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From: Debian Science Maintainers
<debian-science-maintainers@lists.alioth.debian.org>
Date: Mon, 29 Sep 2025 16:11:15 +0200
Subject: tools~cmlwriter.py
changes in the script to provide interactive exports to various formats
---
tools/cmlwriter.py | 85 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 83 insertions(+), 2 deletions(-)
diff --git a/tools/cmlwriter.py b/tools/cmlwriter.py
index dc218b1..2bb52be 100644
--- a/tools/cmlwriter.py
+++ b/tools/cmlwriter.py
@@ -17,6 +17,86 @@ class CMLWriter:
self.fout = fout
self.cml = cml_handler
self.l10n = l10n_handler
+ self.scriptFormat="""
+ <script type='text/javascript'>
+ function getOtherFormat(obj){
+ i=obj.selectedIndex
+ if(i>0){
+ l=document.location+''
+ ext=obj.options[i].value
+ mol=l.replace(/.*chemical-structures\/(.*)_[a-z]*\.html$/,'$1')
+ newl='../convert.cgi?mol='+escape(mol)+"&ext="+ext
+ document.location=newl
+ }
+ }
+ </script>
+"""
+ self.selection="""
+ <select id="format" name="format" onChange="getOtherFormat(this)">
+ <option value="none">----------------</option>
+ <option value="alc">ALC -- Alchemy format</option>
+ <option value="bgf">BGF -- MSI BGF format</option>
+ <option value="box">BOX -- Dock 3.5 Box format</option>
+ <option value="bs">BS -- Ball and Stick format</option>
+ <option value="c3d1">C3D1 -- Chem3D Cartesian 1 format</option>
+ <option value="c3d2">C3D2 -- Chem3D Cartesian 2 format</option>
+ <option value="caccrt">CACCRT -- Cacao Cartesian format</option>
+ <option value="cache">CACHE -- CAChe MolStruct format [Write-only]</option>
+ <option value="cacint">CACINT -- Cacao Internal format [Write-only]</option>
+ <option value="cht">CHT -- Chemtool format [Write-only]</option>
+ <option value="cml">CML -- Chemical Markup Language</option>
+ <option value="cmlr">CMLR -- CML Reaction format</option>
+ <option value="com">COM -- Gaussian 98/03 Cartesian Input [Write-only]</option>
+ <option value="copy">COPY -- Copies raw text [Write-only]</option>
+ <option value="crk2d">CRK2D -- Chemical Resource Kit diagram format (2D)</option>
+ <option value="crk3d">CRK3D -- Chemical Resource Kit 3D format</option>
+ <option value="csr">CSR -- Accelrys/MSI Quanta CSR format [Write-only]</option>
+ <option value="cssr">CSSR -- CSD CSSR format [Write-only]</option>
+ <option value="ct">CT -- ChemDraw Connection Table format </option>
+ <option value="dmol">DMOL -- DMol3 coordinates format</option>
+ <option value="ent">ENT -- Protein Data Bank format</option>
+ <option value="feat">FEAT -- Feature format</option>
+ <option value="fh">FH -- Fenske-Hall Z-Matrix format [Write-only]</option>
+ <option value="fix">FIX -- SMILES FIX format [Write-only]</option>
+ <option value="fpt">FPT -- Fingerprint format [Write-only]</option>
+ <option value="fract">FRACT -- Free Form Fractional format</option>
+ <option value="fs">FS -- FastSearching</option>
+ <option value="gamin">GAMIN -- GAMESS Input [Write-only]</option>
+ <option value="gau">GAU -- Gaussian 98/03 Cartesian Input [Write-only]</option>
+ <option value="gpr">GPR -- Ghemical format</option>
+ <option value="gr96">GR96 -- GROMOS96 format [Write-only]</option>
+ <option value="hin">HIN -- HyperChem HIN format</option>
+ <option value="inp">INP -- GAMESS Input [Write-only]</option>
+ <option value="jin">JIN -- Jaguar input format [Write-only]</option>
+ <option value="mdl">MDL -- MDL MOL format</option>
+ <option value="mmd">MMD -- MacroModel format</option>
+ <option value="mmod">MMOD -- MacroModel format</option>
+ <option value="mol">MOL -- MDL MOL format</option>
+ <option value="mol2">MOL2 -- Sybyl Mol2 format</option>
+ <option value="mopcrt">MOPCRT -- MOPAC Cartesian format</option>
+ <option value="mpd">MPD -- Sybyl descriptor format [Write-only]</option>
+ <option value="mpqcin">MPQCIN -- MPQC simplified input format [Write-only]</option>
+ <option value="nw">NW -- NWChem input format [Write-only]</option>
+ <option value="pcm">PCM -- PCModel Format</option>
+ <option value="pdb">PDB -- Protein Data Bank format</option>
+ <option value="pov">POV -- POV-Ray input format [Write-only]</option>
+ <option value="pqs">PQS -- Parallel Quantum Solutions format</option>
+ <option value="qcin">QCIN -- Q-Chem input format [Write-only]</option>
+ <option value="report">REPORT -- Open Babel report format [Write-only]</option>
+ <option value="rxn">RXN -- MDL RXN format</option>
+ <option value="sd">SD -- MDL MOL format</option>
+ <option value="sdf">SDF -- MDL MOL format</option>
+ <option value="smi">SMI -- SMILES format</option>
+ <option value="tmol">TMOL -- TurboMole Coordinate format</option>
+ <option value="txyz">TXYZ -- Tinker MM2 format [Write-only]</option>
+ <option value="unixyz">UNIXYZ -- UniChem XYZ format</option>
+ <option value="vmol">VMOL -- ViewMol format</option>
+ <option value="xed">XED -- XED format [Write-only]</option>
+ <option value="xyz">XYZ -- XYZ cartesian coordinates format</option>
+ <option value="yob">YOB -- YASARA.org YOB format</option>
+ <option value="zin">ZIN -- ZINDO input format [Write-only]</option>
+ </select>
+"""
def parseFormula(self, raw_formula):
"""Parse formula and return the HTML formula
@@ -57,8 +137,8 @@ class CMLWriter:
xhtmlout.setOutput(self.fout)
xhtmlout.setTitle(title)
xhtmlout.addHead(' <script src="' + '../' * level + 'jmol/Jmol.js" type="text/javascript"></script>')
- xhtmlout.addHead(' <link rel="stylesheet" type="text/css" href="' + '../' * level + 'styles/style.css" />')
- xhtmlout.addHead(' <link rel="shortcut icon" href="' + '../' * level + 'images/favicon.ico" />')
+ xhtmlout.addHead(' <link href="' + '../' * level + 'styles/style.css" rel="stylesheet" type="text/css" />')
+ xhtmlout.addBody(self.scriptFormat)
xhtmlout.addBody(' <div id="header">')
xhtmlout.addBody(' <img src="'+ '../' * level + 'images/header.png" alt="Header image" />')
xhtmlout.addBody(' </div>')
@@ -152,6 +232,7 @@ class CMLWriter:
xhtmlout.addBody(' <li>' + self.l10n.translate('In CML format', lang) + ' <a href="' + cml_file + '" title="CML"><img src="' + '../'*level + 'images/download.png" alt="Download cml file" /></a></li>')
if os.path.isfile(mol_file):
xhtmlout.addBody(' <li>' + self.l10n.translate('In MOL format', lang) + ' <a href="' + mol_file + '" title="MOL"><img src="' + '../'*level + 'images/download.png" alt="Download mol file" /></a></li>')
+ xhtmlout.addBody(' <li>' + self.l10n.translate('Other formats', lang) + ' '+self.selection+'</li>')
xhtmlout.addBody(' </ul>')
xhtmlout.addBody(' </div>')
xhtmlout.addBody(' <div id="inchi">')
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