trunk/proteinstructure/MsdsdPdb.java

package proteinstructure;

import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.HashMap;

import tools.MySQLConnection;

/**
 * A single chain pdb protein structure loaded from a MSDSD database
 * See http://www.ebi.ac.uk/msd-srv/docs/dbdoc/refaindex.html to know what MSDSD is
 * 
 * @author              Jose Duarte
 * Class:               MsdsdPdb
 * Package:             proteinstructure
 */
public class MsdsdPdb extends Pdb {
        
        private final static String MYSQLSERVER="white";
        private final static String MYSQLUSER=MySQLConnection.getUserName();
        private final static String MYSQLPWD="nieve";
        //private final static String DEFAULT_MYMSDSD_DB="my_msdsd_00_07_a";
        private final static String DEFAULT_MSDSD_DB="msdsd_00_07_a";

        private MySQLConnection conn;
        
        private int chainid;
        private int modelid;

        // TODO for this to be able to be used by other people we need to do things without a myMsdsdDb (or also distribute our fixes database)
        private String myMsdsdDb; // our database with add-ons and fixes to msdsd

        /**
         * Constructs Pdb object given pdb code and pdb chain code. 
         * Model will be DEFAULT_MODEL
         * MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
         * Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
         * @param pdbCode
         * @param pdbChainCode
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
                this(pdbCode,pdbChainCode,DEFAULT_MODEL,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));          
        }

        /**
         * Constructs Pdb object given pdb code, pdb chain code, db and MySQLConnection
         * Model will be DEFAULT_MODEL
         * db must be a msdsd database
         * @param pdbCode
         * @param pdbChainCode
         * @param db
         * @param conn
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {          
                this(pdbCode,pdbChainCode,DEFAULT_MODEL,db,conn);               
        }
        
        /**
         * Constructs Pdb object given pdb code, pdb chain code and a model serial
         * MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
         * Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
         * @param pdbCode
         * @param pdbChainCode
         * @param model_serial
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
                this(pdbCode,pdbChainCode,model_serial,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));           
        }

        /**
         * Constructs Pdb object given pdb code, pdb chain code, model serial, a source db and a MySQLConnection.
         * db must be a msdsd database
         * @param pdbCode
         * @param pdbChainCode
         * @param model_serial
         * @param db
         * @param conn
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this.pdbCode=pdbCode;
                this.pdbChainCode=pdbChainCode;
                this.model=model_serial;
                this.db=db;
                this.myMsdsdDb="my_"+db;  // i.e. for db=msdsd_00_07_a then myMsdsdDb=my_msdsd_00_07_a

                this.conn = conn;
                
                this.getchainid();// initialises chainid, modelid and chainCode
        
                if (check_inconsistent_res_numbering()){
            throw new MsdsdInconsistentResidueNumbersError("Inconsistent residue numbering in msdsd for accession_code "+this.pdbCode+", chain_pdb_code "+this.pdbChainCode);
        }
                
                this.sequence = read_seq();
                this.pdbresser2resser = get_ressers_mapping();

                this.read_atomData();
                
                // we initialise resser2pdbresser from the pdbresser2resser HashMap
                this.resser2pdbresser = new HashMap<Integer, String>();
                for (String pdbresser:pdbresser2resser.keySet()){
                        resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
                }
        }

        private void getchainid() throws MsdsdAcCodeNotFoundError {
                chainid=0;
                String chaincodestr="='"+pdbChainCode+"'";
                if (pdbChainCode.equals("NULL")){
                        chaincodestr="IS NULL";
                }
                String sql = "SELECT chain_id, model_id, pchain_code " +
                                " FROM "+myMsdsdDb+".mmol_chain_info " +
                                " WHERE accession_code='"+pdbCode+"' " +
                                " AND chain_pdb_code "+chaincodestr +
                                " AND chain_type='C' " +
                                " AND asu_chain=1 " +
                                " AND model_serial="+model;
                try {
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        if (rsst.next()) {
                                chainid = rsst.getInt(1);
                                modelid = rsst.getInt(2);
                                chainCode=rsst.getString(3);
                                if (! rsst.isLast()) {
                                        System.err.println("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                                        throw new MsdsdAcCodeNotFoundError("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);                                  
                                }
                        } else {
                                System.err.println("No chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                                throw new MsdsdAcCodeNotFoundError("No chain_id could be matched for accession_code "+pdbCode+", chain_pdb_code "+pdbChainCode);
                        } 
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }

        }
        
        private boolean check_inconsistent_res_numbering(){
                int count=0;
                int numserial=0;
                try {
                        String sql="SELECT count(*) " +
                        " FROM "+myMsdsdDb+".problem_serial_chain " +
                        " WHERE chain_id="+chainid +
                        " AND (min_serial!=1 OR num_serial!=num_dist_serial OR num_serial!=max_serial-min_serial+1)";
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                count = rsst.getInt(1);
                                if (count>0){
                                        return true;
                                }
                        }
                        sql="SELECT num_serial FROM "+myMsdsdDb+".problem_serial_chain WHERE chain_id="+chainid;
                        rsst = stmt.executeQuery(sql);
                        int check = 0;
                        while (rsst.next()){
                                check++;
                                numserial=rsst.getInt(1);
                        }
                        if (check!=1){
                                System.err.println("No num_serial match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                        }
                        String allresseq = read_seq();
                        if (allresseq.length()!=numserial){
                                System.err.println("num_serial and length of all_res_seq don't match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                                return true;
                        }
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }
                return false;
        }
        
        private void read_atomData(){
                resser_atom2atomserial = new HashMap<String,Integer>();
                resser2restype = new HashMap<Integer,String>();
                atomser2coord = new HashMap<Integer,Double[]>();
                atomser2resser = new HashMap<Integer,Integer>();

                String sql = "SELECT serial,chem_atom_name,code_3_letter,residue_serial,x,y,z " +
                                " FROM "+db+".atom_data " +
                                " WHERE (model_id = "+modelid+") " +
                                " AND (chain_id = "+chainid+") " +
                                " AND (graph_alt_code_used = 1) " +
                                " AND (graph_standard_aa=1) " +
                                " AND (pdb_group = 'A')" +
                                " ORDER BY chain_code, residue_serial, serial";
                try {
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        int count=0;
                        while (rsst.next()){
                                count++;
                                
                                int atomserial = rsst.getInt(1);                        // atomserial
                                String atom = rsst.getString(2).trim();         // atom
                                String res_type = rsst.getString(3).trim(); // res_type
                                int res_serial = rsst.getInt(4);                        // res_serial
                                double x = rsst.getDouble(5);                           // x
                                double y = rsst.getDouble(6);                           // y
                                double z = rsst.getDouble(7);                           // z
                                Double[] coords = {x, y, z};
                                ArrayList<String> aalist=AA.aas();
                                if (aalist.contains(res_type)) {
                                        atomser2coord.put(atomserial, coords);
                                        atomser2resser.put(atomserial, res_serial);
                                        resser2restype.put(res_serial, res_type);
                                        ArrayList<String> atomlist = aas2atoms.get(res_type);
                                        if (atomlist.contains(atom)){
                                                resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
                                        }
                                }

                                
                        }
                        if (count==0){
                                System.err.println("atom data query returned no data at all for model_id="+modelid+", model_id="+modelid);
                        }
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }
        }
        
        private String read_seq(){
                String allresseq="";
                String sql="SELECT all_res_seq FROM "+myMsdsdDb+".chain_seq WHERE chain_id="+chainid;
                try {
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        int check = 0;
                        if (rsst.next()) {
                                check++;
                                allresseq=rsst.getString(1);
                        } 
                        if (check!=1) {
                                System.err.println("No all_res_seq match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", chain_id="+chainid);
                        } 
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }

                return allresseq;
        }
        
        private HashMap<String,Integer> get_ressers_mapping() {
                HashMap<String,Integer> map = new HashMap<String, Integer>();
                String sql="SELECT serial, concat(pdb_seq,IF(pdb_insert_code IS NULL,'',pdb_insert_code)) " +
                                " FROM "+db+".residue " +
                                " WHERE chain_id="+chainid+
                                " AND pdb_seq IS NOT NULL";
                try {
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        int count=0;
                        while (rsst.next()) {
                                count++;
                                int resser = rsst.getInt(1);
                                String pdbresser = rsst.getString(2);
                                map.put(pdbresser, resser);
                        } 
                        if (count==0) {
                                System.err.println("No residue serials mapping data match for chain_id="+chainid);
                        }
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }

                return map;
        }
        
}
Revision:	207
Committed:	Wed Jun 27 11:06:34 2007 UTC (17 years, 3 months ago) by duarte
File size:	10120 byte(s)
Log Message:	Restructured construction of Pdb and Graph objects: now subclasses for each case Cleaned up and made consistent database connections Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection) PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively Updated following this changes testPdb and compareCMs
Line	User	Rev	File contents
1	duarte	207	package proteinstructure;
2
3			import java.sql.ResultSet;
4			import java.sql.SQLException;
5			import java.sql.Statement;
6			import java.util.ArrayList;
7			import java.util.HashMap;
8
9			import tools.MySQLConnection;
10
11			/**
12			* A single chain pdb protein structure loaded from a MSDSD database
13			* See http://www.ebi.ac.uk/msd-srv/docs/dbdoc/refaindex.html to know what MSDSD is
14			*
15			* @author Jose Duarte
16			* Class: MsdsdPdb
17			* Package: proteinstructure
18			*/
19			public class MsdsdPdb extends Pdb {
20
21			private final static String MYSQLSERVER="white";
22			private final static String MYSQLUSER=MySQLConnection.getUserName();
23			private final static String MYSQLPWD="nieve";
24			//private final static String DEFAULT_MYMSDSD_DB="my_msdsd_00_07_a";
25			private final static String DEFAULT_MSDSD_DB="msdsd_00_07_a";
26
27			private MySQLConnection conn;
28
29			private int chainid;
30			private int modelid;
31
32			// TODO for this to be able to be used by other people we need to do things without a myMsdsdDb (or also distribute our fixes database)
33			private String myMsdsdDb; // our database with add-ons and fixes to msdsd
34
35			/**
36			* Constructs Pdb object given pdb code and pdb chain code.
37			* Model will be DEFAULT_MODEL
38			* MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
39			* Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
40			* @param pdbCode
41			* @param pdbChainCode
42			* @throws MsdsdAcCodeNotFoundError
43			* @throws MsdsdInconsistentResidueNumbersError
44			* @throws SQLException
45			*/
46			public MsdsdPdb (String pdbCode, String pdbChainCode) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
47			this(pdbCode,pdbChainCode,DEFAULT_MODEL,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
48			}
49
50			/**
51			* Constructs Pdb object given pdb code, pdb chain code, db and MySQLConnection
52			* Model will be DEFAULT_MODEL
53			* db must be a msdsd database
54			* @param pdbCode
55			* @param pdbChainCode
56			* @param db
57			* @param conn
58			* @throws MsdsdAcCodeNotFoundError
59			* @throws MsdsdInconsistentResidueNumbersError
60			*/
61			public MsdsdPdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
62			this(pdbCode,pdbChainCode,DEFAULT_MODEL,db,conn);
63			}
64
65			/**
66			* Constructs Pdb object given pdb code, pdb chain code and a model serial
67			* MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
68			* Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
69			* @param pdbCode
70			* @param pdbChainCode
71			* @param model_serial
72			* @throws MsdsdAcCodeNotFoundError
73			* @throws MsdsdInconsistentResidueNumbersError
74			* @throws SQLException
75			*/
76			public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
77			this(pdbCode,pdbChainCode,model_serial,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
78			}
79
80			/**
81			* Constructs Pdb object given pdb code, pdb chain code, model serial, a source db and a MySQLConnection.
82			* db must be a msdsd database
83			* @param pdbCode
84			* @param pdbChainCode
85			* @param model_serial
86			* @param db
87			* @param conn
88			* @throws MsdsdAcCodeNotFoundError
89			* @throws MsdsdInconsistentResidueNumbersError
90			*/
91			public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
92			this.pdbCode=pdbCode;
93			this.pdbChainCode=pdbChainCode;
94			this.model=model_serial;
95			this.db=db;
96			this.myMsdsdDb="my_"+db; // i.e. for db=msdsd_00_07_a then myMsdsdDb=my_msdsd_00_07_a
97
98			this.conn = conn;
99
100			this.getchainid();// initialises chainid, modelid and chainCode
101
102			if (check_inconsistent_res_numbering()){
103			throw new MsdsdInconsistentResidueNumbersError("Inconsistent residue numbering in msdsd for accession_code "+this.pdbCode+", chain_pdb_code "+this.pdbChainCode);
104			}
105
106			this.sequence = read_seq();
107			this.pdbresser2resser = get_ressers_mapping();
108
109			this.read_atomData();
110
111			// we initialise resser2pdbresser from the pdbresser2resser HashMap
112			this.resser2pdbresser = new HashMap<Integer, String>();
113			for (String pdbresser:pdbresser2resser.keySet()){
114			resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
115			}
116			}
117
118			private void getchainid() throws MsdsdAcCodeNotFoundError {
119			chainid=0;
120			String chaincodestr="='"+pdbChainCode+"'";
121			if (pdbChainCode.equals("NULL")){
122			chaincodestr="IS NULL";
123			}
124			String sql = "SELECT chain_id, model_id, pchain_code " +
125			" FROM "+myMsdsdDb+".mmol_chain_info " +
126			" WHERE accession_code='"+pdbCode+"' " +
127			" AND chain_pdb_code "+chaincodestr +
128			" AND chain_type='C' " +
129			" AND asu_chain=1 " +
130			" AND model_serial="+model;
131			try {
132			Statement stmt = conn.createStatement();
133			ResultSet rsst = stmt.executeQuery(sql);
134			if (rsst.next()) {
135			chainid = rsst.getInt(1);
136			modelid = rsst.getInt(2);
137			chainCode=rsst.getString(3);
138			if (! rsst.isLast()) {
139			System.err.println("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
140			throw new MsdsdAcCodeNotFoundError("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
141			}
142			} else {
143			System.err.println("No chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
144			throw new MsdsdAcCodeNotFoundError("No chain_id could be matched for accession_code "+pdbCode+", chain_pdb_code "+pdbChainCode);
145			}
146			rsst.close();
147			stmt.close();
148			} catch (SQLException e) {
149			e.printStackTrace();
150			}
151
152			}
153
154			private boolean check_inconsistent_res_numbering(){
155			int count=0;
156			int numserial=0;
157			try {
158			String sql="SELECT count(*) " +
159			" FROM "+myMsdsdDb+".problem_serial_chain " +
160			" WHERE chain_id="+chainid +
161			" AND (min_serial!=1 OR num_serial!=num_dist_serial OR num_serial!=max_serial-min_serial+1)";
162			Statement stmt = conn.createStatement();
163			ResultSet rsst = stmt.executeQuery(sql);
164			while (rsst.next()) {
165			count = rsst.getInt(1);
166			if (count>0){
167			return true;
168			}
169			}
170			sql="SELECT num_serial FROM "+myMsdsdDb+".problem_serial_chain WHERE chain_id="+chainid;
171			rsst = stmt.executeQuery(sql);
172			int check = 0;
173			while (rsst.next()){
174			check++;
175			numserial=rsst.getInt(1);
176			}
177			if (check!=1){
178			System.err.println("No num_serial match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
179			}
180			String allresseq = read_seq();
181			if (allresseq.length()!=numserial){
182			System.err.println("num_serial and length of all_res_seq don't match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
183			return true;
184			}
185			rsst.close();
186			stmt.close();
187			} catch (SQLException e) {
188			e.printStackTrace();
189			}
190			return false;
191			}
192
193			private void read_atomData(){
194			resser_atom2atomserial = new HashMap<String,Integer>();
195			resser2restype = new HashMap<Integer,String>();
196			atomser2coord = new HashMap<Integer,Double[]>();
197			atomser2resser = new HashMap<Integer,Integer>();
198
199			String sql = "SELECT serial,chem_atom_name,code_3_letter,residue_serial,x,y,z " +
200			" FROM "+db+".atom_data " +
201			" WHERE (model_id = "+modelid+") " +
202			" AND (chain_id = "+chainid+") " +
203			" AND (graph_alt_code_used = 1) " +
204			" AND (graph_standard_aa=1) " +
205			" AND (pdb_group = 'A')" +
206			" ORDER BY chain_code, residue_serial, serial";
207			try {
208			Statement stmt = conn.createStatement();
209			ResultSet rsst = stmt.executeQuery(sql);
210			int count=0;
211			while (rsst.next()){
212			count++;
213
214			int atomserial = rsst.getInt(1); // atomserial
215			String atom = rsst.getString(2).trim(); // atom
216			String res_type = rsst.getString(3).trim(); // res_type
217			int res_serial = rsst.getInt(4); // res_serial
218			double x = rsst.getDouble(5); // x
219			double y = rsst.getDouble(6); // y
220			double z = rsst.getDouble(7); // z
221			Double[] coords = {x, y, z};
222			ArrayList<String> aalist=AA.aas();
223			if (aalist.contains(res_type)) {
224			atomser2coord.put(atomserial, coords);
225			atomser2resser.put(atomserial, res_serial);
226			resser2restype.put(res_serial, res_type);
227			ArrayList<String> atomlist = aas2atoms.get(res_type);
228			if (atomlist.contains(atom)){
229			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
230			}
231			}
232
233
234			}
235			if (count==0){
236			System.err.println("atom data query returned no data at all for model_id="+modelid+", model_id="+modelid);
237			}
238			rsst.close();
239			stmt.close();
240			} catch (SQLException e) {
241			e.printStackTrace();
242			}
243			}
244
245			private String read_seq(){
246			String allresseq="";
247			String sql="SELECT all_res_seq FROM "+myMsdsdDb+".chain_seq WHERE chain_id="+chainid;
248			try {
249			Statement stmt = conn.createStatement();
250			ResultSet rsst = stmt.executeQuery(sql);
251			int check = 0;
252			if (rsst.next()) {
253			check++;
254			allresseq=rsst.getString(1);
255			}
256			if (check!=1) {
257			System.err.println("No all_res_seq match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", chain_id="+chainid);
258			}
259			rsst.close();
260			stmt.close();
261			} catch (SQLException e) {
262			e.printStackTrace();
263			}
264
265			return allresseq;
266			}
267
268			private HashMap<String,Integer> get_ressers_mapping() {
269			HashMap<String,Integer> map = new HashMap<String, Integer>();
270			String sql="SELECT serial, concat(pdb_seq,IF(pdb_insert_code IS NULL,'',pdb_insert_code)) " +
271			" FROM "+db+".residue " +
272			" WHERE chain_id="+chainid+
273			" AND pdb_seq IS NOT NULL";
274			try {
275			Statement stmt = conn.createStatement();
276			ResultSet rsst = stmt.executeQuery(sql);
277			int count=0;
278			while (rsst.next()) {
279			count++;
280			int resser = rsst.getInt(1);
281			String pdbresser = rsst.getString(2);
282			map.put(pdbresser, resser);
283			}
284			if (count==0) {
285			System.err.println("No residue serials mapping data match for chain_id="+chainid);
286			}
287			rsst.close();
288			stmt.close();
289			} catch (SQLException e) {
290			e.printStackTrace();
291			}
292
293			return map;
294			}
295
296			}