org.rcsb.mmtf.dataholders.NoCoordDataStruct Maven / Gradle / Ivy
package org.rcsb.mmtf.dataholders;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.rcsb.mmtf.dataholders.PDBGroup;
/**
* A bean to store information about non coordinate information - fields are related strongly
* to the mmCif field they come from.
*
* @author anthony
*/
public class NoCoordDataStruct extends CoreDataStruct {
/** The _atom_site_symbol. */
// The symbol of thae atom
private List _atom_site_symbol = new ArrayList();
// This data item is an author defined alternative to the value of
// _atom_site_label_asym_id_ This item holds the PDB chain
/** The _atom_site_asym_id. */
// identifier_
private List _atom_site_asym_id = new ArrayList();
// This data item is an author defined alternative to the value of
// _atom_site_label_atom_id_ This item holds the PDB atom name_
// private List _atom_site_auth_atom_id = new ArrayList();
// This data item is an author defined alternative to the value of
// _atom_site_label_comp_id_ This item holds the PDB 3-letter-code
// residue names
// private List _atom_site_auth_comp_id = new ArrayList();
// This data item is an author defined alternative to the value of
/** The _atom_site_auth_seq_id. */
// _atom_site_label_seq_id_ This item holds the PDB residue number_
private List _atom_site_auth_seq_id = new ArrayList();
/** The _atom_site_label_entity_poly_seq_num. */
private List _atom_site_label_entity_poly_seq_num= new ArrayList();
/** The _atom_site_pdbx_ pd b_ins_code. */
// This data item corresponds to the PDB insertion code_
private List _atom_site_pdbx_PDB_ins_code = new ArrayList();
// This data item identifies the model number in an ensemble of
// coordinate data_
// private List _atom_site_pdbx_PDB_model_num = new ArrayList();
// This data item is a place holder for the tags used by the PDB to
/** The _atom_site_group_ pdb. */
// identify coordinate records (e_g_ ATOM or HETATM)_
private List _atom_site_group_PDB = new ArrayList();
// This item is a uniquely identifies for each alternative site for
/** The _atom_site_label_alt_id. */
// this atom position_
private List _atom_site_label_alt_id= new ArrayList();
/** The _atom_site_label_asym_id. */
// This data item is reference to item _struct_asym_id defined in
private List _atom_site_label_asym_id= new ArrayList();
// This data item is a reference to item _chem_comp_atom_atom_id
// defined in category CHEM_COMP_ATOM which is stored in the
// Chemical Component Dictionary_ This atom identifier uniquely
/** The _atom_site_label_atom_id. */
// identifies each atom within each chemical component_
private List _atom_site_label_atom_id= new ArrayList();
// This data item is a reference to item _chem_comp_id defined in
// category CHEM_COMP_ This item is the primary identifier for
// chemical components which may either be mononers in a polymeric
/** The _atom_site_label_comp_id. */
// entity or complete non-polymer entities_
private List _atom_site_label_comp_id= new ArrayList();
// This data item is a reference to _entity_id defined in the ENTITY
// category_ This item is used to identify chemically distinct
// portions of the molecular structure (e_g_ polymer chains,
// ligands, solvent)_
// This data item is a reference to _entity_poly_seq_num defined in
// the ENTITY_POLY_SEQ category_ This item is used to maintain the
// correspondence between the chemical sequence of a polymeric
// entity and the sequence information in the coordinate list and in
// may other structural categories_ This identifier has no meaning
/** The _atom_site_label_entity_id. */
// for non-polymer entities_
private List _atom_site_label_entity_id= new ArrayList();
/** The inter group bond inds. */
// The indices and orders of bonds between groups
private List interGroupBondInds = new ArrayList();
/** The inter group bond orders. */
private List interGroupBondOrders = new ArrayList();
/** The sec struct. */
private List secStruct = new ArrayList();
/** The res order. */
private List resOrder = new ArrayList();
/** The group list. */
private List> groupList = new ArrayList>();
/**
* Gets the _atom_site_symbol.
*
* @return the _atom_site_symbol
*/
public List get_atom_site_symbol() {
return _atom_site_symbol;
}
/**
* Sets the _atom_site_symbol.
*
* @param _atom_site_symbol the new _atom_site_symbol
*/
public void set_atom_site_symbol(List _atom_site_symbol) {
this._atom_site_symbol = _atom_site_symbol;
}
/**
* Gets the _atom_site_asym_id.
*
* @return the _atom_site_asym_id
*/
public List get_atom_site_asym_id() {
return _atom_site_asym_id;
}
/**
* Sets the _atom_site_asym_id.
*
* @param _atom_site_asym_id the new _atom_site_asym_id
*/
public void set_atom_site_asym_id(List _atom_site_asym_id) {
this._atom_site_asym_id = _atom_site_asym_id;
}
/**
* Gets the _atom_site_auth_seq_id.
*
* @return the _atom_site_auth_seq_id
*/
public List get_atom_site_auth_seq_id() {
return _atom_site_auth_seq_id;
}
/**
* Sets the _atom_site_auth_seq_id.
*
* @param _atom_site_auth_seq_id the new _atom_site_auth_seq_id
*/
public void set_atom_site_auth_seq_id(List _atom_site_auth_seq_id) {
this._atom_site_auth_seq_id = _atom_site_auth_seq_id;
}
/**
* Gets the _atom_site_pdbx_ pd b_ins_code.
*
* @return the _atom_site_pdbx_ pd b_ins_code
*/
public List get_atom_site_pdbx_PDB_ins_code() {
return _atom_site_pdbx_PDB_ins_code;
}
/**
* Sets the _atom_site_pdbx_ pd b_ins_code.
*
* @param _atom_site_pdbx_PDB_ins_code the new _atom_site_pdbx_ pd b_ins_code
*/
public void set_atom_site_pdbx_PDB_ins_code(List _atom_site_pdbx_PDB_ins_code) {
this._atom_site_pdbx_PDB_ins_code = _atom_site_pdbx_PDB_ins_code;
}
/**
* Gets the _atom_site_group_ pdb.
*
* @return the _atom_site_group_ pdb
*/
public List get_atom_site_group_PDB() {
return _atom_site_group_PDB;
}
/**
* Sets the _atom_site_group_ pdb.
*
* @param _atom_site_group_PDB the new _atom_site_group_ pdb
*/
public void set_atom_site_group_PDB(List _atom_site_group_PDB) {
this._atom_site_group_PDB = _atom_site_group_PDB;
}
/**
* Gets the _atom_site_label_alt_id.
*
* @return the _atom_site_label_alt_id
*/
public List get_atom_site_label_alt_id() {
return _atom_site_label_alt_id;
}
/**
* Sets the _atom_site_label_alt_id.
*
* @param _atom_site_label_alt_id the new _atom_site_label_alt_id
*/
public void set_atom_site_label_alt_id(List _atom_site_label_alt_id) {
this._atom_site_label_alt_id = _atom_site_label_alt_id;
}
/**
* Gets the _atom_site_label_asym_id.
*
* @return the _atom_site_label_asym_id
*/
public List get_atom_site_label_asym_id() {
return _atom_site_label_asym_id;
}
/**
* Sets the _atom_site_label_asym_id.
*
* @param _atom_site_label_asym_id the new _atom_site_label_asym_id
*/
public void set_atom_site_label_asym_id(List _atom_site_label_asym_id) {
this._atom_site_label_asym_id = _atom_site_label_asym_id;
}
/**
* Gets the _atom_site_label_atom_id.
*
* @return the _atom_site_label_atom_id
*/
public List get_atom_site_label_atom_id() {
return _atom_site_label_atom_id;
}
/**
* Sets the _atom_site_label_atom_id.
*
* @param _atom_site_label_atom_id the new _atom_site_label_atom_id
*/
public void set_atom_site_label_atom_id(List _atom_site_label_atom_id) {
this._atom_site_label_atom_id = _atom_site_label_atom_id;
}
/**
* Gets the _atom_site_label_comp_id.
*
* @return the _atom_site_label_comp_id
*/
public List get_atom_site_label_comp_id() {
return _atom_site_label_comp_id;
}
/**
* Sets the _atom_site_label_comp_id.
*
* @param _atom_site_label_comp_id the new _atom_site_label_comp_id
*/
public void set_atom_site_label_comp_id(List _atom_site_label_comp_id) {
this._atom_site_label_comp_id = _atom_site_label_comp_id;
}
/**
* Gets the _atom_site_label_entity_id.
*
* @return the _atom_site_label_entity_id
*/
public List get_atom_site_label_entity_id() {
return _atom_site_label_entity_id;
}
/**
* Sets the _atom_site_label_entity_id.
*
* @param _atom_site_label_entity_id the new _atom_site_label_entity_id
*/
public void set_atom_site_label_entity_id(List _atom_site_label_entity_id) {
this._atom_site_label_entity_id = _atom_site_label_entity_id;
}
/**
* Gets the _atom_site_label_entity_poly_seq_num.
*
* @return the _atom_site_label_entity_poly_seq_num
*/
public List get_atom_site_label_entity_poly_seq_num() {
return _atom_site_label_entity_poly_seq_num;
}
/**
* Sets the _atom_site_label_entity_poly_seq_num.
*
* @param _atom_site_label_entity_poly_seq_num the new _atom_site_label_entity_poly_seq_num
*/
public void set_atom_site_label_entity_poly_seq_num(List _atom_site_label_entity_poly_seq_num) {
this._atom_site_label_entity_poly_seq_num = _atom_site_label_entity_poly_seq_num;
}
/**
* Gets the group map.
*
* @return the group map
*/
public Map getGroupMap() {
return groupMap;
}
/**
* Sets the group map.
*
* @param groupMap the group map
*/
public void setGroupMap(Map groupMap) {
this.groupMap = groupMap;
}
/**
* Gets the group list.
*
* @return the group list
*/
public List> getGroupList() {
return groupList;
}
/**
* Sets the group list.
*
* @param groupList the new group list
*/
public void setGroupList(List> groupList) {
this.groupList = groupList;
}
/**
* Gets the res order.
*
* @return the res order
*/
public List getResOrder() {
return resOrder;
}
/**
* Sets the res order.
*
* @param resOrder the new res order
*/
public void setResOrder(List resOrder) {
this.resOrder = resOrder;
}
/**
* Gets the sec struct.
*
* @return the sec struct
*/
public List getSecStruct() {
return secStruct;
}
/**
* Sets the sec struct.
*
* @param secStruct the new sec struct
*/
public void setSecStruct(List secStruct) {
this.secStruct = secStruct;
}
/**
* Gets the inter group bond inds.
*
* @return the inter group bond inds
*/
public List getInterGroupBondInds() {
return interGroupBondInds;
}
/**
* Sets the inter group bond inds.
*
* @param interGroupBondInds the new inter group bond inds
*/
public void setInterGroupBondInds(List interGroupBondInds) {
this.interGroupBondInds = interGroupBondInds;
}
/**
* Gets the inter group bond orders.
*
* @return the inter group bond orders
*/
public List getInterGroupBondOrders() {
return interGroupBondOrders;
}
/**
* Sets the inter group bond orders.
*
* @param interGroupBondOrders the new inter group bond orders
*/
public void setInterGroupBondOrders(List interGroupBondOrders) {
this.interGroupBondOrders = interGroupBondOrders;
}
/** The group map. */
protected Map groupMap = new HashMap();
}