org.rcsb.mmtf.dataholders.BioDataStructBean Maven / Gradle / Ivy
package org.rcsb.mmtf.dataholders;
import java.util.ArrayList;
import java.util.List;
/**
* A bean to store the information about the protein structure.
*
* @author Anthony Bradley
*/
public class BioDataStructBean extends NoCoordDataStruct implements BioBean {
// Coordinate infroramtion
/** The _atom_site_cartn_x. */
protected List _atom_site_Cartn_x = new ArrayList();
/** The _atom_site_ cartn_y. */
protected List _atom_site_Cartn_y = new ArrayList();
/** The _atom_site_ cartn_z. */
protected List _atom_site_Cartn_z = new ArrayList();
/** The _atom_site_ b_iso_or_equiv. */
// Isotropic atomic displacement parameter
protected List _atom_site_B_iso_or_equiv= new ArrayList();
/** The _atom_site_occupancy. */
// The fraction of the atom present at this atom position_
protected List _atom_site_occupancy= new ArrayList();
/** The secondary structure list. */
// An array to store the secondary structure data
private List secStruct = new ArrayList();
/** The residue order list. */
// An array to store the sequence of residues
private List resOrder = new ArrayList();
/** The inter-group bond indicess. */
// Arrays to store the indices and bond orders of inter residue bonds
private List interGroupBondInds = new ArrayList();
/** The inter-group bond orders. */
private List interGroupBondOrders = new ArrayList();
/**
* Gets the _atom_site_id.
*
* @return the _atom_site_id
*/
public List get_atom_site_id() {
return _atom_site_id;
}
/**
* Sets the _atom_site_id.
*
* @param _atom_site_id the new _atom_site_id
*/
public void set_atom_site_id(List _atom_site_id) {
this._atom_site_id = _atom_site_id;
}
/** The _atom_site_id. */
private List _atom_site_id = new ArrayList();
/**
* Gets the _atom_site_ cartn_x.
*
* @return the _atom_site_ cartn_x
*/
public List get_atom_site_Cartn_x() {
return _atom_site_Cartn_x;
}
/**
* Sets the _atom_site_ cartn_x.
*
* @param _atom_site_Cartn_x the new _atom_site_ cartn_x
*/
public void set_atom_site_Cartn_x(ArrayList _atom_site_Cartn_x) {
this._atom_site_Cartn_x = _atom_site_Cartn_x;
}
/**
* Gets the _atom_site_ cartn_y.
*
* @return the _atom_site_ cartn_y
*/
public List get_atom_site_Cartn_y() {
return _atom_site_Cartn_y;
}
/**
* Sets the _atom_site_ cartn_y.
*
* @param _atom_site_Cartn_y the new _atom_site_ cartn_y
*/
public void set_atom_site_Cartn_y(ArrayList _atom_site_Cartn_y) {
this._atom_site_Cartn_y = _atom_site_Cartn_y;
}
/**
* Gets the _atom_site_ cartn_z.
*
* @return the _atom_site_ cartn_z
*/
public List get_atom_site_Cartn_z() {
return _atom_site_Cartn_z;
}
/**
* Sets the _atom_site_ cartn_z.
*
* @param _atom_site_Cartn_z the new _atom_site_ cartn_z
*/
public void set_atom_site_Cartn_z(ArrayList _atom_site_Cartn_z) {
this._atom_site_Cartn_z = _atom_site_Cartn_z;
}
/**
* Gets the _atom_site_ b_iso_or_equiv.
*
* @return the _atom_site_ b_iso_or_equiv
*/
public List get_atom_site_B_iso_or_equiv() {
return _atom_site_B_iso_or_equiv;
}
/**
* Sets the _atom_site_ b_iso_or_equiv.
*
* @param _atom_site_B_iso_or_equiv the new _atom_site_ b_iso_or_equiv
*/
public void set_atom_site_B_iso_or_equiv(ArrayList _atom_site_B_iso_or_equiv) {
this._atom_site_B_iso_or_equiv = _atom_site_B_iso_or_equiv;
}
/**
* Gets the _atom_site_occupancy.
*
* @return the _atom_site_occupancy
*/
public List get_atom_site_occupancy() {
return _atom_site_occupancy;
}
/**
* Sets the _atom_site_occupancy.
*
* @param _atom_site_occupancy the new _atom_site_occupancy
*/
public void set_atom_site_occupancy(ArrayList _atom_site_occupancy) {
this._atom_site_occupancy = _atom_site_occupancy;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#getResOrder()
*/
public List getResOrder() {
return resOrder;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#setResOrder(java.util.List)
*/
public void setResOrder(List resOrder) {
this.resOrder = resOrder;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#getSecStruct()
*/
public List getSecStruct() {
return secStruct;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#setSecStruct(java.util.List)
*/
public void setSecStruct(List secStruct) {
this.secStruct = secStruct;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#getInterGroupBondOrders()
*/
public List getInterGroupBondOrders() {
return interGroupBondOrders;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#setInterGroupBondOrders(java.util.List)
*/
public void setInterGroupBondOrders(List interGroupBondOrders) {
this.interGroupBondOrders = interGroupBondOrders;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#getInterGroupBondInds()
*/
public List getInterGroupBondInds() {
return interGroupBondInds;
}
/* (non-Javadoc)
* @see org.rcsb.mmtf.dataholders.NoCoordDataStruct#setInterGroupBondInds(java.util.List)
*/
public void setInterGroupBondInds(List interGroupBondInds) {
this.interGroupBondInds = interGroupBondInds;
}
}