Uses of Class
org.proteinshader.structure.enums.AtomEnum

Packages that use AtomEnum

org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.enums	Holds the enums needed by org.proteinshader.structure and its subpackages.
org.proteinshader.structure.exceptions	Holds the exception classes needed by org.proteinshader.structure and its subpackages.
org.proteinshader.structure.io	Holds the classes needed for reading Protein Data Bank structure files.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.

Uses of AtomEnum in org.proteinshader.structure

Methods in org.proteinshader.structure that return AtomEnum

AtomEnum

Atom.getType() Returns the Atom's type as an enum based on the periodic table of the elements.

Methods in org.proteinshader.structure with parameters of type AtomEnum

Atom	AminoAcid.addNewAtom(int serialNo, AtomEnum type, String atomID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new Atom with the type and Atom ID given as arguments, adds the Atom to the Residue's collection of Atoms, and returns a reference to the new Atom.
Atom	Residue.addNewAtom(int serialNo, AtomEnum type, String atomID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new Atom with the type and Atom ID given as arguments, adds the Atom to the Residue's collection of Atoms, and returns a reference to the new Atom.
Atom	Structure.addNewAtom(int atomSerialNo, AtomEnum atomType, String atomID, String aminoAcidType, String residueID, String chainID, String modelID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new atom with the atomID given as an argument, adds the new Atom to the requested Model-Chain-AminoAcid, and then returns a reference to the new Atom.
Atom	Structure.addNewHetAtom(int atomSerialNo, AtomEnum atomType, String atomID, String hetName, String residueID, String chainID, String modelID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new atom with the atomID given as an argument, adds the new Atom to the requested Model-Chain-(Heterogen or Water), and then returns a reference to the new Atom.

Constructors in org.proteinshader.structure with parameters of type AtomEnum

Atom(int serialNo, AtomEnum type, String atomID, String residueID, String chainID, String modelID, String structureID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility)
This constructor uses the type argument (an AtomEnum) to set the default radius and CPK color for the Atom.

Uses of AtomEnum in org.proteinshader.structure.enums

Methods in org.proteinshader.structure.enums that return AtomEnum

static AtomEnum	AtomEnum.valueOf(String name) Returns the enum constant of this type with the specified name.
static AtomEnum[]	AtomEnum.values() Returns an array containing the constants of this enum type, in the order they're declared.

Uses of AtomEnum in org.proteinshader.structure.exceptions

Methods in org.proteinshader.structure.exceptions that return AtomEnum

AtomEnum	BondLengthException.getDstAtomType() Returns the destination Atom type as an AtomEnum.
AtomEnum	BondLengthException.getSrcAtomType() Returns the source Atom type as an AtomEnum.

Constructors in org.proteinshader.structure.exceptions with parameters of type AtomEnum

BondLengthException(double calculatedLength, double expectedLength, double toleranceFactor, AtomEnum srcAtomType, AtomEnum dstAtomType, int srcAtomSerialNo, int dstAtomSerialNo)
Sets the default message to "A Bond length was unacceptable".

BondLengthException(String message, double calculatedLength, double expectedLength, double toleranceFactor, AtomEnum srcAtomType, AtomEnum dstAtomType, int srcAtomSerialNo, int dstAtomSerialNo)
The message given this constructor can be retrieved using getMessage().

Uses of AtomEnum in org.proteinshader.structure.io

Methods in org.proteinshader.structure.io that return AtomEnum

AtomEnum

PDBAtomFieldExtractor.extractAtomType(String line) Obtains the atom type (chemical element) from an ATOM or HETATM record.

Uses of AtomEnum in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type AtomEnum

void	Visitor.setMode(AtomEnum atomType) Sets the traversal mode with regard to Atom type.