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.TreeMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

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.chainCode = getChainCode();
                this.sequence = read_seq();
                this.pdbresser2resser = get_ressers_mapping();
    
                this.read_atomData(); // populates resser_atom2atomserial, resser2restype, atomser2coord, atomser2resser

                // we initialise resser2pdbresser from the pdbresser2resser HashMap
                this.resser2pdbresser = new HashMap<Integer, String>();
                for (String pdbresser:pdbresser2resser.keySet()){
                        resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
                }
                
                readSecStructure();
        }

        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,Double[]>();
                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
                        Double[] coords = {x, y, z};
                        ArrayList<String> aalist=AA.aas();
                        if (aalist.contains(res_type)) {
                                atomser2coord.put(atomserial, coords);
                                atomser2resser.put(atomserial, res_serial);
                                resser2restype.put(res_serial, res_type);
                                ArrayList<String> atomlist = aas2atoms.get(res_type);
                                if (atomlist.contains(atom)){
                                        resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
                                }
                        }

                }
                if (count==0){
                        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);
        ArrayList<String> aalist=AA.aas();
        int count=0;
        while (rsst.next()) {
                count++;
                String res_type = rsst.getString(1);
                if (aalist.contains(res_type)){
                        sequence+=AA.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>();
                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.resser2secstruct = new HashMap<Integer, String>();
                this.secstruct2resinterval = new TreeMap<String, Interval>();
                
                // 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);
                        secstruct2resinterval.put(ssId, new Interval(beg,end));
                        for (int i=beg;i<=end;i++){
                                if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
                                        System.err.println("Inconsistency in secondary structure assignment. " +
                                                        "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
                                }
                                resser2secstruct.put(i,ssId);
                        }
                } 
                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="S"+sheetid+id; // e.g.: SA1, SA2..., SB1, SB2,...
                        secstruct2resinterval.put(ssId, new Interval(beg,end));
                        for (int i=beg;i<=end;i++){
                                if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
                                        System.err.println("Inconsistency in secondary structure assignment. " +
                                                        "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
                                }
                                resser2secstruct.put(i,ssId); 
                        }
                } 
                rsst.close();
                stmt.close();

        }
}
Revision:	222
Committed:	Wed Jul 4 15:39:01 2007 UTC (17 years, 3 months ago) by duarte
File size:	15481 byte(s)
Log Message:	New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals New class Interval
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.TreeMap;
10	import java.util.regex.Matcher;
11	import java.util.regex.Pattern;
12
13	import tools.MySQLConnection;
14
15	/**
16	* A single chain pdb protein structure loaded from a PDBASE database
17	* See http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/guides/PDBase.html to know what PDBASE is
18	*
19	* @author Jose Duarte
20	* Class: PdbasePdb
21	* Package: proteinstructure
22	*/
23	public class PdbasePdb extends Pdb {
24
25	private final static String MYSQLSERVER="white";
26	private final static String MYSQLUSER=MySQLConnection.getUserName();
27	private final static String MYSQLPWD="nieve";
28	private final static String DEFAULT_PDBASE_DB="pdbase";
29
30	private MySQLConnection conn;
31
32	private int entrykey;
33	private String asymid;
34	private int entitykey;
35	private String alt_locs_sql_str;
36
37	/**
38	* Constructs Pdb object given pdb code and pdb chain code.
39	* Model will be DEFAULT_MODEL
40	* MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
41	* Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
42	* @param pdbCode
43	* @param pdbChainCode
44	* @throws PdbaseInconsistencyError
45	* @throws PdbCodeNotFoundError
46	* @throws SQLException
47	* @throws PdbChainCodeNotFoundError
48	*/
49	public PdbasePdb (String pdbCode, String pdbChainCode) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
50	this(pdbCode, pdbChainCode, DEFAULT_MODEL, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
51	}
52
53	/**
54	* Constructs Pdb object given pdb code, pdb chain code, source db and a MySQLConnection
55	* Model will be DEFAULT_MODEL
56	* The db must be a pdbase database
57	* @param pdbCode
58	* @param pdbChainCode
59	* @param db
60	* @param conn
61	* @throws PdbaseInconsistencyError
62	* @throws PdbCodeNotFoundError
63	* @throws SQLException
64	* @throws PdbChainCodeNotFoundError
65	*/
66	public PdbasePdb (String pdbCode, String pdbChainCode, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
67	this(pdbCode,pdbChainCode,DEFAULT_MODEL,db, conn);
68	}
69
70	/**
71	* Constructs Pdb object given pdb code, pdb chain code and model serial.
72	* MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
73	* Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
74	* @param pdbCode
75	* @param pdbChainCode
76	* @param model_serial
77	* @throws PdbaseInconsistencyError
78	* @throws PdbCodeNotFoundError
79	* @throws SQLException
80	* @throws PdbChainCodeNotFoundError
81	*/
82	public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
83	this(pdbCode, pdbChainCode, model_serial, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
84	}
85
86	/**
87	* Constructs Pdb object given pdb code, pdb chain code, model serial, source db and a MySQLConnection.
88	* The db must be a pdbase database
89	* @param pdbCode
90	* @param pdbChainCode
91	* @param model_serial
92	* @param db
93	* @param conn
94	* @throws PdbaseInconsistencyError
95	* @throws PdbCodeNotFoundError
96	* @throws SQLException
97	* @throws PdbChainCodeNotFoundError
98	*/
99	public PdbasePdb (String pdbCode, String pdbChainCode, int model_serial, String db, MySQLConnection conn) throws PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError {
100	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
101	this.pdbChainCode=pdbChainCode.toUpperCase(); // our convention: chain codes are upper case
102	this.model=model_serial;
103	this.db=db;
104
105	this.conn = conn;
106	this.entrykey=get_entry_key();
107	this.asymid=get_asym_id(); // sets asymid and chainCode
108	this.entitykey=get_entity_key();
109	this.alt_locs_sql_str=get_atom_alt_locs();
110
111	this.chainCode = getChainCode();
112	this.sequence = read_seq();
113	this.pdbresser2resser = get_ressers_mapping();
114
115	this.read_atomData(); // populates resser_atom2atomserial, resser2restype, atomser2coord, atomser2resser
116
117	// we initialise resser2pdbresser from the pdbresser2resser HashMap
118	this.resser2pdbresser = new HashMap<Integer, String>();
119	for (String pdbresser:pdbresser2resser.keySet()){
120	resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
121	}
122
123	readSecStructure();
124	}
125
126	private int get_entry_key() throws PdbCodeNotFoundError, SQLException {
127	String sql="SELECT entry_key FROM "+db+".struct WHERE entry_id='"+pdbCode.toUpperCase()+"'";
128	Statement stmt = conn.createStatement();
129	ResultSet rsst = stmt.executeQuery(sql);
130	if (rsst.next()) {
131	entrykey = rsst.getInt(1);
132	if (! rsst.isLast()) {
133	//System.err.println("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
134	throw new PdbCodeNotFoundError("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
135	}
136	} else {
137	//System.err.println("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
138	throw new PdbCodeNotFoundError("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
139	}
140	rsst.close();
141	stmt.close();
142	return entrykey;
143	}
144
145	private String get_asym_id() throws PdbChainCodeNotFoundError, SQLException {
146	String pdbstrandid=pdbChainCode;
147	if (pdbChainCode.equals("NULL")){
148	pdbstrandid="A";
149	}
150	String sql="SELECT asym_id " +
151	" FROM "+db+".pdbx_poly_seq_scheme " +
152	" WHERE entry_key=" + entrykey +
153	" AND pdb_strand_id='"+pdbstrandid+"' " +
154	" LIMIT 1";
155
156	Statement stmt = conn.createStatement();
157	ResultSet rsst = stmt.executeQuery(sql);
158	if (rsst.next()) {
159	asymid = rsst.getString(1);
160	} else {
161	//System.err.println("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
162	throw new PdbChainCodeNotFoundError("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
163	}
164	rsst.close();
165	stmt.close();
166	// we set the internal chain identifier chainCode from asymid
167	chainCode = asymid;
168	return asymid;
169	}
170
171	private int get_entity_key() throws PdbaseInconsistencyError, SQLException {
172	String sql="SELECT entity_key " +
173	" FROM "+db+".struct_asym " +
174	" WHERE entry_key="+ entrykey +
175	" AND id='"+asymid+"'";
176
177	Statement stmt = conn.createStatement();
178	ResultSet rsst = stmt.executeQuery(sql);
179	if (rsst.next()) {
180	entitykey = rsst.getInt(1);
181	if (! rsst.isLast()) {
182	//System.err.println("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
183	throw new PdbaseInconsistencyError("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
184	}
185	} else {
186	//System.err.println("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
187	throw new PdbaseInconsistencyError("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
188	}
189	rsst.close();
190	stmt.close();
191	return entitykey;
192	}
193
194	private String get_atom_alt_locs() throws PdbaseInconsistencyError, SQLException{
195	ArrayList<String> alt_ids = new ArrayList<String>();
196	HashMap<String,Integer> alt_ids2keys = new HashMap<String,Integer>();
197	String alt_loc_field="label_alt_key";
198	String sql="SELECT id, atom_sites_alt_key FROM "+db+".atom_sites_alt WHERE entry_key="+entrykey;
199
200	Statement stmt = conn.createStatement();
201	ResultSet rsst = stmt.executeQuery(sql);
202	int count=0;
203	while (rsst.next()) {
204	count++;
205	alt_ids.add(rsst.getString(1));
206	alt_ids2keys.put(rsst.getString(1), rsst.getInt(2));
207	}
208	if (count!=0){
209	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
210	//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!");
211	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!");
212	}
213	alt_ids.remove(".");
214	Collections.sort(alt_ids);
215	String lowest_alt_id = alt_ids.get(0);
216	alt_locs_sql_str = "("+alt_loc_field+"="+alt_ids2keys.get(".")+" OR "+alt_loc_field+"="+alt_ids2keys.get(lowest_alt_id)+")";
217	} else {
218	alt_locs_sql_str=alt_loc_field+" IS NULL";
219	}
220
221	rsst.close();
222	stmt.close();
223
224	return alt_locs_sql_str;
225	}
226
227	private void read_atomData() throws PdbaseInconsistencyError, SQLException{
228	resser_atom2atomserial = new HashMap<String,Integer>();
229	resser2restype = new HashMap<Integer,String>();
230	atomser2coord = new HashMap<Integer,Double[]>();
231	atomser2resser = new HashMap<Integer,Integer>();
232
233
234	String sql = "SELECT id, label_atom_id, label_comp_id, label_seq_id, Cartn_x, Cartn_y, Cartn_z " +
235	" FROM "+db+".atom_site " +
236	" WHERE entry_key="+entrykey +
237	" AND label_asym_id='"+asymid+"' " +
238	" AND label_entity_key="+ entitykey +
239	" AND model_num="+ model +
240	" AND "+alt_locs_sql_str;
241
242	Statement stmt = conn.createStatement();
243	ResultSet rsst = stmt.executeQuery(sql);
244	int count=0;
245	while (rsst.next()){
246	count++;
247
248	int atomserial = rsst.getInt(1); // atomserial
249	String atom = rsst.getString(2).trim(); // atom
250	String res_type = rsst.getString(3).trim(); // res_type
251	int res_serial = rsst.getInt(4); // res_serial
252	double x = rsst.getDouble(5); // x
253	double y = rsst.getDouble(6); // y
254	double z = rsst.getDouble(7); // z
255	Double[] coords = {x, y, z};
256	ArrayList<String> aalist=AA.aas();
257	if (aalist.contains(res_type)) {
258	atomser2coord.put(atomserial, coords);
259	atomser2resser.put(atomserial, res_serial);
260	resser2restype.put(res_serial, res_type);
261	ArrayList<String> atomlist = aas2atoms.get(res_type);
262	if (atomlist.contains(atom)){
263	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
264	}
265	}
266
267	}
268	if (count==0){
269	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+"'");
270	}
271	rsst.close();
272	stmt.close();
273	}
274
275	private String read_seq() throws PdbaseInconsistencyError, SQLException{
276	String sequence="";
277	String pdbstrandid=pdbChainCode;
278	if (pdbChainCode.equals("NULL")){
279	pdbstrandid="A";
280	}
281	// we use seq_id+0 (implicitly converts to int) in ORDER BY because seq_id is varchar!!
282	String sql="SELECT mon_id" +
283	" FROM "+db+".pdbx_poly_seq_scheme " +
284	" WHERE entry_key=" + entrykey +
285	" AND asym_id='"+asymid+"' " +
286	" AND pdb_strand_id='"+pdbstrandid+"' " +
287	" ORDER BY seq_id+0";
288
289	Statement stmt = conn.createStatement();
290	ResultSet rsst = stmt.executeQuery(sql);
291	ArrayList<String> aalist=AA.aas();
292	int count=0;
293	while (rsst.next()) {
294	count++;
295	String res_type = rsst.getString(1);
296	if (aalist.contains(res_type)){
297	sequence+=AA.threeletter2oneletter(res_type);
298	} else {
299	sequence+=NONSTANDARD_AA_LETTER;
300	}
301	}
302	if (count==0) {
303	//System.err.println("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
304	throw new PdbaseInconsistencyError("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
305	}
306	rsst.close();
307	stmt.close();
308
309	return sequence;
310	}
311
312	private HashMap<String,Integer> get_ressers_mapping() throws PdbaseInconsistencyError, SQLException{
313	String pdbstrandid=pdbChainCode;
314	if (pdbChainCode.equals("NULL")){
315	pdbstrandid="A";
316	}
317
318	HashMap<String,Integer> map = new HashMap<String, Integer>();
319	String sql="SELECT seq_id, concat(auth_seq_num,IF(pdb_ins_code='.','',pdb_ins_code))" +
320	" FROM "+db+".pdbx_poly_seq_scheme " +
321	" WHERE entry_key=" + entrykey +
322	" AND asym_id='"+asymid+"' " +
323	" AND pdb_strand_id='"+pdbstrandid+"' " +
324	" AND auth_seq_num!='?'" +
325	" ORDER BY seq_id+0";
326
327	Statement stmt = conn.createStatement();
328	ResultSet rsst = stmt.executeQuery(sql);
329	int count=0;
330	while (rsst.next()) {
331	count++;
332	int resser = Integer.parseInt(rsst.getString(1));
333	String pdbresser = rsst.getString(2);
334	map.put(pdbresser, resser);
335	}
336	if (count==0) {
337	//System.err.println("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
338	throw new PdbaseInconsistencyError("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
339	}
340	rsst.close();
341	stmt.close();
342
343	return map;
344	}
345
346	private void readSecStructure() throws SQLException {
347	this.resser2secstruct = new HashMap<Integer, String>();
348	this.secstruct2resinterval = new TreeMap<String, Interval>();
349
350	// HELIX AND TURN -- struct_conf table
351	String sql = "SELECT id,beg_label_seq_id,end_label_seq_id " +
352	" FROM "+db+".struct_conf " +
353	" WHERE entry_key="+entrykey+
354	" AND beg_label_asym_id='"+asymid+"'";
355	Statement stmt = conn.createStatement();
356	ResultSet rsst = stmt.executeQuery(sql);
357	int count=0;
358	while (rsst.next()) {
359	count++;
360	String id = rsst.getString(1).trim(); // id is either HELIX_Pnn or TURN_Pnn
361	Pattern p = Pattern.compile("^(\\w).+_P(\\d)+$");
362	Matcher m = p.matcher(id);
363	String ssId="Unknown";
364	if (m.find()){
365	ssId = m.group(1)+m.group(2); // e.g.: Hnn (helices) or Tnn (turns)
366	}
367	int beg = rsst.getInt(2);
368	int end =rsst.getInt(3);
369	secstruct2resinterval.put(ssId, new Interval(beg,end));
370	for (int i=beg;i<=end;i++){
371	if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
372	System.err.println("Inconsistency in secondary structure assignment. " +
373	"Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
374	}
375	resser2secstruct.put(i,ssId);
376	}
377	}
378	rsst.close();
379	stmt.close();
380
381	// SHEET -- struct_sheet_range table
382	sql = "SELECT sheet_id, id, beg_label_seq_id, end_label_seq_id " +
383	" FROM "+db+".struct_sheet_range " +
384	" WHERE entry_key="+entrykey+
385	" AND beg_label_asym_id='"+asymid+"'";
386	stmt = conn.createStatement();
387	rsst = stmt.executeQuery(sql);
388	count=0;
389	while (rsst.next()) {
390	count++;
391	String sheetid = rsst.getString(1).trim();
392	int id = rsst.getInt(2);
393	int beg = rsst.getInt(3);
394	int end =rsst.getInt(4);
395	String ssId="S"+sheetid+id; // e.g.: SA1, SA2..., SB1, SB2,...
396	secstruct2resinterval.put(ssId, new Interval(beg,end));
397	for (int i=beg;i<=end;i++){
398	if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
399	System.err.println("Inconsistency in secondary structure assignment. " +
400	"Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
401	}
402	resser2secstruct.put(i,ssId);
403	}
404	}
405	rsst.close();
406	stmt.close();
407
408	}
409	}