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 
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {            
                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 
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
                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, SQLException {
                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;

                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();
        }
        
        private boolean check_inconsistent_res_numbering() throws SQLException{
                int count=0;
                int numserial=0;

                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();
                return false;
        }
        
        private void read_atomData() throws SQLException{
                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";

                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();
        }
        
        private String read_seq() throws SQLException{
                String allresseq="";
                String sql="SELECT all_res_seq FROM "+myMsdsdDb+".chain_seq WHERE chain_id="+chainid;

                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();

                return allresseq;
        }
        
        private HashMap<String,Integer> get_ressers_mapping() throws SQLException {
                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";

                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();

                return map;
        }
        
}
Revision:	210
Committed:	Wed Jun 27 15:57:39 2007 UTC (17 years, 3 months ago) by duarte
File size:	9865 byte(s)
Log Message:	Now throwing also SQLExceptions for individual queries, not just for connections
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	duarte	210	* @throws SQLException
61	duarte	207	*/
62	duarte	210	public MsdsdPdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
63	duarte	207	this(pdbCode,pdbChainCode,DEFAULT_MODEL,db,conn);
64			}
65
66			/**
67			* Constructs Pdb object given pdb code, pdb chain code and a model serial
68			* MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
69			* Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
70			* @param pdbCode
71			* @param pdbChainCode
72			* @param model_serial
73			* @throws MsdsdAcCodeNotFoundError
74			* @throws MsdsdInconsistentResidueNumbersError
75			* @throws SQLException
76			*/
77			public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
78			this(pdbCode,pdbChainCode,model_serial,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
79			}
80
81			/**
82			* Constructs Pdb object given pdb code, pdb chain code, model serial, a source db and a MySQLConnection.
83			* db must be a msdsd database
84			* @param pdbCode
85			* @param pdbChainCode
86			* @param model_serial
87			* @param db
88			* @param conn
89			* @throws MsdsdAcCodeNotFoundError
90			* @throws MsdsdInconsistentResidueNumbersError
91	duarte	210	* @throws SQLException
92	duarte	207	*/
93	duarte	210	public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
94	duarte	207	this.pdbCode=pdbCode;
95			this.pdbChainCode=pdbChainCode;
96			this.model=model_serial;
97			this.db=db;
98			this.myMsdsdDb="my_"+db; // i.e. for db=msdsd_00_07_a then myMsdsdDb=my_msdsd_00_07_a
99
100			this.conn = conn;
101
102			this.getchainid();// initialises chainid, modelid and chainCode
103
104			if (check_inconsistent_res_numbering()){
105			throw new MsdsdInconsistentResidueNumbersError("Inconsistent residue numbering in msdsd for accession_code "+this.pdbCode+", chain_pdb_code "+this.pdbChainCode);
106			}
107
108			this.sequence = read_seq();
109			this.pdbresser2resser = get_ressers_mapping();
110
111			this.read_atomData();
112
113			// we initialise resser2pdbresser from the pdbresser2resser HashMap
114			this.resser2pdbresser = new HashMap<Integer, String>();
115			for (String pdbresser:pdbresser2resser.keySet()){
116			resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
117			}
118			}
119
120	duarte	210	private void getchainid() throws MsdsdAcCodeNotFoundError, SQLException {
121	duarte	207	chainid=0;
122			String chaincodestr="='"+pdbChainCode+"'";
123			if (pdbChainCode.equals("NULL")){
124			chaincodestr="IS NULL";
125			}
126			String sql = "SELECT chain_id, model_id, pchain_code " +
127			" FROM "+myMsdsdDb+".mmol_chain_info " +
128			" WHERE accession_code='"+pdbCode+"' " +
129			" AND chain_pdb_code "+chaincodestr +
130			" AND chain_type='C' " +
131			" AND asu_chain=1 " +
132			" AND model_serial="+model;
133
134	duarte	210	Statement stmt = conn.createStatement();
135			ResultSet rsst = stmt.executeQuery(sql);
136			if (rsst.next()) {
137			chainid = rsst.getInt(1);
138			modelid = rsst.getInt(2);
139			chainCode=rsst.getString(3);
140			if (! rsst.isLast()) {
141			System.err.println("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
142			throw new MsdsdAcCodeNotFoundError("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
143			}
144			} else {
145			System.err.println("No chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
146			throw new MsdsdAcCodeNotFoundError("No chain_id could be matched for accession_code "+pdbCode+", chain_pdb_code "+pdbChainCode);
147			}
148			rsst.close();
149			stmt.close();
150	duarte	207	}
151
152	duarte	210	private boolean check_inconsistent_res_numbering() throws SQLException{
153	duarte	207	int count=0;
154			int numserial=0;
155	duarte	210
156			String sql="SELECT count(*) " +
157			" FROM "+myMsdsdDb+".problem_serial_chain " +
158			" WHERE chain_id="+chainid +
159			" AND (min_serial!=1 OR num_serial!=num_dist_serial OR num_serial!=max_serial-min_serial+1)";
160			Statement stmt = conn.createStatement();
161			ResultSet rsst = stmt.executeQuery(sql);
162			while (rsst.next()) {
163			count = rsst.getInt(1);
164			if (count>0){
165	duarte	207	return true;
166			}
167			}
168	duarte	210	sql="SELECT num_serial FROM "+myMsdsdDb+".problem_serial_chain WHERE chain_id="+chainid;
169			rsst = stmt.executeQuery(sql);
170			int check = 0;
171			while (rsst.next()){
172			check++;
173			numserial=rsst.getInt(1);
174			}
175			if (check!=1){
176			System.err.println("No num_serial match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
177			}
178			String allresseq = read_seq();
179			if (allresseq.length()!=numserial){
180			System.err.println("num_serial and length of all_res_seq don't match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
181			return true;
182			}
183			rsst.close();
184			stmt.close();
185	duarte	207	return false;
186			}
187
188	duarte	210	private void read_atomData() throws SQLException{
189	duarte	207	resser_atom2atomserial = new HashMap<String,Integer>();
190			resser2restype = new HashMap<Integer,String>();
191			atomser2coord = new HashMap<Integer,Double[]>();
192			atomser2resser = new HashMap<Integer,Integer>();
193
194			String sql = "SELECT serial,chem_atom_name,code_3_letter,residue_serial,x,y,z " +
195			" FROM "+db+".atom_data " +
196			" WHERE (model_id = "+modelid+") " +
197			" AND (chain_id = "+chainid+") " +
198			" AND (graph_alt_code_used = 1) " +
199			" AND (graph_standard_aa=1) " +
200			" AND (pdb_group = 'A')" +
201			" ORDER BY chain_code, residue_serial, serial";
202
203	duarte	210	Statement stmt = conn.createStatement();
204			ResultSet rsst = stmt.executeQuery(sql);
205			int count=0;
206			while (rsst.next()){
207			count++;
208
209			int atomserial = rsst.getInt(1); // atomserial
210			String atom = rsst.getString(2).trim(); // atom
211			String res_type = rsst.getString(3).trim(); // res_type
212			int res_serial = rsst.getInt(4); // res_serial
213			double x = rsst.getDouble(5); // x
214			double y = rsst.getDouble(6); // y
215			double z = rsst.getDouble(7); // z
216			Double[] coords = {x, y, z};
217			ArrayList<String> aalist=AA.aas();
218			if (aalist.contains(res_type)) {
219			atomser2coord.put(atomserial, coords);
220			atomser2resser.put(atomserial, res_serial);
221			resser2restype.put(res_serial, res_type);
222			ArrayList<String> atomlist = aas2atoms.get(res_type);
223			if (atomlist.contains(atom)){
224			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
225			}
226	duarte	207	}
227	duarte	210
228
229	duarte	207	}
230	duarte	210	if (count==0){
231			System.err.println("atom data query returned no data at all for model_id="+modelid+", model_id="+modelid);
232			}
233			rsst.close();
234			stmt.close();
235	duarte	207	}
236
237	duarte	210	private String read_seq() throws SQLException{
238	duarte	207	String allresseq="";
239			String sql="SELECT all_res_seq FROM "+myMsdsdDb+".chain_seq WHERE chain_id="+chainid;
240
241	duarte	210	Statement stmt = conn.createStatement();
242			ResultSet rsst = stmt.executeQuery(sql);
243			int check = 0;
244			if (rsst.next()) {
245			check++;
246			allresseq=rsst.getString(1);
247			}
248			if (check!=1) {
249			System.err.println("No all_res_seq match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", chain_id="+chainid);
250			}
251			rsst.close();
252			stmt.close();
253
254	duarte	207	return allresseq;
255			}
256
257	duarte	210	private HashMap<String,Integer> get_ressers_mapping() throws SQLException {
258	duarte	207	HashMap<String,Integer> map = new HashMap<String, Integer>();
259			String sql="SELECT serial, concat(pdb_seq,IF(pdb_insert_code IS NULL,'',pdb_insert_code)) " +
260			" FROM "+db+".residue " +
261			" WHERE chain_id="+chainid+
262			" AND pdb_seq IS NOT NULL";
263	duarte	210
264			Statement stmt = conn.createStatement();
265			ResultSet rsst = stmt.executeQuery(sql);
266			int count=0;
267			while (rsst.next()) {
268			count++;
269			int resser = rsst.getInt(1);
270			String pdbresser = rsst.getString(2);
271			map.put(pdbresser, resser);
272			}
273			if (count==0) {
274			System.err.println("No residue serials mapping data match for chain_id="+chainid);
275	duarte	207	}
276	duarte	210	rsst.close();
277			stmt.close();
278	duarte	207
279			return map;
280			}
281
282			}