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 java.util.TreeSet;

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 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 an empty Pdb object given pdb code 
         * Data will be loaded from database upon call of load(pdbChainCode, modelSerial)  
         * 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
         * @throws SQLException 
         */
        public MsdsdPdb (String pdbCode) throws SQLException {
                this(pdbCode,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));             
        }

        /**
         * Constructs an empty Pdb object given pdb code, a source db and a MySQLConnection.
         * Data will be loaded from database upon call of load(pdbChainCode, modelSerial) 
         * @param pdbCode
         * @param db a msdsd database
         * @param conn
         */
        public MsdsdPdb (String pdbCode, String db, MySQLConnection conn) {
                this.pdbCode=pdbCode.toLowerCase();                             // our convention: pdb codes are lower case
                this.db=db;
                this.myMsdsdDb="my_"+db;  // i.e. for db=msdsd_00_07_a then myMsdsdDb=my_msdsd_00_07_a
                this.dataLoaded = false;

                this.conn = conn;
                
        }

        public void load(String pdbChainCode, int modelSerial) throws PdbLoadError {
                this.model = modelSerial;
                this.pdbChainCode=pdbChainCode; // NOTE! pdb chain codes are case sensitive!
                try {
                        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);
                        }
                        
                        dataLoaded = true;
                        
                } catch (PdbCodeNotFoundError e) {
                        throw new PdbLoadError(e);
                } catch (SQLException e) {
                        throw new PdbLoadError(e);
                } catch (MsdsdInconsistentResidueNumbersError e) {
                        throw new PdbLoadError(e);
                }
                
        }
        
        public String[] getChains()     throws PdbLoadError {
                TreeSet<String> chains = new TreeSet<String>();
                try {
                        String sql = "SELECT DISTINCT chain_pdb_code " + // the DISTINCT is because there can be a multi model entry
                        " FROM "+myMsdsdDb+".mmol_chain_info " +
                        " WHERE accession_code='"+pdbCode+"' " +
                        " AND chain_type='C' " +
                        " AND asu_chain=1 ";
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                String chain = rsst.getString(1);
                                if (chain==null) chain="NULL";
                                chains.add(chain);
                        }
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        throw new PdbLoadError(e);
                }
                
                if (chains.isEmpty()) return null;
                
                String[] chainsArray = new String[chains.size()];
                chains.toArray(chainsArray);
                return chainsArray;
        }
        
        public Integer[] getModels() throws PdbLoadError {
                TreeSet<Integer> models = new TreeSet<Integer>();
                try {
                        String sql = "SELECT DISTINCT model_serial " +
                        " FROM "+myMsdsdDb+".mmol_chain_info " +
                        " WHERE accession_code='"+pdbCode+"' " +
                        " AND chain_type='C' " +
                        " AND asu_chain=1 ";
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                models.add(rsst.getInt(1));
                        }
                        rsst.close();
                        stmt.close();
        
                } catch (SQLException e) {
                        throw new PdbLoadError(e);
                }
                
                if (models.isEmpty()) return null;              
                Integer[] modelsArray = new Integer[models.size()];
                models.toArray(modelsArray);
                return modelsArray;
        }
        
        private void getchainid() throws PdbCodeNotFoundError, SQLException {
                chainid=0;
                String chaincodestr="='"+pdbChainCode+"'";
                if (pdbChainCode.equals(Pdb.NULL_CHAIN_CODE)){
                        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);
                        if (AAinfo.isValidAA(res_type)) {
                                atomser2coord.put(atomserial, coords);
                                atomser2resser.put(atomserial, res_serial);
                                resser2restype.put(res_serial, res_type);
                                if (AAinfo.isValidAtomWithOXT(res_type,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:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 9 months ago) by duarte
File size:	14582 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
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	441	import java.util.TreeSet;
11	duarte	207
12	duarte	226	import javax.vecmath.Point3d;
13
14	duarte	207	import tools.MySQLConnection;
15
16			/**
17			* A single chain pdb protein structure loaded from a MSDSD database
18			* See http://www.ebi.ac.uk/msd-srv/docs/dbdoc/refaindex.html to know what MSDSD is
19			*
20			* @author Jose Duarte
21			* Class: MsdsdPdb
22			* Package: proteinstructure
23			*/
24			public class MsdsdPdb extends Pdb {
25
26			private final static String MYSQLSERVER="white";
27			private final static String MYSQLUSER=MySQLConnection.getUserName();
28			private final static String MYSQLPWD="nieve";
29			//private final static String DEFAULT_MYMSDSD_DB="my_msdsd_00_07_a";
30			private final static String DEFAULT_MSDSD_DB="msdsd_00_07_a";
31
32			private MySQLConnection conn;
33
34			private int chainid;
35			private int modelid;
36
37	duarte	441	// TODO for this to be used by other people we need to do things without a myMsdsdDb (or also distribute our fixes database)
38	duarte	207	private String myMsdsdDb; // our database with add-ons and fixes to msdsd
39
40			/**
41	duarte	441	* Constructs an empty Pdb object given pdb code
42			* Data will be loaded from database upon call of load(pdbChainCode, modelSerial)
43	duarte	207	* MySQLConnection is taken from defaults in MsdsdPdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
44			* Database is taken from default msdsd database in MsdsdPdb class: DEFAULT_MSDSD_DB
45			* @param pdbCode
46			* @throws SQLException
47			*/
48	duarte	441	public MsdsdPdb (String pdbCode) throws SQLException {
49			this(pdbCode,DEFAULT_MSDSD_DB,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
50	duarte	207	}
51
52			/**
53	duarte	441	* Constructs an empty Pdb object given pdb code, a source db and a MySQLConnection.
54			* Data will be loaded from database upon call of load(pdbChainCode, modelSerial)
55	duarte	207	* @param pdbCode
56	duarte	441	* @param db a msdsd database
57	duarte	207	* @param conn
58			*/
59	duarte	441	public MsdsdPdb (String pdbCode, String db, MySQLConnection conn) {
60	stehr	217	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
61	duarte	207	this.db=db;
62			this.myMsdsdDb="my_"+db; // i.e. for db=msdsd_00_07_a then myMsdsdDb=my_msdsd_00_07_a
63	duarte	441	this.dataLoaded = false;
64	duarte	207
65			this.conn = conn;
66
67	duarte	441	}
68	duarte	207
69	duarte	441	public void load(String pdbChainCode, int modelSerial) throws PdbLoadError {
70			this.model = modelSerial;
71			this.pdbChainCode=pdbChainCode; // NOTE! pdb chain codes are case sensitive!
72			try {
73			this.getchainid();// initialises chainid, modelid and chainCode
74
75			if (check_inconsistent_res_numbering()){
76			throw new MsdsdInconsistentResidueNumbersError("Inconsistent residue numbering in msdsd for accession_code "+this.pdbCode+", chain_pdb_code "+this.pdbChainCode);
77			}
78
79			this.sequence = read_seq();
80			this.fullLength = sequence.length();
81
82			this.pdbresser2resser = get_ressers_mapping();
83
84			this.read_atomData();
85
86			this.obsLength = resser2restype.size();
87
88			// we initialise resser2pdbresser from the pdbresser2resser HashMap
89			this.resser2pdbresser = new HashMap<Integer, String>();
90			for (String pdbresser:pdbresser2resser.keySet()){
91			resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
92			}
93
94			secondaryStructure = new SecondaryStructure(); // create empty secondary structure first to make sure object is not null
95			readSecStructure();
96			if(!secondaryStructure.isEmpty()) {
97			secondaryStructure.setComment("MSDSD");
98			}
99
100			// initialising atomser2atom from resser_atom2atomserial
101			atomser2atom = new HashMap<Integer, String>();
102			for (String resser_atom:resser_atom2atomserial.keySet()){
103			int atomserial = resser_atom2atomserial.get(resser_atom);
104			String atom = resser_atom.split("_")[1];
105			atomser2atom.put(atomserial,atom);
106			}
107
108			dataLoaded = true;
109
110			} catch (PdbCodeNotFoundError e) {
111			throw new PdbLoadError(e);
112			} catch (SQLException e) {
113			throw new PdbLoadError(e);
114			} catch (MsdsdInconsistentResidueNumbersError e) {
115			throw new PdbLoadError(e);
116			}
117	duarte	207
118	duarte	441	}
119
120	stehr	470	public String[] getChains() throws PdbLoadError {
121	duarte	441	TreeSet<String> chains = new TreeSet<String>();
122			try {
123			String sql = "SELECT DISTINCT chain_pdb_code " + // the DISTINCT is because there can be a multi model entry
124			" FROM "+myMsdsdDb+".mmol_chain_info " +
125			" WHERE accession_code='"+pdbCode+"' " +
126			" AND chain_type='C' " +
127			" AND asu_chain=1 ";
128			Statement stmt = conn.createStatement();
129			ResultSet rsst = stmt.executeQuery(sql);
130			while (rsst.next()) {
131			String chain = rsst.getString(1);
132			if (chain==null) chain="NULL";
133			chains.add(chain);
134			}
135			rsst.close();
136			stmt.close();
137			} catch (SQLException e) {
138	stehr	470	throw new PdbLoadError(e);
139	duarte	207	}
140	duarte	219
141	duarte	441	if (chains.isEmpty()) return null;
142
143			String[] chainsArray = new String[chains.size()];
144			chains.toArray(chainsArray);
145			return chainsArray;
146			}
147
148	stehr	470	public Integer[] getModels() throws PdbLoadError {
149	duarte	441	TreeSet<Integer> models = new TreeSet<Integer>();
150			try {
151			String sql = "SELECT DISTINCT model_serial " +
152			" FROM "+myMsdsdDb+".mmol_chain_info " +
153			" WHERE accession_code='"+pdbCode+"' " +
154			" AND chain_type='C' " +
155			" AND asu_chain=1 ";
156			Statement stmt = conn.createStatement();
157			ResultSet rsst = stmt.executeQuery(sql);
158			while (rsst.next()) {
159			models.add(rsst.getInt(1));
160			}
161			rsst.close();
162			stmt.close();
163
164			} catch (SQLException e) {
165	stehr	470	throw new PdbLoadError(e);
166	stehr	259	}
167	duarte	237
168	duarte	441	if (models.isEmpty()) return null;
169			Integer[] modelsArray = new Integer[models.size()];
170			models.toArray(modelsArray);
171			return modelsArray;
172	duarte	207	}
173	duarte	441
174	stehr	215	private void getchainid() throws PdbCodeNotFoundError, SQLException {
175	duarte	207	chainid=0;
176			String chaincodestr="='"+pdbChainCode+"'";
177	stehr	336	if (pdbChainCode.equals(Pdb.NULL_CHAIN_CODE)){
178	duarte	207	chaincodestr="IS NULL";
179			}
180			String sql = "SELECT chain_id, model_id, pchain_code " +
181			" FROM "+myMsdsdDb+".mmol_chain_info " +
182			" WHERE accession_code='"+pdbCode+"' " +
183			" AND chain_pdb_code "+chaincodestr +
184			" AND chain_type='C' " +
185			" AND asu_chain=1 " +
186			" AND model_serial="+model;
187
188	duarte	210	Statement stmt = conn.createStatement();
189			ResultSet rsst = stmt.executeQuery(sql);
190			if (rsst.next()) {
191			chainid = rsst.getInt(1);
192			modelid = rsst.getInt(2);
193			chainCode=rsst.getString(3);
194			if (! rsst.isLast()) {
195	stehr	215	//System.err.println("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
196			throw new PdbCodeNotFoundError("More than 1 chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
197	duarte	210	}
198			} else {
199	stehr	215	//System.err.println("No chain_id match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
200			throw new PdbCodeNotFoundError("No chain_id could be matched for accession_code "+pdbCode+", chain_pdb_code "+pdbChainCode);
201	duarte	210	}
202			rsst.close();
203			stmt.close();
204	duarte	207	}
205
206	duarte	210	private boolean check_inconsistent_res_numbering() throws SQLException{
207	duarte	207	int count=0;
208			int numserial=0;
209	duarte	210
210			String sql="SELECT count(*) " +
211			" FROM "+myMsdsdDb+".problem_serial_chain " +
212			" WHERE chain_id="+chainid +
213			" AND (min_serial!=1 OR num_serial!=num_dist_serial OR num_serial!=max_serial-min_serial+1)";
214			Statement stmt = conn.createStatement();
215			ResultSet rsst = stmt.executeQuery(sql);
216			while (rsst.next()) {
217			count = rsst.getInt(1);
218			if (count>0){
219	duarte	207	return true;
220			}
221			}
222	duarte	210	sql="SELECT num_serial FROM "+myMsdsdDb+".problem_serial_chain WHERE chain_id="+chainid;
223			rsst = stmt.executeQuery(sql);
224			int check = 0;
225			while (rsst.next()){
226			check++;
227			numserial=rsst.getInt(1);
228			}
229			if (check!=1){
230			System.err.println("No num_serial match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
231			}
232			String allresseq = read_seq();
233			if (allresseq.length()!=numserial){
234			System.err.println("num_serial and length of all_res_seq don't match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
235			return true;
236			}
237			rsst.close();
238			stmt.close();
239	duarte	207	return false;
240			}
241
242	duarte	210	private void read_atomData() throws SQLException{
243	duarte	207	resser_atom2atomserial = new HashMap<String,Integer>();
244			resser2restype = new HashMap<Integer,String>();
245	duarte	226	atomser2coord = new HashMap<Integer,Point3d>();
246	duarte	207	atomser2resser = new HashMap<Integer,Integer>();
247
248			String sql = "SELECT serial,chem_atom_name,code_3_letter,residue_serial,x,y,z " +
249			" FROM "+db+".atom_data " +
250			" WHERE (model_id = "+modelid+") " +
251			" AND (chain_id = "+chainid+") " +
252			" AND (graph_alt_code_used = 1) " +
253			" AND (graph_standard_aa=1) " +
254			" AND (pdb_group = 'A')" +
255			" ORDER BY chain_code, residue_serial, serial";
256
257	duarte	210	Statement stmt = conn.createStatement();
258			ResultSet rsst = stmt.executeQuery(sql);
259			int count=0;
260			while (rsst.next()){
261			count++;
262
263			int atomserial = rsst.getInt(1); // atomserial
264			String atom = rsst.getString(2).trim(); // atom
265			String res_type = rsst.getString(3).trim(); // res_type
266			int res_serial = rsst.getInt(4); // res_serial
267			double x = rsst.getDouble(5); // x
268			double y = rsst.getDouble(6); // y
269			double z = rsst.getDouble(7); // z
270	duarte	226	Point3d coords = new Point3d(x, y, z);
271	duarte	326	if (AAinfo.isValidAA(res_type)) {
272	duarte	210	atomser2coord.put(atomserial, coords);
273			atomser2resser.put(atomserial, res_serial);
274			resser2restype.put(res_serial, res_type);
275	duarte	326	if (AAinfo.isValidAtomWithOXT(res_type,atom)){
276	duarte	210	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
277			}
278	duarte	207	}
279	duarte	210
280
281	duarte	207	}
282	duarte	210	if (count==0){
283			System.err.println("atom data query returned no data at all for model_id="+modelid+", model_id="+modelid);
284			}
285			rsst.close();
286			stmt.close();
287	duarte	207	}
288
289	duarte	210	private String read_seq() throws SQLException{
290	duarte	207	String allresseq="";
291			String sql="SELECT all_res_seq FROM "+myMsdsdDb+".chain_seq WHERE chain_id="+chainid;
292
293	duarte	210	Statement stmt = conn.createStatement();
294			ResultSet rsst = stmt.executeQuery(sql);
295			int check = 0;
296			if (rsst.next()) {
297			check++;
298			allresseq=rsst.getString(1);
299			}
300			if (check!=1) {
301			System.err.println("No all_res_seq match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", chain_id="+chainid);
302			}
303			rsst.close();
304			stmt.close();
305
306	duarte	207	return allresseq;
307			}
308
309	duarte	210	private HashMap<String,Integer> get_ressers_mapping() throws SQLException {
310	duarte	207	HashMap<String,Integer> map = new HashMap<String, Integer>();
311			String sql="SELECT serial, concat(pdb_seq,IF(pdb_insert_code IS NULL,'',pdb_insert_code)) " +
312			" FROM "+db+".residue " +
313			" WHERE chain_id="+chainid+
314			" AND pdb_seq IS NOT NULL";
315	duarte	210
316			Statement stmt = conn.createStatement();
317			ResultSet rsst = stmt.executeQuery(sql);
318			int count=0;
319			while (rsst.next()) {
320			count++;
321			int resser = rsst.getInt(1);
322			String pdbresser = rsst.getString(2);
323			map.put(pdbresser, resser);
324			}
325			if (count==0) {
326			System.err.println("No residue serials mapping data match for chain_id="+chainid);
327	duarte	207	}
328	duarte	210	rsst.close();
329			stmt.close();
330	duarte	207
331			return map;
332			}
333
334	duarte	219	private void readSecStructure() throws SQLException{
335	stehr	274	this.secondaryStructure = new SecondaryStructure();
336	duarte	219
337			//HELIX -- helix table
338			String sql = "SELECT helix_serial, beg_residue_serial, end_residue_serial " +
339			" FROM "+db+".helix " +
340			" WHERE (model_id = "+modelid+") " +
341			" AND (chain_id = "+chainid+") ";
342			Statement stmt = conn.createStatement();
343			ResultSet rsst = stmt.executeQuery(sql);
344			int count=0;
345			while (rsst.next()) {
346			count++;
347			int serial = rsst.getInt(1);
348			int beg = rsst.getInt(2);
349			int end =rsst.getInt(3);
350	stehr	274	String ssId = "" + SecStrucElement.HELIX+serial;
351			SecStrucElement ssElem = new SecStrucElement(SecStrucElement.HELIX,beg,end,ssId);
352			secondaryStructure.add(ssElem);
353	duarte	219	}
354			rsst.close();
355			stmt.close();
356			//SHEET -- strand table
357			sql = "SELECT sheet_serial, strand_serial, strand_beg_residue_serial, strand_end_residue_serial " +
358			" FROM "+db+".strand " +
359			" WHERE (model_id = "+modelid+") " +
360			" AND (chain_id = "+chainid+") ";
361			stmt = conn.createStatement();
362			rsst = stmt.executeQuery(sql);
363			// we store everything in these 2 maps to assign later to resser2secstruct based on our own ids (ids are not very consistent in msdsd)
364	duarte	222	HashMap<Integer,Interval> strands2begEnd = new HashMap<Integer, Interval>();
365	duarte	219	TreeMap<Integer,ArrayList<Integer>> sheets2strands = new TreeMap<Integer, ArrayList<Integer>>();
366			count=0;
367			while (rsst.next()) {
368			count++;
369			int sheetSerial = rsst.getInt(1);
370			int strandSerial = rsst.getInt(2);
371			int beg = rsst.getInt(3);
372			int end =rsst.getInt(4);
373	duarte	222	strands2begEnd.put(strandSerial, new Interval(beg,end));
374	duarte	219	if (sheets2strands.containsKey(sheetSerial)){
375			sheets2strands.get(sheetSerial).add(strandSerial);
376			} else {
377			ArrayList<Integer> strands = new ArrayList<Integer>();
378			strands.add(strandSerial);
379			sheets2strands.put(sheetSerial, strands);
380			}
381			}
382			rsst.close();
383			stmt.close();
384			char sheet='A';
385			for (int sheetSerial:sheets2strands.keySet()){
386			int strand=1;
387			for (int strandSerial:sheets2strands.get(sheetSerial)){
388	duarte	222	Interval begEnd = strands2begEnd.get(strandSerial);
389	stehr	274	String ssId = ""+SecStrucElement.STRAND+sheet+strand;
390			SecStrucElement ssElem = new SecStrucElement(SecStrucElement.STRAND,begEnd.beg,begEnd.end,ssId);
391			secondaryStructure.add(ssElem);
392	duarte	219	strand++;
393			}
394			sheet++;
395			}
396
397			//TURN -- turn table
398			// 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
399			sql = "SELECT turn_id, res_1_residue_serial, res_2_residue_serial, res_3_residue_serial, res_4_residue_serial " +
400			" FROM "+db+".turn " +
401			" WHERE (model_id = "+modelid+") " +
402			" AND (chain_id = "+chainid+") ";
403			stmt = conn.createStatement();
404			rsst = stmt.executeQuery(sql);
405	duarte	222	TreeMap<Integer,ArrayList<Integer>> turns = new TreeMap<Integer, ArrayList<Integer>>();
406	duarte	219	count=0;
407			while (rsst.next()) {
408			count++;
409			int dbId = rsst.getInt(1);
410			int res1 = rsst.getInt(2);
411			int res2 = rsst.getInt(3);
412			int res3 = rsst.getInt(4);
413			int res4 = rsst.getInt(5);
414	duarte	222	ArrayList<Integer> residues = new ArrayList<Integer>();
415			if (res1!=0) residues.add(res1); // res is 0 when the field is NULL in database
416			if (res2!=0) residues.add(res2);
417			if (res3!=0) residues.add(res3);
418			if (res4!=0) residues.add(res4);
419	duarte	219	turns.put(dbId, residues);
420			}
421			rsst.close();
422			stmt.close();
423			int serial=1;
424			for (int dbId:turns.keySet()){
425	stehr	274	String ssId = "" + SecStrucElement.TURN + serial;
426	duarte	222	int beg = Collections.min(turns.get(dbId));
427			int end = Collections.max(turns.get(dbId));
428	stehr	274	SecStrucElement ssElem = new SecStrucElement(SecStrucElement.TURN,beg,end,ssId);
429			secondaryStructure.add(ssElem);
430	duarte	219	serial++;
431			}
432
433			}
434	duarte	207	}