.tleap_cond.tleap_cmd == "saveAmberParmNetcdf":
saveAmberParmNetcdf ${cmd.tleap_cond.arg_unit} out/saveAmberParmNetcdf_topologyfilename_${i}_1.top out/saveAmberParmNetcdf_coordinatefilename_${i}_2.coord
#elif $cmd.tleap_cond.tleap_cmd == "saveAmberParmPert":
saveAmberParmPert ${cmd.tleap_cond.arg_unit} out/saveAmberParmPert_topologyfilename_${i}_1.top out/saveAmberParmPert_coordinatefilename_${i}_2.coord
#elif $cmd.tleap_cond.tleap_cmd == "saveAmberParmPol":
saveAmberParmPol ${cmd.tleap_cond.arg_unit} out/saveAmberParmPol_topologyfilename_${i}_1.top out/saveAmberParmPol_coordinatefilename_${i}_2.coord
#elif $cmd.tleap_cond.tleap_cmd == "saveAmberParmPolPert":
saveAmberParmPolPert ${cmd.tleap_cond.arg_unit} out/saveAmberParmPolPert_topologyfilename_${i}_1.top out/saveAmberParmPolPert_coordinatefilename_${i}_2.coord
#elif $cmd.tleap_cond.tleap_cmd == "saveAmberPrep":
saveAmberPrep ${cmd.tleap_cond.arg_unit} out/saveAmberPrep_filename_${i}_1.txt
#elif $cmd.tleap_cond.tleap_cmd == "saveMol2":
saveMol2 ${cmd.tleap_cond.arg_unit} out/saveMol2_filename_${i}_1.mol2 ${cmd.tleap_cond.arg_option}
#elif $cmd.tleap_cond.tleap_cmd == "saveMol3":
saveMol3 ${cmd.tleap_cond.arg_unit} out/saveMol3_filename_${i}_1.mol3 ${cmd.tleap_cond.arg_option}
#elif $cmd.tleap_cond.tleap_cmd == "saveOff":
saveOff ${cmd.tleap_cond.arg_obj} out/saveOff_filename_${i}_1.txt
#elif $cmd.tleap_cond.tleap_cmd == "savePdb":
savePdb ${cmd.tleap_cond.arg_unit} out/savePdb_filename_${i}_1.pdb
#elif $cmd.tleap_cond.tleap_cmd == "scaleCharges":
scaleCharges ${cmd.tleap_cond.arg_container} ${cmd.tleap_cond.arg_scale_factor}
#elif $cmd.tleap_cond.tleap_cmd == "select":
select ${cmd.tleap_cond.arg_obj}
#elif $cmd.tleap_cond.tleap_cmd == "sequence":
#if $cmd.tleap_cond.sequence_assign:
${cmd.tleap_cond.sequence_assign} = sequence { ${cmd.tleap_cond.arg_list} }
#else:
sequence { ${cmd.tleap_cond.arg_list} }
#end if
#elif $cmd.tleap_cond.tleap_cmd == "set":
set ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_container} ${cmd.tleap_cond.arg_dim}
#elif $cmd.tleap_cond.tleap_cmd == "set_default":
#for $setdefaultsvar in $cmd.tleap_cond.defaults:
set default ${setdefaultsvar.settingsvariable} ${setdefaultsvar.usersetting}
#end for 
#elif $cmd.tleap_cond.tleap_cmd == "setBox":
setBox ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_enclosure} ${cmd.tleap_cond.arg_buffer} 
#elif $cmd.tleap_cond.tleap_cmd == "showdefault":
showdefault
#elif $cmd.tleap_cond.tleap_cmd == "solvateBox":
solvateBox ${cmd.tleap_cond.arg_solute} ${cmd.tleap_cond.arg_solvent} ${cmd.tleap_cond.arg_buffer} ${cmd.tleap_cond.arg_iso} ${cmd.tleap_cond.arg_closeness}
#elif $cmd.tleap_cond.tleap_cmd == "solvateCap":
solvateCap ${cmd.tleap_cond.arg_solute} ${cmd.tleap_cond.arg_solvent} ${cmd.tleap_cond.arg_position} ${cmd.tleap_cond.arg_radius} ${cmd.tleap_cond.arg_closeness} 
#elif $cmd.tleap_cond.tleap_cmd == "solvateDontClip":
solvateDontClip ${cmd.tleap_cond.arg_solute} ${cmd.tleap_cond.arg_solvent} ${cmd.tleap_cond.arg_buffer} ${cmd.tleap_cond.arg_closeness}
#elif $cmd.tleap_cond.tleap_cmd == "solvateOct":
solvateOct ${cmd.tleap_cond.arg_solute} ${cmd.tleap_cond.arg_solvent} ${cmd.tleap_cond.arg_buffer} ${cmd.tleap_cond.arg_iso} ${cmd.tleap_cond.arg_closeness}
#elif $cmd.tleap_cond.tleap_cmd == "solvateShell":
solvateShell ${cmd.tleap_cond.arg_solute} ${cmd.tleap_cond.arg_solvent} ${cmd.tleap_cond.arg_thickness} ${cmd.tleap_cond.arg_closeness}
#elif $cmd.tleap_cond.tleap_cmd == "source":
source ${cmd.tleap_cond.arg_filename}
#elif $cmd.tleap_cond.tleap_cmd == "transform":
transform ${cmd.tleap_cond.arg_atoms} {
     { ${cmd.tleap_cond.arg_matrix_row1} }
     { ${cmd.tleap_cond.arg_matrix_row2} }
     { ${cmd.tleap_cond.arg_matrix_row3} }
     { 0 0 0 1 } 
     }
#elif $cmd.tleap_cond.tleap_cmd == "translate":
translate ${cmd.tleap_cond.arg_atoms} { ${cmd.tleap_cond.arg_direction} }
#elif $cmd.tleap_cond.tleap_cmd == "verbosity":
verbosity ${cmd.tleap_cond.arg_level}
#elif $cmd.tleap_cond.tleap_cmd == "zMatrix":
zMatrix ${cmd.tleap_cond.arg_obj} ${cmd.tleap_cond.arg_zmatrix}
#end if
#end for]]>
quit
          </configfile>
     </configfiles>

     <inputs>

          <repeat name="tleap_cmds" title="Add tLEaP command" min="1">
               <conditional name="tleap_cond">
                    <param type="select" name="tleap_cmd" label="Choose tLEaP command">
                         <option value="add">add</option>
                         <option value="addAtomTypes">addAtomTypes</option>
                         <option value="addH">addH</option>
                         <option value="addIons">addIons</option>
                         <option value="addIons2">addIons2</option>
                         <option value="addIonsRand">addIonsRand</option>
                         <option value="addPath">addPath</option>
                         <option value="addPdbAtomMap">addPdbAtomMap</option>
                         <option value="addPdbResMap">addPdbResMap</option>
                         <option value="alignAxes">alignAxes</option>
                         <option value="bond">bond</option>
                         <option value="bondByDistance">bondByDistance</option>
                         <option value="center">center</option>
                         <option value="charge">charge</option>
                         <option value="check">check</option>
                         <option value="clearPdbAtomMap">clearPdbAtomMap</option>
                         <option value="clearPdbResMap">clearPdbResMap</option>
                         <option value="clearVariables">clearVariables</option>
                         <option value="combine">combine</option>
                         <option value="copy">copy</option>
                         <option value="createAtom">createAtom</option>
                         <option value="createParmset">createParmset</option>
                         <option value="createResidue">createResidue</option>
                         <option value="createUnit">createUnit</option>
                         <option value="crossLink">crossLink</option>
                         <option value="debugOff">debugOff</option>
                         <option value="debugOn">debugOn</option>
                         <option value="debugStatus">debugStatus</option>
                         <option value="deleteBond">deleteBond</option>
                         <option value="deleteOffLibEntry">deleteOffLibEntry</option>
                         <option value="deleteRestraint">deleteRestraint</option>
                         <option value="desc">desc</option>
                         <option value="deSelect">deSelect</option>
                         <option value="displayPdbAtomMap">displayPdbAtomMap</option>
                         <option value="displayPdbResMap">displayPdbResMap</option>
                         <option value="edit">edit</option>
                         <option value="flip">flip</option>
                         <option value="groupSelectedAtoms">groupSelectedAtoms</option>
                         <option value="help">help</option>
                         <option value="impose">impose</option>
                         <option value="list">list</option>
                         <option value="listOff">listOff</option>
                         <option value="loadAmberParams">loadAmberParams</option>
                         <option value="loadAmberPrep">loadAmberPrep</option>
                         <option value="loadMol2">loadMol2</option>
                         <option value="loadMol3">loadMol3</option>
                         <option value="loadOff">loadOff</option>
                         <option value="loadPdb">loadPdb</option>
                         <option value="loadPdbUsingSeq">loadPdbUsingSeq</option>
                         <option value="logFile">logFile</option>
                         <option value="matchVariables">matchVariables</option>
                         <option value="measureGeom">measureGeom</option>
                         <option value="relax">relax</option>
                         <option value="remove">remove</option>
                         <option value="restrainAngle">restrainAngle</option>
                         <option value="restrainBond">restrainBond</option>
                         <option value="restrainTorsion">restrainTorsion</option>
                         <option value="saveAmberParm">saveAmberParm</option>
                         <option value="saveAmberParmNetcdf">saveAmberParmNetcdf</option>
                         <option value="saveAmberParmPert">saveAmberParmPert</option>
                         <option value="saveAmberParmPol">saveAmberParmPol</option>
                         <option value="saveAmberParmPolPert">saveAmberParmPolPert</option>
                         <option value="saveAmberPrep">saveAmberPrep</option>
                         <option value="saveMol2">saveMol2</option>
                         <option value="saveMol3">saveMol3</option>
                         <option value="saveOff">saveOff</option>
                         <option value="savePdb">savePdb</option>
                         <option value="scaleCharges">scaleCharges</option>
                         <option value="select">select</option>
                         <option value="sequence">sequence</option>
                         <option value="set">set</option>
                         <option value="set_default">set_default</option>
                         <option value="setBox">setBox</option>
                         <option value="showdefault">showdefault</option>
                         <option value="solvateBox">solvateBox</option>
                         <option value="solvateCap">solvateCap</option>
                         <option value="solvateDontClip">solvateDontClip</option>
                         <option value="solvateOct">solvateOct</option>
                         <option value="solvateShell">solvateShell</option>
                         <option value="source">source</option>
                         <option value="transform">transform</option>
                         <option value="translate">translate</option>
                         <option value="verbosity">verbosity</option>
                         <option value="zMatrix">zMatrix</option>
                    </param>
                    <when value="add">
                         <param name="arg_a" label="a value" type="text" value="" help="UNIT/RESIDUE/ATOM"/>
                         <param name="arg_b" label="b value" type="text" value="" help="UNIT/RESIDUE/ATOM"/>
                    </when>
                    <when value="addAtomTypes">
                         <repeat name="atomtypevars" title="new atom type parameters" min="1">
                              <param name="arg_addAtomTypes_var1" label="name" type="text" value="" help="designated name in the force field"/>
                              <param name="arg_addAtomTypes_var2" label="element" type="text" value="" help="atom name as it appear in the periodic table"/>
                              <param name="arg_addAtomTypes_var3" label="hybridization state" type="text" value="" help="sp2, sp3, etc."/>
                         </repeat>
                    </when>
                    <when value="addH">
                         <param name="arg_obj" label="Assign to UNIT with variable name:" type="text" value="" help="this should be the same variable given to a previously loaded target structure"/>
                    </when>
                    <when value="addIons">
                         <expand macro="addingions" />
                    </when>
                    <when value="addIons2">
                         <expand macro="addingions" />
                    </when>
                    <when value="addIonsRand">
                         <expand macro="addingions" />
                         <param name="arg_separation" label="separation value" type="text" value="" help="This value guarantees a minimum distance between inserted ions, in angstsroms."/>
                    </when>
                    <when value="addPath">
                         <param name="arg_path" label="path to directory" type="text" value="" help="Specify additional paths for leap to search for files when executing commands."/>
                    </when>
                    <when value="addPdbAtomMap">
                         <repeat name="AtomMapList" title="Add atom name from a pdb file to a list" min="1">
                              <param name="oddpdbname" label="Odd atom type from pdb file" type="text" value="" help=""/>
                              <param name="libpdbname" label="Atom type to reference in the library" type="text" value="" help=""/>
                         </repeat>
                    </when>
                    <when value="addPdbResMap">
                         <repeat name="resmap" title="Add atom name from a pdb file to a residue map in LEaP" min="1">
                              <param name="terminalflag" label="If terminal atom, select type:" type="text" value="" help="select 0 for beginning residues (N-terminal for proteins, 5' for nucleic acids) and 1 for ending residues (C-terminal for proteins, 3' for nucleic acids). Leave blank if neither. "/>
                              <param name="pdbname" label="atom name in pdb file" type="text" value="" help=""/>
                              <param name="leapvar" label="variable name within leap to map onto" type="text" value="" help=""/>
                         </repeat>
                    </when>
                    <when value="alignAxes">
                         <expand macro="unitvariable" />
                    </when>
                    <when value="bond">
                         <param name="arg_atom1" label="Bonding atom 1" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype', where the assigned UNITvariable is the same one used to define your structure in loadPdb, saveAmberParm, savePdb, and other commands in your tleap script. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'. "/>
                         <param name="arg_atom2" label="Bonding atom 2" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype', where the assigned UNITvariable is the same one used to define your structure in loadPdb, saveAmberParm, savePdb, and other commands in your tleap script. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'. "/>
                         <param name="arg_order" label="order value" type="select" value="" help="Choose 'S' for single bond, 'D' for double bond, 'T' for triple bond, or 'A' for aromatic bond. The default value is 'S' if left blank.">
                              <option value="">default</option>
                              <option value="S">single bond</option>
                              <option value="D">double bond</option>
                              <option value="T">triple bond</option>
                              <option value="A">aromatic bond</option>
                         </param>
                    </when>
                    <when value="bondByDistance">
                         <expand macro="container" />
                         <param name="arg_maxBond" label="maxBond value" type="text" value="" help="maximum distance, in angstroms"/>
                    </when>
                    <when value="center">
                         <expand macro="container"/>
                    </when>
                    <when value="charge">
                         <expand macro="container"/>
                    </when>
                    <when value="check">
                         <expand macro="unitvariable" />
                         <param name="arg_parmset" label="parmset value" type="text" value="" help="PARMSET/STRING where all mising parameters are placed. This is optional."/>
                    </when>
                    <when value="clearPdbAtomMap">
                    </when>
                    <when value="clearPdbResMap">
                    </when>
                    <when value="clearVariables">
                         <param name="arg_list" label="list of variables to clear" type="text" value="" help="This is optional. Use only if a specific set of variables need to be cleared. If left empty, all variables will be cleared by default."/>
                    </when>
                    <when value="combine">
                         <param name="combine_assign" label="Name of the new combined list of variables" type="text" value=""/>
                         <param name="arg_list" label="list of variables" type="text" value="" help="Write the name of previously defined variables that you'd like to combine into this new list. "/>
                    </when>
                    <when value="copy">
                         <param name="copy_assign" label="Name of the newly copied variable:" type="text" value=""/>
                         <param name="arg_variable" label="Variable you are making a copy of:" type="text" value="" help=""/>
                    </when>
                    <when value="createAtom">
                         <expand macro="create" />
                         <param name="arg_type" label="new atom type" type="text" value="" help="STRING"/>
                         <param name="arg_charge" label="atomic charge" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="createParmset">
                         <expand macro="create" />
                    </when>
                    <when value="createResidue">
                         <expand macro="create" />
                    </when>
                    <when value="createUnit">
                         <expand macro="create" />
                    </when>
                    <when value="crossLink">
                         <param name="arg_res1" label="res1 value" type="text" value="" help="Residue 1"/>
                         <param name="arg_conn1" label="conn1 value" type="text" value="" help="connecting atom on residue 1"/>
                         <param name="arg_res2" label="res2 value" type="text" value="" help="Residue 2"/>
                         <param name="arg_conn2" label="conn2 value" type="text" value="" help="connecting atom on residue 2"/>
                    </when>
                    <when value="debugOff">
                         <expand macro="builtin_amberfiles" />
                    </when>
                    <when value="debugOn">
                         <expand macro="builtin_amberfiles" />
                    </when>
                    <when value="debugStatus">
                    </when>
                    <when value="deleteBond">
                         <param name="arg_atom1" label="Bonding atom 1" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype', where the assigned UNITvariable is the same one used to define your structure in loadPdb, saveAmberParm, savePdb, and other commands in your tleap script. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'. "/>
                         <param name="arg_atom2" label="Bonding atom 2" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype', where the assigned UNITvariable is the same one used to define your structure in loadPdb, saveAmberParm, savePdb, and other commands in your tleap script. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'. "/>
                    </when>
                    <when value="deleteOffLibEntry">
                         <param name="arg_library" label="library value" type="text" format="txt" value="" help="STRING"/>
                         <param name="arg_entry" label="entry value" type="text" value="" help="STRING"/>
                    </when>
                    <when value="deleteRestraint">
                         <expand macro="unitvariable" />
                         <param name="arg_a" label="a value" type="text" value="" help="ATOM"/>
                         <param name="arg_b" label="b value" type="text" value="" help="ATOM"/>
                         <param name="arg_c" label="c value" type="text" value="" help="ATOM"/>
                         <param name="arg_d" label="d value" type="text" value="" help="ATOM"/>
                    </when>
                    <when value="desc">
                         <expand macro="unitvariable" />
                    </when>
                    <when value="deSelect">
                         <expand macro="object" />
                    </when>
                    <when value="displayPdbAtomMap">
                    </when>
                    <when value="displayPdbResMap">
                    </when>
                    <when value="edit">
                         <param name="arg_unit_parmset" label="unit-parmset value" type="text" value="" help="UNIT/PARMSET"/>
                    </when>
                    <when value="flip">
                         <expand macro="object" />
                    </when>
                    <when value="groupSelectedAtoms">
                         <expand macro="unitvariable" />
                         <param name="arg_name" label="name value" type="text" value="" help="STRING"/>
                    </when>
                    <when value="help">
                         <param name="arg_string" label="string value" type="text" value="" help="STRING"/>
                    </when>
                    <when value="impose">
                         <expand macro="unitvariable" />
                         <param name="arg_seqlist" label="seqlist value" type="text" value="" help="LIST"/>
                         <param name="arg_internals_atom1" label="internals atom1" type="text" value="" help=""/>
                         <param name="arg_internals_atom2" label="internals atom2" type="text" value="" help=""/>
                         <param name="arg_internals_displacement" label="displacement" type="text" value="" help="can be positive or negative, in angstroms"/>
                    </when>
                    <when value="list">
                    </when>
                    <when value="listOff">
                         <param name="arg_library" label="library value" type="data" value="" format="txt" help="STRING"/>
                    </when>
                    <when value="loadAmberParams">
                         <param name="loadAmberParams_assign" label="Assign to variable named" type="text" value=""/>
                         <expand macro="amberfiles_conditional" />
                    </when>
                    <when value="loadAmberPrep">
                         <expand macro="amberfiles_conditional" />
                         <param name="arg_prefix" label="prefix value" type="text" value="" help="STRING"/>
                    </when>
                    <when value="loadMol2">
                         <param name="loadMol2_assign" label="Assign to variable named" type="text" value="" help="This is the molecule's residue name as it appears in the mol2 file."/>
                         <expand macro="loadfile" data_format="mol2"/>
                    </when>
                    <when value="loadMol3">
                         <param name="loadMol3_assign" label="Assign to variable named" type="text" value="" help="This is the molecule's residue name as it appears in the mol2 file."/>
                         <expand macro="loadfile" data_format="mol3"/>
                    </when>
                    <when value="loadOff">
                         <expand macro="loadfile" />
                    </when>
                    <when value="loadPdb">
                         <param name="loadPdb_assign" label="Assign to variable named" type="text" value="" help="The variable name that your system's components are assigned to. This should generally be the same variable used when saving the output files (when using savePdb, saveAmberParm, etc.)."/>
                         <expand macro="loadfile" data_format="pdb"/>
                    </when>
                    <when value="loadPdbUsingSeq">
                         <expand macro="loadfile" data_format="pdb"/>
                         <param name="arg_unitlist" label="unitlist value" type="text" value="" help="LIST"/>
                    </when>
                    <when value="logFile">
                         <expand macro="loadfile" />
>
                    </when>
                    <when value="matchVariables">
                         <param name="matchVariables_assign" label="Assign to variable named" type="text" value=""/>
                         <param name="arg_string" label="string value" type="text" value="" help="STRING"/>
                    </when>
                    <when value="measureGeom">
                         <param name="arg_atom1" label="atom1" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_atom2" label="atom2" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_atom3" label="atom3" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_atom4" label="atom4" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber.atomtype'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                    </when>
                    <when value="relax">
                         <expand macro="object" />
                    </when>
                    <when value="remove">
                         <param name="arg_a" label="a value --> Object you are removing contents FROM" type="text" value="" help="UNIT/RESIDUE/ATOM. The object can be a specific residue [ type 'UNITvariable.residuenumber(or name)' ], or an entire UNIT [ only type 'UNITvariable' ]. "/>
                         <param name="arg_b" label="b value --> The specific content you are removing" type="text" value="" help="UNIT/RESIDUE/ATOM. The contents can be a single atom [type 'UNITvariable.residuenumber(or name).atomtype(or number)' ], or an entire residue [type 'UNITvariable.residuenumber(or name)' ]. "/>
                    </when>
                    <when value="restrainAngle">
                         <expand macro="unitvariable" />
                         <param name="arg_a" label="atom1" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_b" label="atom2 or the middle atom" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_c" label="atom3" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_force" label="Force constant K_theta" type="text" value="" help="This is the force constant value you are setting to restrain this angle, in kcal/mol/radian^2."/>
                         <param name="arg_angle" label="Equilibrium angle theta" type="text" value="" help="This is the equilibrium angle, in degrees, between these 3 interacting atoms."/>
                    </when>
                    <when value="restrainBond">
                         <expand macro="unitvariable" />
                         <param name="arg_a" label="atom1" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_b" label="atom2" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_force" label="Force constant K_b" type="text" value="" help="This is the force constant value you are setting to restrain this length, in kcal/mol/angstrom^2. "/>
                         <param name="arg_length" label="Equilibrium length" type="text" value="" help="This is the equilibrium bond length between these two atoms."/>
                    </when>
                    <when value="restrainTorsion">
                         <expand macro="unitvariable" />
                         <param name="arg_a" label="atom1" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_b" label="atom2" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_c" label="atom3" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_d" label="atom4" type="text" value="" help="Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'." />
                         <param name="arg_force" label="Force constant K_phi" type="text" value="" help="This is the force constant you are setting to restrain this dihedral."/>
                         <param name="arg_phi" label="Equilibrium torsion angle phi" type="text" value="" help="This is the equilibrium torsion angle for this dihedral."/>
                         <param name="arg_multiplicity" label="multiplicity value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="saveAmberParm">
                         <param name="arg_unit" label="Assign to variable named" type="text" value="" help="The variable name that your system's components are assigned to. This should generally be the same variable used previously with input commands like 'loadPdb'."/>
                    </when>
                    <when value="saveAmberParmNetcdf">
                         <expand macro="unitvariable" />
                    </when>
                    <when value="saveAmberParmPert">
                         <expand macro="unitvariable" />
                    </when>
                    <when value="saveAmberParmPol">
                         <expand macro="unitvariable" />
                    </when>
                    <when value="saveAmberParmPolPert">
                         <expand macro="unitvariable" />
                    </when>
                    <when value="saveAmberPrep">
                         <expand macro="unitvariable" />
                         <expand macro="newfile" />
                    </when>
                    <when value="saveMol2">
                         <expand macro="unitvariable" />

                         <param name="arg_option" label="option value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="saveMol3">
                         <expand macro="unitvariable" />
                         <param name="arg_option" label="option value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="saveOff">
                         <expand macro="object" />
                    </when>
                    <when value="savePdb">
                         <param name="arg_unit" label="Assign to variable named" type="text" value="" help="The variable name that your system's components are assigned to. This should generally be the same variable used previously with input commands like 'loadPdb'."/>
                    </when>
                    <when value="scaleCharges">
                         <expand macro="container" />
                         <param name="arg_scale_factor" label="scale_factor value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="select">
                         <expand macro="object" />
                    </when>
                    <when value="sequence">
                         <param name="sequence_assign" label="Assign to variable named" type="text" value=""/>
                         <param name="arg_list" label="list value" type="text" value="" help="LIST"/>
                    </when>
                    <when value="set">
                         <param name="arg_variable" label="variable value" type="text" value="" help="the variable name that your components are assigned to"/>
                         <param name="arg_container" label="container value" type="text" value="" help="type'box' if you are using this command to set box dimensions"/>
                         <param name="arg_dim" label="dimensions value" type="text" value="" help="dimension magnitude for X, Y, and Z"/>
                    </when>
                    <when value="set_default">
                         <repeat name="defaults" title="Default setting to adjust:">
                              <expand macro="defaultsettings" />
                              <expand macro="settingoptions" />
                         </repeat>
                    </when>
                    <when value="setBox">
                         <expand macro="unitvariable" />
                         <param name="arg_enclosure" label="enclosure value" type="text" value="" help="type 'vdw' or 'centers'"/>
                         <param name="arg_buffer" label="buffer value" type="text" value="" help="object"/>
                    </when>
                    <when value="showdefault">
                    </when>
                    <when value="solvateBox">
                         <expand macro="solvateparams" />
                         <param name="arg_iso" label="iso value" type="text" value="" help="type 'iso' if using this option"/>
                    </when>
                    <when value="solvateCap">
                         <expand macro="solvateparams" />
                         <param name="arg_position" label="position value" type="text" value="" help="Defines the center of the solvent cap. Can be listed directly using coordinates for { X Y Z }, or you can specify a UNIT, RESIDUE, ATOM, or LIST of any of these 3 as a reference for position."/>
                         <param name="arg_radius" label="radius value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="solvateDontClip">
                         <expand macro="solvateparams" />
                         <param name="arg_closeness" label="closeness value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="solvateOct">
                         <expand macro="solvateparams" />
                         <param name="arg_iso" label="iso value" type="text" value="" help="type 'iso' if choosing this option"/>
                    </when>
                    <when value="solvateShell">
                         <expand macro="solvateparams" />
                         <param name="arg_thickness" label="thickness value" type="text" value="" help="NUMBER"/>
                    </when>
                    <when value="source">
                         <expand macro="builtin_amberfiles" />
                    </when>
                    <when value="transform">
                         <param name="arg_atoms" label="atoms value" type="text" value="" help="UNIT/RESIDUE/ATOM. You can transform an entire UNIT, an entire RESIDUE, or a specific atom. Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'. Multiple selections can be typed into this list so a transformation is performed on several components of your system at once, just separate each choice of UNIT/RESIDUE/ATOM with a single space in between. " />
                         <param name="arg_matrix_row1" label="Row 1 of matrix" type="text" value="" help="type the following: ' r11  r12  r13  -tx ', where r11-r13 are matrix elements for the X dimension. If you would like to translate along this dimension, assign a value to -tx, in angstroms. For a simple reflection along this axis, set this row to r11=-1, r12=0, r13=0. "/>
                         <param name="arg_matrix_row2" label="Row 2 of matrix" type="text" value="" help="type the following: ' r21  r22  r23  -tx ', where r21-r23 are matrix elements for the Y dimension. If you would like to translate along this dimension, assign a value to -ty, in angstroms. For a simple reflection along this axis, set this row to r21=0, r22=-1, r23=0. "/>
                         <param name="arg_matrix_row3" label="Row 3 of matrix" type="text" value="" help="type the following: ' r31  r32  r33  -tz ', where r31-r33 are matrix elements for the Z dimension. If you would like to translate along this dimension, assign a value to -tz, in angstroms. For a simple reflection along this axis, set this row to r31=0, r32=0, r33=-1. "/>
                    </when>
                    <when value="translate">
                         <param name="arg_atoms" label="list of atoms" type="text" value="" help="UNIT/RESIDUE/ATOM. You can translate an entire UNIT, an entire RESIDUE, or a specific atom. Each atom is defined as 'UNITvariable.residuenumber(or name).atomtype(or number)'. For example, typing 'mol.5.SG' tells tleap that the bonding atom is assigned to the variable 'mol', in residue number 5, and is the atom type 'SG'. Multiple selections can be typed into this list so a transformation is performed on several components of your system at once, just separate each choice of UNIT/RESIDUE/ATOM with a single space in between. " />
                         <param name="arg_direction" label="direction value in each dimension" type="text" value="" help="Displace by this amount { X Y Z }. The direction is based on whether each vector is positive or negative. "/>
                    </when>
                    <when value="verbosity">
                         <param name="arg_level" label="level value" type="text" value="" help="This command sets the level of output that LEaP provides the user. A value of 0 is the default, providing the minimum of messages. A value of 1 will produce more output, and a value of 2 will produce all of the output of level 1 and display the text of the script lines executed with the source command."/>
                    </when>
                    <when value="zMatrix">
                         <param name="arg_obj" label="obj value" type="text" value="" help="UNIT/RESIDUE/ATOM"/>
                         <param name="arg_zmatrix" label="zmatrix value" type="text" value="" help="LIST"/>
                    </when>
               </conditional>
          </repeat>
     </inputs>
     <outputs>
          <data format="txt" name="output_tleap_in" label="Build tLEaP: tleap.in"/>
          <data format="txt" name="output_tleap" label="Build tLEaP: tleap.log"/>
          <collection name="output_pdb" type="list" label="Collection of pdb" format="pdb">
               <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdb" directory="out" format="pdb"/>
          </collection>
          <collection name="output_top" type="list" label="Collection of topology files" format="prmtop">
               <discover_datasets pattern="(?P&lt;designation&gt;.+)\.prmtop" directory="out" format="prmtop"/>
          </collection>
          <collection name="output_txt" type="list" label="Collection of txt" format="txt">
               <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="out" format="txt"/>
          </collection>
          <collection name="output_coord" type="list" label="Collection of coordinate files" format="inpcrd">
               <discover_datasets pattern="(?P&lt;designation&gt;.+)\.inpcrd" directory="out" format="inpcrd"/>
          </collection>
          <collection name="output_mol2" type="list" label="Collection of mol2" format="mol2">
               <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mol2" directory="out" format="mol2"/>
          </collection>
          <collection name="output_mol3" type="list" label="Collection of mol3" format="mol3">
               <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mol3" directory="out" format="mol3"/>
          </collection>
     </outputs>
     <tests>
          <test expect_num_outputs="8">
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="source"/>
                         <param name="arg_filename" value="oldff/leaprc.ff14SB"/>
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="loadAmberParams" />
                         <conditional name="file_source">
                              <param name="file_source_selector" value="builtin"/>
                              <param name="arg_filename" value="frcmod.ff14SB"/>
                         </conditional>
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="loadAmberParams" />
                         <conditional name="file_source">
                              <param name="file_source_selector" value="builtin"/>
                              <param name="arg_filename" value="frcmod.ionsjc_tip4pew"/>
                         </conditional>
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="loadAmberPrep" />
                         <conditional name="file_source">
                              <param name="file_source_selector" value="history"/>
                              <param name="arg_filename" value="ZAFF.prep"/>
                         </conditional>
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="loadAmberParams" />
                         <conditional name="file_source">
                              <param name="file_source_selector" value="history"/>
                              <param name="arg_filename" value="ZAFF.frcmod"/>
                         </conditional>
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="loadPdb" />
                         <param name="loadPdb_assign" value="mol" />
                         <param name="arg_filename" value="sarscov2_helicase_ZincBindingDomain.pdb"/>
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="bond" />
                         <param name="arg_atom1" value="mol.114.ZN" />
                         <param name="arg_atom2" value="mol.5.SG" />
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="set" />
                         <param name="arg_variable" value="mol" />
                         <param name="arg_container" value="box" />
                         <param name="arg_dim" value="12" />
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="addIons" />
                         <param name="arg_variable" value="mol" />
                         <param name="arg_ion1" value="Cl-" />
                         <param name="arg__ion1" value="0" />
                         <param name="arg_ion2" value="Na+" />
                         <param name="arg__ion2" value="0" />
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="saveAmberParm" />
                         <param name="arg_unit" value="mol" />
                    </conditional>
               </repeat>
               <repeat name="tleap_cmds">
                    <conditional name="tleap_cond">
                         <param name="tleap_cmd" value="savePdb" />
                         <param name="arg_unit" value="mol" />
                    </conditional>
               </repeat>
               <output name="output_tleap_in" value="leap_testfile.txt" lines_diff="6">
                    <assert_contents>
                         <has_text text="loadAmberParams frcmod.ff14SB" />
                         <has_text text="bond mol.114.ZN mol.5.SG" />
                         <has_text text="quit" />
                    </assert_contents>
               </output>
               <output name="output_tleap">
                    <assert_contents>
                         <has_text text="Welcome to LEaP!" />
                    </assert_contents>
               </output>
               <output_collection name="output_top" type="list" count="1">
                    <element name="saveAmberParm_topologyfilename_9_1">
                         <assert_contents>
                              <has_text text="N   H1  H2  H3  CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB  CG1" />
                         </assert_contents>
                    </element>
               </output_collection>
               <output_collection name="output_coord" type="list" count="1">
                    <element name="saveAmberParm_coordinatefilename_9_2">
                         <assert_contents>
                              <has_text text="12.0000000  12.0000000  12.0000000  90.0000000  90.0000000  90.0000000" />
                         </assert_contents>
                    </element>
               </output_collection>
               <output_collection name="output_pdb" type="list" count="1">
                    <element name="savePdb_filename_10_1">
                         <assert_contents>
                              <has_text text="CRYST1   12.000   12.000   12.000  90.00  90.00  90.00 P 1           1" />
                         </assert_contents>
                    </element>
               </output_collection>
          </test>
     </tests>
     <help><![CDATA[
::

  add a b
  
        UNIT/RESIDUE/ATOM          _a_
        UNIT/RESIDUE/ATOM          _b_
  
  Add the object _b_ to the object _a_.   This command is used to place
  ATOMs within RESIDUEs, and RESIDUEs within UNITs.
  
  addAtomTypes {
          { "H"   "H" "sp3" }
          { "HO"  "H" "sp3" }
          ...
      }
  Add mapping of AMBER atom type to element and hybridization. Typically in
  leaprc.
  
  addH obj
  
        UNIT                       _obj_
  
  Add missing hydrogens and build external coordinates for _obj_.
  
  addIons unit ion1 #ion1 [ion2 #ion2]
        UNIT                      _unit_
        UNIT                      _ion1_
        NUMBER                    _#ion1_
        UNIT                      _ion2_
        NUMBER                    _#ion2_
  Adds counterions in a shell around _unit_ using a Coulombic potential
  on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
  opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
  the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
  If solvent is present, it is ignored in the charge and steric calculations,
  and if an ion has a steric conflict with a solvent molecule, the ion is
  moved to the center of said molecule, and the latter is deleted. (To
  avoid this behavior, either solvate _after_ addIons, or use addIons2.)
  Ions must be monoatomic. Note that the one-at-a-time procedure is not
  guaranteed to globally minimize the electrostatic energy. When neutralizing
  regular-backbone nucleic acids, the first cations will generally be added
  between phosphates, leaving the final two ions to be placed somewhere around
  the middle of the molecule.
  The default grid resolution is 1 Angstrom, extending from an inner radius
  of (max ion size + max solute atom size) to an outer radius 4 Angstroms
  beyond. A distance-dependent dielectric is used for speed.
  
  addIons2 unit ion1 #ion1 [ion2 #ion2]
          UNIT                    _unit_
          UNIT                    _ion1_
          NUMBER                  _#ion1_
          UNIT                    _ion2_
          NUMBER                  _#ion2_
  Same as addIons, except solvent and solute are treated the same.
  
  addIonsRand unit ion1 #ion1 [ion2 #ion2] [separation]
  
          UNIT      _unit_
          UNIT      _ion1_
          NUMBER    _#ion1_
          UNIT      _ion2_
          NUMBER    _#ion2_
          NUMBER    _separation_
  
  Adds counterions in a shell around _unit_ by replacing random solvent
  molecules. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
  opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
  the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
  If _separation_ is specified, ions will be guaranteed to be more than that
  distance apart in Angstroms.
  
  Ions must be monoatomic. This procedure is much faster than addIons, as
  it does not calculate charges. Solvent must be present. It must be possible
  to position the requested number of ions with the given separation in the
  solvent.
  
  addPath path
  
        STRING                       _path_
  
  Add the directory in _path_ to the list of directories that are searched
  for files specified by other commands.
  
  addPdbAtomMap list
        LIST                         _list_
  
  The atom Name Map is used to try to map atom names read from PDB files
  to atoms within residue UNITs when the atom name in the PDB file does
  not match an atom in the residue.  This enables PDB files to be read
  in without extensive editing of atom names.  The LIST is a LIST of LISTs:
        { {sublist} {sublist} ... }
  where each sublist is of the form
        { "OddAtomName" "LibAtomName" }
  Many `odd' atom names can map to one `standard' atom name, but any single
  odd atom name maps only to the last standard atom name it was mapped to.
  
  addPdbResMap list
        LIST                         _list_
  
  The Name Map is used to map residue names read from PDB files to variable
  names within LEaP.  The LIST is a LIST of LISTs:
        { {sublist} {sublist} ... }
  Each sublist contains two or three entries to add to the Name Map:
        { [terminalflag] PDBName LEaPVar }
  where the PDBName will be mapped to the LEaPVar. The terminalflag indicates
  the special cases of terminal residues: allowable values are 0 for beginning
  residues (N-terminal for proteins, 5' for nucleic acids) and 1 for ending
  residues (C-terminal for proteins, 3' for nucleic acids).  If the
  terminalflag is given, the PDBName->LEaPVar name map will only be applied
  for the appropriate terminal residue.  The `leaprc' file included with
  the distribution contains default mappings.
  
  alias [alias[ string]]
        STRING                    _alias_
        STRING                    _string_
  
  alias string1 command - equivalence string1 to command.
  alias string1         - delete the alias for string1.
  alias                 - report all current aliases.
  
  alignAxes unit
  
        UNIT                         _unit_
  
  Translate the geometric center of _unit_ to the origin and align
  the principle axes of the ATOMs within _unit_ along the coordinate
  axes.  This is done by calculating the moment of inertia of the UNIT
  using unit mass for each ATOM, and then diagonalizing the resulting
  matrix and aligning the eigenvectors along the coordinate axes.
  This command modifies the coordinates of the UNIT. It may be
  especially useful for preparing long solutes such as nucleic acids
  for solvation.
  
  bond atom1 atom2 [ order ]
  
        ATOM                         _atom1_
        ATOM                         _atom2_
        STRING                       _order_
  
  Create a bond between _atom1_ and _atom2_.  Both of these ATOMs must
  be contained by the same UNIT. By default, the bond will be a single
  bond.  By specifying "S", "D", "T", or "A" as the optional argument
  _order_ the user can specify a single, double, triple, or aromatic
  bond.
  
  bondByDistance container [ maxBond ]
  
        UNIT/RESIDUE/ATOM         _container_
        NUMBER                    _maxBond_
  
  Create single bonds between all ATOMs in _container_ that are within
  _maxBond_ angstroms of each other.   If _maxBond_ is not specified,
  a default distance of 2 angstroms used.
  
  center container
        UNIT/RESIDUE/ATOM          _container_
  
  Display the coordinates of the geometric center of the ATOMs within
  _container_.
  
  charge container
  
        UNIT/RESIDUE/ATOM          _container_
  
  This command calculates the total charge of the ATOMs within _container_.
  The unperturbed and perturbed total charge are displayed.
  
  check unit [ parmset ]
        UNIT                      _unit_
        PARMSET/STRING            _parmset_
  
  This command can be used to check the UNIT for internal inconsistencies
  that could cause problems when performing calculations.  This is
  a very useful command that should be used before a UNIT is saved
  with saveAmberParm or its variations.
  With the optional parmset, all missing parameters are placed in the
  PARMSET to allow for easy editing of those parameters.  If a string is
  passed, a PARMSET will be created with that name.
  Currently it checks for the following possible problems:
  
     - Long bonds.  A long bond is greater than 3.0 angstroms.
  
     - Short bonds.  A short bond is less than 0.5 angstroms.
  
     - Non-integral total charge of the UNIT.
  
     - Missing types.
  
     - Close contacts between non-bonded ATOMs.  A close contact is
       less than 1.5 angstroms.
  
  clearPdbAtomMap
  
  Clear the Name Map used for ``second-chance'' mapping of atom names in
  PDB files to atoms within residue UNITs.  See addPdbAtomMap.
  
  clearPdbResMap
  
  Clear the Name Map used to map residue names in PDB files to variable
  names within LEaP.  See addPdbResMap.
  
  clearVariables [ list ]
  
        LIST                         _list_
  
  This command removes variables from LEaP. If the _list_ argument
  is provided, then only the variables in the LIST will be removed.
  If no argument is provided then ALL variables will be removed.
  
  variable = combine list
        object                       _variable_
        LIST                         _list_
  
  Combine the contents of the UNITs within _list_ into a single UNIT.
  The new UNIT is placed in _variable_.   This command is similar to
  the sequence command except it does not link the ATOMs of the UNITs
  together.
  
  newvariable = copy variable
  
        object                       _newvariable_
        object                       _variable_
  
  Create an exact duplicate of the object _variable_. Changing the object
  _variable_ will not affect the object _newvariable_.
  This is in contrast to the situation created by "newvariable = variable"
  in which both names reference the same object.
  
  variable = createAtom name type charge
  
        ATOM                         _variable_
        STRING                       _name_
        STRING                       _type_
        NUMBER                       _charge_
  
  Return a new ATOM with _name_, _type_, and _charge_.
  
  variable = createParmset name
        PARMSET                   _variable_
        STRING                    _name_
  
  Return a new and empty PARMSET with the name _name_.
  
  variable = createResidue name
        RESIDUE                      _variable_
        STRING                       _name_
  
  Return a new and empty RESIDUE with the name _name_.
  
  variable = createUnit name
        UNIT                         _variable_
        STRING                       _name_
  
  Return a new and empty UNIT with the name _name_.
  
  crossLink res1 conn1 res2 conn2
  
        RESIDUE                      _res1_
        STRING                       _connect1_
        RESIDUE                      _res2_
        STRING                       _connect2_
  
  Create a bond between ATOMs at the connection point specified by
  _conn1_ and _conn2_.   The argument _conn1_ and _conn2_ can have the
  following values:
  
  Name_           Alternatives__
  $connect0      $nend, $firstend
  $connect1      $cend, $lastend
  $connect2      $send, $disulphide
  $connect3
  $connect4
  $connect5
  
  debugOff filename
  
        STRING                       _filename_
  
  This command is a system debugging function.  It turns off debugging
  messages from the source (.c) file _filename_.   The symbol *
  matches all files.  The default for all filenames is `off'.
  Note that system debugging is in effect only if LEaP was compiled
  with the preprocessor macro DEBUG defined.
  
  debugOn filename
  
        STRING                       _filename_
  
  This command is a system debugging function.  It turns on debugging
  messages from the source (.c) file _filename_.   The symbol *
  matches all files.  The default for all filenames is `off'.
  Note that system debugging is in effect only if LEaP was compiled
  with the preprocessor macro DEBUG defined.
  
  debugStatus
  This command is a memory debugging function.  It displays various
  messages that describe LEaP's usage of system resources.
  Note that memory debugging is in effect only if LEaP was compiled
  with the preprocessor macro MEMORY_DEBUG defined; MEMORY_DEBUG values
  range from 1 through 4 with the greatest being the most aggressive.
  
  deleteBond atom1 atom2
  
        ATOM                         _atom1_
        ATOM                         _atom2_
  
  Remove the bond between the ATOMs _atom1_ and _atom2_.   If no bond
  exists, an error will be displayed.
  
  deleteOffLibEntry library entry
        STRING                       _library_
        STRING                       _entry_
  
  Delete _entry_ from the Object File Format file named _library_.
  
  deleteRestraint unit a b [c [d]]
  
        UNIT                         _unit_
        ATOM                         _a_
        ATOM                         _b_
        ATOM                         _c_
        ATOM                         _d_
  
  Remove a bond, angle, or torsion restraint from _unit_, depending
  on the number of ATOMs specified.
  
  desc variable
        object                       _variable_
  
  Print a description of the object.
  
  deSelect obj
  
        UNIT/RESIDUE/ATOM          _obj_
  
  Clears the SELECT flag on all ATOMs within _obj_.  See the select command.
  
  displayPdbAtomMap
  
  Display the Name Map used for ``second chance'' mapping of atom names
  in PDB files to atoms within residue UNITs.  See addPdbAtomMap.
  
  displayPdbResMap
  
  Display the Name Map used to map residue names in PDB files to variable
  names within LEaP.  See addPdbResMap.
  
  edit unit-parmset
        UNIT/PARMSET              _unit-parmset_
  
  In xLEaP this command creates a unit editor or parameter set editor
  that contains the UNIT or PARMSET _unit-parmset_.   The user can view
  and edit the contents of the UNIT or PARMSET by using the mouse.
  If _unit-parmset_ is a PARMSET, then the user may select the Atom, Bond,
  Angle, Torsion, Improper Torsion, or Hydrogen Bond Parameters to
  edit by selecting the appropriate button.
  In tLEaP this command prints an error message.
  
  flip obj
  
        UNIT                       _obj_
  
  Flips the chirality of the selected atoms within _obj_.
  
  groupSelectedAtoms unit name
  
        UNIT                         _unit_
        STRING                       _name_
  
  Create a group within _unit_ with the name _name_ using all of the
  ATOMs within the UNIT that are selected.  If the group has already
  been defined then overwrite the old group.
  
  help [string]
  
        STRING                       _string_
  
  This command prints a description of the command in _string_.  If
  the STRING is not given then a list of legal STRINGs is provided.
  
  impose unit seqlist internals
  
        UNIT                         _unit_
        LIST                         _seqlist_
        LIST                         _internals_
  
  The impose command allows the user to impose internal coordinates
  on the UNIT. The list of RESIDUEs to impose the internal coordinates
  upon is in _seqlist_.  The internal coordinates to impose are in
  the LIST _internals_.
  The command works by looking into each RESIDUE within the UNIT that
  is listed in the _seqlist_ argument and attempts to apply each of
  the internal coordinates within _internals_.  The _seqlist_ argument
  is a LIST of NUMBERs that represent sequence numbers or ranges of
  sequence numbers.  Ranges of sequence numbers are represented by
  two-element LISTs that contain the first and last sequence number
  in the range.  The user can specify sequence number ranges that are
  larger than what is found in the UNIT. For example the range { 1 999 }
  represents all RESIDUEs in a 200 RESIDUE UNIT.
  The _internals_ argument is a LIST of LISTs.  Each sublist contains
  a sequence of ATOM names which are of type STRING followed by the
  value of the internal coordinate.  See the output of help _types_ for
  details on specifying STRINGs.  Examples of the impose command are:
  
  impose peptide { 1 2 3 } { { $N $CA  $C $N -40.0 } { $C $N  $CA $C
  -60.0 } }
  
  The RESIDUEs with sequence numbers 1, 2, and 5 within the UNIT peptide
  will assume an alpha helix conformation.
  
  impose peptide { 1 2  { 5 10 } 12 }  { { "CA" "CB" 5.0 } }
  
  This will impose on the residues with sequence numbers 1, 2, 5, 6,
  7, 8, 9, 10, and 12 within the UNIT peptide a bond length of 5.0
  angstroms between the alpha and beta carbons.  RESIDUEs without an
  ATOM named $CB (like glycine)  will be unaffected.
  Three types of conformational change are supported; bond length changes,
  bond angle changes, and torsion angle changes.  If the conformational
  change involves a torsion angle, then all dihedrals around the central
  pair of atoms are rotated.   The entire list of internals are applied
  to each RESIDUE.
  
  list
  List all of the variables currently defined.
  
  listOff library
        STRING                       _library_
  
  List the UNITs/PARMSETs stored within the Object File Format file
  named _library_.
  
  variable = loadAmberParams filename
        PARMSET                      _variable_
        STRING                       _filename_
  
  Load an AMBER format parameter set file and place it in _variable_.
  All interactions defined in the parameter set will be contained within
  _variable_.   This command causes the loaded parameter set to be included
  in LEaP's list of parameter sets that are searched when parameters are
  required.  General proper and improper torsion parameters are modified,
  the AMBER general type "X" is replaced with the LEaP general type "?".
  
  loadAmberPrep filename [ prefix ]
  
        STRING                       _filename_
        STRING                       _prefix_
  
  This command loads an AMBER PREP input file.  For each residue that
  is loaded, a new UNIT is constructed that contains a single RESIDUE
  and a variable is created with the same name as the name of the residue
  within the PREP file.   If the optional argument _prefix_ is provided
  it will be prefixed to each variable name; this feature is used to
  prefix united atom residues, which have the same names as all-atom
  residues, with the string $U to distinguish them.
  
  variable = loadMol2 filename
        STRING                       _filename_
  
  Load a Sybyl Mol2-format file with the file name _filename_.  The UNIT
  loaded will have the name specified for the MOLECULE in the input file.
  
  variable = loadMol3 filename
        STRING                       _filename_
  
  Load a Sybyl-derived Mol3-format file with the file name _filename_.
  The UNIT loaded will have the name specified for the MOLECULE in the
  input file.
  
  More information:
  http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
  
  loadOff filename
        STRING                       _filename_
  
  This command loads the Object File Format library within the file named
  _filename_.  All UNITs and PARMSETs within the library will be loaded.
  The objects are loaded into LEaP under the variable names the objects
  had when they were saved.  Variables already in existence that have the
  same names as the objects being loaded will be overwritten.  PARMSETs
  loaded using this command are included in LEaP's library of PARMSETs
  that is searched whenever parameters are required.
  
  variable = loadPdb filename
        STRING                       _filename_
  
  Load a Protein Data Bank format file with the file name _filename_.
  The sequence numbers of the RESIDUEs will be determined from the order
  of residues within the PDB file ATOM records.  For each residue in the
  PDB file, LEaP searches the variables currently defined for variable
  names that match the residue name.  If a match is found then the
  contents of the variable are copied into the UNIT created for the PDB
  structure.  If no PDB `TER' card separates the current residue from the
  previous one, a bond is created between the connect1 ATOM of the
  previous residue and the connect0 atom of the new one.  (A PDB TER
  record is also used to detect a new residue in the case of contiguous
  residues with identical residue sequence numbers.)  As atoms are read
  from the ATOM records, their coordinates are written into the
  correspondingly named ATOMs within the residue being built.  If the
  entire residue is read and it is found that ATOM coordinates are missing
  then external coordinates are built from the internal coordinates that
  were defined in the matching UNIT (residue) variable.  This allows LEaP
  to build coordinates for hydrogens and lone pairs which are not
  specified in PDB files.
  
  loadPdbUsingSeq filename unitlist
  
        STRING                       _filename_
        LIST                         _unitlist_
  
  This command reads a Protein Data Bank format file from the file
  named _filename_.  This command is identical to loadPdb except it
  does not use the residue names within the PDB file.   Instead, the
  sequence is defined by the user in _unitlist_.  For more details
  see loadPdb.
  
  logFile filename
  
        STRING                       _filename_
  
  This command opens the file with the file name _filename_ as a log
  file.  User input and ALL output is written to the log file.  Output
  is written to the log file as if the verbosity level were set to 2.
  
  variable = matchVariables string
  
        LIST                         _variable_
        STRING                       _string_
  
  Create a LIST of variables with names that match _string_. The _string_
  argument can contain the wildcard characters "?" and "*" to match any
  single character or substring of characters, respectively.
  
  measureGeom atom1 atom2 [ atom3 [ atom4 ] ]
        ATOM                _atom1_ _atom2_ _atom3_ _atom4_
  
  Measure the distance, angle, or torsion between two, three, or four ATOMs,
  respectively.
  
  quit
  
  relax obj
  
        UNIT                       _obj_
  
  Relaxes the selected atoms within _obj_.
  
  remove a b
  
        UNIT/RESIDUE/ATOM          _a_
        UNIT/RESIDUE/ATOM          _b_
  
  Remove the object _b_ from the object _a_.   If _a_ is not contained
  by _b_ then an error message will be displayed.  This command is
  used to remove ATOMs from RESIDUEs, and RESIDUEs from UNITs.   If
  the object represented by _b_ is not referenced by some variable
  name then it will be destroyed.
  
  restrainAngle unit a b c force angle
  
        UNIT                         _unit_
        ATOM                         _a_
        ATOM                         _b_
        ATOM                         _c_
        NUMBER                       _force_
        NUMBER                       _angle_
  
  Add an angle restraint to _unit_ between atoms _a_, _b_, and _c_,
  having force constant of _force_, and equilibrium angle _angle_.
  
  restrainBond unit a b force length
  
        UNIT                         _unit_
        ATOM                         _a_
        ATOM                         _b_
        NUMBER                       _force_
        NUMBER                       _length_
  
  Add a bond (distance) restraint to _unit_ between atoms _a_ and _b_
  with a force constant of _force_ and an equilibrium distance of _length_.
  
  restrainTorsion unit a b c d force phi multiplicity
  
        UNIT                         _unit_
        ATOM                         _a_
        ATOM                         _b_
        ATOM                         _c_
        ATOM                         _d_
        NUMBER                       _force_
        NUMBER                       _phi_
        NUMBER                       _multiplicity_
  
  Add a torsion restraint to _unit_ between atoms _a_, _b_, _c_, and
  _d_, with a force constant of _force_, an equilibrium torsion angle
  of _phi_, and a multiplicity of _multiplicity_.
  
  saveAmberParm     unit topologyfilename coordinatefilename
  
        UNIT                         _unit_
        STRING                       _topologyfilename_
        STRING                       _coordinatefilename_
  
  Save the AMBER topology and coordinate files for the UNIT into the
  files named _topologyfilename_ and _coordinatefilename_ respectively.
  This command will cause LEaP to search its list of PARMSETs for
  parameters defining all of the interactions between the ATOMs within
  the UNIT.  This command produces a topology file and a coordinate file
  which are identical in format to those produced by the AMBER program
  PARM, and which can be read into AMBER and SPASMS for energy minimization,
  dynamics, or nmode calculations.
  See also: saveAmberParmPol, saveAmberParmPert, and saveAmberParmPolPert
  for including atomic polarizabilities and preparing free energy
  perturbation calculations and saveAmberParmNetcdf for saving in a
  binary format.
  
  saveAmberParmNetcdf     unit topologyfilename coordinatefilename
  
  UNIT                         _unit_
  STRING                       _topologyfilename_
  STRING                       _coordinatefilename_
  
  Save the AMBER topology and coordinate files for the UNIT into the
  files named _topologyfilename_ and _coordinatefilename_ respectively.
  This command will cause LEaP to search its list of PARMSETs for
  parameters defining all of the interactions between the ATOMs within
  the UNIT.  This command produces a topology file and a coordinate file
  which can be read into AMBER and SPASMS for energy minimization, dynamics,
  or nmode calculations.
  The coordinate file written will be in the binary NetCDF AMBER restart
  format, which enables the writing of larger input files and quicker I/O.
  Use saveAmberParm for the regular ASCII coordinate format.
  
  saveAmberParmPert unit topologyfilename coordinatefilename
  
        UNIT                         _unit_
        STRING                       _topologyfilename_
        STRING                       _coordinatefilename_
  
  Save the AMBER topology and coordinate files for the UNIT into the
  files named _topologyfilename_ and _coordinatefilename_ respectively.
  This command will cause LEaP to search its list of PARMSETs for
  parameters defining all of the interactions between the ATOMs within
  the UNIT - including the perturbed ATOMs (which are ignored by the
  vanilla saveAmberParm command).  This command produces a topology file
  and a coordinate file that are identical in format to those produced by
  the AMBER PARM program using the PERT option, and which can be read into
  AMBER and SPASMS for free energy calculations.
  
  saveAmberParmPol unit topologyfilename coordinatefilename
  
  Like saveAmberParm, but includes atomic polarizabilities in the topology
  file for use with IPOL=1 in Sander. The polarizabilities are according
  to atom type, and are defined in the 'mass' section of the parm.dat or
  frcmod file. Note: charges are normally scaled when polarizabilities are
  used - see scaleCharges for an easy way of doing this.
  
  saveAmberParmPolPert unit topologyfilename coordinatefilename
  
  Like saveAmberParmPert, but includes atomic polarizabilities in the topology
  file for use with IPOL=1 in Gibbs. The polarizabilities are according to
  atom type, and are defined in the 'mass' section of the parm.dat or frcmod
  file. Note: charges are normally scaled when polarizabilities are used -
  see scaleCharges for an easy way of doing this.
  
  saveAmberPrep unit filename
  
        UNIT                         _unit_
        STRING                       _filename_
  
  Save all residues in the UNIT to a prep.in file. All possible improper
  dihedrals are given for each residue, so unwanted ones need to be
  deleted from the file. 'Connect0' and 'connect1' atoms must be defined
  for each residue.
  
  saveMol2 unit filename option
  
        UNIT                         _unit_
        STRING                       _filename_
        NUMBER                       _option_
  
  Write UNIT to the file _filename_ as a Mol2 format file.
  option = 0 for Default atom types
  option = 1 for AMBER atom types
  
  More information:
  https://upjv.q4md-forcefieldtools.org/Tutorial/leap-mol2.php
  
  saveMol3 unit filename option
  
        UNIT                         _unit_
        STRING                       _filename_
        NUMBER                       _option_
  
  Write UNIT to the file _filename_ as a Mol3 format file.
  option = 0 for Default atom types
  option = 1 for AMBER atom types
  
  More information:
  http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
  
  saveOff object filename
  
        object                       _object_
        STRING                       _filename_
  
  The saveOff command allows the user to save UNITs, and PARMSETs to a
  file named _filename_.  The file is written using the Object File
  Format (OFF) and can accommodate an unlimited number of uniquely
  named objects.  The names by which the objects are stored are the
  variable names specified in the argument of this command.  If the
  file _filename_ already exists then the new objects will be added
  to the file.  If there are objects within the file with the same
  names as objects being saved then the old objects will be overwritten.
  The argument _object_ can be a single UNIT, a single PARMSET, or
  a LIST of mixed UNITs and PARMSETs.
  
  savePdb unit filename
  
        UNIT                         _unit_
        STRING                       _filename_
  
  Write UNIT to the file _filename_ as a PDB format file.
  
  scaleCharges container scale_factor
  
        UNIT/RESIDUE/ATOM   _container_
        NUMBER              _scale_factor_
  
  This command scales the charges in the object by _scale_factor_,
  which must be > 0.  It is useful for building systems for use
  with polarizable atoms, e.g.
  > x = copy solute
  > scaleCharges x 0.8
  > y = copy WATBOX216
  > scalecharges y 0.875
  > solvatebox x y 10
  > saveamberparmpol x x.top x.crd
  
  select obj
  
        UNIT/RESIDUE/ATOM          _obj_
  
  Sets the SELECT flag on all ATOMs within _obj_.  See the deSelect command.
  
  variable = sequence list
  
        LIST                         _list_
  
  The sequence command is used to create a new UNIT by copying the
  contents of a LIST of UNITs.  As each UNIT in the list is copied,
  a bond is created between its head atom and the tail ATOM of the
  previous UNIT, if both connect ATOMs are defined.  If only one of
  the connect pair is defined, a warning is generated and no bond is
  created.  If neither connection ATOM is defined then no bond is
  created.  As each RESIDUE within a UNIT is copied, it is assigned a
  sequence number reflecting the order added.  The order of RESIDUEs
  in multi-RESIDUE UNITs is maintained.
  This command builds reasonable starting coordinates for the new UNIT
  by assigning internal coordinates to the linkages between the component
  UNITs and building the Cartesian coordinates from these and the
  internal coordinates of the component UNITs.
  
  set default variable value
        STRING                       _variable_
        STRING                       _value_
  OR
      set container parameter object
        UNIT/RESIDUE/ATOM/STRING     _container_
        STRING                       _parameter_
        object                       _object/value_
  
  This command sets the values of some global parameters (when the first
  argument is "default") or sets various parameters associated with _container_.
  
  To see the possible variables for "set default", type "help set_default".
  
  The box parameter of a UNIT defines the bounding box of the UNIT; this is
  not a UNIT's periodic box.  The setBox and solvate family of commands add a
  periodic box to a UNIT; for a description, type, e.g., "help setBox".
  
  The more useful parameters for each type of _container_ are the following:
    container    parameters           values
  
    UNIT         name                 STRING
                 head, tail           ATOM [e.g. unit.1.1]
                 restype              "protein" "nucleic" "saccharide" "solvent"
                                      "undefined" [sets all residues in UNIT]
                 box                  LIST [side lengths: {A B C}]
                                      or NUMBER [cube side length] or "null"
                 cap                  LIST [center, radius: {X Y Z  R}]
                                      or "null"
  
    RESIDUE      name                 STRING
    [e.g.        restype              [see UNIT]
     unit.1]     connect0, connect1   ATOM [e.g. unit.1.1]
                 imagingAtom          ATOM [e.g. unit.1.1]
  
    ATOM         name, pertName       STRING [<= 4 chars]
    [e.g.        type, pertType       STRING [<= 2 chars]
     unit.1.1]   element              STRING
                 pert                 "true" [or pert flag unset]
                 charge, pertCharge   DOUBLE
                 position             LIST [{X Y Z}]
  
  Allowed arguments to "set default variable value" are these:
    variables        values       descriptions
  
    PdbWriteCharges  "on"         add charges to each ATOM record
                     "off"        don't do this (default)
  
    OldPrmtopFormat  "on"         use prmtop format from Amber6 and earlier
                     "off"        use the new prmtop format (default)
  
    Gibbs            "on"         require perturbed atoms to be set explicitly
                                     (needed for gibbs)
                     "off"        set perturbed if Type != PertType (default)
                                     (OK for sander)
  
    UseResIds        "on"         put cols 22-27 of the input pdb file into
                     "off"        a RESIDUE_ID table in prmtop files; default
                                  is "off"; only works with new prmtop formats,
                                  and when a single loadPdb command is used to
                                  create a unit.
  
    Charmm           "on"         include terms for CHARMM22 force fields
                     "off"        don't include these (default)
  
    DeleteExtraPointAngles
                     "on"         delete angles and torsions relating to
                                     extra points (default)
                     "off"        don't delete these (for older codes only)
  
    FlexibleWater    "on"         allow for flexible 3-point water models
                     "off"        assume 3-point water models are rigid (default)
  
    PBRadii          "bondi"      use Bondi radii for generalized Born
                     "mbondi"     use H-modified Bondi radii (default)
                     "mbondi2"    use H(N)-modified Bondi radii
                     "mbondi3"    ArgH and AspGluO modified Bondi2 radii
                     "parse"      Radii from the Sitkoff et al. parse parameters
                     "pbamber"    Huo and Kollman optimized radii (old!)
                     "amber6"     use radii that were the default in amber6
                                     (only recommended for backwards compat.)
  
    Dielectric       "distance"   use distance-dependent dielectric (default)
                     "constant"   use constant dielectric
  
    dipole_damp_factor    real    sets the default value for "DIPOLE_DAMP_FACTOR"
                                  for dipole screening factors in Thole models.
                                  Valid value > 0.0
  
    sceescalefactor  real         sets the default value for "SCEE_SCALE_FACTOR"
                                  for 1-4 EEL scaling factors. Valid value > 0.0.
                                  Default=1.2.
  
    scnbscalefactor  real         sets the default value for "SCNB_SCALE_FACTOR"
                                  for 1-4 NB scaling factors. Valid value > 0.0.
                                  Default=2.0.
  
    CMAP             "on"         include CMAP corrections for dihedrals
                     "off"        don't include these (default)
  
    PHIPSIMAP        "on"         include residue-based PHIPSI parameters
                     "off"        don't include these (default)
  
    ipol             integer      Sets the default value for IPOL.
                                  Valid values are 0 - 4.
                                  Default value is 0, meaning disabled.
  
    nocenter         "on"         coordinates will not be centered in the
                                  periodic simulation box
                     "off"        coordinates will be centered (default)
  
    reorder_residues "on"         solvent will be moved to the end (default)
                     "off"        residue order will be maintained as input.
                                  Beta feature: use at your own risk!
  
  setBox solute enclosure [ buffer ]
        UNIT                         _solute_
        "vdw" OR "centers"           _enclosure_
        object                       _buffer_
  
  The setBox command creates a periodic box around the _solute_ UNIT, turning
  it into a periodic system for the simulation programs.  It does not add
  any solvent to the system. The choice of "vdw" or "centers" determines
  whether the box encloses all entire atoms or just all atom centers -
  use "centers" if the system has been previously equilibrated as a
  periodic box. See the solvateBox command for a description of the
  buffer object, which extends either type of box by an arbitrary amount.
  
  showDefault [ variable OR all OR * ]
        STRING                       _variable_
  
  The showdefault command shows the values assigned to the variables by
  the "set default" command. Without variable, with "all", or with "*",
  all default variables are shown.
  
  solvateBox solute solvent buffer [ "iso" ] [ closeness ]
  
        UNIT                         _solute_
        UNIT                         _solvent_
        object                       _buffer_
        NUMBER                       _closeness_
  
  The solvateBox command creates a solvent box around the _solute_ UNIT.
  The _solute_ UNIT is modified by the addition of _solvent_ RESIDUEs.
  
  The user may want to first align long solutes that are not expected
  to tumble using alignAxes, in order to minimize box volume.
  
  The normal choice for a TIP3 _solvent_ UNIT is WATBOX216. Note that
  constant pressure equilibration is required to bring the artificial box
  to reasonable density, since Van der Waals voids remain due to the
  impossibility of natural packing of solvent around the solute and at
  the edges of the box.
  
  The solvent box UNIT is copied and repeated in all three spatial directions
  to create a box containing the entire solute and a buffer zone defined
  by the _buffer_ argument. The _buffer_ argument defines the distance,
  in angstroms, between the wall of the box and the closest ATOM in the
  solute.
  
  If the buffer argument is a single NUMBER, then the buffer distance is
  the same for the x, y, and z directions, unless the "iso" option is used
  to make the box isometric, with the shortest box clearance = buffer. If
  "iso" is used, the solute is rotated to orient the principal axes,
  otherwise it is just centered on the origin.
  
  If the buffer argument is a LIST of three NUMBERS, then the NUMBERs are
  applied to the x, y, and z axes respectively. As the larger box is created
  and superimposed on the solute, solvent molecules overlapping the solute
  are removed.
  
  The optional _closeness_ parameter can be used to control the extent to
  which _solvent_ ATOMs overlap _solute_ ATOMs.  The default value of
  the _closeness_ argument is 1.0, which allows no overlap.  Smaller
  values allow solvent ATOMs to overlap _solute_ ATOMs by (1 - closeness) *
  R*ij, where R*ij is the sum of the Van der Waals radii of solute and
  solvent atoms.  Values greater than 1 enforce a minimum gap between
  solvent and solute of (closeness - 1) * R*ij.
  
  This command modifies the _solute_ UNIT in several ways.  First, the
  coordinates of the ATOMs are modified to move the center of a box
  enclosing the Van der Waals radii of the atoms to the origin.  Secondly,
  the UNIT is modified by the addition of _solvent_ RESIDUEs copied from
  the _solvent_ UNIT. Finally, the box parameter of the new system (still
  named for the _solute_) is modified to reflect the fact that a periodic,
  rectilinear solvent box has been created around it.
  
  solvateCap solute solvent position radius [ closeness ]
  
        UNIT                         _solute_
        UNIT                         _solvent_
        object                       _position_
        NUMBER                       _radius_
        NUMBER                       _closeness_
  
  The solvateCap command creates a solvent cap around the _solute_ UNIT
  or a part thereof.  The _solute_ UNIT is modified by the addition of
  _solvent_ RESIDUEs.
  The normal choice for a TIP3 _solvent_ UNIT is WATBOX216. The _solvent_
  box is repeated in all three spatial directions and _solvent_ RESIDUEs
  selected to create a solvent sphere with a radius of _radius_ Angstroms.
  
  The _position_ argument defines where the center of the solvent cap
  is to be placed.   If _position_ is a UNIT, RESIDUE, ATOM, or a LIST
  of UNITs, RESIDUEs, or ATOMs, then the geometric center of the ATOMs
  within the object will be used as the center of the solvent cap sphere.
  If _position_ is a LIST containing three NUMBERs then the _position_
  argument will be treated as a vector that defines the position of
  the solvent cap sphere center.
  
  The optional _closeness_ parameter can be used to control the extent to
  which _solvent_ ATOMs overlap _solute_ ATOMs.  The default value of
  the _closeness_ argument is 1.0, which allows no overlap.  Smaller
  values allow solvent ATOMs to overlap _solute_ ATOMs by (1 - closeness) *
  R*ij, where R*ij is the sum of the Van der Waals radii of solute and
  solvent atoms.  Values greater than 1 enforce a minimum gap between
  solvent and solute of (closeness - 1) * R*ij.
  
  This command modifies the _solute_ UNIT in several ways.  First,
  the UNIT is modified by the addition of _solvent_ RESIDUEs copied
  from the _solvent_ UNIT. Secondly, the cap parameter of the UNIT
  _solute_ is modified to reflect the fact that a solvent cap has been
  created around the solute.
  
  solvateDontClip solute solvent buffer [ closeness ]
  
        UNIT                         _solute_
        UNIT                         _solvent_
        object                       _buffer_
        NUMBER                       _closeness_
  
  This command is identical to the solvateBox command except that the
  solvent box that is created is not clipped to the boundary of the
  _buffer_ region.  This command forms larger solvent boxes than does
  solvateBox because it does not cause solvent that is outside the buffer
  region to be discarded.   This helps to preserve the periodic structure
  of properly constructed solvent boxes, preventing hot-spots from
  forming.
  
  solvateOct solute solvent buffer [ "iso" ] [ closeness ]
  
        UNIT                         _solute_
        UNIT                         _solvent_
        object                       _buffer_
        NUMBER                       _closeness_
  
  The solvateOct command is the same as solvateBox, except the corners
  of the box are sliced off, resulting in a truncated octahedron, which
  typically gives a more uniform distribution of solvent around the
  solute.
  
  In solvateOct, when a LIST is given for the buffer argument, four
  numbers are given instead of three, where the fourth is the diagonal
  clearance. If 0.0 is given as the fourth number, the diagonal clearance
  resulting from the application of the x,y,z clearances is reported. If
  a non-0 value is given, this may require scaling up the other clearances,
  which is also reported. Similarly, if a single number is given, any
  scaleup of the x,y,z buffer to accommodate the diagonal clip is reported.
  
  If the "iso" option is used, the isometric truncated octahedron is
  rotated to an orientation used by the PME code, and the box and angle
  dimensions output by the saveAmberParm* commands are adjusted for PME
  code imaging.
  
  solvateShell solute solvent thickness [ closeness ]
  
        UNIT                         _solute_
        UNIT                         _solvent_
        NUMBER                       _thickness_
        NUMBER                       _closeness_
  
  The solvateShell command creates a solvent shell around the _solute_ UNIT.
  The _solute_ UNIT is modified by the addition of _solvent_ RESIDUEs.
  
  The normal choice for a TIP3 _solvent_ UNIT is WATBOX216. The _solvent_ box
  is repeated in all three spatial directions and _solvent_ RESIDUEs selected
  to create a solvent shell with a radius of _thickness_ Angstroms around the
  _solute_.
  
  The _thickness_ argument defines the maximum distance a _solvent_ ATOM may
  be from the closest _solute_ ATOM.
  
  The optional _closeness_ parameter can be used to control overlap of _solvent_
  with _solute_ ATOMs.   The default value of the _closeness_ argument is
  1.0, which allows contact but no overlap.  Please see the solvateBox
  command for more details on the _closeness_ parameter.
  
  source filename
        STRING                       _filename_
  
  This command executes LEaP commands within a text file.  To display the
  commands as they are read, see the verbosity command.  The text within
  the source file must be formatted exactly like the text the user types
  into LEaP.
  
  transform atoms matrix
  
        CONTAINER/LIST               _atoms_
        LIST                         _matrix_
  
  Translate all of the ATOMs within _atoms_ by the (3X3) or (4X4) matrix
  defined by the 9 or 16 NUMBERs in the LIST of LISTs _matrix_.
      { { r11  r12  r13  -tx }
        { r21  r22  r23  -ty }
        { r31  r32  r33  -tz }
        { 0    0    0     1  } }
  The diagonal upper left elements, rII can be used for symmetry operations,
  e.g. a reflection in the XY plane can be produced with r11=1, r22=1, r33=-1
  where the other rIJ elements are 0. The -t column is used to specify
  translations along the appropriate axes (0 for no translation).
  
  translate atoms direction
  
        UNIT/RESIDUE/ATOM            _atoms_
        LIST                         _direction_
  
  Translate all of the ATOMs within _atoms_ by the vector defined by
  the three NUMBERs in the LIST _ direction_.
  
  verbosity level
  
        NUMBER                       _level_
  
  This command sets the level of output that LEaP provides the user.
  A value of 0 is the default, providing the minimum of messages.  A
  value of 1 will produce more output, and a value of 2 will produce
  all of the output of level 1 and display the text of the script lines
  executed with the source command.
  
  zMatrix obj zmatrix
  
        UNIT/RESIDUE/ATOM            _obj_
        LIST                         _zmatrix_
  
  The zMatrix command is quite complicated.  It is used to define the
  external coordinates of ATOMs within _obj_ using internal coordinates.
  The second parameter of the zMatrix command is a LIST of LISTs; each
  sub-list has several arguments:
  
  { a1 a2 bond12 }
  
  This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
  along the x-axis from ATOM _a2_.   If ATOM _a2_ does not have coordinates
  defined then ATOM _a2_ is placed at the origin.
  
  { a1 a2 a3 bond12 angle123 }
  
  This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
  away from ATOM _a2_ making an angle of _angle123_ degrees between
  _a1_, _a2_ and _a3_.  The angle is measured in a right hand sense
  and in the x-y plane.   ATOMs _a2_ and _a3_ must have coordinates defined.
  
  { a1 a2 a3 a4 bond12 angle123 torsion1234 }
  
  This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
  away from ATOM _a2_, creating an angle of _angle123_ degrees between
  _a1_, _a2_, and _a3_, and making a torsion angle of _torsion1234_ between
  _a1_, _a2_, _a3_, and _a4_.
  
  { a1 a2 a3 a4 bond12 angle123 angle124 orientation }
  
  This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
  away from ATOM _a2_, making angles _angle123_ between ATOMs _a1_,
  _a2_, and _a3_, and _angle124_ between ATOMs _a1_, _a2_, and _a4_.  The
  argument _orientation_ defines whether the ATOM _a1_ is above or below
  a plane defined by the ATOMs _a2_, _a3_, and _a4_.  If _orientation_
  is positive then _a1_ will be placed in such a way so that the inner
  product of (_a3_-_a2_)  cross (_a4_-_a2_) with (_a1_-_a2_) is positive.
  Otherwise _a1_ will be placed on the other side of the plane.  This
  allows the coordinates of a molecule like fluoro-chloro-bromo-methane
  to be defined without having to resort to dummy atoms.
  The first arguments within the zMatrix entries ( _a1_, _a2_, _a3_,
  _a4_ ) are either ATOMs or STRINGs containing names of ATOMs within
  _obj_.   The subsequent arguments are all NUMBERs.   Any ATOM can be
  placed at the _a1_ position, even those that have coordinates defined.
  This feature can be used to provide an endless supply of dummy atoms,
  if they are required.   A predefined dummy atom with the name "*"
  (a single asterisk, no quotes)  can also be used.
  No order is imposed in the sub-lists.  The user can place sub-lists
  in arbitrary order, as long as they maintain the requirement that
  all atoms _a2_, _a3_, and _a4_ must have external coordinates defined,
  except for entries that define the coordinate of an ATOM using only
  a bond length.


    ]]>     </help>
     <expand macro="citations" />
</tool>