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.Collections;
import java.util.HashMap;
import java.util.TreeMap;

import javax.vecmath.Point3d;

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 PdbCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode) throws PdbCodeNotFoundError, 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 PdbCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError 
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws PdbCodeNotFoundError, 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 PdbCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial) throws PdbCodeNotFoundError, 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 PdbCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError 
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws PdbCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
                this.pdbCode=pdbCode.toLowerCase();                             // our convention: pdb codes are lower case
                this.pdbChainCode=pdbChainCode.toUpperCase();   // our convention: chain codes are upper case
                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.fullLength = sequence.length();
                
                this.pdbresser2resser = get_ressers_mapping();

                this.read_atomData();
                
                this.obsLength = resser2restype.size();
                
                // we initialise resser2pdbresser from the pdbresser2resser HashMap
                this.resser2pdbresser = new HashMap<Integer, String>();
                for (String pdbresser:pdbresser2resser.keySet()){
                        resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
                }
                
                secondaryStructure = new SecondaryStructure();  // create empty secondary structure first to make sure object is not null               
                readSecStructure();
                if(!secondaryStructure.isEmpty()) {
                        secondaryStructure.setComment("MSDSD");
                }
                
                // initialising atomser2atom from resser_atom2atomserial
                atomser2atom = new HashMap<Integer, String>();
                for (String resser_atom:resser_atom2atomserial.keySet()){
                        int atomserial = resser_atom2atomserial.get(resser_atom);
                        String atom = resser_atom.split("_")[1];
                        atomser2atom.put(atomserial,atom);
                }
        }

        private void getchainid() throws PdbCodeNotFoundError, 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 PdbCodeNotFoundError("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 PdbCodeNotFoundError("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,Point3d>();
                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
                        Point3d coords = new Point3d(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);
                                atomlist.add("OXT"); // the extra atom OXT is there in the last residue of the chain
                                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;
        }
        
        private void readSecStructure() throws SQLException{
                this.secondaryStructure = new SecondaryStructure();
                
                //HELIX -- helix table
                String sql = "SELECT helix_serial, beg_residue_serial, end_residue_serial " +
                                " FROM "+db+".helix " +
                                " WHERE (model_id = "+modelid+") " +
                                " AND (chain_id = "+chainid+") ";
                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                int count=0;
                while (rsst.next()) {
                        count++;
                        int serial = rsst.getInt(1);
                        int beg = rsst.getInt(2);
                        int end =rsst.getInt(3);
                        String ssId = "" + SecStrucElement.HELIX+serial;
                        SecStrucElement ssElem = new SecStrucElement(SecStrucElement.HELIX,beg,end,ssId);
                        secondaryStructure.add(ssElem);
                } 
                rsst.close();
                stmt.close();
                //SHEET -- strand table
                sql = "SELECT sheet_serial, strand_serial, strand_beg_residue_serial, strand_end_residue_serial " +
                                " FROM "+db+".strand " +
                                " WHERE (model_id = "+modelid+") " +
                                " AND (chain_id = "+chainid+") ";
                stmt = conn.createStatement();
                rsst = stmt.executeQuery(sql);
                // we store everything in these 2 maps to assign later to resser2secstruct based on our own ids (ids are not very consistent in msdsd)
                HashMap<Integer,Interval> strands2begEnd = new HashMap<Integer, Interval>(); 
                TreeMap<Integer,ArrayList<Integer>> sheets2strands = new TreeMap<Integer, ArrayList<Integer>>();
                count=0;
                while (rsst.next()) {
                        count++;
                        int sheetSerial = rsst.getInt(1);
                        int strandSerial = rsst.getInt(2);
                        int beg = rsst.getInt(3);
                        int end =rsst.getInt(4);
                        strands2begEnd.put(strandSerial, new Interval(beg,end));
                        if (sheets2strands.containsKey(sheetSerial)){
                                sheets2strands.get(sheetSerial).add(strandSerial);
                        } else {
                                ArrayList<Integer> strands = new ArrayList<Integer>();
                                strands.add(strandSerial);
                                sheets2strands.put(sheetSerial, strands);
                        }
                } 
                rsst.close();
                stmt.close();
                char sheet='A';
                for (int sheetSerial:sheets2strands.keySet()){
                        int strand=1;
                        for (int strandSerial:sheets2strands.get(sheetSerial)){
                                Interval begEnd = strands2begEnd.get(strandSerial);
                                String ssId = ""+SecStrucElement.STRAND+sheet+strand;
                                SecStrucElement ssElem = new SecStrucElement(SecStrucElement.STRAND,begEnd.beg,begEnd.end,ssId);
                                secondaryStructure.add(ssElem);                         
                                strand++;
                        }
                        sheet++;
                }

                //TURN -- turn table    
                // they forgot to fill up the turn_serial field so we have to use turn_id and get a serial from it that is unique within the chain only
                sql = "SELECT turn_id, res_1_residue_serial, res_2_residue_serial, res_3_residue_serial, res_4_residue_serial " +
                                " FROM "+db+".turn " +
                                " WHERE (model_id = "+modelid+") " +
                                " AND (chain_id = "+chainid+") ";
                stmt = conn.createStatement();
                rsst = stmt.executeQuery(sql);
                TreeMap<Integer,ArrayList<Integer>> turns = new TreeMap<Integer, ArrayList<Integer>>();
                count=0;
                while (rsst.next()) {
                        count++;
                        int dbId = rsst.getInt(1);
                        int res1 = rsst.getInt(2);
                        int res2 = rsst.getInt(3);
                        int res3 = rsst.getInt(4);
                        int res4 = rsst.getInt(5);
                        ArrayList<Integer> residues = new ArrayList<Integer>();
                        if (res1!=0) residues.add(res1); // res is 0 when the field is NULL in database
                        if (res2!=0) residues.add(res2);
                        if (res3!=0) residues.add(res3);
                        if (res4!=0) residues.add(res4);
                        turns.put(dbId, residues);                              
                } 
                rsst.close();
                stmt.close();
                int serial=1;
                for (int dbId:turns.keySet()){
                        String ssId = "" + SecStrucElement.TURN + serial;
                        int beg = Collections.min(turns.get(dbId));
                        int end = Collections.max(turns.get(dbId));
                        SecStrucElement ssElem = new SecStrucElement(SecStrucElement.TURN,beg,end,ssId);
                        secondaryStructure.add(ssElem);
                        serial++;
                }

        }
}
Revision:	278
Committed:	Tue Aug 14 12:14:04 2007 UTC (17 years, 2 months ago) by duarte
File size:	14509 byte(s)
Log Message:	Fixed bug with getFullLength when reading from pdb file Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers New member variables obsLength and fullLength
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	duarte	222	import java.util.Collections;
8	duarte	207	import java.util.HashMap;
9	duarte	219	import java.util.TreeMap;
10	duarte	207
11	duarte	226	import javax.vecmath.Point3d;
12
13	duarte	207	import tools.MySQLConnection;
14
15			/**
16			* A single chain pdb protein structure loaded from a MSDSD database
17			* See http://www.ebi.ac.uk/msd-srv/docs/dbdoc/refaindex.html to know what MSDSD is
18			*
19			* @author Jose Duarte
20			* Class: MsdsdPdb
21			* Package: proteinstructure
22			*/
23			public class MsdsdPdb extends Pdb {
24
25			private final static String MYSQLSERVER="white";
26			private final static String MYSQLUSER=MySQLConnection.getUserName();
27			private final static String MYSQLPWD="nieve";
28			//private final static String DEFAULT_MYMSDSD_DB="my_msdsd_00_07_a";
29			private final static String DEFAULT_MSDSD_DB="msdsd_00_07_a";
30
31			private MySQLConnection conn;
32
33			private int chainid;
34			private int modelid;
35
36			// 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)
37			private String myMsdsdDb; // our database with add-ons and fixes to msdsd
38
39			/**
40			* Constructs Pdb object given pdb code and pdb chain code.
41			* Model will be DEFAULT_MODEL
42			* MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
43			* Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
44			* @param pdbCode
45			* @param pdbChainCode
46	stehr	215	* @throws PdbCodeNotFoundError
47	duarte	207	* @throws MsdsdInconsistentResidueNumbersError
48			* @throws SQLException
49			*/
50	stehr	215	public MsdsdPdb (String pdbCode, String pdbChainCode) throws PdbCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
51	duarte	207	this(pdbCode,pdbChainCode,DEFAULT_MODEL,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
52			}
53
54			/**
55			* Constructs Pdb object given pdb code, pdb chain code, db and MySQLConnection
56			* Model will be DEFAULT_MODEL
57			* db must be a msdsd database
58			* @param pdbCode
59			* @param pdbChainCode
60			* @param db
61			* @param conn
62	stehr	215	* @throws PdbCodeNotFoundError
63	duarte	207	* @throws MsdsdInconsistentResidueNumbersError
64	duarte	210	* @throws SQLException
65	duarte	207	*/
66	stehr	215	public MsdsdPdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws PdbCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
67	duarte	207	this(pdbCode,pdbChainCode,DEFAULT_MODEL,db,conn);
68			}
69
70			/**
71			* Constructs Pdb object given pdb code, pdb chain code and a model serial
72			* MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
73			* Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
74			* @param pdbCode
75			* @param pdbChainCode
76			* @param model_serial
77	stehr	215	* @throws PdbCodeNotFoundError
78	duarte	207	* @throws MsdsdInconsistentResidueNumbersError
79			* @throws SQLException
80			*/
81	stehr	215	public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial) throws PdbCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
82	duarte	207	this(pdbCode,pdbChainCode,model_serial,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
83			}
84
85			/**
86			* Constructs Pdb object given pdb code, pdb chain code, model serial, a source db and a MySQLConnection.
87			* db must be a msdsd database
88			* @param pdbCode
89			* @param pdbChainCode
90			* @param model_serial
91			* @param db
92			* @param conn
93	stehr	215	* @throws PdbCodeNotFoundError
94	duarte	207	* @throws MsdsdInconsistentResidueNumbersError
95	duarte	210	* @throws SQLException
96	duarte	207	*/
97	stehr	215	public MsdsdPdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws PdbCodeNotFoundError, MsdsdInconsistentResidueNumbersError, SQLException {
98	stehr	217	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
99			this.pdbChainCode=pdbChainCode.toUpperCase(); // our convention: chain codes are upper case
100	duarte	207	this.model=model_serial;
101			this.db=db;
102			this.myMsdsdDb="my_"+db; // i.e. for db=msdsd_00_07_a then myMsdsdDb=my_msdsd_00_07_a
103
104			this.conn = conn;
105
106			this.getchainid();// initialises chainid, modelid and chainCode
107
108			if (check_inconsistent_res_numbering()){
109			throw new MsdsdInconsistentResidueNumbersError("Inconsistent residue numbering in msdsd for accession_code "+this.pdbCode+", chain_pdb_code "+this.pdbChainCode);
110			}
111
112			this.sequence = read_seq();
113	duarte	278	this.fullLength = sequence.length();
114
115	duarte	207	this.pdbresser2resser = get_ressers_mapping();
116
117			this.read_atomData();
118
119	duarte	278	this.obsLength = resser2restype.size();
120
121	duarte	207	// we initialise resser2pdbresser from the pdbresser2resser HashMap
122			this.resser2pdbresser = new HashMap<Integer, String>();
123			for (String pdbresser:pdbresser2resser.keySet()){
124			resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
125			}
126	duarte	219
127	stehr	274	secondaryStructure = new SecondaryStructure(); // create empty secondary structure first to make sure object is not null
128			readSecStructure();
129			if(!secondaryStructure.isEmpty()) {
130			secondaryStructure.setComment("MSDSD");
131	stehr	259	}
132	duarte	237
133			// initialising atomser2atom from resser_atom2atomserial
134			atomser2atom = new HashMap<Integer, String>();
135			for (String resser_atom:resser_atom2atomserial.keySet()){
136			int atomserial = resser_atom2atomserial.get(resser_atom);
137			String atom = resser_atom.split("_")[1];
138			atomser2atom.put(atomserial,atom);
139			}
140	duarte	207	}
141
142	stehr	215	private void getchainid() throws PdbCodeNotFoundError, SQLException {
143	duarte	207	chainid=0;
144			String chaincodestr="='"+pdbChainCode+"'";
145			if (pdbChainCode.equals("NULL")){
146			chaincodestr="IS NULL";
147			}
148			String sql = "SELECT chain_id, model_id, pchain_code " +
149			" FROM "+myMsdsdDb+".mmol_chain_info " +
150			" WHERE accession_code='"+pdbCode+"' " +
151			" AND chain_pdb_code "+chaincodestr +
152			" AND chain_type='C' " +
153			" AND asu_chain=1 " +
154			" AND model_serial="+model;
155
156	duarte	210	Statement stmt = conn.createStatement();
157			ResultSet rsst = stmt.executeQuery(sql);
158			if (rsst.next()) {
159			chainid = rsst.getInt(1);
160			modelid = rsst.getInt(2);
161			chainCode=rsst.getString(3);
162			if (! rsst.isLast()) {
163	stehr	215	//System.err.println("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
164			throw new PdbCodeNotFoundError("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
165	duarte	210	}
166			} else {
167	stehr	215	//System.err.println("No chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
168			throw new PdbCodeNotFoundError("No chain_id could be matched for accession_code "+pdbCode+", chain_pdb_code "+pdbChainCode);
169	duarte	210	}
170			rsst.close();
171			stmt.close();
172	duarte	207	}
173
174	duarte	210	private boolean check_inconsistent_res_numbering() throws SQLException{
175	duarte	207	int count=0;
176			int numserial=0;
177	duarte	210
178			String sql="SELECT count(*) " +
179			" FROM "+myMsdsdDb+".problem_serial_chain " +
180			" WHERE chain_id="+chainid +
181			" AND (min_serial!=1 OR num_serial!=num_dist_serial OR num_serial!=max_serial-min_serial+1)";
182			Statement stmt = conn.createStatement();
183			ResultSet rsst = stmt.executeQuery(sql);
184			while (rsst.next()) {
185			count = rsst.getInt(1);
186			if (count>0){
187	duarte	207	return true;
188			}
189			}
190	duarte	210	sql="SELECT num_serial FROM "+myMsdsdDb+".problem_serial_chain WHERE chain_id="+chainid;
191			rsst = stmt.executeQuery(sql);
192			int check = 0;
193			while (rsst.next()){
194			check++;
195			numserial=rsst.getInt(1);
196			}
197			if (check!=1){
198			System.err.println("No num_serial match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
199			}
200			String allresseq = read_seq();
201			if (allresseq.length()!=numserial){
202			System.err.println("num_serial and length of all_res_seq don't match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
203			return true;
204			}
205			rsst.close();
206			stmt.close();
207	duarte	207	return false;
208			}
209
210	duarte	210	private void read_atomData() throws SQLException{
211	duarte	207	resser_atom2atomserial = new HashMap<String,Integer>();
212			resser2restype = new HashMap<Integer,String>();
213	duarte	226	atomser2coord = new HashMap<Integer,Point3d>();
214	duarte	207	atomser2resser = new HashMap<Integer,Integer>();
215
216			String sql = "SELECT serial,chem_atom_name,code_3_letter,residue_serial,x,y,z " +
217			" FROM "+db+".atom_data " +
218			" WHERE (model_id = "+modelid+") " +
219			" AND (chain_id = "+chainid+") " +
220			" AND (graph_alt_code_used = 1) " +
221			" AND (graph_standard_aa=1) " +
222			" AND (pdb_group = 'A')" +
223			" ORDER BY chain_code, residue_serial, serial";
224
225	duarte	210	Statement stmt = conn.createStatement();
226			ResultSet rsst = stmt.executeQuery(sql);
227			int count=0;
228			while (rsst.next()){
229			count++;
230
231			int atomserial = rsst.getInt(1); // atomserial
232			String atom = rsst.getString(2).trim(); // atom
233			String res_type = rsst.getString(3).trim(); // res_type
234			int res_serial = rsst.getInt(4); // res_serial
235			double x = rsst.getDouble(5); // x
236			double y = rsst.getDouble(6); // y
237			double z = rsst.getDouble(7); // z
238	duarte	226	Point3d coords = new Point3d(x, y, z);
239	duarte	210	ArrayList<String> aalist=AA.aas();
240			if (aalist.contains(res_type)) {
241			atomser2coord.put(atomserial, coords);
242			atomser2resser.put(atomserial, res_serial);
243			resser2restype.put(res_serial, res_type);
244			ArrayList<String> atomlist = aas2atoms.get(res_type);
245	duarte	275	atomlist.add("OXT"); // the extra atom OXT is there in the last residue of the chain
246	duarte	210	if (atomlist.contains(atom)){
247			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
248			}
249	duarte	207	}
250	duarte	210
251
252	duarte	207	}
253	duarte	210	if (count==0){
254			System.err.println("atom data query returned no data at all for model_id="+modelid+", model_id="+modelid);
255			}
256			rsst.close();
257			stmt.close();
258	duarte	207	}
259
260	duarte	210	private String read_seq() throws SQLException{
261	duarte	207	String allresseq="";
262			String sql="SELECT all_res_seq FROM "+myMsdsdDb+".chain_seq WHERE chain_id="+chainid;
263
264	duarte	210	Statement stmt = conn.createStatement();
265			ResultSet rsst = stmt.executeQuery(sql);
266			int check = 0;
267			if (rsst.next()) {
268			check++;
269			allresseq=rsst.getString(1);
270			}
271			if (check!=1) {
272			System.err.println("No all_res_seq match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", chain_id="+chainid);
273			}
274			rsst.close();
275			stmt.close();
276
277	duarte	207	return allresseq;
278			}
279
280	duarte	210	private HashMap<String,Integer> get_ressers_mapping() throws SQLException {
281	duarte	207	HashMap<String,Integer> map = new HashMap<String, Integer>();
282			String sql="SELECT serial, concat(pdb_seq,IF(pdb_insert_code IS NULL,'',pdb_insert_code)) " +
283			" FROM "+db+".residue " +
284			" WHERE chain_id="+chainid+
285			" AND pdb_seq IS NOT NULL";
286	duarte	210
287			Statement stmt = conn.createStatement();
288			ResultSet rsst = stmt.executeQuery(sql);
289			int count=0;
290			while (rsst.next()) {
291			count++;
292			int resser = rsst.getInt(1);
293			String pdbresser = rsst.getString(2);
294			map.put(pdbresser, resser);
295			}
296			if (count==0) {
297			System.err.println("No residue serials mapping data match for chain_id="+chainid);
298	duarte	207	}
299	duarte	210	rsst.close();
300			stmt.close();
301	duarte	207
302			return map;
303			}
304
305	duarte	219	private void readSecStructure() throws SQLException{
306	stehr	274	this.secondaryStructure = new SecondaryStructure();
307	duarte	219
308			//HELIX -- helix table
309			String sql = "SELECT helix_serial, beg_residue_serial, end_residue_serial " +
310			" FROM "+db+".helix " +
311			" WHERE (model_id = "+modelid+") " +
312			" AND (chain_id = "+chainid+") ";
313			Statement stmt = conn.createStatement();
314			ResultSet rsst = stmt.executeQuery(sql);
315			int count=0;
316			while (rsst.next()) {
317			count++;
318			int serial = rsst.getInt(1);
319			int beg = rsst.getInt(2);
320			int end =rsst.getInt(3);
321	stehr	274	String ssId = "" + SecStrucElement.HELIX+serial;
322			SecStrucElement ssElem = new SecStrucElement(SecStrucElement.HELIX,beg,end,ssId);
323			secondaryStructure.add(ssElem);
324	duarte	219	}
325			rsst.close();
326			stmt.close();
327			//SHEET -- strand table
328			sql = "SELECT sheet_serial, strand_serial, strand_beg_residue_serial, strand_end_residue_serial " +
329			" FROM "+db+".strand " +
330			" WHERE (model_id = "+modelid+") " +
331			" AND (chain_id = "+chainid+") ";
332			stmt = conn.createStatement();
333			rsst = stmt.executeQuery(sql);
334			// we store everything in these 2 maps to assign later to resser2secstruct based on our own ids (ids are not very consistent in msdsd)
335	duarte	222	HashMap<Integer,Interval> strands2begEnd = new HashMap<Integer, Interval>();
336	duarte	219	TreeMap<Integer,ArrayList<Integer>> sheets2strands = new TreeMap<Integer, ArrayList<Integer>>();
337			count=0;
338			while (rsst.next()) {
339			count++;
340			int sheetSerial = rsst.getInt(1);
341			int strandSerial = rsst.getInt(2);
342			int beg = rsst.getInt(3);
343			int end =rsst.getInt(4);
344	duarte	222	strands2begEnd.put(strandSerial, new Interval(beg,end));
345	duarte	219	if (sheets2strands.containsKey(sheetSerial)){
346			sheets2strands.get(sheetSerial).add(strandSerial);
347			} else {
348			ArrayList<Integer> strands = new ArrayList<Integer>();
349			strands.add(strandSerial);
350			sheets2strands.put(sheetSerial, strands);
351			}
352			}
353			rsst.close();
354			stmt.close();
355			char sheet='A';
356			for (int sheetSerial:sheets2strands.keySet()){
357			int strand=1;
358			for (int strandSerial:sheets2strands.get(sheetSerial)){
359	duarte	222	Interval begEnd = strands2begEnd.get(strandSerial);
360	stehr	274	String ssId = ""+SecStrucElement.STRAND+sheet+strand;
361			SecStrucElement ssElem = new SecStrucElement(SecStrucElement.STRAND,begEnd.beg,begEnd.end,ssId);
362			secondaryStructure.add(ssElem);
363	duarte	219	strand++;
364			}
365			sheet++;
366			}
367
368			//TURN -- turn table
369			// they forgot to fill up the turn_serial field so we have to use turn_id and get a serial from it that is unique within the chain only
370			sql = "SELECT turn_id, res_1_residue_serial, res_2_residue_serial, res_3_residue_serial, res_4_residue_serial " +
371			" FROM "+db+".turn " +
372			" WHERE (model_id = "+modelid+") " +
373			" AND (chain_id = "+chainid+") ";
374			stmt = conn.createStatement();
375			rsst = stmt.executeQuery(sql);
376	duarte	222	TreeMap<Integer,ArrayList<Integer>> turns = new TreeMap<Integer, ArrayList<Integer>>();
377	duarte	219	count=0;
378			while (rsst.next()) {
379			count++;
380			int dbId = rsst.getInt(1);
381			int res1 = rsst.getInt(2);
382			int res2 = rsst.getInt(3);
383			int res3 = rsst.getInt(4);
384			int res4 = rsst.getInt(5);
385	duarte	222	ArrayList<Integer> residues = new ArrayList<Integer>();
386			if (res1!=0) residues.add(res1); // res is 0 when the field is NULL in database
387			if (res2!=0) residues.add(res2);
388			if (res3!=0) residues.add(res3);
389			if (res4!=0) residues.add(res4);
390	duarte	219	turns.put(dbId, residues);
391			}
392			rsst.close();
393			stmt.close();
394			int serial=1;
395			for (int dbId:turns.keySet()){
396	stehr	274	String ssId = "" + SecStrucElement.TURN + serial;
397	duarte	222	int beg = Collections.min(turns.get(dbId));
398			int end = Collections.max(turns.get(dbId));
399	stehr	274	SecStrucElement ssElem = new SecStrucElement(SecStrucElement.TURN,beg,end,ssId);
400			secondaryStructure.add(ssElem);
401	duarte	219	serial++;
402			}
403
404			}
405	duarte	207	}