org.rcsb.mmtf.dataholders.MmtfBean Maven / Gradle / Ivy
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package org.rcsb.mmtf.dataholders;
import java.util.List;
import java.util.Map;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* A class to store the data sent in an MMTF data source.
*
* @author anthony
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class MmtfBean {
/** The mmtf version. */
private String mmtfVersion;
/** The mmtf producer. */
private String mmtfProducer;
/** The number of bonds. */
private int numBonds;
/** The pdb id. */
private String pdbId;
/** The title. */
private String title;
/** The number of atoms. */
private int numAtoms;
/** 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 List unitCell;
/** The bio assembly. */
private Map bioAssembly;
/** The bond atom (indices) list. */
private byte[] bondAtomList;
/** The bond order list. */
private byte[] bondOrderList;
/** The group map. */
// Map of all the data
private Map groupMap;
/** The x coord big. 4 byte integers in pairs. */
private byte[] xCoordBig;
/** The y coord big. 4 byte integers in pairs. */
private byte[] yCoordBig;
/** The z coord big. 4 byte integers in pairs. */
private byte[] zCoordBig;
/** The b factor big. 4 byte integers in pairs. */
private byte[] bFactorBig;
/** The x coord small. 2 byte integers. */
private byte[] xCoordSmall;
/** The y coord small. 2 byte integers.*/
private byte[] yCoordSmall;
/** The z coord small. 2 byte integers.*/
private byte[] zCoordSmall;
/** The b factor small. 2 byte integers.*/
private byte[] bFactorSmall;
/** The secondary structure list. Stored as 1 byte ints. */
private byte[] secStructList;
/** The occupancy list. */
private byte[] occList;
/** The alt label list. */
private List altLabelList;
/** The insertion code list. */
private List 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 sequence, per asym chain. */
private List chainSeqList;
/** The SeqRes group ids. */
private byte[] seqResIdList;
/** The experimental method(s). */
private List experimentalMethods;
/** The resolution in Angstrom. -1.0 if not applicable*/
private float resolution;
/** The rfree. -1.0 if not applicable */
private float rFree;
/** The r-work. -1.0 if not applicable */
private float rWork;
/** The list of entities in this structure. */
private Entity[] entityList;
/** Constructor to set the default values for floats */
public MmtfBean() {
/** The mmtf version. Set here. */
mmtfVersion = "0.1";
/** The mmtf producer. NA is default and means error. */
mmtfProducer = "NA";
/** The resolution in Angstrom. -1.0 if not applicable*/
resolution = (float) -1.0;
/** The rfree. -1.0 if not applicable */
rFree = (float) -1.0;
/** 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() {
return resolution;
}
/**
* @param resolution the resolution to set
*/
public void setResolution(float resolution) {
this.resolution = resolution;
}
/**
* @return the rFree
*/
public float getrFree() {
return rFree;
}
/**
* @param rFree the rFree to set
*/
public void setrFree(float rFree) {
this.rFree = rFree;
}
/**
* @return the rWork
*/
public float getrWork() {
return rWork;
}
/**
* @param rWork the rWork to set
*/
public void setrWork(float rWork) {
this.rWork = rWork;
}
/*
/**
* Gets the space group.
*
* @return the space group
*/
public final String getSpaceGroup() {
return spaceGroup;
}
/**
* Sets the space group.
*
* @param inputSpaceGroup the new space group
*/
public final void setSpaceGroup(final String inputSpaceGroup) {
this.spaceGroup = inputSpaceGroup;
}
/**
* Gets the unit cell.
*
* @return the unit cell
*/
public final List getUnitCell() {
return unitCell;
}
/**
* Sets the unit cell.
*
* @param inputUnitCell the new unit cell
*/
public final void setUnitCell(final List inputUnitCell) {
this.unitCell = inputUnitCell;
}
/**
* Gets the group num list.
*
* @return the group num list
*/
public final byte[] getGroupIdList() {
return groupIdList;
}
/**
* Sets the group num list.
*
* @param inputGroupNumList the new group num list
*/
public final void setGroupIdList(final byte[] inputGroupNumList) {
this.groupIdList = inputGroupNumList;
}
/**
* Gets the x coord big.
*
* @return the x coord big
*/
public final byte[] getxCoordBig() {
return xCoordBig;
}
/**
* Sets the x coord big.
*
* @param inputXCoordBig the new 4 byte integer x coord array
*/
public final void setxCoordBig(final byte[] inputXCoordBig) {
this.xCoordBig = inputXCoordBig;
}
/**
* Gets the y coord big.
*
* @return the y coord big
*/
public final byte[] getyCoordBig() {
return yCoordBig;
}
/**
* Sets the y coord big.
*
* @param inputYCoordBig the new 4 byte integer y coord array
*/
public final void setyCoordBig(final byte[] inputYCoordBig) {
this.yCoordBig = inputYCoordBig;
}
/**
* Gets the z coord big.
*
* @return the z coord big
*/
public final byte[] getzCoordBig() {
return zCoordBig;
}
/**
* Sets the z coord big.
*
* @param inputZCoordBig the new 4 byte integer z coord array
*/
public final void setzCoordBig(final byte[] inputZCoordBig) {
this.zCoordBig = inputZCoordBig;
}
/**
* Gets the x coord small.
*
* @return the x coord small
*/
public final byte[] getxCoordSmall() {
return xCoordSmall;
}
/**
* Sets the x coord small.
*
* @param inputXCoordSmall the new 2 byte integer x coord array
*/
public final void setxCoordSmall(final byte[] inputXCoordSmall) {
this.xCoordSmall = inputXCoordSmall;
}
/**
* Gets the y coord small.
*
* @return the y coord small
*/
public final byte[] getyCoordSmall() {
return yCoordSmall;
}
/**
* Sets the y coord small.
*
* @param inputYCoordSmall the new 2 byte integer y coord array
*/
public final void setyCoordSmall(final byte[] inputYCoordSmall) {
this.yCoordSmall = inputYCoordSmall;
}
/**
* Gets the z coord small.
*
* @return the z coord small
*/
public final byte[] getzCoordSmall() {
return zCoordSmall;
}
/**
* Sets the z coord small.
*
* @param inputZCoordSmall the new 2 byte integer z coord array
*/
public final void setzCoordSmall(final byte[] inputZCoordSmall) {
this.zCoordSmall = inputZCoordSmall;
}
/**
* Gets the b factor big.
*
* @return the b factor big
*/
public final byte[] getbFactorBig() {
return bFactorBig;
}
/**
* Sets the b factor big.
*
* @param inputBigBFactor the new b factor big
*/
public final void setbFactorBig(final byte[] inputBigBFactor) {
this.bFactorBig = inputBigBFactor;
}
/**
* Gets the b factor small.
*
* @return the b factor small
*/
public final byte[] getbFactorSmall() {
return bFactorSmall;
}
/**
* Sets the b factor small.
*
* @param inputSmallBFactor the new b factor 2 byte array
*/
public final void setbFactorSmall(final byte[] inputSmallBFactor) {
this.bFactorSmall = inputSmallBFactor;
}
/**
* Gets the alt label list.
*
* @return the alt label list
*/
public final List getAltLabelList() {
return altLabelList;
}
/**
* Sets the alt label list.
*
* @param inputAltIdList the new alt id label list
*/
public final void setAltLabelList(final List inputAltIdList) {
this.altLabelList = inputAltIdList;
}
/**
* Gets the bio assembly.
*
* @return the bio assembly
*/
public final Map getBioAssembly() {
return bioAssembly;
}
/**
* 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 final 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 final void setChainNameList(final byte[] inputChainList) {
this.chainNameList = inputChainList;
}
/**
* Sets the bioassembly information.
*
* @param inputBioAssembly the bio assembly
*/
public final void setBioAssembly(final Map inputBioAssembly) {
this.bioAssembly = inputBioAssembly;
}
/**
* Gets the num atoms.
*
* @return the num atoms
*/
public final int getNumAtoms() {
return numAtoms;
}
/**
* Sets the num atoms.
*
* @param inputNumAtoms the new num atoms
*/
public final void setNumAtoms(final int inputNumAtoms) {
this.numAtoms = inputNumAtoms;
}
/**
* Gets the occ list.
*
* @return the occ list
*/
public final byte[] getOccList() {
return occList;
}
/**
* Sets the occ list.
*
* @param occupancy the new occ list
*/
public final void setOccList(final byte[] occupancy) {
this.occList = occupancy;
}
/**
* Gets the insertion code list.
*
* @return the insertion code list
*/
public final List getInsCodeList() {
return insCodeList;
}
/**
* Sets the ins code list.
*
* @param inputInsertionCodeList the new insertion code list
*/
public final void setInsCodeList(final List inputInsertionCodeList) {
this.insCodeList = inputInsertionCodeList;
}
/**
* Gets the group map.
*
* @return the group map
*/
public final Map getGroupMap() {
return groupMap;
}
/**
* Sets the group map.
*
* @param inputGroupMap the group map
*/
public final void setGroupMap(final Map inputGroupMap) {
this.groupMap = inputGroupMap;
}
/**
* Gets the sec struct list.
*
* @return the sec struct list
*/
public final byte[] getSecStructList() {
return secStructList;
}
/**
* Sets the sec struct list.
*
* @param secStruct the new sec struct list
*/
public final void setSecStructList(final byte[] secStruct) {
this.secStructList = secStruct;
}
/**
* Gets the group type list.
*
* @return the group type list
*/
public final byte[] getGroupTypeList() {
return groupTypeList;
}
/**
* Sets the group type list.
*
* @param resOrder the new group type list
*/
public final void setGroupTypeList(final byte[] resOrder) {
this.groupTypeList = resOrder;
}
/**
* Gets the atom id list.
*
* @return the atom id list
*/
public final byte[] getAtomIdList() {
return atomIdList;
}
/**
* Sets the atom id list.
*
* @param inputAtomIdList the new atom id list
*/
public final void setAtomIdList(final byte[] inputAtomIdList) {
this.atomIdList = inputAtomIdList;
}
/**
* Gets the title.
*
* @return the title
*/
public final String getTitle() {
return title;
}
/**
* Sets the title.
*
* @param inputTitle the new title
*/
public final void setTitle(final String inputTitle) {
this.title = inputTitle;
}
/**
* Gets the pdb id.
*
* @return the pdb id
*/
public final String getPdbId() {
return pdbId;
}
/**
* Sets the pdb id.
*
* @param pdbCode the new pdb id
*/
public final void setPdbId(final String pdbCode) {
this.pdbId = pdbCode;
}
/**
* Gets the mmtf producer.
*
* @return the mmtf producer
*/
public final String getMmtfProducer() {
return mmtfProducer;
}
/**
* Sets the mmtf producer.
*
* @param inputMmtfProducer the new mmtf producer
*/
public final void setMmtfProducer(final String inputMmtfProducer) {
this.mmtfProducer = inputMmtfProducer;
}
/**
* Gets the mmtf version.
*
* @return the mmtf version
*/
public final String getMmtfVersion() {
return mmtfVersion;
}
/**
* Sets the mmtf version.
*
* @param inputMmtfVersion the new mmtf version
*/
public final void setMmtfVersion(final String inputMmtfVersion) {
this.mmtfVersion = inputMmtfVersion;
}
/**
* Gets the num bonds.
*
* @return the num bonds
*/
public final int getNumBonds() {
return numBonds;
}
/**
* Sets the number of bonds.
*
* @param inputNumBonds the new num bonds
*/
public final void setNumBonds(final int inputNumBonds) {
this.numBonds = inputNumBonds;
}
/**
* Gets the bond atom list.
*
* @return the bond atom list
*/
public final byte[] getBondAtomList() {
return bondAtomList;
}
/**
* Sets the bond atom list.
*
* @param inputBondAtomList the new bond atom list
*/
public final void setBondAtomList(final byte[] inputBondAtomList) {
this.bondAtomList = inputBondAtomList;
}
/**
* Gets the bond order list.
*
* @return the bond order list
*/
public final byte[] getBondOrderList() {
return bondOrderList;
}
/**
* Sets the bond order list.
*
* @param inputBondOrderList the new bond order list
*/
public final void setBondOrderList(final 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 final 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 final void setChainsPerModel(final int[]
inputInternalChainsPerModel) {
this.chainsPerModel = inputInternalChainsPerModel;
}
/**
* Gets the number of groups per chain.
*
* @return the internal groups per chain
*/
public final int[] getGroupsPerChain() {
return groupsPerChain;
}
/**
* Sets the number of groups in a chain.
*
* @param inputGroupsPerChain the new internal groups per chain
*/
public final void setGroupsPerChain(final int[]
inputGroupsPerChain) {
this.groupsPerChain = inputGroupsPerChain;
}
/**
* Gets the internal chain list.
*
* @return the internal chain list
*/
public final byte[] getChainIdList() {
return chainIdList;
}
/**
* Sets the internal chain list.
*
* @param inputInternalChainList the new internal chain list
*/
public final void setChainIdList(final byte[] inputInternalChainList) {
this.chainIdList = inputInternalChainList;
}
/**
* @return the experimental methods
*/
public List getExperimentalMethods() {
return experimentalMethods;
}
/**
* @param experimentalMethods the experimental methods to set
*/
public void setExperimentalMethods(List experimentalMethods) {
this.experimentalMethods = experimentalMethods;
}
/**
* @return the sequence on a per (asym) chain level.
*/
public List getChainSeqList() {
return chainSeqList;
}
/**
* @param sequence the list of strings (sequences per asym chain) to set.
*/
public void setChainSeqList(List sequence) {
this.chainSeqList = sequence;
}
/**
* @return the seqResGroupIds
*/
public byte[] getSeqResIdList() {
return seqResIdList;
}
/**
* @param seqResGroupIds the seqResGroupIds to set
*/
public void setSeqResIdList(byte[] seqResGroupIds) {
this.seqResIdList = seqResGroupIds;
}
/**
* Get the entity list
* @return
*/
public Entity[] getEntityList() {
return entityList;
}
/**
* Set the entity list
* @param entityList
*/
public void setEntityList(Entity[] entityList) {
this.entityList = entityList;
}
}
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