Mercurial > repos > bgruening > openbabel

changeset 3:282503f242cf

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Uploaded
author bgruening
date Fri, 26 Apr 2013 09:07:43 -0400
parents efe00424f82b
children d7bf9b4e3183
files convert/ob_convert.xml tool_dependencies.xml
diffstat 2 files changed, 33 insertions(+), 102 deletions(-) [+]
line wrap: on
line diff
--- a/convert/ob_convert.xml	Sun Mar 31 13:10:35 2013 -0400
+++ b/convert/ob_convert.xml	Fri Apr 26 09:07:43 2013 -0400
@@ -43,75 +43,6 @@
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/>
-        <!--<param name="format1" type="select" label="Input format">
-            <option value="acr">Carine ASCI Crystal</option>
-            <option value="alc">Alchemy format</option>
-            <option value="arc">Accelrys/MSI Biosym/Insight II CAR format [Read-only]</option>
-            <option value="bgf">MSI BGF format</option>
-            <option value="box">Dock 3.5 Box format</option>
-            <option value="bs">Ball and Stick format</option>
-            <option value="c3d1">Chem3D Cartesian 1 format</option>
-            <option value="c3d2">Chem3D Cartesian 2 format</option>
-            <option value="caccrt">Cacao Cartesian format</option>
-            <option value="can">Canonical SMILES format</option>
-            <option value="car">Accelrys/MSI Biosym/Insight II CAR format [Read-only]</option>
-            <option value="ccc">CCC format [Read-only]</option>
-            <option value="cdx">ChemDraw binary format [Read-only]</option>
-            <option value="cdxml">ChemDraw CDXML format</option>
-            <option value="cif">Crystallographic Information File</option>
-            <option value="cml">Chemical Markup Language</option>
-            <option value="cmlr">CML Reaction format</option>
-            <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
-            <option value="crk3d">Chemical Resource Kit 3D format</option>
-            <option value="ct">ChemDraw Connection Table format</option>
-            <option value="dmol">DMol3 coordinates format</option>
-            <option value="ent">Protein Data Bank format</option>
-            <option value="fch">Gaussian formatted checkpoint file format [Read-only]</option>
-            <option value="fchk">Gaussian formatted checkpoint file format [Read-only]</option>
-            <option value="fck">Gaussian formatted checkpoint file format [Read-only]</option>
-            <option value="feat">Feature format</option>
-            <option value="fract">Free Form Fractional format</option>
-            <option value="fs">Open Babel FastSearching database</option>
-            <option value="g03">Gaussian 98/03 Output [Read-only]</option>
-            <option value="g98">Gaussian 98/03 Output [Read-only]</option>
-            <option value="gam">GAMESS Output [Read-only]</option>
-            <option value="gamout">GAMESS Output [Read-only]</option>
-            <option value="gpr">Ghemical format</option>
-            <option value="hin">HyperChem HIN format</option>
-            <option value="ins">ShelX format [Read-only]</option>
-            <option value="jout">Jaguar output format [Read-only]</option>
-            <option value="mdl">MDL MOL format</option>
-            <option value="mmd">MacroModel format</option>
-            <option value="mmod">MacroModel format</option>
-            <option value="mol">MDL MOL format</option>
-            <option value="mol2">Sybyl Mol2 format</option>
-            <option value="moo">MOPAC Output format [Read-only]</option>
-            <option value="mop">MOPAC Cartesian format</option>
-            <option value="mopcrt">MOPAC Cartesian format</option>
-            <option value="mopin">MOPAC Internal</option>
-            <option value="mopout">MOPAC Output format [Read-only]</option>
-            <option value="mpc">MOPAC Cartesian format</option>
-            <option value="mpqc">MPQC output format [Read-only]</option>
-            <option value="nwo">NWChem output format [Read-only]</option>
-            <option value="pc">PubChem format [Read-only]</option>
-            <option value="pcm">PCModel format</option>
-            <option value="pdb">Protein Data Bank format</option>
-            <option value="pqs">Parallel Quantum Solutions format</option>
-            <option value="prep">Amber Prep format [Read-only]</option>
-            <option value="qcout">Q-Chem output format [Read-only]</option>
-            <option value="res">ShelX format [Read-only]</option>
-            <option value="rxn">MDL RXN format</option>
-            <option value="sdf">MDL MOL format</option>
-            <option value="smi">SMILES format</option>
-            <option value="tdd">Thermo format</option>
-            <option value="therm">Thermo format</option>
-            <option value="tmol">TurboMole Coordinate format</option>
-            <option value="unixyz">UniChem XYZ format</option>
-            <option value="vmol">ViewMol format</option>
-            <option value="xml">General XML format [Read-only]</option>
-            <option value="xyz">XYZ cartesian coordinates format</option>
-            <option value="yob">YASARA.org YOB format</option>
-        </param>-->
         <param name="out_format" type="select" label="Output format">
             <option value="acr">Carine ASCI Crystal</option>
             <option value="alc">Alchemy format</option>
@@ -121,77 +52,77 @@
             <option value="c3d1">Chem3D Cartesian 1 format</option>
             <option value="c3d2">Chem3D Cartesian 2 format</option>
             <option value="caccrt">Cacao Cartesian format</option>
-            <option value="cache">CAChe MolStruct format [Write-only]</option>
-            <option value="cacint">Cacao Internal format [Write-only]</option>
+            <option value="cache">CAChe MolStruct format</option>
+            <option value="cacint">Cacao Internal format</option>
             <option value="can">Canonical SMILES format (can)</option>
             <option value="cdxml">ChemDraw CDXML format</option>
-            <option value="cht">Chemtool format [Write-only]</option>
+            <option value="cht">Chemtool format</option>
             <option value="cif">Crystallographic Information File</option>
             <option value="cml">Chemical Markup Language</option>
             <option value="cmlr">CML Reaction format</option>
-            <option value="com">Gaussian 98/03 Cartesian Input [Write-only]</option>
-            <option value="copy">Copies raw text [Write-only]</option>
+            <option value="com">Gaussian 98/03 Cartesian Input</option>
+            <option value="copy">Copies raw text</option>
             <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
             <option value="crk3d">Chemical Resource Kit 3D format</option>
-            <option value="csr">Accelrys/MSI Quanta CSR format [Write-only]</option>
-            <option value="cssr">CSD CSSR format [Write-only]</option>
+            <option value="csr">Accelrys/MSI Quanta CSR format</option>
+            <option value="cssr">CSD CSSR format</option>
             <option value="ct">ChemDraw Connection Table format</option>
             <option value="dmol">DMol3 coordinates format</option>
             <!--<option value="ent">Protein Data Bank format</option>
-            <option value="fa">FASTA format [Write-only]</option>-->
-            <option value="fasta">FASTA format [Write-only]</option>
+            <option value="fa">FASTA format</option>-->
+            <option value="fasta">FASTA format</option>
             <option value="feat">Feature format</option>
-            <option value="fh">Fenske-Hall Z-Matrix format [Write-only]</option>
-            <option value="fix">SMILES FIX format [Write-only]</option>
-            <option value="fpt">Fingerprint format [Write-only]</option>
+            <option value="fh">Fenske-Hall Z-Matrix format</option>
+            <option value="fix">SMILES FIX format</option>
+            <option value="fpt">Fingerprint format</option>
             <option value="fract">Free Form Fractional format</option>
             <option value="fs">Open Babel FastSearching database (fs)</option>
-            <!--<option value="fsa">FASTA format [Write-only]</option>-->
-            <option value="gamin">GAMESS Input [Write-only]</option>
-            <option value="gau">Gaussian 98/03 Cartesian Input [Write-only]</option>
-            <!--<option value="gjc">Gaussian 98/03 Cartesian Input [Write-only]</option>
-            <option value="gjf">Gaussian 98/03 Cartesian Input [Write-only]</option>-->
+            <!--<option value="fsa">FASTA format</option>-->
+            <option value="gamin">GAMESS Input</option>
+            <option value="gau">Gaussian 98/03 Cartesian Input</option>
+            <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option>
+            <option value="gjf">Gaussian 98/03 Cartesian Input</option>-->
             <option value="gpr">Ghemical format</option>
-            <option value="gr96">GROMOS96 format [Write-only]</option>
+            <option value="gr96">GROMOS96 format</option>
             <option value="hin">HyperChem HIN format</option>
-            <option value="inchi">IUPAC InChI [Write-only]</option>
-            <option value="inp">GAMESS Input [Write-only]</option>
-            <option value="jin">Jaguar input format [Write-only]</option>
+            <option value="inchi">IUPAC InChI</option>
+            <option value="inp">GAMESS Input</option>
+            <option value="jin">Jaguar input format</option>
             <!--<option value="mdl">MDL MOL format (mol)</option>-->
             <option value="mmd">MacroModel format</option>
             <option value="mmod">MacroModel format</option>
             <option value="mol">MDL MOL format (mol)</option>
             <option value="mol2">Sybyl Mol2 format (mol2)</option>
-            <option value="molreport">Open Babel molecule report [Write-only]</option>
+            <option value="molreport">Open Babel molecule report</option>
             <option value="mop">MOPAC Cartesian format</option>
             <option value="mopcrt">MOPAC Cartesian format</option>
             <option value="mopin">MOPAC Internal</option>
             <option value="mpc">MOPAC Cartesian format</option>
-            <option value="mpd">Sybyl descriptor format [Write-only]</option>
-            <option value="mpqcin">MPQC simplified input format [Write-only]</option>
-            <option value="nw">NWChem input format [Write-only]</option>
+            <option value="mpd">Sybyl descriptor format</option>
+            <option value="mpqcin">MPQC simplified input format</option>
+            <option value="nw">NWChem input format</option>
             <option value="pcm">PCModel format</option>
             <option value="pdb">Protein Data Bank format (pdb)</option>
-            <option value="pov">POV-Ray input format [Write-only]</option>
+            <option value="pov">POV-Ray input format</option>
             <option value="pqs">Parallel Quantum Solutions format</option>
-            <option value="qcin">Q-Chem input format [Write-only]</option>
-            <option value="report">Open Babel report format [Write-only]</option>
+            <option value="qcin">Q-Chem input format</option>
+            <option value="report">Open Babel report format</option>
             <option value="rxn">MDL RXN format</option>
             <!--<option value="sd">MDL MOL format</option>-->
             <option value="sdf">MDL MOL format (sdf)</option>
             <option value="smi">SMILES format (smi)</option>
             <!--<option value="sy2">Sybyl Mol2 format</option>-->
             <option value="tdd">Thermo format</option>
-            <option value="test">Test format [Write-only]</option>
+            <option value="test">Test format</option>
             <option value="therm">Thermo format</option>
             <option value="tmol">TurboMole Coordinate format</option>
-            <option value="txyz">Tinker MM2 format [Write-only]</option>
+            <option value="txyz">Tinker MM2 format</option>
             <option value="unixyz">UniChem XYZ format</option>
             <option value="vmol">ViewMol format</option>
-            <option value="xed">XED format [Write-only]</option>
+            <option value="xed">XED format</option>
             <option value="xyz">XYZ cartesian coordinates format</option>
             <option value="yob">YASARA.org YOB format</option>
-            <option value="zin">ZINDO input format [Write-only]</option>
+            <option value="zin">ZINDO input format</option>
         </param>
         <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
         <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
--- a/tool_dependencies.xml	Sun Mar 31 13:10:35 2013 -0400
+++ b/tool_dependencies.xml	Fri Apr 26 09:07:43 2013 -0400
@@ -1,6 +1,6 @@
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-	<repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="9e07452137da" />
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="6fd6b904eeff" />
     </package>
     <package name="cheminfolib" version="0.1">
         <install version="1.0">