trunk/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
                this.pdbChainCode=pdbChainCode.toUpperCase();   // our convention: chain codes are upper case
                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")){
                        pdbstrandid="A";
                }
                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;  
        }
        
        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>();

                
                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="";
                String pdbstrandid=pdbChainCode;
                if (pdbChainCode.equals("NULL")){
                        pdbstrandid="A";
                }
        // 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+"' " +
                        " 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++;
                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+", pdb_strand_id="+pdbstrandid);
        }
        rsst.close();
        stmt.close();

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

                HashMap<String,Integer> map = new HashMap<String, Integer>();
                //TODO revise: do we want auth_seq_num or pdb_seq_num here??
                String sql="SELECT seq_id, concat(auth_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+"' " +
                                        " AND auth_seq_num!='?'" +
                                        " 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:	326
Committed:	Thu Sep 20 14:49:55 2007 UTC (17 years, 1 month ago) by duarte
File size:	15753 byte(s)
Log Message:	Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
Line	File contents
1	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	import java.util.regex.Matcher;
10	import java.util.regex.Pattern;
11
12	import javax.vecmath.Point3d;
13
14	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	* @throws PdbCodeNotFoundError
47	* @throws SQLException
48	* @throws PdbChainCodeNotFoundError
49	*/
50	public PdbasePdb (String pdbCode, String pdbChainCode) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
51	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	* @throws PdbCodeNotFoundError
64	* @throws SQLException
65	* @throws PdbChainCodeNotFoundError
66	*/
67	public PdbasePdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
68	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	* @throws PdbCodeNotFoundError
80	* @throws SQLException
81	* @throws PdbChainCodeNotFoundError
82	*/
83	public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
84	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	* @throws PdbCodeNotFoundError
97	* @throws SQLException
98	* @throws PdbChainCodeNotFoundError
99	*/
100	public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
101	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
102	this.pdbChainCode=pdbChainCode.toUpperCase(); // our convention: chain codes are upper case
103	this.model=model_serial;
104	this.db=db;
105
106	this.conn = conn;
107	this.entrykey=get_entry_key();
108	this.asymid=get_asym_id(); // sets asymid and chainCode
109	this.entitykey=get_entity_key();
110	this.alt_locs_sql_str=get_atom_alt_locs();
111
112	this.sequence = read_seq();
113	this.fullLength = sequence.length();
114
115	this.pdbresser2resser = get_ressers_mapping();
116
117	this.read_atomData(); // populates resser_atom2atomserial, resser2restype, atomser2coord, atomser2resser
118
119	this.obsLength = resser2restype.size();
120
121	// 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
127	secondaryStructure = new SecondaryStructure(); // create empty secondary structure first to make sure object is not null
128	readSecStructure();
129	if(!secondaryStructure.isEmpty()) {
130	secondaryStructure.setComment("Pdbase");
131	}
132
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	}
141
142	private int get_entry_key() throws PdbCodeNotFoundError, SQLException {
143	String sql="SELECT entry_key FROM "+db+".struct WHERE entry_id='"+pdbCode.toUpperCase()+"'";
144	Statement stmt = conn.createStatement();
145	ResultSet rsst = stmt.executeQuery(sql);
146	if (rsst.next()) {
147	entrykey = rsst.getInt(1);
148	if (! rsst.isLast()) {
149	//System.err.println("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
150	throw new PdbCodeNotFoundError("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
151	}
152	} else {
153	//System.err.println("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
154	throw new PdbCodeNotFoundError("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
155	}
156	rsst.close();
157	stmt.close();
158	return entrykey;
159	}
160
161	private String get_asym_id() throws PdbChainCodeNotFoundError, SQLException {
162	String pdbstrandid=pdbChainCode;
163	if (pdbChainCode.equals("NULL")){
164	pdbstrandid="A";
165	}
166	String sql="SELECT asym_id " +
167	" FROM "+db+".pdbx_poly_seq_scheme " +
168	" WHERE entry_key=" + entrykey +
169	" AND pdb_strand_id='"+pdbstrandid+"' " +
170	" LIMIT 1";
171
172	Statement stmt = conn.createStatement();
173	ResultSet rsst = stmt.executeQuery(sql);
174	if (rsst.next()) {
175	asymid = rsst.getString(1);
176	} else {
177	//System.err.println("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
178	throw new PdbChainCodeNotFoundError("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
179	}
180	rsst.close();
181	stmt.close();
182	// we set the internal chain identifier chainCode from asymid
183	chainCode = asymid;
184	return asymid;
185	}
186
187	private int get_entity_key() throws PdbaseInconsistencyError, SQLException {
188	String sql="SELECT entity_key " +
189	" FROM "+db+".struct_asym " +
190	" WHERE entry_key="+ entrykey +
191	" AND id='"+asymid+"'";
192
193	Statement stmt = conn.createStatement();
194	ResultSet rsst = stmt.executeQuery(sql);
195	if (rsst.next()) {
196	entitykey = rsst.getInt(1);
197	if (! rsst.isLast()) {
198	//System.err.println("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
199	throw new PdbaseInconsistencyError("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
200	}
201	} else {
202	//System.err.println("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
203	throw new PdbaseInconsistencyError("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
204	}
205	rsst.close();
206	stmt.close();
207	return entitykey;
208	}
209
210	private String get_atom_alt_locs() throws PdbaseInconsistencyError, SQLException{
211	ArrayList<String> alt_ids = new ArrayList<String>();
212	HashMap<String,Integer> alt_ids2keys = new HashMap<String,Integer>();
213	String alt_loc_field="label_alt_key";
214	String sql="SELECT id, atom_sites_alt_key FROM "+db+".atom_sites_alt WHERE entry_key="+entrykey;
215
216	Statement stmt = conn.createStatement();
217	ResultSet rsst = stmt.executeQuery(sql);
218	int count=0;
219	while (rsst.next()) {
220	count++;
221	alt_ids.add(rsst.getString(1));
222	alt_ids2keys.put(rsst.getString(1), rsst.getInt(2));
223	}
224	if (count!=0){
225	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
226	//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!");
227	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!");
228	}
229	alt_ids.remove(".");
230	Collections.sort(alt_ids);
231	String lowest_alt_id = alt_ids.get(0);
232	alt_locs_sql_str = "("+alt_loc_field+"="+alt_ids2keys.get(".")+" OR "+alt_loc_field+"="+alt_ids2keys.get(lowest_alt_id)+")";
233	} else {
234	alt_locs_sql_str=alt_loc_field+" IS NULL";
235	}
236
237	rsst.close();
238	stmt.close();
239
240	return alt_locs_sql_str;
241	}
242
243	private void read_atomData() throws PdbaseInconsistencyError, SQLException{
244	resser_atom2atomserial = new HashMap<String,Integer>();
245	resser2restype = new HashMap<Integer,String>();
246	atomser2coord = new HashMap<Integer,Point3d>();
247	atomser2resser = new HashMap<Integer,Integer>();
248
249
250	String sql = "SELECT id, label_atom_id, label_comp_id, label_seq_id, Cartn_x, Cartn_y, Cartn_z " +
251	" FROM "+db+".atom_site " +
252	" WHERE entry_key="+entrykey +
253	" AND label_asym_id='"+asymid+"' " +
254	" AND label_entity_key="+ entitykey +
255	" AND model_num="+ model +
256	" AND "+alt_locs_sql_str;
257
258	Statement stmt = conn.createStatement();
259	ResultSet rsst = stmt.executeQuery(sql);
260	int count=0;
261	while (rsst.next()){
262	count++;
263
264	int atomserial = rsst.getInt(1); // atomserial
265	String atom = rsst.getString(2).trim(); // atom
266	String res_type = rsst.getString(3).trim(); // res_type
267	int res_serial = rsst.getInt(4); // res_serial
268	double x = rsst.getDouble(5); // x
269	double y = rsst.getDouble(6); // y
270	double z = rsst.getDouble(7); // z
271	Point3d coords = new Point3d(x, y, z);
272	if (AAinfo.isValidAA(res_type)) {
273	atomser2coord.put(atomserial, coords);
274	atomser2resser.put(atomserial, res_serial);
275	resser2restype.put(res_serial, res_type);
276	if (AAinfo.isValidAtomWithOXT(res_type,atom)){
277	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
278	}
279	}
280
281	}
282	if (count==0){
283	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+"'");
284	}
285	rsst.close();
286	stmt.close();
287	}
288
289	private String read_seq() throws PdbaseInconsistencyError, SQLException{
290	String sequence="";
291	String pdbstrandid=pdbChainCode;
292	if (pdbChainCode.equals("NULL")){
293	pdbstrandid="A";
294	}
295	// we use seq_id+0 (implicitly converts to int) in ORDER BY because seq_id is varchar!!
296	String sql="SELECT mon_id" +
297	" FROM "+db+".pdbx_poly_seq_scheme " +
298	" WHERE entry_key=" + entrykey +
299	" AND asym_id='"+asymid+"' " +
300	" AND pdb_strand_id='"+pdbstrandid+"' " +
301	" ORDER BY seq_id+0";
302
303	Statement stmt = conn.createStatement();
304	ResultSet rsst = stmt.executeQuery(sql);
305	int count=0;
306	while (rsst.next()) {
307	count++;
308	String res_type = rsst.getString(1);
309	if (AAinfo.isValidAA(res_type)){
310	sequence+=AAinfo.threeletter2oneletter(res_type);
311	} else {
312	sequence+=NONSTANDARD_AA_LETTER;
313	}
314	}
315	if (count==0) {
316	//System.err.println("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
317	throw new PdbaseInconsistencyError("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
318	}
319	rsst.close();
320	stmt.close();
321
322	return sequence;
323	}
324
325	private HashMap<String,Integer> get_ressers_mapping() throws PdbaseInconsistencyError, SQLException{
326	String pdbstrandid=pdbChainCode;
327	if (pdbChainCode.equals("NULL")){
328	pdbstrandid="A";
329	}
330
331	HashMap<String,Integer> map = new HashMap<String, Integer>();
332	//TODO revise: do we want auth_seq_num or pdb_seq_num here??
333	String sql="SELECT seq_id, concat(auth_seq_num,IF(pdb_ins_code='.','',pdb_ins_code))" +
334	" FROM "+db+".pdbx_poly_seq_scheme " +
335	" WHERE entry_key=" + entrykey +
336	" AND asym_id='"+asymid+"' " +
337	" AND pdb_strand_id='"+pdbstrandid+"' " +
338	" AND auth_seq_num!='?'" +
339	" ORDER BY seq_id+0";
340
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	//System.err.println("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
352	throw new PdbaseInconsistencyError("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
353	}
354	rsst.close();
355	stmt.close();
356
357	return map;
358	}
359
360	private void readSecStructure() throws SQLException {
361	this.secondaryStructure = new SecondaryStructure();
362
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	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	}
390	if(ssType != SecStrucElement.OTHER) {
391	SecStrucElement ssElem = new SecStrucElement(ssType, beg, end, ssId);
392	secondaryStructure.add(ssElem);
393	}
394	}
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	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	}
416	rsst.close();
417	stmt.close();
418
419	}
420	}