Mercurial > repos > bgruening > openbabel
comparison convert/ob_convert.xml @ 3:282503f242cf
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 26 Apr 2013 09:07:43 -0400 |
| parents | 6493d130f018 |
| children | 12822efbd4a4 |
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| 2:efe00424f82b | 3:282503f242cf |
|---|---|
| 41 #end if | 41 #end if |
| 42 2>&1 | 42 2>&1 |
| 43 </command> | 43 </command> |
| 44 <inputs> | 44 <inputs> |
| 45 <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/> | 45 <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/> |
| 46 <!--<param name="format1" type="select" label="Input format"> | |
| 47 <option value="acr">Carine ASCI Crystal</option> | |
| 48 <option value="alc">Alchemy format</option> | |
| 49 <option value="arc">Accelrys/MSI Biosym/Insight II CAR format [Read-only]</option> | |
| 50 <option value="bgf">MSI BGF format</option> | |
| 51 <option value="box">Dock 3.5 Box format</option> | |
| 52 <option value="bs">Ball and Stick format</option> | |
| 53 <option value="c3d1">Chem3D Cartesian 1 format</option> | |
| 54 <option value="c3d2">Chem3D Cartesian 2 format</option> | |
| 55 <option value="caccrt">Cacao Cartesian format</option> | |
| 56 <option value="can">Canonical SMILES format</option> | |
| 57 <option value="car">Accelrys/MSI Biosym/Insight II CAR format [Read-only]</option> | |
| 58 <option value="ccc">CCC format [Read-only]</option> | |
| 59 <option value="cdx">ChemDraw binary format [Read-only]</option> | |
| 60 <option value="cdxml">ChemDraw CDXML format</option> | |
| 61 <option value="cif">Crystallographic Information File</option> | |
| 62 <option value="cml">Chemical Markup Language</option> | |
| 63 <option value="cmlr">CML Reaction format</option> | |
| 64 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> | |
| 65 <option value="crk3d">Chemical Resource Kit 3D format</option> | |
| 66 <option value="ct">ChemDraw Connection Table format</option> | |
| 67 <option value="dmol">DMol3 coordinates format</option> | |
| 68 <option value="ent">Protein Data Bank format</option> | |
| 69 <option value="fch">Gaussian formatted checkpoint file format [Read-only]</option> | |
| 70 <option value="fchk">Gaussian formatted checkpoint file format [Read-only]</option> | |
| 71 <option value="fck">Gaussian formatted checkpoint file format [Read-only]</option> | |
| 72 <option value="feat">Feature format</option> | |
| 73 <option value="fract">Free Form Fractional format</option> | |
| 74 <option value="fs">Open Babel FastSearching database</option> | |
| 75 <option value="g03">Gaussian 98/03 Output [Read-only]</option> | |
| 76 <option value="g98">Gaussian 98/03 Output [Read-only]</option> | |
| 77 <option value="gam">GAMESS Output [Read-only]</option> | |
| 78 <option value="gamout">GAMESS Output [Read-only]</option> | |
| 79 <option value="gpr">Ghemical format</option> | |
| 80 <option value="hin">HyperChem HIN format</option> | |
| 81 <option value="ins">ShelX format [Read-only]</option> | |
| 82 <option value="jout">Jaguar output format [Read-only]</option> | |
| 83 <option value="mdl">MDL MOL format</option> | |
| 84 <option value="mmd">MacroModel format</option> | |
| 85 <option value="mmod">MacroModel format</option> | |
| 86 <option value="mol">MDL MOL format</option> | |
| 87 <option value="mol2">Sybyl Mol2 format</option> | |
| 88 <option value="moo">MOPAC Output format [Read-only]</option> | |
| 89 <option value="mop">MOPAC Cartesian format</option> | |
| 90 <option value="mopcrt">MOPAC Cartesian format</option> | |
| 91 <option value="mopin">MOPAC Internal</option> | |
| 92 <option value="mopout">MOPAC Output format [Read-only]</option> | |
| 93 <option value="mpc">MOPAC Cartesian format</option> | |
| 94 <option value="mpqc">MPQC output format [Read-only]</option> | |
| 95 <option value="nwo">NWChem output format [Read-only]</option> | |
| 96 <option value="pc">PubChem format [Read-only]</option> | |
| 97 <option value="pcm">PCModel format</option> | |
| 98 <option value="pdb">Protein Data Bank format</option> | |
| 99 <option value="pqs">Parallel Quantum Solutions format</option> | |
| 100 <option value="prep">Amber Prep format [Read-only]</option> | |
| 101 <option value="qcout">Q-Chem output format [Read-only]</option> | |
| 102 <option value="res">ShelX format [Read-only]</option> | |
| 103 <option value="rxn">MDL RXN format</option> | |
| 104 <option value="sdf">MDL MOL format</option> | |
| 105 <option value="smi">SMILES format</option> | |
| 106 <option value="tdd">Thermo format</option> | |
| 107 <option value="therm">Thermo format</option> | |
| 108 <option value="tmol">TurboMole Coordinate format</option> | |
| 109 <option value="unixyz">UniChem XYZ format</option> | |
| 110 <option value="vmol">ViewMol format</option> | |
| 111 <option value="xml">General XML format [Read-only]</option> | |
| 112 <option value="xyz">XYZ cartesian coordinates format</option> | |
| 113 <option value="yob">YASARA.org YOB format</option> | |
| 114 </param>--> | |
| 115 <param name="out_format" type="select" label="Output format"> | 46 <param name="out_format" type="select" label="Output format"> |
| 116 <option value="acr">Carine ASCI Crystal</option> | 47 <option value="acr">Carine ASCI Crystal</option> |
| 117 <option value="alc">Alchemy format</option> | 48 <option value="alc">Alchemy format</option> |
| 118 <option value="bgf">MSI BGF format</option> | 49 <option value="bgf">MSI BGF format</option> |
| 119 <option value="box">Dock 3.5 Box format</option> | 50 <option value="box">Dock 3.5 Box format</option> |
| 120 <option value="bs">Ball and Stick format</option> | 51 <option value="bs">Ball and Stick format</option> |
| 121 <option value="c3d1">Chem3D Cartesian 1 format</option> | 52 <option value="c3d1">Chem3D Cartesian 1 format</option> |
| 122 <option value="c3d2">Chem3D Cartesian 2 format</option> | 53 <option value="c3d2">Chem3D Cartesian 2 format</option> |
| 123 <option value="caccrt">Cacao Cartesian format</option> | 54 <option value="caccrt">Cacao Cartesian format</option> |
| 124 <option value="cache">CAChe MolStruct format [Write-only]</option> | 55 <option value="cache">CAChe MolStruct format</option> |
| 125 <option value="cacint">Cacao Internal format [Write-only]</option> | 56 <option value="cacint">Cacao Internal format</option> |
| 126 <option value="can">Canonical SMILES format (can)</option> | 57 <option value="can">Canonical SMILES format (can)</option> |
| 127 <option value="cdxml">ChemDraw CDXML format</option> | 58 <option value="cdxml">ChemDraw CDXML format</option> |
| 128 <option value="cht">Chemtool format [Write-only]</option> | 59 <option value="cht">Chemtool format</option> |
| 129 <option value="cif">Crystallographic Information File</option> | 60 <option value="cif">Crystallographic Information File</option> |
| 130 <option value="cml">Chemical Markup Language</option> | 61 <option value="cml">Chemical Markup Language</option> |
| 131 <option value="cmlr">CML Reaction format</option> | 62 <option value="cmlr">CML Reaction format</option> |
| 132 <option value="com">Gaussian 98/03 Cartesian Input [Write-only]</option> | 63 <option value="com">Gaussian 98/03 Cartesian Input</option> |
| 133 <option value="copy">Copies raw text [Write-only]</option> | 64 <option value="copy">Copies raw text</option> |
| 134 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> | 65 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> |
| 135 <option value="crk3d">Chemical Resource Kit 3D format</option> | 66 <option value="crk3d">Chemical Resource Kit 3D format</option> |
| 136 <option value="csr">Accelrys/MSI Quanta CSR format [Write-only]</option> | 67 <option value="csr">Accelrys/MSI Quanta CSR format</option> |
| 137 <option value="cssr">CSD CSSR format [Write-only]</option> | 68 <option value="cssr">CSD CSSR format</option> |
| 138 <option value="ct">ChemDraw Connection Table format</option> | 69 <option value="ct">ChemDraw Connection Table format</option> |
| 139 <option value="dmol">DMol3 coordinates format</option> | 70 <option value="dmol">DMol3 coordinates format</option> |
| 140 <!--<option value="ent">Protein Data Bank format</option> | 71 <!--<option value="ent">Protein Data Bank format</option> |
| 141 <option value="fa">FASTA format [Write-only]</option>--> | 72 <option value="fa">FASTA format</option>--> |
| 142 <option value="fasta">FASTA format [Write-only]</option> | 73 <option value="fasta">FASTA format</option> |
| 143 <option value="feat">Feature format</option> | 74 <option value="feat">Feature format</option> |
| 144 <option value="fh">Fenske-Hall Z-Matrix format [Write-only]</option> | 75 <option value="fh">Fenske-Hall Z-Matrix format</option> |
| 145 <option value="fix">SMILES FIX format [Write-only]</option> | 76 <option value="fix">SMILES FIX format</option> |
| 146 <option value="fpt">Fingerprint format [Write-only]</option> | 77 <option value="fpt">Fingerprint format</option> |
| 147 <option value="fract">Free Form Fractional format</option> | 78 <option value="fract">Free Form Fractional format</option> |
| 148 <option value="fs">Open Babel FastSearching database (fs)</option> | 79 <option value="fs">Open Babel FastSearching database (fs)</option> |
| 149 <!--<option value="fsa">FASTA format [Write-only]</option>--> | 80 <!--<option value="fsa">FASTA format</option>--> |
| 150 <option value="gamin">GAMESS Input [Write-only]</option> | 81 <option value="gamin">GAMESS Input</option> |
| 151 <option value="gau">Gaussian 98/03 Cartesian Input [Write-only]</option> | 82 <option value="gau">Gaussian 98/03 Cartesian Input</option> |
| 152 <!--<option value="gjc">Gaussian 98/03 Cartesian Input [Write-only]</option> | 83 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option> |
| 153 <option value="gjf">Gaussian 98/03 Cartesian Input [Write-only]</option>--> | 84 <option value="gjf">Gaussian 98/03 Cartesian Input</option>--> |
| 154 <option value="gpr">Ghemical format</option> | 85 <option value="gpr">Ghemical format</option> |
| 155 <option value="gr96">GROMOS96 format [Write-only]</option> | 86 <option value="gr96">GROMOS96 format</option> |
| 156 <option value="hin">HyperChem HIN format</option> | 87 <option value="hin">HyperChem HIN format</option> |
| 157 <option value="inchi">IUPAC InChI [Write-only]</option> | 88 <option value="inchi">IUPAC InChI</option> |
| 158 <option value="inp">GAMESS Input [Write-only]</option> | 89 <option value="inp">GAMESS Input</option> |
| 159 <option value="jin">Jaguar input format [Write-only]</option> | 90 <option value="jin">Jaguar input format</option> |
| 160 <!--<option value="mdl">MDL MOL format (mol)</option>--> | 91 <!--<option value="mdl">MDL MOL format (mol)</option>--> |
| 161 <option value="mmd">MacroModel format</option> | 92 <option value="mmd">MacroModel format</option> |
| 162 <option value="mmod">MacroModel format</option> | 93 <option value="mmod">MacroModel format</option> |
| 163 <option value="mol">MDL MOL format (mol)</option> | 94 <option value="mol">MDL MOL format (mol)</option> |
| 164 <option value="mol2">Sybyl Mol2 format (mol2)</option> | 95 <option value="mol2">Sybyl Mol2 format (mol2)</option> |
| 165 <option value="molreport">Open Babel molecule report [Write-only]</option> | 96 <option value="molreport">Open Babel molecule report</option> |
| 166 <option value="mop">MOPAC Cartesian format</option> | 97 <option value="mop">MOPAC Cartesian format</option> |
| 167 <option value="mopcrt">MOPAC Cartesian format</option> | 98 <option value="mopcrt">MOPAC Cartesian format</option> |
| 168 <option value="mopin">MOPAC Internal</option> | 99 <option value="mopin">MOPAC Internal</option> |
| 169 <option value="mpc">MOPAC Cartesian format</option> | 100 <option value="mpc">MOPAC Cartesian format</option> |
| 170 <option value="mpd">Sybyl descriptor format [Write-only]</option> | 101 <option value="mpd">Sybyl descriptor format</option> |
| 171 <option value="mpqcin">MPQC simplified input format [Write-only]</option> | 102 <option value="mpqcin">MPQC simplified input format</option> |
| 172 <option value="nw">NWChem input format [Write-only]</option> | 103 <option value="nw">NWChem input format</option> |
| 173 <option value="pcm">PCModel format</option> | 104 <option value="pcm">PCModel format</option> |
| 174 <option value="pdb">Protein Data Bank format (pdb)</option> | 105 <option value="pdb">Protein Data Bank format (pdb)</option> |
| 175 <option value="pov">POV-Ray input format [Write-only]</option> | 106 <option value="pov">POV-Ray input format</option> |
| 176 <option value="pqs">Parallel Quantum Solutions format</option> | 107 <option value="pqs">Parallel Quantum Solutions format</option> |
| 177 <option value="qcin">Q-Chem input format [Write-only]</option> | 108 <option value="qcin">Q-Chem input format</option> |
| 178 <option value="report">Open Babel report format [Write-only]</option> | 109 <option value="report">Open Babel report format</option> |
| 179 <option value="rxn">MDL RXN format</option> | 110 <option value="rxn">MDL RXN format</option> |
| 180 <!--<option value="sd">MDL MOL format</option>--> | 111 <!--<option value="sd">MDL MOL format</option>--> |
| 181 <option value="sdf">MDL MOL format (sdf)</option> | 112 <option value="sdf">MDL MOL format (sdf)</option> |
| 182 <option value="smi">SMILES format (smi)</option> | 113 <option value="smi">SMILES format (smi)</option> |
| 183 <!--<option value="sy2">Sybyl Mol2 format</option>--> | 114 <!--<option value="sy2">Sybyl Mol2 format</option>--> |
| 184 <option value="tdd">Thermo format</option> | 115 <option value="tdd">Thermo format</option> |
| 185 <option value="test">Test format [Write-only]</option> | 116 <option value="test">Test format</option> |
| 186 <option value="therm">Thermo format</option> | 117 <option value="therm">Thermo format</option> |
| 187 <option value="tmol">TurboMole Coordinate format</option> | 118 <option value="tmol">TurboMole Coordinate format</option> |
| 188 <option value="txyz">Tinker MM2 format [Write-only]</option> | 119 <option value="txyz">Tinker MM2 format</option> |
| 189 <option value="unixyz">UniChem XYZ format</option> | 120 <option value="unixyz">UniChem XYZ format</option> |
| 190 <option value="vmol">ViewMol format</option> | 121 <option value="vmol">ViewMol format</option> |
| 191 <option value="xed">XED format [Write-only]</option> | 122 <option value="xed">XED format</option> |
| 192 <option value="xyz">XYZ cartesian coordinates format</option> | 123 <option value="xyz">XYZ cartesian coordinates format</option> |
| 193 <option value="yob">YASARA.org YOB format</option> | 124 <option value="yob">YASARA.org YOB format</option> |
| 194 <option value="zin">ZINDO input format [Write-only]</option> | 125 <option value="zin">ZINDO input format</option> |
| 195 </param> | 126 </param> |
| 196 <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" /> | 127 <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" /> |
| 197 <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" /> | 128 <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" /> |
| 198 <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" /> | 129 <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" /> |
| 199 <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" /> | 130 <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" /> |