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JUMBO
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"JUMBO" is a collective term for CML-aware software components. They are intended to be definitive for the CML language, and provide validation and examples. CMLXOM and JUMBO are under SCM at http://cml.svn.sourceforge.net/viewvc/cml/ on Sourceforge
A set of components directly supporting the elements and attributes in CML. Every element has a Java class, e.g.:
In general the classes support management of
* required or common childElements, * required or common attributes
CMLXOM represents an in-memory and serializable CML object of any complexity. In general CML can be read into CMLXOM and processed with Java code or XPath expressions. CMLXOM does not support complex chemical calculations (which are in JUMBO and JUMBOConverters). For example CMLXOM will support the management of bond information but not the generation of SMILES.
Provides a large set of "tools" which generally support the CMLXOM classes but also provide general functionality. Typically:
These might provide, respectively, molecular geometry, fragment analysis, properties ; and stoichiometry, identification of catalysts, etc.
A large set of modular components for carrying out 1:1 transformations. The simplest are Foo2CMLConverter and CML2FooConverter where Foo is a legacy format. This supports major formats in:
* crystallography * computational chemistry * molecules * reactions * spectroscopy
There are gaps but many of these are due to the unclear nature of the legacy. It took me a long day to write most of a GAMESSUK2CMLConverter but some have taken longer, especially where bonding algorithms, geometry, etc. are required
See also JUMBO-Converters
The subtrees at SF (20101008) are described below with a star rating as to their current importance (* = used but specialist, ** = widely used, *** almost essential if using JUMBO for CML, - no longer used but may be mined)
As at 20101008 on bitbucket/petermr
As at 20101008 on bitbucket/wwmm