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


Package Samples:

• org.xmlcml.simplecml

Classes:

• SimpleMolecule: SimpleMolecule manages a subset of CML functionality for molecules. It lacks many of the more sophisticated methods and exposes the atoms and bonds as public vectors It should only be used with SimpleBond and SimpleAtom. Typical code: SimpleMolecule mol = new SimpleMolecule(); SimpleAtom atom1 = new SimpleAtom(); atom1.elementType="C"; atom1.id="c1"; atomVector.addElement(atom1); SimpleAtom atom2 = new SimpleAtom(); atom2.elementType="O"; atom2.id="o2"; atomVector.addElement(atom2); SimpleBond bond = new SimpleBond(); bond.atomRef1 = atom1; bond.atomRef2 = atom2; bond.order = "T"; bondVector.a ...
• CMLEventHandler: SAX-like CML reader, hacked from David Megginson's AElfred demo; although this is deprecated, it is used to provide 1.02 compatibility also it is unlikely that its problems will be relevant in chemistry. Methods in this class are not called directly, but by Aelfred. Typical usage: try { CMLEventHandler evh = new CMLEventHandler(); evh.doParse(fileName); SimpleMolecule mol = evh.topMolecule; } catch (Exception e) { e.printStackTrace(); System.out.println("Failed to read file: "+e); } mol can then be used as a SimpleMolecule
• SimpleBond: SimpleBond manages a subset of CML functionality for atoms. It lacks many of the more sophisticated setters and getters and exposes the bond children directly (e.g. order). It should only be used with SimpleMolecule and SimpleAtom. Typical code: SimpleAtom bond = new SimpleBond(); bond.atomRef1 = atom23; bond.atomRef2 = atom25; bond.order = "S";
• SimpleAtom: SimpleAtom manages a subset of CML functionality for atoms. It lacks many of the more sophisticated setters and getters and exposes the atom children directly (e.g. hydrogenCount). It should only be used with SimpleMolecule and SimpleBond. Typical code: SimpleAtom atom = new SimpleAtom(); atom.id = "a123"; atom.elementType="Na"; atom.formalCharge=1;

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