MolAtom

The chemaxon.struc.MolAtom class is used to represent chemical atoms. To create a MolAtom object, one of these constructor methods can be used:

MolAtom(int Z, double x, double y, double z);
MolAtom(int Z, double x, double y);
MolAtom(int Z);

Here int Z is the atomic number; double x, double y, double z, are the coordinates of the atom. If the coordinates are not given, they are automatically set to zero. The atomic number can be specified using the constants in the static class, chemaxon.struc.PeriodicSystem.

Code example: Create an oxygen MolAtom object

      MolAtom o = new MolAtom(PeriodicSystem.O);

If the constructed MolAtom object is supposed to be a part of MoleculeGraph (or its subclasses), then it should be added to it using the add(MolAtom) method:

    molecule.add(o);

The following table summerizes if the properties of the MolAtom have set or get methods.

property	set	get	note
Index	×	✔	assigned automatically
Bonds	✔	✔
Atomic number, type	✔	✔
Atomic mass	✔	✔
Radical	✔	✔
Charge	✔	✔
Coordinates	✔	✔
Atomic map	✔	✔
Alias string	✔	✔
Valence	✔	✔	calculated
Implicit hydrogen count	✔	✔	calculated
Hybrization	✔	✔	calculated separately

Molecule Graph	Table of contents	MolBond
Previous chapter		Next chapter