README

A PHP 8.4+ package that parses Chemical Structure Markup Language (CSML) documents and renders them as SVG images.

CSML is an XML-based markup language for describing molecular structures with full topological, geometric, and repeating-unit information. This package provides the reference PHP implementation for parsing and visualizing CSML documents.

Installation

composer require chemstrucml/csml-parser

Requirements

PHP 8.4 or higher
ext-simplexml
ext-dom
ext-libxml

Quick Start

use ChemStrucML\Csml\CsmlRenderer;

$renderer = new CsmlRenderer();

// Render from a file
$svg = $renderer->renderFile('benzene.csml');

// Render from a string
$svg = $renderer->renderString('<csml version="0.1">
  <molecule id="water" name="Water">
    <atom id="O1" element="O" />
    <atom id="H1" element="H" />
    <atom id="H2" element="H" />
    <bond from="O1" to="H1" order="single" />
    <bond from="O1" to="H2" order="single" />
  </molecule>
</csml>');

// Save to file
file_put_contents('molecule.svg', $svg);

Usage

Parse and Render Separately

use ChemStrucML\Csml\CsmlRenderer;

$renderer = new CsmlRenderer();

// Parse to inspect the document model
$document = $renderer->parse($csmlString);

echo $document->version;                    // "0.1"
echo $document->molecules[0]->name;         // "Benzene"
echo count($document->molecules[0]->atoms); // 6

// Render to SVG
$svg = $renderer->render($document);

Custom Rendering Configuration

use ChemStrucML\Csml\CsmlRenderer;
use ChemStrucML\Csml\Config\RenderConfig;

$config = new RenderConfig(
    bondLength: 80.0,           // Bond length in SVG pixels (default: 60.0)
    bondWidth: 2.0,             // Stroke width (default: 1.5)
    fontSize: 16.0,             // Atom label font size (default: 14.0)
    fontFamily: 'monospace',    // Font family (default: 'Arial, Helvetica, sans-serif')
    padding: 30.0,              // SVG padding (default: 20.0)
    showAllCarbons: false,      // Show carbon labels in skeletal mode (default: false)
    showImplicitHydrogens: true, // Show implicit H labels (default: true)
    useColoredAtoms: true,      // CPK coloring for atoms (default: true)
    backgroundColor: 'white',   // SVG background (default: 'transparent')
);

$renderer = new CsmlRenderer(config: $config);
$svg = $renderer->renderFile('molecule.csml');

Using the Parser Directly

use ChemStrucML\Csml\Parser\XmlParser;

$parser = new XmlParser();
$document = $parser->parseFile('molecule.csml');

foreach ($document->molecules as $molecule) {
    echo "Molecule: {$molecule->name}\n";
    echo "  Atoms: " . count($molecule->atoms) . "\n";
    echo "  Bonds: " . count($molecule->bonds) . "\n";
    echo "  Rings: " . count($molecule->rings) . "\n";
}

Supported CSML Features

Feature	Elements	Status
Atoms	`<atom>`, `<atom-list>`	Supported
Bonds	`<bond>`, `<bond-chain>`	Supported
Ring systems	`<ring>`, `<fused-ring>`	Supported
Groups & fragments	`<group>`, `<group-ref>`, `<anchor>`, `<attach>`	Supported
Repeat units	`<repeat>`, `<connector>`, `<cap>`	Supported
Branching	`<branch>`	Supported
Copolymers	`<copolymer>`	Supported
Coordinates	`<coordinates>`, `<point>`	Supported
Metadata	`<meta>`	Supported
Implicit hydrogens	`implicit-h="auto"`	Supported
Stereochemistry	`chirality`, `stereo` attributes	Parsed
Geometry constraints	`<angle>`, `<torsion>`, `<length>`	Parsed

Bond Rendering Styles

Single, double, triple bonds with proper parallel line offset
Aromatic rings with inscribed circle
Wedge bonds (filled triangle for stereo-up)
Hatch bonds (dashed lines for stereo-down)
Dashed bonds (hydrogen bonds, partial bonds)

Atom Rendering

The renderer follows skeletal formula conventions by default:

Carbon atoms are not labeled (unless they carry a charge, isotope, or explicit label)
Non-carbon atoms display their element symbol with CPK coloring (O = red, N = blue, S = yellow, etc.)
Implicit hydrogens are shown as subscripts (e.g. NH, OH, NH₂)
Charges are rendered as superscripts (e.g. O⁻, NH₃⁺)

CSML Examples

Benzene

<csml version="0.1">
  <molecule id="benzene" name="Benzene">
    <atom-list element="C" prefix="C" from="1" to="6" />
    <ring id="benz" size="6" aromatic="true">
      <member atom="C1" /><member atom="C2" /><member atom="C3" />
      <member atom="C4" /><member atom="C5" /><member atom="C6" />
    </ring>
  </molecule>
</csml>

1-Hexanol

<csml version="0.1">
  <molecule id="1-hexanol" name="1-Hexanol">
    <atom-list element="C" prefix="C" from="1" to="6" />
    <atom id="O1" element="O" />
    <bond-chain atoms="C1 C2 C3 C4 C5 C6" order="single" />
    <bond from="C6" to="O1" order="single" />
  </molecule>
</csml>

Naphthalene (Fused Rings)

<csml version="0.1">
  <molecule id="naphthalene" name="Naphthalene">
    <atom-list element="C" prefix="C" from="1" to="10" />
    <ring id="ring_a" size="6" aromatic="true">
      <member atom="C1" /><member atom="C2" /><member atom="C3" />
      <member atom="C4" /><member atom="C5" /><member atom="C6" />
    </ring>
    <ring id="ring_b" size="6" aromatic="true">
      <member atom="C5" /><member atom="C6" /><member atom="C7" />
      <member atom="C8" /><member atom="C9" /><member atom="C10" />
    </ring>
    <fused-ring rings="ring_a ring_b" shared-atoms="C5 C6" />
  </molecule>
</csml>

Why CSML?

Feature	CSML	SMILES	MOL/SDF	CML	InChI
Human-readable	Yes	Yes	No	Yes	No
Polymer repeat units	Yes	No	Partial	No	No
Copolymer patterns	Yes	No	No	No	No
Reusable fragments	Yes	No	No	Partial	No
Extensible (namespaces)	Yes	No	No	Yes	No
End-group specification	Yes	No	No	No	No

CSML separates topology (what is connected to what) from geometry (angles, lengths) and from presentation (how to draw it), making it uniquely suited for polymer science, materials engineering, and structural chemistry applications where existing formats fall short.

License

MIT

chemstrucml / csml-parser

Maintainers

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