edu.sdsc.mbt
Class Structure

java.lang.Object
  edu.sdsc.mbt.Structure

All Implemented Interfaces:

java.io.Serializable

public abstract class Structure

extends java.lang.Object

implements java.io.Serializable

This class provides the primary interface for a molecular structure object.

Note that since there are currently no "set" methods in this class, there are also currently no StructureComponentEvent handling methods.

Author:

John L. Moreland

See Also:

StructureComponentEvent,

, Serialized Form

Constructor Summary

Structure()

Method Summary

StructureComponentIterator	createStructureComponentIterator(StructureComponentFilter filter) Given a StructureComponentFilter, create and return an iterator which will selectively return a subset of structure components.
abstract StructureComponent	getStructureComponentByIndex(java.lang.String structureComponentType, int index) Get the values for any StructureSomponent subclass by its type-specific index.
abstract int	getStructureComponentCount(java.lang.String scType) Counts components of the specified type that exist in the structure.
StructureComponentIterator	getStructureComponentRelations(java.lang.String relation_name, StructureComponent structureComponent) Given a StructureComponentRelation name and a StructureComponent, create and return a StructureComponentIterator which will selectively return the related subset of StructureComponent objects.
StructureMap	getStructureMap() Return the StructureMap object that describes the derived (implied) hierarchy of primary and secondary structure data for the Structure.
abstract java.lang.String	getUrlString() This method returns a string which represents the URL from which the structure instance was produced.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Structure

public Structure()

Method Detail

getUrlString

public abstract java.lang.String getUrlString()

This method returns a string which represents the URL from which the structure instance was produced. Examples: file://c:/myFiles/5ebx.pdb // a local PDB file file://c:/myFiles/5ebx.mmCIF // a local mmCIF file ftp://ftp.rcsb.org/2cpk.pdb // a remote pdb file ftp://ftp.rcsb.org/4hhb.mmCIF // a remote mmCIF file iiop://corba.sdsc.edu/2cpk // an openMMS reference This URL can be handed back to the StructureFactory in order to re-load the structure.

getStructureComponentCount

public abstract int getStructureComponentCount(java.lang.String scType)

Counts components of the specified type that exist in the structure. TYPE values are defined in the StructureComponentRegistry class.

createStructureComponentIterator

public StructureComponentIterator createStructureComponentIterator(StructureComponentFilter filter)

Given a StructureComponentFilter, create and return an iterator which will selectively return a subset of structure components.

getStructureComponentRelations

public StructureComponentIterator getStructureComponentRelations(java.lang.String relation_name,
                                                                 StructureComponent structureComponent)
                                                          throws java.lang.IllegalArgumentException

Given a StructureComponentRelation name and a StructureComponent, create and return a StructureComponentIterator which will selectively return the related subset of StructureComponent objects. This is acheaved by creating a RelationFilter with relation name and StructureComponent parameters then simply calling the createStructureComponentIterator method with that filter.

Throws:

java.lang.IllegalArgumentException

getStructureComponentByIndex

public abstract StructureComponent getStructureComponentByIndex(java.lang.String structureComponentType,
                                                                int index)
                                                         throws java.lang.IndexOutOfBoundsException,
                                                                java.lang.IllegalArgumentException

Get the values for any StructureSomponent subclass by its type-specific index. For example: Atom, Residue, Conformation, etc.

Note that it is the caller's responsibility to cast the returned object to the corresponding StructureComponent sublcass type. For example, an application might do something like this:

 // First load a structure using the StructureFactory, and then...
 int atom_count =
   structure.getStructureComponentCount( StructureComponentRegistry.TYPE_ATOM );
 for ( int i=0; i

getStructureMap
public StructureMap getStructureMap()

Return the StructureMap object that describes the derived (implied)
 hierarchy of primary and secondary structure data for the Structure.
 This mapping provides a means to iteratate over components of the
 structure in an ordered and efficient manner.