Package org.biojava.nbio.structure.io.mmtf

Class MmtfStructureReader

java.lang.Object

org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

All Implemented Interfaces:

Serializable, org.rcsb.mmtf.api.StructureAdapterInterface

public class MmtfStructureReader
extends Object
implements org.rcsb.mmtf.api.StructureAdapterInterface, 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	Description
MmtfStructureReader()	Instantiates a new bio java structure decoder.

Method Summary

Modifier and Type	Method	Description
void	finalizeStructure()
Structure	getStructure()	Gets the structure.
void	initStructure(int totalNumBonds, 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	setBioAssemblyTrans(int bioAssemblyId, int[] inputChainIndices, double[] inputTransform, String name)
void	setChainInfo(String chainId, String chainName, int groupCount)
void	setEntityInfo(int[] chainIndices, String sequence, String description, String type)
void	setGroupBond(int indOne, int indTwo, int bondOrder)
void	setGroupInfo(String groupName, int groupNumber, char insertionCode, String chemCompType, int atomCount, int bondCount, char singleLetterCode, int sequenceIndexId, int secStructType)
void	setHeaderInfo(float rFree, float rWork, float resolution, String title, String depositionDate, String releaseDate, String[] experimentalMethods)
void	setInterGroupBond(int indOne, int indTwo, int bondOrder)
void	setModelInfo(int inputModelNumber, int chainCount)
void	setXtalInfo(String spaceGroupString, float[] unitCell, double[][] ncsOperMatrixList)

Methods inherited from class java.lang.Object

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

Constructor Detail

MmtfStructureReader

public MmtfStructureReader()

Instantiates a new bio java structure decoder.

Method Detail

getStructure

public Structure getStructure()

Gets the structure.

Returns:

the structure

finalizeStructure

public void finalizeStructure()

Specified by:

finalizeStructure in interface org.rcsb.mmtf.api.StructureAdapterInterface

initStructure

public void initStructure(int totalNumBonds,
                          int totalNumAtoms,
                          int totalNumGroups,
                          int totalNumChains,
                          int totalNumModels,
                          String modelId)

Specified by:

initStructure in interface org.rcsb.mmtf.api.StructureAdapterInterface

setModelInfo

public void setModelInfo(int inputModelNumber,
                         int chainCount)

Specified by:

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

setChainInfo

public void setChainInfo(String chainId,
                         String chainName,
                         int groupCount)

Specified by:

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

setGroupInfo

public void setGroupInfo(String groupName,
                         int groupNumber,
                         char insertionCode,
                         String chemCompType,
                         int atomCount,
                         int bondCount,
                         char singleLetterCode,
                         int sequenceIndexId,
                         int secStructType)

Specified by:

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

setAtomInfo

public 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.StructureAdapterInterface

setGroupBond

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

Specified by:

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

setInterGroupBond

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

Specified by:

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

setXtalInfo

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

Specified by:

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

setBioAssemblyTrans

public void setBioAssemblyTrans(int bioAssemblyId,
                                int[] inputChainIndices,
                                double[] inputTransform,
                                String name)

Specified by:

setBioAssemblyTrans in interface org.rcsb.mmtf.api.StructureAdapterInterface

setEntityInfo

public void setEntityInfo(int[] chainIndices,
                          String sequence,
                          String description,
                          String type)

Specified by:

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

setHeaderInfo

public void setHeaderInfo(float rFree,
                          float rWork,
                          float resolution,
                          String title,
                          String depositionDate,
                          String releaseDate,
                          String[] experimentalMethods)

Specified by:

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