aglappe-jung/proteinstructure/PdbasePdb.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.regex.Matcher;
import java.util.regex.Pattern;

import javax.vecmath.Point3d;

import tools.MySQLConnection;

/**
 * A single chain pdb protein structure loaded from a PDBASE database
 * See http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/guides/PDBase.html to know what PDBASE is
 * 
 * @author              Jose Duarte
 * Class:               PdbasePdb
 * Package:             proteinstructure
 */
public class PdbasePdb 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_PDBASE_DB="pdbase";

        private MySQLConnection conn;
        
        private int entrykey;
        private String asymid;
        private int entitykey;
        private String alt_locs_sql_str;

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

        /**
         * Constructs Pdb object given pdb code, pdb chain code, source db and a MySQLConnection 
         * Model will be DEFAULT_MODEL
         * The db must be a pdbase database
         * @param pdbCode
         * @param pdbChainCode
         * @param db
         * @param conn
         * @throws PdbaseInconsistencyError
         * @throws PdbCodeNotFoundError 
         * @throws SQLException 
         * @throws PdbChainCodeNotFoundError 
         */
        public PdbasePdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
                this(pdbCode,pdbChainCode,DEFAULT_MODEL,db, conn);              
        }

        /**
         * Constructs Pdb object given pdb code, pdb chain code and model serial.
         * MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
         * Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
         * @param pdbCode
         * @param pdbChainCode
         * @param model_serial
         * @throws PdbaseInconsistencyError
         * @throws PdbCodeNotFoundError
         * @throws SQLException
         * @throws PdbChainCodeNotFoundError 
         */
        public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
                this(pdbCode, pdbChainCode, model_serial, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
        }
        
        /**
         * Constructs Pdb object given pdb code, pdb chain code, model serial, source db and a MySQLConnection.
         * The db must be a pdbase database 
         * @param pdbCode
         * @param pdbChainCode
         * @param model_serial
         * @param db
         * @param conn
         * @throws PdbaseInconsistencyError
         * @throws PdbCodeNotFoundError 
         * @throws SQLException 
         * @throws PdbChainCodeNotFoundError 
         */
        public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
                this.pdbCode=pdbCode.toLowerCase();                             // our convention: pdb codes are lower case
                //NOTE:a case sensitive pdb_strand_id can be mapped to more than one asym_ids!!!!!!!!!!
                this.pdbChainCode=pdbChainCode;                                 // NOTE! pdb chain code are case sensitive!
                this.model=model_serial;
                this.db=db;
                
                this.conn = conn;
        this.entrykey=get_entry_key();
        this.asymid=get_asym_id();              // sets asymid and chainCode
        this.entitykey=get_entity_key();
        this.alt_locs_sql_str=get_atom_alt_locs();
                
                this.sequence = read_seq();
                this.fullLength = sequence.length();
                
                this.pdbresser2resser = get_ressers_mapping();
    
                this.read_atomData(); // populates resser_atom2atomserial, resser2restype, atomser2coord, atomser2resser

                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("Pdbase");
                }
                
                // 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 int get_entry_key() throws PdbCodeNotFoundError, SQLException {
                String sql="SELECT entry_key FROM "+db+".struct WHERE entry_id='"+pdbCode.toUpperCase()+"'";
                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                if (rsst.next()) {
                        entrykey = rsst.getInt(1);
                        if (! rsst.isLast()) {
                                //System.err.println("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                                throw new PdbCodeNotFoundError("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);                                     
                        }
                } else {
                        //System.err.println("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                        throw new PdbCodeNotFoundError("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
                }
                rsst.close();
                stmt.close();
                return entrykey;
        }
        
        private String get_asym_id() throws PdbChainCodeNotFoundError, SQLException {
                String pdbstrandid=pdbChainCode;
                if (pdbChainCode.equals(NULL_CHAIN_CODE)){
                        pdbstrandid="A";
                }
                // NOTE: 'limit 1' not really needed since there can be only one asym_id
                // per entry_key,pdb_strand_id combination (pdb_strand_id case sensitive!)
                String sql="SELECT asym_id " +
                                " FROM "+db+".pdbx_poly_seq_scheme " +
                                " WHERE entry_key=" + entrykey +
                                " AND pdb_strand_id='"+pdbstrandid+"' " +
                                " LIMIT 1";

                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                if (rsst.next()) {
                        asymid = rsst.getString(1);
                } else {
                        //System.err.println("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
                        throw new PdbChainCodeNotFoundError("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
                }
                rsst.close();
                stmt.close();
                // we set the internal chain identifier chainCode from asymid
                chainCode = asymid;
                return asymid;  
        }
        
        // NOTE: Entity key not really needed since there can be only one entity_key
        // per entry_key,asym_id combination 
        private int get_entity_key() throws PdbaseInconsistencyError, SQLException {
                String sql="SELECT entity_key " +
                                " FROM "+db+".struct_asym " +
                                " WHERE entry_key="+ entrykey +
                                " AND id='"+asymid+"'";

                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                if (rsst.next()) {
                        entitykey = rsst.getInt(1);
                        if (! rsst.isLast()) {
                                //System.err.println("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
                                throw new PdbaseInconsistencyError("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);                                 
                        }
                } else {
                        //System.err.println("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
                        throw new PdbaseInconsistencyError("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
                }
                rsst.close();
                stmt.close();
                return entitykey;
        }
        
        private String get_atom_alt_locs() throws PdbaseInconsistencyError, SQLException{
                ArrayList<String> alt_ids = new ArrayList<String>();
                HashMap<String,Integer> alt_ids2keys = new HashMap<String,Integer>();
                String alt_loc_field="label_alt_key";
                String sql="SELECT id, atom_sites_alt_key FROM "+db+".atom_sites_alt WHERE entry_key="+entrykey;

                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                int count=0;
                while (rsst.next()) {
                        count++;
                        alt_ids.add(rsst.getString(1));
                        alt_ids2keys.put(rsst.getString(1), rsst.getInt(2));
                }
                if (count!=0){
                        if ((! alt_ids.contains(".")) || alt_ids.indexOf(".")!=alt_ids.lastIndexOf(".")){ // second term is a way of finding out if there is more than 1 ocurrence of "." in the ArrayList 
                                //System.err.println("alt_codes exist for entry_key "+entrykey+" but there is either no default value '.' or more than 1 '.'. Something wrong with this entry_key or with "+DEFAULT_PDBASE_DB+" db!");
                                throw new PdbaseInconsistencyError("alt_codes exist for entry_key "+entrykey+" but there is either no default value '.' or more than 1 '.'. Something wrong with this entry_key or with "+DEFAULT_PDBASE_DB+" db!");
                        }
                        alt_ids.remove(".");
                        Collections.sort(alt_ids);
                        String lowest_alt_id = alt_ids.get(0);
                        alt_locs_sql_str = "("+alt_loc_field+"="+alt_ids2keys.get(".")+" OR "+alt_loc_field+"="+alt_ids2keys.get(lowest_alt_id)+")";
                } else {
                        alt_locs_sql_str=alt_loc_field+" IS NULL";
                } 

                rsst.close();
                stmt.close();

                return alt_locs_sql_str;
        }
        
        private void read_atomData() throws PdbaseInconsistencyError, SQLException{
                resser_atom2atomserial = new HashMap<String,Integer>();
                resser2restype = new HashMap<Integer,String>();
                atomser2coord = new HashMap<Integer,Point3d>();
                atomser2resser = new HashMap<Integer,Integer>();

                // NOTE: label_entity_key not really needed since there can be only one entity_key
                // per entry_key,asym_id combination
                String sql = "SELECT id, label_atom_id, label_comp_id, label_seq_id, Cartn_x, Cartn_y, Cartn_z " +
                                " FROM "+db+".atom_site " +
                                " WHERE entry_key="+entrykey +
                                " AND label_asym_id='"+asymid+"' " +
                                " AND label_entity_key="+ entitykey +
                                " AND model_num="+ model +
                                " AND "+alt_locs_sql_str;

                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){
                        throw new PdbaseInconsistencyError("atom data query returned no data at all for entry_key="+entrykey+", asym_id="+asymid+", entity_key="+entitykey+", model_num="+model+", alt_locs_sql_str='"+alt_locs_sql_str+"'");
                }
                rsst.close();
                stmt.close();
        }
        
        private String read_seq() throws PdbaseInconsistencyError, SQLException{
                String sequence="";

        // we use seq_id+0 (implicitly converts to int) in ORDER BY because seq_id is varchar!!
        String sql="SELECT mon_id" +
                        " FROM "+db+".pdbx_poly_seq_scheme " +
                        " WHERE entry_key=" + entrykey +
                        " AND asym_id='"+asymid+"' " +
                        " ORDER BY seq_id+0";

        Statement stmt = conn.createStatement();
        ResultSet rsst = stmt.executeQuery(sql);
        int count=0;
        while (rsst.next()) {
                count++;
                String res_type = rsst.getString(1);
                if (AAinfo.isValidAA(res_type)){
                        sequence+=AAinfo.threeletter2oneletter(res_type);
                } else {
                        sequence+=NONSTANDARD_AA_LETTER;
                }
        } 
        if (count==0) {
                //System.err.println("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
                throw new PdbaseInconsistencyError("No sequence data match for entry_key="+entrykey+", asym_id="+asymid);
        }
        rsst.close();
        stmt.close();

                return sequence;
        }
        
        private HashMap<String,Integer> get_ressers_mapping() throws PdbaseInconsistencyError, SQLException{
                String pdbstrandid=pdbChainCode;
                if (pdbChainCode.equals(NULL_CHAIN_CODE)){
                        pdbstrandid="A";
                }

                HashMap<String,Integer> map = new HashMap<String, Integer>();
                String sql="SELECT seq_id, concat(pdb_seq_num,IF(pdb_ins_code='.','',pdb_ins_code))" +
                                        " FROM "+db+".pdbx_poly_seq_scheme " +
                                        " WHERE entry_key=" + entrykey +
                                        " AND asym_id='"+asymid+"' " +
                                        " AND pdb_strand_id='"+pdbstrandid+"' " +
                                        " ORDER BY seq_id+0";

                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                int count=0;
                while (rsst.next()) {
                        count++;
                        int resser = Integer.parseInt(rsst.getString(1));
                        String pdbresser = rsst.getString(2);
                        map.put(pdbresser, resser);
                } 
                if (count==0) {
                        //System.err.println("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
                        throw new PdbaseInconsistencyError("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
                }
                rsst.close();
                stmt.close();

                return map;
        }

        private void readSecStructure() throws SQLException {
                this.secondaryStructure = new SecondaryStructure();
                
                // HELIX AND TURN -- struct_conf table
                String sql = "SELECT id,beg_label_seq_id,end_label_seq_id " +
                                " FROM "+db+".struct_conf " +
                                " WHERE entry_key="+entrykey+
                                " AND beg_label_asym_id='"+asymid+"'";
                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                int count=0;
                while (rsst.next()) {
                        count++;
                        String id = rsst.getString(1).trim(); // id is either HELIX_Pnn or TURN_Pnn
                        Pattern p = Pattern.compile("^(\\w).+_P(\\d)+$");
                        Matcher m = p.matcher(id);
                        String ssId="Unknown";
                        if (m.find()){
                                ssId = m.group(1)+m.group(2); // e.g.: Hnn (helices) or Tnn (turns)                             
                        }
                        int beg = rsst.getInt(2);
                        int end =rsst.getInt(3);
                        char ssType = SecStrucElement.OTHER;
                        if(id.startsWith("H")) {
                                ssType = SecStrucElement.HELIX;
                        } else if(id.startsWith("T")) {
                                ssType = SecStrucElement.TURN;
                        } else {
                                System.err.println("Unknown secondary structure type " + id + " encountered when reading from Pdbase. Skipping.");
                        }
                        if(ssType != SecStrucElement.OTHER) {
                                SecStrucElement ssElem = new SecStrucElement(ssType, beg, end, ssId);
                                secondaryStructure.add(ssElem);
                        }
                } 
                rsst.close();
                stmt.close();
                
                // SHEET -- struct_sheet_range table
                sql = "SELECT sheet_id, id, beg_label_seq_id, end_label_seq_id " +
                                " FROM "+db+".struct_sheet_range " +
                                " WHERE entry_key="+entrykey+
                                " AND beg_label_asym_id='"+asymid+"'";
                stmt = conn.createStatement();
                rsst = stmt.executeQuery(sql);
                count=0;
                while (rsst.next()) {
                        count++;
                        String sheetid = rsst.getString(1).trim();
                        int id = rsst.getInt(2);
                        int beg = rsst.getInt(3);
                        int end =rsst.getInt(4);
                        String ssId=SecStrucElement.STRAND+sheetid+id; // e.g.: SA1, SA2..., SB1, SB2,...
                        SecStrucElement ssElem = new SecStrucElement(SecStrucElement.STRAND, beg, end, ssId);
                        secondaryStructure.add(ssElem);
                } 
                rsst.close();
                stmt.close();

        }
}
Revision:	419
Committed:	Thu Nov 22 14:09:18 2007 UTC (16 years, 11 months ago) by duarte
File size:	15966 byte(s)
Log Message:	Re-branching for JUNG2 development
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.Collections;
8			import java.util.HashMap;
9	duarte	219	import java.util.regex.Matcher;
10			import java.util.regex.Pattern;
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 PDBASE database
18			* See http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/guides/PDBase.html to know what PDBASE is
19			*
20			* @author Jose Duarte
21			* Class: PdbasePdb
22			* Package: proteinstructure
23			*/
24			public class PdbasePdb 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_PDBASE_DB="pdbase";
30
31			private MySQLConnection conn;
32
33			private int entrykey;
34			private String asymid;
35			private int entitykey;
36			private String alt_locs_sql_str;
37
38			/**
39			* Constructs Pdb object given pdb code and pdb chain code.
40			* Model will be DEFAULT_MODEL
41			* MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
42			* Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
43			* @param pdbCode
44			* @param pdbChainCode
45			* @throws PdbaseInconsistencyError
46	stehr	215	* @throws PdbCodeNotFoundError
47	duarte	207	* @throws SQLException
48	stehr	215	* @throws PdbChainCodeNotFoundError
49	duarte	207	*/
50	stehr	215	public PdbasePdb (String pdbCode, String pdbChainCode) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
51	duarte	207	this(pdbCode, pdbChainCode, DEFAULT_MODEL, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
52			}
53
54			/**
55			* Constructs Pdb object given pdb code, pdb chain code, source db and a MySQLConnection
56			* Model will be DEFAULT_MODEL
57			* The db must be a pdbase database
58			* @param pdbCode
59			* @param pdbChainCode
60			* @param db
61			* @param conn
62			* @throws PdbaseInconsistencyError
63	stehr	215	* @throws PdbCodeNotFoundError
64	duarte	210	* @throws SQLException
65	stehr	215	* @throws PdbChainCodeNotFoundError
66	duarte	207	*/
67	stehr	215	public PdbasePdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
68	duarte	207	this(pdbCode,pdbChainCode,DEFAULT_MODEL,db, conn);
69			}
70
71			/**
72			* Constructs Pdb object given pdb code, pdb chain code and model serial.
73			* MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
74			* Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
75			* @param pdbCode
76			* @param pdbChainCode
77			* @param model_serial
78			* @throws PdbaseInconsistencyError
79	stehr	215	* @throws PdbCodeNotFoundError
80	duarte	207	* @throws SQLException
81	stehr	215	* @throws PdbChainCodeNotFoundError
82	duarte	207	*/
83	stehr	215	public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
84	duarte	207	this(pdbCode, pdbChainCode, model_serial, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
85			}
86
87			/**
88			* Constructs Pdb object given pdb code, pdb chain code, model serial, source db and a MySQLConnection.
89			* The db must be a pdbase database
90			* @param pdbCode
91			* @param pdbChainCode
92			* @param model_serial
93			* @param db
94			* @param conn
95			* @throws PdbaseInconsistencyError
96	stehr	215	* @throws PdbCodeNotFoundError
97	duarte	210	* @throws SQLException
98	stehr	215	* @throws PdbChainCodeNotFoundError
99	duarte	207	*/
100	stehr	215	public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
101	stehr	217	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
102	duarte	401	//NOTE:a case sensitive pdb_strand_id can be mapped to more than one asym_ids!!!!!!!!!!
103			this.pdbChainCode=pdbChainCode; // NOTE! pdb chain code are case sensitive!
104	duarte	207	this.model=model_serial;
105			this.db=db;
106
107			this.conn = conn;
108			this.entrykey=get_entry_key();
109			this.asymid=get_asym_id(); // sets asymid and chainCode
110			this.entitykey=get_entity_key();
111			this.alt_locs_sql_str=get_atom_alt_locs();
112
113			this.sequence = read_seq();
114	duarte	278	this.fullLength = sequence.length();
115
116	duarte	207	this.pdbresser2resser = get_ressers_mapping();
117
118			this.read_atomData(); // populates resser_atom2atomserial, resser2restype, atomser2coord, atomser2resser
119
120	duarte	278	this.obsLength = resser2restype.size();
121
122	duarte	207	// we initialise resser2pdbresser from the pdbresser2resser HashMap
123			this.resser2pdbresser = new HashMap<Integer, String>();
124			for (String pdbresser:pdbresser2resser.keySet()){
125			resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
126			}
127	duarte	219
128	stehr	274	secondaryStructure = new SecondaryStructure(); // create empty secondary structure first to make sure object is not null
129	duarte	219	readSecStructure();
130	stehr	274	if(!secondaryStructure.isEmpty()) {
131			secondaryStructure.setComment("Pdbase");
132	stehr	259	}
133	duarte	237
134			// initialising atomser2atom from resser_atom2atomserial
135			atomser2atom = new HashMap<Integer, String>();
136			for (String resser_atom:resser_atom2atomserial.keySet()){
137			int atomserial = resser_atom2atomserial.get(resser_atom);
138			String atom = resser_atom.split("_")[1];
139			atomser2atom.put(atomserial,atom);
140			}
141	duarte	207	}
142
143	stehr	215	private int get_entry_key() throws PdbCodeNotFoundError, SQLException {
144	duarte	207	String sql="SELECT entry_key FROM "+db+".struct WHERE entry_id='"+pdbCode.toUpperCase()+"'";
145	duarte	210	Statement stmt = conn.createStatement();
146			ResultSet rsst = stmt.executeQuery(sql);
147			if (rsst.next()) {
148			entrykey = rsst.getInt(1);
149			if (! rsst.isLast()) {
150	stehr	215	//System.err.println("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
151			throw new PdbCodeNotFoundError("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
152	duarte	207	}
153	duarte	210	} else {
154	stehr	215	//System.err.println("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
155			throw new PdbCodeNotFoundError("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
156	duarte	207	}
157	duarte	210	rsst.close();
158			stmt.close();
159	duarte	207	return entrykey;
160			}
161
162	stehr	215	private String get_asym_id() throws PdbChainCodeNotFoundError, SQLException {
163	duarte	207	String pdbstrandid=pdbChainCode;
164	stehr	336	if (pdbChainCode.equals(NULL_CHAIN_CODE)){
165	duarte	207	pdbstrandid="A";
166			}
167	filippis	400	// NOTE: 'limit 1' not really needed since there can be only one asym_id
168			// per entry_key,pdb_strand_id combination (pdb_strand_id case sensitive!)
169	duarte	207	String sql="SELECT asym_id " +
170			" FROM "+db+".pdbx_poly_seq_scheme " +
171			" WHERE entry_key=" + entrykey +
172			" AND pdb_strand_id='"+pdbstrandid+"' " +
173			" LIMIT 1";
174	duarte	210
175			Statement stmt = conn.createStatement();
176			ResultSet rsst = stmt.executeQuery(sql);
177			if (rsst.next()) {
178			asymid = rsst.getString(1);
179			} else {
180	stehr	215	//System.err.println("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
181			throw new PdbChainCodeNotFoundError("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
182	duarte	207	}
183	duarte	210	rsst.close();
184			stmt.close();
185	duarte	207	// we set the internal chain identifier chainCode from asymid
186			chainCode = asymid;
187			return asymid;
188			}
189
190	filippis	400	// NOTE: Entity key not really needed since there can be only one entity_key
191			// per entry_key,asym_id combination
192	duarte	210	private int get_entity_key() throws PdbaseInconsistencyError, SQLException {
193	duarte	207	String sql="SELECT entity_key " +
194			" FROM "+db+".struct_asym " +
195			" WHERE entry_key="+ entrykey +
196			" AND id='"+asymid+"'";
197	duarte	210
198			Statement stmt = conn.createStatement();
199			ResultSet rsst = stmt.executeQuery(sql);
200			if (rsst.next()) {
201			entitykey = rsst.getInt(1);
202			if (! rsst.isLast()) {
203	stehr	215	//System.err.println("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
204	duarte	210	throw new PdbaseInconsistencyError("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
205	duarte	207	}
206	duarte	210	} else {
207	stehr	215	//System.err.println("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
208	duarte	210	throw new PdbaseInconsistencyError("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
209	duarte	207	}
210	duarte	210	rsst.close();
211			stmt.close();
212	duarte	207	return entitykey;
213			}
214
215	duarte	210	private String get_atom_alt_locs() throws PdbaseInconsistencyError, SQLException{
216	duarte	207	ArrayList<String> alt_ids = new ArrayList<String>();
217			HashMap<String,Integer> alt_ids2keys = new HashMap<String,Integer>();
218			String alt_loc_field="label_alt_key";
219			String sql="SELECT id, atom_sites_alt_key FROM "+db+".atom_sites_alt WHERE entry_key="+entrykey;
220
221	duarte	210	Statement stmt = conn.createStatement();
222			ResultSet rsst = stmt.executeQuery(sql);
223			int count=0;
224			while (rsst.next()) {
225			count++;
226			alt_ids.add(rsst.getString(1));
227			alt_ids2keys.put(rsst.getString(1), rsst.getInt(2));
228	duarte	207	}
229	duarte	210	if (count!=0){
230			if ((! alt_ids.contains(".")) \|\| alt_ids.indexOf(".")!=alt_ids.lastIndexOf(".")){ // second term is a way of finding out if there is more than 1 ocurrence of "." in the ArrayList
231	stehr	215	//System.err.println("alt_codes exist for entry_key "+entrykey+" but there is either no default value '.' or more than 1 '.'. Something wrong with this entry_key or with "+DEFAULT_PDBASE_DB+" db!");
232	duarte	210	throw new PdbaseInconsistencyError("alt_codes exist for entry_key "+entrykey+" but there is either no default value '.' or more than 1 '.'. Something wrong with this entry_key or with "+DEFAULT_PDBASE_DB+" db!");
233			}
234			alt_ids.remove(".");
235			Collections.sort(alt_ids);
236			String lowest_alt_id = alt_ids.get(0);
237			alt_locs_sql_str = "("+alt_loc_field+"="+alt_ids2keys.get(".")+" OR "+alt_loc_field+"="+alt_ids2keys.get(lowest_alt_id)+")";
238			} else {
239			alt_locs_sql_str=alt_loc_field+" IS NULL";
240			}
241
242			rsst.close();
243			stmt.close();
244
245	duarte	207	return alt_locs_sql_str;
246			}
247
248	duarte	210	private void read_atomData() throws PdbaseInconsistencyError, SQLException{
249	duarte	207	resser_atom2atomserial = new HashMap<String,Integer>();
250			resser2restype = new HashMap<Integer,String>();
251	duarte	226	atomser2coord = new HashMap<Integer,Point3d>();
252	duarte	207	atomser2resser = new HashMap<Integer,Integer>();
253
254	filippis	400	// NOTE: label_entity_key not really needed since there can be only one entity_key
255			// per entry_key,asym_id combination
256	duarte	207	String sql = "SELECT id, label_atom_id, label_comp_id, label_seq_id, Cartn_x, Cartn_y, Cartn_z " +
257			" FROM "+db+".atom_site " +
258			" WHERE entry_key="+entrykey +
259			" AND label_asym_id='"+asymid+"' " +
260			" AND label_entity_key="+ entitykey +
261			" AND model_num="+ model +
262			" AND "+alt_locs_sql_str;
263
264	duarte	210	Statement stmt = conn.createStatement();
265			ResultSet rsst = stmt.executeQuery(sql);
266			int count=0;
267			while (rsst.next()){
268			count++;
269
270			int atomserial = rsst.getInt(1); // atomserial
271			String atom = rsst.getString(2).trim(); // atom
272			String res_type = rsst.getString(3).trim(); // res_type
273			int res_serial = rsst.getInt(4); // res_serial
274			double x = rsst.getDouble(5); // x
275			double y = rsst.getDouble(6); // y
276			double z = rsst.getDouble(7); // z
277	duarte	226	Point3d coords = new Point3d(x, y, z);
278	duarte	326	if (AAinfo.isValidAA(res_type)) {
279	duarte	210	atomser2coord.put(atomserial, coords);
280			atomser2resser.put(atomserial, res_serial);
281			resser2restype.put(res_serial, res_type);
282	duarte	326	if (AAinfo.isValidAtomWithOXT(res_type,atom)){
283	duarte	210	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
284	duarte	207	}
285			}
286	duarte	210
287	duarte	207	}
288	duarte	210	if (count==0){
289			throw new PdbaseInconsistencyError("atom data query returned no data at all for entry_key="+entrykey+", asym_id="+asymid+", entity_key="+entitykey+", model_num="+model+", alt_locs_sql_str='"+alt_locs_sql_str+"'");
290			}
291			rsst.close();
292			stmt.close();
293	duarte	207	}
294
295	duarte	210	private String read_seq() throws PdbaseInconsistencyError, SQLException{
296	duarte	207	String sequence="";
297	filippis	400
298	duarte	207	// we use seq_id+0 (implicitly converts to int) in ORDER BY because seq_id is varchar!!
299			String sql="SELECT mon_id" +
300			" FROM "+db+".pdbx_poly_seq_scheme " +
301			" WHERE entry_key=" + entrykey +
302			" AND asym_id='"+asymid+"' " +
303			" ORDER BY seq_id+0";
304
305	duarte	210	Statement stmt = conn.createStatement();
306			ResultSet rsst = stmt.executeQuery(sql);
307			int count=0;
308			while (rsst.next()) {
309			count++;
310			String res_type = rsst.getString(1);
311	duarte	326	if (AAinfo.isValidAA(res_type)){
312			sequence+=AAinfo.threeletter2oneletter(res_type);
313	duarte	210	} else {
314			sequence+=NONSTANDARD_AA_LETTER;
315			}
316			}
317			if (count==0) {
318	stehr	215	//System.err.println("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
319	filippis	400	throw new PdbaseInconsistencyError("No sequence data match for entry_key="+entrykey+", asym_id="+asymid);
320	duarte	210	}
321			rsst.close();
322			stmt.close();
323
324	duarte	207	return sequence;
325			}
326
327	duarte	210	private HashMap<String,Integer> get_ressers_mapping() throws PdbaseInconsistencyError, SQLException{
328	duarte	207	String pdbstrandid=pdbChainCode;
329	stehr	336	if (pdbChainCode.equals(NULL_CHAIN_CODE)){
330	duarte	207	pdbstrandid="A";
331			}
332
333			HashMap<String,Integer> map = new HashMap<String, Integer>();
334	filippis	400	String sql="SELECT seq_id, concat(pdb_seq_num,IF(pdb_ins_code='.','',pdb_ins_code))" +
335	duarte	207	" FROM "+db+".pdbx_poly_seq_scheme " +
336			" WHERE entry_key=" + entrykey +
337			" AND asym_id='"+asymid+"' " +
338			" AND pdb_strand_id='"+pdbstrandid+"' " +
339			" ORDER BY seq_id+0";
340	duarte	210
341			Statement stmt = conn.createStatement();
342			ResultSet rsst = stmt.executeQuery(sql);
343			int count=0;
344			while (rsst.next()) {
345			count++;
346			int resser = Integer.parseInt(rsst.getString(1));
347			String pdbresser = rsst.getString(2);
348			map.put(pdbresser, resser);
349			}
350			if (count==0) {
351	stehr	215	//System.err.println("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
352	duarte	210	throw new PdbaseInconsistencyError("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
353	duarte	207	}
354	duarte	210	rsst.close();
355			stmt.close();
356	duarte	207
357			return map;
358			}
359
360	duarte	219	private void readSecStructure() throws SQLException {
361	stehr	274	this.secondaryStructure = new SecondaryStructure();
362	duarte	219
363			// HELIX AND TURN -- struct_conf table
364			String sql = "SELECT id,beg_label_seq_id,end_label_seq_id " +
365			" FROM "+db+".struct_conf " +
366			" WHERE entry_key="+entrykey+
367			" AND beg_label_asym_id='"+asymid+"'";
368			Statement stmt = conn.createStatement();
369			ResultSet rsst = stmt.executeQuery(sql);
370			int count=0;
371			while (rsst.next()) {
372			count++;
373			String id = rsst.getString(1).trim(); // id is either HELIX_Pnn or TURN_Pnn
374			Pattern p = Pattern.compile("^(\\w).+_P(\\d)+$");
375			Matcher m = p.matcher(id);
376			String ssId="Unknown";
377			if (m.find()){
378			ssId = m.group(1)+m.group(2); // e.g.: Hnn (helices) or Tnn (turns)
379			}
380			int beg = rsst.getInt(2);
381			int end =rsst.getInt(3);
382	stehr	274	char ssType = SecStrucElement.OTHER;
383			if(id.startsWith("H")) {
384			ssType = SecStrucElement.HELIX;
385			} else if(id.startsWith("T")) {
386			ssType = SecStrucElement.TURN;
387			} else {
388			System.err.println("Unknown secondary structure type " + id + " encountered when reading from Pdbase. Skipping.");
389	duarte	219	}
390	stehr	274	if(ssType != SecStrucElement.OTHER) {
391			SecStrucElement ssElem = new SecStrucElement(ssType, beg, end, ssId);
392			secondaryStructure.add(ssElem);
393			}
394	duarte	219	}
395			rsst.close();
396			stmt.close();
397
398			// SHEET -- struct_sheet_range table
399			sql = "SELECT sheet_id, id, beg_label_seq_id, end_label_seq_id " +
400			" FROM "+db+".struct_sheet_range " +
401			" WHERE entry_key="+entrykey+
402			" AND beg_label_asym_id='"+asymid+"'";
403			stmt = conn.createStatement();
404			rsst = stmt.executeQuery(sql);
405			count=0;
406			while (rsst.next()) {
407			count++;
408			String sheetid = rsst.getString(1).trim();
409			int id = rsst.getInt(2);
410			int beg = rsst.getInt(3);
411			int end =rsst.getInt(4);
412	stehr	274	String ssId=SecStrucElement.STRAND+sheetid+id; // e.g.: SA1, SA2..., SB1, SB2,...
413			SecStrucElement ssElem = new SecStrucElement(SecStrucElement.STRAND, beg, end, ssId);
414			secondaryStructure.add(ssElem);
415	duarte	219	}
416			rsst.close();
417			stmt.close();
418
419			}
420	duarte	207	}