* See the "PROGRAMMING NOTE" section of the StructureComponent class. *
* @see edu.sdsc.mbt.StructureComponent * @see edu.sdsc.mbt.Structure * @see edu.sdsc.mbt.StructureComponentIterator *
* @author John L. Moreland */ public class Atom extends StructureComponent implements java.lang.Cloneable, java.io.Serializable { public static short SP3 = 0; public static short SP2 = 1; public static short SP = 2; // // Constructor // /** * Creates a new Atom object and initializes the StructureComponent * "structure" field. */ public Atom( ) { } // // StructureComponent methods // /** * Copy all of the field values from the parameter object into "this". */ public void copy( StructureComponent structureComponent ) { structure = structureComponent.getStructure(); Atom atom = (Atom) structureComponent; element = atom.element; name = atom.name; number = atom.number; // altLoc = atom.altLoc; compound = atom.compound; residue_id = atom.residue_id; coordinate[0] = atom.coordinate[0]; coordinate[1] = atom.coordinate[1]; coordinate[2] = atom.coordinate[2]; // occupancy = atom.occupancy; // bfactor = atom.bfactor; backbone = atom.backbone; } /** * Clone this object. */ public Object clone( ) throws CloneNotSupportedException { return super.clone( ); } /** * This method returns the fully qualified name of this class. *
* This name is used by the StructureComponentRegistry class to enable * dynamic registration and discovery of new StructureComponent * sub-classes/types. The name is also used to create a unique integer * indentifier for each type in order to make run-time type comparisons * fast. */ private static String className = null; public static String getClassName() { if ( className == null ) className = ((new Throwable()).getStackTrace())[0].getClassName(); return className; } /** * This method returns the fully qualified name of this class. */ public String getStructureComponentType( ) { return className; } // // Atom fields // /** * The element symbol. * For example, "C", "O", "N", "H", etc. */ // public String element; // _atom_site.type_symbol - removed: waste of memory public short element = 0; public String getElement(){ return PeriodicTable.getElementSymbol(element); } public void setElement(String symbol){ element = (short)PeriodicTable.getElementNumber(symbol); } // public int atomicNumber = 1; /** * The macromolecular ID (element name). * For example, "CA", "CB", "OG1", "N", etc. */ public String name; // _atom_site.label_atom_id /** * The atom serial number. */ public int number = -1; // _atom_site.id /** * Compound 3-letter code. * For example, "VAL", "THR", "ILE", etc. */ public String compound; // _atom_site.label_comp_id public short formalCharge = 0; /** * Chain/Asymetric unit ID. * For example, "A", "B", "C", etc. */ public String chain_id; // _atom_site.label_asym_id /** * Residue/Sequence ID. * Must be a positive integer. * For example, "10", "11", "13", etc. */ public int residue_id = -1; // _atom_site.label_seq_id public Residue residue; /** * The x,y,z coordinate in angstroms. * For example, (21.023, 30.128, 12.340). */ public double coordinate[] = { 0.0, 0.0, 0.0 }; // _atom_site.Cartn_x,y,z /** * The fraction (0.0-1.0) of the atom element. * For example, "1.0", "0.5", "0.58", etc. */ // public float occupancy = 0.0f; // _atom_site.occupancy /** * Temperature B-Factor. * For example, "17.12", "26.28", etc. */ // public float bfactor = 0.0f; // _atom_site.B_iso_or_equiv /** * Radius */ // public float radius = 0.0f; /** * Whether this atom is a part of the protein backbone */ public boolean backbone = false; /** * Alternate Location Identifier (single character) * should be specified when occupancy < 1. * For example, "", "A", "B", "C", etc. *
* @see #occupancy *
*/ // public String altLoc = null; // _atom_site.label_alt_id /** * Partial Charge (-1.0 - 3.0). * For example, "0.3", "1.1", etc. */ public float partialCharge = 0.0f; // _atom_site.??? /** * Atomic orbital hybridization state. Needed for molecular mechanics calculations */ public short hybridization = SP3; /** * Force field type indicates the kind of atom depending on the atoms it's bonded to */ public String forceFieldType; /** * Inidcates whether this atom is ionized, hence which radius should be used for rendering */ // public boolean ion = false; public short render = (short)StylesPreferences.renderingMode; public short quality = (short)StylesPreferences.startupRenderingQuality; public boolean visible = true; public boolean isVisible(){ return visible; } }