Codename: cml
Marvin is capable of importing and exporting files in the Chemical Markup Language. Special atom types are lost during export.
Import. The following CML2 standard tags are recognized:
<cml>
Children:
title
Children:
<property dictRef="name" title="name"> - A property.
<scalar [dataType="dataType"]> value</scalar> - Supported data types: "string" (default), "boolean", "integer", "double", "ENTITY" (for special property classes).
<array dataType="dataType" [delimiter="delimiter"]>list of values</array> - Currently, only the "integer" data type is supported. The default delimiter is the space character.
<atomArray>
Attributes:
atomID, elementType, x2, y2, x3, y3, z3, formalCharge, hydrogenCount, isotope
Children:
<atom>
Attributes:
id, elementType, x2, y2, x3, y3, z3, formalCharge, hydrogenCount, isotope
<bondArray>
Attributes:
atomRefs1, atomRefs2, order
Children:
<bond atomRefs2="a1
a2" order="order" >
The
atom references a1 and a2 must be valid atom ids.
The order value can be "1", "S"
(single), "2", "D" (double), "3",
"T" (triple) or "A" (aromatic).
Children:
<bondStereo>value</bondStereo>
-
Value can be "W" (wedge - up), "H" (hatch -
down), "C" (cis) or "T" (trans)
<bondStereo convention="convention" conventionValue="value" />
|
convention |
conventionValue |
meaning |
|---|---|---|
|
MDL |
1 |
up |
|
MDL |
6 |
down |
|
MDL |
4 |
either |
|
MDL |
3 |
cis or trans |
|
ChemAxon |
CTUnspec |
cis/trans or unspecified |
A <bond> tag is recognized at import even if the bondArray container is not present.
title
Children:
<reactantList>
<molecule>
<productList>
<molecule>
<propertyList> - Reaction properties
The argument of MolConverter, MolExporter and the getMol/getM
functions (of the applets and beans) is the format string. The format
specification ("cml") is followed by ":" and the
selected option(s) for cml export.
|
:... |
|
|
:A |
Atom attributes are stored
in arrays. For 2D molecules, only the x, y coordinates are stored.
This is a more compact form of storage than the default (using
|
|
:P |
Create human readable output: put new xml elements in new lines and indent for embedded elements. |
|
:CN |
The accuracy of the exported coordinates can be given: N is the length of the decimals of the coordinate, 0 < N ≤ 9 |
|
:D |
This option is important if the molecule has parity information and has 0 dimension.
By default during the export, a clean method is invoked on the structure
and the generated coordinates and wedge information are exported into CML format
but NOT the parity information. However, using this option coordinates and wedge information
are not generated but parity information is exported. |
|
:I |
Ignore unexportable molecule properties. Without this option the exporter will throw an exception when reach an unexportable property. |
|
:BOM |
Write the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8. |
For example: cml:A or cml:C5.
Example of CML file exported without options:
<?xml version="1.0"?><cml xmlns="http://www.xml-cml.org/schema" xmlns:convention="http://www.xml-cml.org/convention" convention="convention:molecular" xmlns:marvin="http://www.chemaxon.com/marvin/marvinDictRef"> <molecule title="Ethane" id="m1"><atomArray><atom id="a1" elementType="C" x2="0.0" y2="0.0"></atom><atom id="a2" elementType="C" x2="0.0" y2="1.54"></atom></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"></bond></bondArray></molecule> </cml>
Example of CML file exported with option "A":
<?xml version="1.0"?><cml xmlns="http://www.xml-cml.org/schema" xmlns:convention="http://www.xml-cml.org/convention" convention="convention:molecular" xmlns:marvin="http://www.chemaxon.com/marvin/marvinDictRef"> <molecule title="Ethane" id="m1"><atomArray atomID="a1 a2" elementType="C C" x2="0.0 0.0" y2="0.0 1.54"></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"></bond></bondArray></molecule> </cml>
Example of CML file exported with option "P":
<?xml version="1.0"?>
<cml xmlns="http://www.xml-cml.org/schema" xmlns:convention="http://www.xml-cml.org/convention" convention="convention:molecular" xmlns:marvin="http://www.chemaxon.com/marvin/marvinDictRef">
<molecule title="Ethane" id="m1">
<atomArray>
<atom id="a1" elementType="C" x2="0.0" y2="0.0"/>
<atom id="a2" elementType="C" x2="0.0" y2="1.54"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
</bondArray>
</molecule>
</cml>
Example of CML file exported with options "AP":
<?xml version="1.0"?>
<cml xmlns="http://www.xml-cml.org/schema" xmlns:convention="http://www.xml-cml.org/convention" convention="convention:molecular" xmlns:marvin="http://www.chemaxon.com/marvin/marvinDictRef">
<molecule title="Ethane" id="m1">
<atomArray atomID="a1 a2" elementType="C C" x2="0.0 0.0" y2="0.0 1.54"/>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
</bondArray>
</molecule>
</cml>
JChemPaint (last version tested: 1.9.8) and Marvin imports each other's CML files.
Jmol 8 imports CML files exported by Marvin that contain 3D structures. Jmol is a 3D viewer that does not import bonds but calculates them from atomic distances. This means that bonds are not imported correctly if the molecule is 2D.