org.biojava.nbio.structure.io.mmtf

Class BioJavaStructureDecoder

java.lang.Object

org.biojava.nbio.structure.io.mmtf.BioJavaStructureDecoder

All Implemented Interfaces:

Serializable, org.rcsb.mmtf.api.StructureDecoderInterface

public class BioJavaStructureDecoder
extends Object
implements org.rcsb.mmtf.api.StructureDecoderInterface, Serializable

A biojava specific structure inflator for MMTF. Should be ported to biojava code.

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
BioJavaStructureDecoder() Instantiates a new bio java structure decoder.

Method Summary

Modifier and Type	Method and Description
void	cleanUpStructure()
Structure	getStructure() Gets the structure.
void	prepareStructure(int totalNumAtoms, int totalNumGroups, int totalNumChains, int totalNumModels)
void	setAtomInfo(String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, String element, int charge)
void	setBioAssembly(Map<Integer,org.rcsb.mmtf.dataholders.BioAssemblyData> inputBioassemblies)
void	setChainInfo(String chainId, int groupCount)
void	setGroupBonds(int indOne, int indTwo, int bondOrder)
void	setGroupInfo(String groupName, int groupNumber, char insertionCode, String chemCompType, int atomCount)
void	setInterGroupBonds(int indOne, int indTwo, int bondOrder)
void	setModelCount(int inputModelCount)
void	setModelInfo(int inputModelNumber, int chainCount)
void	setXtalInfo(String spaceGroupString, List<Float> unitCell)
void	updateChainInfo(String chainId, int groupCount)

Methods inherited from class java.lang.Object

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

Constructor Detail

BioJavaStructureDecoder

public BioJavaStructureDecoder()

Instantiates a new bio java structure decoder.

Method Detail

getStructure

public final Structure getStructure()

Gets the structure.

Returns:

the structure

setModelCount

public void setModelCount(int inputModelCount)

Specified by:

setModelCount in interface org.rcsb.mmtf.api.StructureDecoderInterface

setModelInfo

public final void setModelInfo(int inputModelNumber,
                               int chainCount)

Specified by:

setModelInfo in interface org.rcsb.mmtf.api.StructureDecoderInterface

setChainInfo

public final void setChainInfo(String chainId,
                               int groupCount)

Specified by:

setChainInfo in interface org.rcsb.mmtf.api.StructureDecoderInterface

setGroupInfo

public final void setGroupInfo(String groupName,
                               int groupNumber,
                               char insertionCode,
                               String chemCompType,
                               int atomCount)

Specified by:

setGroupInfo in interface org.rcsb.mmtf.api.StructureDecoderInterface

setAtomInfo

public final void setAtomInfo(String atomName,
                              int serialNumber,
                              char alternativeLocationId,
                              float x,
                              float y,
                              float z,
                              float occupancy,
                              float temperatureFactor,
                              String element,
                              int charge)

Specified by:

setAtomInfo in interface org.rcsb.mmtf.api.StructureDecoderInterface

setGroupBonds

public final void setGroupBonds(int indOne,
                                int indTwo,
                                int bondOrder)

Specified by:

setGroupBonds in interface org.rcsb.mmtf.api.StructureDecoderInterface

setInterGroupBonds

public final void setInterGroupBonds(int indOne,
                                     int indTwo,
                                     int bondOrder)

Specified by:

setInterGroupBonds in interface org.rcsb.mmtf.api.StructureDecoderInterface

setXtalInfo

public final void setXtalInfo(String spaceGroupString,
                              List<Float> unitCell)

Specified by:

setXtalInfo in interface org.rcsb.mmtf.api.StructureDecoderInterface

updateChainInfo

public final void updateChainInfo(String chainId,
                                  int groupCount)

Specified by:

updateChainInfo in interface org.rcsb.mmtf.api.StructureDecoderInterface

setBioAssembly

public void setBioAssembly(Map<Integer,org.rcsb.mmtf.dataholders.BioAssemblyData> inputBioassemblies)

Specified by:

setBioAssembly in interface org.rcsb.mmtf.api.StructureDecoderInterface

cleanUpStructure

public void cleanUpStructure()

Specified by:

cleanUpStructure in interface org.rcsb.mmtf.api.StructureDecoderInterface

prepareStructure

public void prepareStructure(int totalNumAtoms,
                             int totalNumGroups,
                             int totalNumChains,
                             int totalNumModels)

Specified by:

prepareStructure in interface org.rcsb.mmtf.api.StructureDecoderInterface