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• org.xmlcml.noncml: Javadoc index of package org.xmlcml.noncml.


Package Samples:

• org.xmlcml.noncml

Classes:

• SMILESAtom: parse a SMILES atom [....]. Interprets leading characters of a String as a SMILES atom (used for parsing SMILES. Typical usage: s = "[13C@H3-2]NOS" SMILESAtom sa = new SMILESAtom(s); String rest = s.substring(sa.getLength()); int isotope = sa.getIsotope(); String element = sa.getElementType(); String chiral = sa.getChiral(); int hCount = sa.getHydrogenCount(); int ch = sa.getFormalCharge() At present SMARTS is not supported
• MDLMol: class to read (? and write?) mdl-molfiles as described in chemical MIME. NOTE: I have not been able to find any public statement of the format and am unable to guarantee the correctness of any code which interprets Mol files.
• MDLMolImpl: class to read (? and write?) mdl-molfiles as described in chemical MIME. NOTE: I have not been able to find any public statement of the format and am unable to guarantee the correctness of any code which interprets Mol files.
• NonCMLDocument: an interface for input/output of non-CML information (e.g. MOL, SMILES). The foreign document is held as a CMLDOM and accessed by input.output methods.
• Chemime: manages chemical/ files - still experimental. For most file tpes see NonCMLDocumentImpl
• CIFCore1DataBlockAdapter: an adapter class to provide convenience methods for access to data in dataBlocks
• MIFCore1DataBlockAdapter: an adapter class to provide convenience methods for access to data in dataBlocks
• Format: class for formatted files (e.g. PDB, etc.) Preliminary markup into sections.
• PreStyle: class for formatted files (e.g. PDB, etc.) Preliminary markup into sections.
• PDBConect: class to read (? and write?) PDBConect files (e.g. HET dictionary).
• PDBConectImpl: class to read (? and write?) PDBConect files (e.g. HET dictionary).
• CASTEPImpl: class to read (? and write?) CASTEP files NOT COMPLETE
• GAMESSImpl: class to read (? and write?) GAMESS files NOT COMPLETE
• DummyImpl: class to read (? and write?) Dummy files NOT COMPLETE
• JCAMPImpl: class to read (? and write?) JCAMP files NOT COMPLETE
• MOPACImpl: class to read (? and write?) MOPAC files NOT COMPLETE
• MOPACInImpl: class to read (? and write?) MOPAC files NOT COMPLETE
• VAMPImpl: class to read (? and write?) VAMP files NOT COMPLETE
• G94Impl: class to read (? and write?) G94 files NOT COMPLETE
• JMEImpl: class to read and write JME files (Peter Ertl's applet)
• XYZImpl: class to read and write xyz files (Peter Ertl's applet)
• SwissF: class for SwissProt files using legacyParser
• JME: class for JME files (Peter Ertl's applet);
• MOPACFImpl: class to read MOPAC files using parser
• SwissFImpl: class to read Swiss files using parser

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