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package org.rcsb.mmtf.dataholders;

import java.io.Serializable;
import java.util.Arrays;

import com.fasterxml.jackson.annotation.JsonIgnoreProperties;

/**
 * Group (residue) level data store.
 * @author Anthony Bradley
 *
 */
@JsonIgnoreProperties(ignoreUnknown = true)
public class Group implements Serializable {

	/** Serial id for this version of the format. */
	private static final long serialVersionUID = 2880633780569899800L;

	/** The group name. (e.g. HIS) */
	private String groupName;

	/** The atom names. A list of strings indicating
	 * the atom names (e.g. CA for C-alpha). */
	private String[] atomNameList;

	/** The element names. A list of strings indicating
	 * the element names (e.g. Ca for Calcium). */
	private String[] elementList;

	/** The bond orders. A list of integers indicating the bond orders*/
	private int[] bondOrderList;

	/** The bond indices (in pairs).
	 * (e.g. 0,1 means there is bond between atom 0 and 1).*/
	private int[] bondAtomList;

	/** The formal charges on the atoms. */
	private int[] formalChargeList;

	/** The single letter code. */
	private char singleLetterCode;

	/** A string (taken from the chemical component dictionary) indicating 
	 * the type of the group. Corresponds to: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_chem_comp.type.html */
	private String chemCompType;

	/* (non-Javadoc)
	 * @see java.lang.Object#hashCode()
	 */
	@Override
	public int hashCode() {
		final int prime = 31;
		int result = 1;
		result = prime * result + Arrays.hashCode(formalChargeList);
		result = prime * result + Arrays.hashCode(atomNameList);
		result = prime * result + Arrays.hashCode(bondAtomList);
		result = prime * result + Arrays.hashCode(bondOrderList);
		result = prime * result + ((chemCompType == null) ? 0 : chemCompType.hashCode());
		result = prime * result + Arrays.hashCode(elementList);
		result = prime * result + ((groupName == null) ? 0 : groupName.hashCode());
		result = prime * result + singleLetterCode;
		return result;
	}

	/* (non-Javadoc)
	 * @see java.lang.Object#equals(java.lang.Object)
	 */
	@Override
	public boolean equals(Object obj) {
		if (this == obj)
			return true;
		if (obj == null)
			return false;
		if (getClass() != obj.getClass())
			return false;
		Group other = (Group) obj;
		if (!Arrays.equals(formalChargeList, other.formalChargeList))
			return false;
		if (!Arrays.equals(atomNameList, other.atomNameList))
			return false;
		if (!Arrays.equals(bondAtomList, other.bondAtomList))
			return false;
		if (!Arrays.equals(bondOrderList, other.bondOrderList))
			return false;
		if (chemCompType == null) {
			if (other.chemCompType != null)
				return false;
		} else if (!chemCompType.equals(other.chemCompType))
			return false;
		if (!Arrays.equals(elementList, other.elementList))
			return false;
		if (groupName == null) {
			if (other.groupName != null)
				return false;
		} else if (!groupName.equals(other.groupName))
			return false;
		if (singleLetterCode != other.singleLetterCode)
			return false;
		return true;
	}

	/**
	 * Gets the atom info.
	 *
	 * @return the atom info
	 */
	// Generic getter and setter functions
	public String[] getAtomNameList() {
		return atomNameList;
	}

	/**
	 * Sets the atom info.
	 *
	 * @param inputAtomInfo the new atom info
	 */
	public void setAtomNameList(String[] inputAtomInfo) {
		this.atomNameList = inputAtomInfo;
	}

	/**
	 * Gets the bond orders.
	 *
	 * @return the bond orders
	 */
	public int[] getBondOrderList() {
		return bondOrderList;
	}

	/**
	 * Sets the bond orders.
	 *
	 * @param inputBondOrders the new bond orders
	 */
	public void setBondOrderList(int[] inputBondOrders) {
		this.bondOrderList = inputBondOrders;
	}

	/**
	 * Gets the bond indices.
	 *
	 * @return the bond indices
	 */
	public int[] getBondAtomList() {
		return bondAtomList;
	}

	/**
	 * Sets the bond indices.
	 *
	 * @param inputBondIndices the new bond indices
	 */
	public void setBondAtomList(int[] inputBondIndices) {
		this.bondAtomList = inputBondIndices;
	}

	/**
	 * Gets the group name.
	 *
	 * @return the group name
	 */
	public String getGroupName() {
		return groupName;
	}

	/**
	 * Sets the group name.
	 *
	 * @param resName the new group name
	 */
	public void setGroupName(String resName) {
		this.groupName = resName;
	}

	/**
	 * Gets the atom charges.
	 *
	 * @return the atom charges
	 */
	public int[] getFormalChargeList() {
		return formalChargeList;
	}

	/**
	 * Sets the atom charges.
	 *
	 * @param inputAtomCharges the new atom charges
	 */
	public void setFormalChargeList(int[] inputAtomCharges) {
		this.formalChargeList = inputAtomCharges;
	}

	/**
	 * Gets the single letter code.
	 *
	 * @return the single letter code
	 */
	public char getSingleLetterCode() {
		return singleLetterCode;
	}

	/**
	 * Sets the single letter code.
	 *
	 * @param inputSingleLetterCode the new single letter code
	 */
	public void setSingleLetterCode(char inputSingleLetterCode) {
		this.singleLetterCode = inputSingleLetterCode;
	}

	/**
	 * Get the chemical component type (in mmCIF as _chem_comp.type).
	 * 
	 * @return the groupType - corresponds to _chem_comp.type
	 */
	public String getChemCompType() {
		return chemCompType;
	}

	/**
	 * @param groupType the groupType (corresponds to _chem_comp.type) to set
	 */
	public void setChemCompType(String groupType) {
		this.chemCompType = groupType;
	}

	/**
	 * @return the list of elements (e.g. C for Carbon and Ca for Calcium)
	 */
	public String[] getElementList() {
		return elementList;
	}

	/**
	 * @param elementList the  list of elements (e.g. C for Carbon and Ca for Calcium)
	 */
	public void setElementList(String[] elementList) {
		this.elementList = elementList;
	}

}