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, String modelId)
void	setAtomInfo(String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, String element, int charge)
void	setBioAssemblyList(List<org.rcsb.mmtf.dataholders.BioAssemblyData> inputBioassemblies)
void	setChainInfo(String chainId, int groupCount)
void	setEntityInfo(String[] chainIds, String sequence, String description, String title)
void	setGroupBond(int indOne, int indTwo, int bondOrder)
void	setGroupInfo(String groupName, int groupNumber, char insertionCode, String chemCompType, int atomCount)
void	setHeaderInfo(float rFree, float rWork, float resolution, String title, List<String> experimnetalMethods)
void	setInterGroupBond(int indOne, int indTwo, int bondOrder)
void	setModelCount(int inputModelCount)
void	setModelInfo(int inputModelNumber, int chainCount)
void	setXtalInfo(String spaceGroupString, float[] unitCell)

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

setGroupBond

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

Specified by:

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

setInterGroupBond

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

Specified by:

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

setXtalInfo

public final void setXtalInfo(String spaceGroupString,
                              float[] unitCell)

Specified by:

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

setBioAssemblyList

public void setBioAssemblyList(List<org.rcsb.mmtf.dataholders.BioAssemblyData> inputBioassemblies)

Specified by:

setBioAssemblyList 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,
                             String modelId)

Specified by:

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

setEntityInfo

public void setEntityInfo(String[] chainIds,
                          String sequence,
                          String description,
                          String title)

Specified by:

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

setHeaderInfo

public void setHeaderInfo(float rFree,
                          float rWork,
                          float resolution,
                          String title,
                          List<String> experimnetalMethods)

Specified by:

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