org.rcsb.mmtf.dataholders.MmtfStructure Maven / Gradle / Ivy
package org.rcsb.mmtf.dataholders;
import java.io.Serializable;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* A class to store the data sent in an MMTF data source.
*
* @author Anthony Bradley
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class MmtfStructure implements Serializable {
/** The number to divide coordinate int values by. */
public static final int COORD_DIVIDER = 1000;
/** The number to divide occupancy and bfactor int values by. */
public static final int OCCUPANCY_BFACTOR_DIVIDER = 100;
/** The default value for Rfree and Rwork */
public static final float UNAVAILABLE_R_VALUE = 1.0f;
/** The default value for resolution when not available or not applicable */
public static final float UNAVAILABLE_RESOLUTION_VALUE = 99.0f;
/** The default value for a missing or null string field */
public static final char UNAVAILABLE_CHAR_VALUE = '\0';
/** The number of characters in a chain.*/
public static final int CHAIN_LENGTH = 4;
/** The version of MMTF */
public static final String VERSION = "0.2.0";
/** Serial id for this version of the format. */
private static final long serialVersionUID = 384559979573830324L;
/** The mmtf version. */
private String mmtfVersion;
/** The mmtf producer. */
private String mmtfProducer;
/** The number of bonds. */
private int numBonds;
/** The number of atoms. */
private int numAtoms;
/** The number of groups. */
private int numGroups;
/** The number of chains. */
private int numChains;
/** The number of models. */
private int numModels;
/** The structure Id. Most commonly this will be the four character PDB id. */
private String structureId;
/** The title. */
private String title;
/** The number of chains per model. */
private int[] chainsPerModel;
/** The internal groups per chain. */
private int[] groupsPerChain;
/** The names of the chains. Each chain is allocated four bytes. Chain names can be up to four characters long. 0 bytes indicate the end of the chain name. These are taken from the auth id. */
private byte[] chainNameList;
/** The names of the chains. Each chain is allocated four bytes. Chain names can be up to four characters long. 0 bytes indicate the end of the chain name. These are taken from the asym id. */
private byte[] chainIdList;
/** The space group. */
private String spaceGroup;
/** The unit cell. */
private float[] unitCell;
/** The bio assembly. */
private List bioAssemblyList;
/** The bond atom (indices) list. */
private byte[] bondAtomList;
/** The bond order list. */
private byte[] bondOrderList;
/** The list of different PDBGroups in the structure. */
private Group[] groupList;
/** The encoded X coordinates. */
private byte[] xCoordList;
/** The encoded Y coordinates. */
private byte[] yCoordList;
/** The encoded Z coordinates. */
private byte[] zCoordList;
/** The encoded B-factors. */
private byte[] bFactorList;
/** The secondary structure list. Stored as 1 byte ints. */
private byte[] secStructList;
/** The occupancy list. */
private byte[] occupancyList;
/** The list of alternate location ids. */
private byte[] altLocList;
/** The insertion code list. */
private byte[] insCodeList;
/** The group type list. */
private byte[] groupTypeList;
/** The group id list. Identifies each group along the chain. */
private byte[] groupIdList;
/** The atom id list. */
private byte[] atomIdList;
/** The SeqRes group ids. */
private byte[] sequenceIndexList;
/** The experimental method(s). */
private String[] experimentalMethods;
/** The resolution in Angstrom. Null if not applicable*/
private float resolution;
/** The rfree. Null if not applicable */
private float rFree;
/** The r-work. Null if not applicable */
private float rWork;
/** The list of entities in this structure. */
private Entity[] entityList;
/** The deposition date of the structure in ISO time standard format. https://www.cl.cam.ac.uk/~mgk25/iso-time.html */
private String depositionDate;
/** The release data of the structure in ISO time standard format. https://www.cl.cam.ac.uk/~mgk25/iso-time.html */
private String releaseDate;
/** A float array for the NCS operator expression matrices, derived from the mmCIF file. */
private double[][] ncsOperatorList;
/** Constructor to set the default values for floats */
public MmtfStructure() {
/** The mmtf version. Set here. */
mmtfVersion = MmtfStructure.VERSION;
/** The mmtf producer. NA is default and for RCSB PDB data indicates an error. */
mmtfProducer = "NA";
/** The resolution in Angstrom. -1.0 if not applicable*/
resolution = UNAVAILABLE_RESOLUTION_VALUE;
/** The rfree. 1.0 if not applicable */
rFree = UNAVAILABLE_R_VALUE;
rWork = UNAVAILABLE_R_VALUE;
/** The number of atoms. Default is -1 indicates error */
numAtoms = -1;
/** The number of bonds. Default of -1 indicates error*/
numBonds = -1;
}
/**
* @return the resolution
*/
public Float getResolution() {
if (resolution==UNAVAILABLE_RESOLUTION_VALUE) {
return null;
}
return resolution;
}
/**
* @param resolution the resolution to set
*/
public void setResolution(float resolution) {
if (resolution==0.0) {
this.resolution = UNAVAILABLE_RESOLUTION_VALUE;
}
else{
this.resolution = resolution;
}
}
/**
* @return the rFree
*/
public Float getrFree() {
if (rFree==UNAVAILABLE_R_VALUE) {
return null;
}
return rFree;
}
/**
* @param rFree the rFree to set
*/
public void setrFree(float rFree) {
if (rFree==0.0){
this.rFree = UNAVAILABLE_R_VALUE;
}
else{
this.rFree = rFree;
}
}
/**
* @return the rWork
*/
public Float getrWork() {
if (rWork==UNAVAILABLE_R_VALUE) {
return null;
}
return rWork;
}
/**
* @param rWork the rWork to set
*/
public void setrWork(float rWork) {
if (rWork==0.0){
this.rWork = UNAVAILABLE_R_VALUE;
}
else{
this.rWork = rWork;
}
}
/**
* Gets the space group.
*
* @return the space group
*/
public String getSpaceGroup() {
return spaceGroup;
}
/**
* Sets the space group.
*
* @param inputSpaceGroup the new space group
*/
public void setSpaceGroup(String inputSpaceGroup) {
this.spaceGroup = inputSpaceGroup;
}
/**
* Gets the unit cell.
*
* @return the unit cell
*/
public float[] getUnitCell() {
return unitCell;
}
/**
* Sets the unit cell.
*
* @param inputUnitCell the new unit cell
*/
public void setUnitCell(float[] inputUnitCell) {
this.unitCell = inputUnitCell;
}
/**
* Gets the group num list.
*
* @return the group num list
*/
public byte[] getGroupIdList() {
return groupIdList;
}
/**
* Sets the group num list.
*
* @param inputGroupNumList the new group num list
*/
public void setGroupIdList(byte[] inputGroupNumList) {
this.groupIdList = inputGroupNumList;
}
/**
* Gets the alternate location list.
*
* @return the alternate location list
*/
public byte[] getAltLocList() {
return altLocList;
}
/**
* Sets the alt label list.
*
* @param inputAltLocList the new alternation location label list
*/
public void setAltLocList(byte[] inputAltLocList) {
this.altLocList = inputAltLocList;
}
/**
* Gets the bio assembly.
*
* @return the bio assembly
*/
public List getBioAssemblyList() {
return bioAssemblyList;
}
/**
* Gets the chain names. The byte array indicating the (up to four characters) name of the chain. This is taken from the auth id.
*
* @return the chain list
*/
public byte[] getChainNameList() {
return chainNameList;
}
/**
* Sets the chain names. The byte array indicating the (up to four characters) name of the chain. This is taken from the auth id.
*
* @param inputChainList the new chain list
*/
public void setChainNameList(byte[] inputChainList) {
this.chainNameList = inputChainList;
}
/**
* Sets the bioassembly information.
*
* @param inputBioAssembly the bio assembly
*/
public void setBioAssemblyList(List inputBioAssembly) {
this.bioAssemblyList = inputBioAssembly;
}
/**
* Gets the num atoms.
*
* @return the num atoms
*/
public int getNumAtoms() {
return numAtoms;
}
/**
* Sets the num atoms.
*
* @param inputNumAtoms the new num atoms
*/
public void setNumAtoms(int inputNumAtoms) {
this.numAtoms = inputNumAtoms;
}
/**
* Gets the occupancy list - an encoded per atom list of occupancy values.
*
* @return the occupancy list - an encoded per atom list of occupancy values.
*/
public byte[] getOccupancyList() {
return occupancyList;
}
/**
* Sets the occupancy list - an encoded per atom list of occupancy values.
*
* @param inputOccupancyList the occupancy list - an encoded per atom list of occupancy values.
*/
public void setOccupancyList(byte[] inputOccupancyList) {
this.occupancyList = inputOccupancyList;
}
/**
* Gets the insertion code list.
*
* @return the insertion code list
*/
public byte[] getInsCodeList() {
return insCodeList;
}
/**
* Sets the ins code list.
*
* @param inputInsertionCodeList the new insertion code list
*/
public void setInsCodeList(byte[] inputInsertionCodeList) {
this.insCodeList = inputInsertionCodeList;
}
/**
* Gets the group map.
*
* @return the group map
*/
public Group[] getGroupList() {
return groupList;
}
/**
* Sets the group map.
*
* @param inputGroupMap the group map
*/
public void setGroupList(Group[] inputGroupMap) {
this.groupList = inputGroupMap;
}
/**
* Gets the sec struct list.
*
* @return the sec struct list
*/
public byte[] getSecStructList() {
return secStructList;
}
/**
* Sets the sec struct list.
*
* @param secStruct the new sec struct list
*/
public void setSecStructList(byte[] secStruct) {
this.secStructList = secStruct;
}
/**
* Gets the group type list.
*
* @return the group type list
*/
public byte[] getGroupTypeList() {
return groupTypeList;
}
/**
* Sets the group type list.
*
* @param resOrder the new group type list
*/
public void setGroupTypeList(byte[] resOrder) {
this.groupTypeList = resOrder;
}
/**
* Gets the atom id list.
*
* @return the atom id list
*/
public byte[] getAtomIdList() {
return atomIdList;
}
/**
* Sets the atom id list.
*
* @param inputAtomIdList the new atom id list
*/
public void setAtomIdList(byte[] inputAtomIdList) {
this.atomIdList = inputAtomIdList;
}
/**
* Gets the title.
*
* @return the title
*/
public String getTitle() {
return title;
}
/**
* Sets the title.
*
* @param inputTitle the new title
*/
public void setTitle(String inputTitle) {
this.title = inputTitle;
}
/**
* Gets the structure id. Should be used as a unique identifier of this structure.
*
* @return the the structure id a unique String id of this structure.
*/
public String getStructureId() {
return structureId;
}
/**
* Sets the structure id. Should be used as a unique identifier of this structure.
*
* @param inputId a unique String id of this structure.
*/
public void setStructureId(String inputId) {
this.structureId = inputId;
}
/**
* Gets the mmtf producer.
*
* @return the mmtf producer
*/
public String getMmtfProducer() {
return mmtfProducer;
}
/**
* Sets the mmtf producer.
*
* @param inputMmtfProducer the new mmtf producer
*/
public void setMmtfProducer(String inputMmtfProducer) {
this.mmtfProducer = inputMmtfProducer;
}
/**
* Gets the mmtf version.
*
* @return the mmtf version
*/
public String getMmtfVersion() {
return mmtfVersion;
}
/**
* Sets the mmtf version.
*
* @param inputMmtfVersion the new mmtf version
*/
public void setMmtfVersion(String inputMmtfVersion) {
this.mmtfVersion = inputMmtfVersion;
}
/**
* Gets the num bonds.
*
* @return the num bonds
*/
public int getNumBonds() {
return numBonds;
}
/**
* Sets the number of bonds.
*
* @param inputNumBonds the new num bonds
*/
public void setNumBonds(int inputNumBonds) {
this.numBonds = inputNumBonds;
}
/**
* Gets the bond atom list.
*
* @return the bond atom list
*/
public byte[] getBondAtomList() {
return bondAtomList;
}
/**
* Sets the bond atom list.
*
* @param inputBondAtomList the new bond atom list
*/
public void setBondAtomList(byte[] inputBondAtomList) {
this.bondAtomList = inputBondAtomList;
}
/**
* Gets the bond order list.
*
* @return the bond order list
*/
public byte[] getBondOrderList() {
return bondOrderList;
}
/**
* Sets the bond order list.
*
* @param inputBondOrderList the new bond order list
*/
public void setBondOrderList(byte[] inputBondOrderList) {
this.bondOrderList = inputBondOrderList;
}
/**
* Gets the number of chains per model. Chains are currently specified by asym (internal) chain ids.
*
* @return the list of chains per model.
*/
public int[] getChainsPerModel() {
return chainsPerModel;
}
/**
* Sets the number of chains per model. Currently specified by asy (internal) chain ids.
*
* @param inputInternalChainsPerModel the new list of chains per model.
*/
public void setChainsPerModel(int[]
inputInternalChainsPerModel) {
this.chainsPerModel = inputInternalChainsPerModel;
}
/**
* Gets the number of groups per chain.
*
* @return the internal groups per chain
*/
public int[] getGroupsPerChain() {
return groupsPerChain;
}
/**
* Sets the number of groups in a chain.
*
* @param inputGroupsPerChain the new internal groups per chain
*/
public void setGroupsPerChain(int[]
inputGroupsPerChain) {
this.groupsPerChain = inputGroupsPerChain;
}
/**
* Gets the internal chain list.
*
* @return the internal chain list
*/
public byte[] getChainIdList() {
return chainIdList;
}
/**
* Sets the internal chain list.
*
* @param inputInternalChainList the new internal chain list
*/
public void setChainIdList(byte[] inputInternalChainList) {
this.chainIdList = inputInternalChainList;
}
/**
* @return the experimental methods
*/
public String[] getExperimentalMethods() {
return experimentalMethods;
}
/**
* @param experimentalMethods the experimental methods to set
*/
public void setExperimentalMethods(String[] experimentalMethods) {
this.experimentalMethods = experimentalMethods;
}
/**
* @return the seqResGroupIds
*/
public byte[] getSequenceIndexList() {
return sequenceIndexList;
}
/**
* @param seqResGroupIds the seqResGroupIds to set
*/
public void setSequenceIndexList(byte[] seqResGroupIds) {
this.sequenceIndexList = seqResGroupIds;
}
/**
* Get the entity list.
* @return the list of entities for this structure.
*/
public Entity[] getEntityList() {
return entityList;
}
/**
* Set the entity list.
* @param entityList the input list of entities.
*/
public void setEntityList(Entity[] entityList) {
this.entityList = entityList;
}
/**
* @return the deposition date of the structure in ISO time standard.
*/
public String getDepositionDate() {
return depositionDate;
}
/**
* @param depositionDate a string indicating the deposition date to set.
*/
public void setDepositionDate(String depositionDate) {
this.depositionDate = depositionDate;
}
/**
* @return the release date of the structure in ISO time standard.
*/
public String getReleaseDate() {
return releaseDate;
}
/**
* @param releaseDate a string indicating the deposition date to set.
*/
public void setReleaseDate(String releaseDate) {
this.releaseDate = releaseDate;
}
/**
* @return the X coords as an encoded byte array.
*/
public byte[] getxCoordList() {
return xCoordList;
}
/**
* @param xCoords the X coords as an encoded byte array.
*/
public void setxCoordList(byte[] xCoords) {
this.xCoordList = xCoords;
}
/**
* @return the the Y coords as an encoded byte array.
*/
public byte[] getyCoordList() {
return yCoordList;
}
/**
* @param yCoords the Y coords as an encoded byte array.
*/
public void setyCoordList(byte[] yCoords) {
this.yCoordList = yCoords;
}
/**
* @return the Z coords as an encoded byte array.
*/
public byte[] getzCoordList() {
return zCoordList;
}
/**
* @param zCoords the Z coords as an encoded byte array.
*/
public void setzCoordList(byte[] zCoords) {
this.zCoordList = zCoords;
}
/**
* @return the atomic B-factors as an encoded byte array.
*/
public byte[] getbFactorList() {
return bFactorList;
}
/**
* @param bFactors the atomic B-factors as an encoded byte array.
*/
public void setbFactorList(byte[] bFactors) {
this.bFactorList = bFactors;
}
/**
* @return the number of groups in the structure
*/
public int getNumGroups() {
return numGroups;
}
/**
* @param numGroups the number of groups in the structure
*/
public void setNumGroups(int numGroups) {
this.numGroups = numGroups;
}
/**
* @return the number of chains in the structure
*/
public int getNumChains() {
return numChains;
}
/**
* @param numChains the number of chains in the structure
*/
public void setNumChains(int numChains) {
this.numChains = numChains;
}
/**
* @return the number of models in the structure
*/
public int getNumModels() {
return numModels;
}
/**
* @param numModels the number of models in the structure
*/
public void setNumModels(int numModels) {
this.numModels = numModels;
}
/**
* @return the ncsOperMatrixList
*/
public double[][] getNcsOperatorList() {
return ncsOperatorList;
}
/**
* @param ncsOperatorList the ncsOperMatrixList to set
*/
public void setNcsOperatorList(double[][] ncsOperatorList) {
this.ncsOperatorList = ncsOperatorList;
}
}
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