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.TreeSet;
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 an empty Pdb object given pdb code
         * Data will be loaded from database upon call of load(pdbChainCode, modelSerial)
         * MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
         * Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
         * @param pdbCode
         * @throws SQLException  
         * @throws PdbCodeNotFoundError 
         */
        public PdbasePdb (String pdbCode) throws SQLException, PdbCodeNotFoundError {
                this(pdbCode, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
        }

        /**
         * Constructs an empty Pdb object given pdb code, source db and a MySQLConnection.
         * Data will be loaded from database upon call of load(pdbChainCode, modelSerial)  
         * @param pdbCode
         * @param db a pdbase database
         * @param conn
         * @throws SQLException 
         * @throws PdbCodeNotFoundError 
         */
        public PdbasePdb (String pdbCode, String db, MySQLConnection conn) throws PdbCodeNotFoundError, SQLException  {
                this.pdbCode=pdbCode.toLowerCase();                             // our convention: pdb codes are lower case
                this.db=db;
                this.dataLoaded = false;
                
                this.conn = conn;
                
                // this makes sure that we find the pdb code in the database
                this.entrykey = get_entry_key();
        }

        public void load(String pdbChainCode, int modelSerial) throws PdbLoadError {
                try {
                        this.model = modelSerial;
                        this.pdbChainCode=pdbChainCode;                                 // NOTE! pdb chain code are case sensitive!
                        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);
                        }
                        
                        dataLoaded = true;
                        
                } catch (SQLException e) {
                        throw new PdbLoadError(e);
                } catch (PdbChainCodeNotFoundError e) {
                        throw new PdbLoadError(e);
                } catch (PdbaseInconsistencyError e) {
                        throw new PdbLoadError(e);
                }

        }
        
        public String[] getChains()     throws PdbLoadError {
                TreeSet<String> chains = new TreeSet<String>();
                try {
                        String sql = "SELECT DISTINCT pdb_strand_id FROM "+db+".pdbx_poly_seq_scheme WHERE entry_key="+entrykey;
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                chains.add(rsst.getString(1));
                        }
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        throw new PdbLoadError(e);
                }
                
                if (chains.isEmpty()) return null;
                
                String[] chainsArray = new String[chains.size()];
                chains.toArray(chainsArray);
                return chainsArray;
        }
        
        public Integer[] getModels() throws PdbLoadError {
                TreeSet<Integer> models = new TreeSet<Integer>();
                try {
                        String sql = "SELECT DISTINCT model_num FROM "+db+".atom_site WHERE entry_key="+entrykey;
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                models.add(rsst.getInt(1));
                        }
                        rsst.close();
                        stmt.close();
        
                } catch (SQLException e) {
                        throw new PdbLoadError(e);
                }
                
                if (models.isEmpty()) return null;              
                Integer[] modelsArray = new Integer[models.size()];
                models.toArray(modelsArray);
                return modelsArray;
        }
        
        private 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:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 9 months ago) by duarte
File size:	15840 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
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.TreeSet;
10	import java.util.regex.Matcher;
11	import java.util.regex.Pattern;
12
13	import javax.vecmath.Point3d;
14
15	import tools.MySQLConnection;
16
17	/**
18	* A single chain pdb protein structure loaded from a PDBASE database
19	* See http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/guides/PDBase.html to know what PDBASE is
20	*
21	* @author Jose Duarte
22	* Class: PdbasePdb
23	* Package: proteinstructure
24	*/
25	public class PdbasePdb extends Pdb {
26
27	private final static String MYSQLSERVER="white";
28	private final static String MYSQLUSER=MySQLConnection.getUserName();
29	private final static String MYSQLPWD="nieve";
30	private final static String DEFAULT_PDBASE_DB="pdbase";
31
32	private MySQLConnection conn;
33
34	private int entrykey;
35	private String asymid;
36	private int entitykey;
37	private String alt_locs_sql_str;
38
39	/**
40	* Constructs an empty Pdb object given pdb code
41	* Data will be loaded from database upon call of load(pdbChainCode, modelSerial)
42	* MySQLConnection is taken from defaults in PdbasePdb class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
43	* Database is taken from default pdbase database in PdbasePdb class: DEFAULT_PDBASE_DB
44	* @param pdbCode
45	* @throws SQLException
46	* @throws PdbCodeNotFoundError
47	*/
48	public PdbasePdb (String pdbCode) throws SQLException, PdbCodeNotFoundError {
49	this(pdbCode, DEFAULT_PDBASE_DB, new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD));
50	}
51
52	/**
53	* Constructs an empty Pdb object given pdb code, source db and a MySQLConnection.
54	* Data will be loaded from database upon call of load(pdbChainCode, modelSerial)
55	* @param pdbCode
56	* @param db a pdbase database
57	* @param conn
58	* @throws SQLException
59	* @throws PdbCodeNotFoundError
60	*/
61	public PdbasePdb (String pdbCode, String db, MySQLConnection conn) throws PdbCodeNotFoundError, SQLException {
62	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
63	this.db=db;
64	this.dataLoaded = false;
65
66	this.conn = conn;
67
68	// this makes sure that we find the pdb code in the database
69	this.entrykey = get_entry_key();
70	}
71
72	public void load(String pdbChainCode, int modelSerial) throws PdbLoadError {
73	try {
74	this.model = modelSerial;
75	this.pdbChainCode=pdbChainCode; // NOTE! pdb chain code are case sensitive!
76	this.asymid=get_asym_id(); // sets asymid and chainCode
77	this.entitykey=get_entity_key();
78	this.alt_locs_sql_str=get_atom_alt_locs();
79
80	this.sequence = read_seq();
81	this.fullLength = sequence.length();
82
83	this.pdbresser2resser = get_ressers_mapping();
84
85	this.read_atomData(); // populates resser_atom2atomserial, resser2restype, atomser2coord, atomser2resser
86
87	this.obsLength = resser2restype.size();
88
89	// we initialise resser2pdbresser from the pdbresser2resser HashMap
90	this.resser2pdbresser = new HashMap<Integer, String>();
91	for (String pdbresser:pdbresser2resser.keySet()){
92	resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
93	}
94
95	secondaryStructure = new SecondaryStructure(); // create empty secondary structure first to make sure object is not null
96	readSecStructure();
97	if(!secondaryStructure.isEmpty()) {
98	secondaryStructure.setComment("Pdbase");
99	}
100
101	// initialising atomser2atom from resser_atom2atomserial
102	atomser2atom = new HashMap<Integer, String>();
103	for (String resser_atom:resser_atom2atomserial.keySet()){
104	int atomserial = resser_atom2atomserial.get(resser_atom);
105	String atom = resser_atom.split("_")[1];
106	atomser2atom.put(atomserial,atom);
107	}
108
109	dataLoaded = true;
110
111	} catch (SQLException e) {
112	throw new PdbLoadError(e);
113	} catch (PdbChainCodeNotFoundError e) {
114	throw new PdbLoadError(e);
115	} catch (PdbaseInconsistencyError e) {
116	throw new PdbLoadError(e);
117	}
118
119	}
120
121	public String[] getChains() throws PdbLoadError {
122	TreeSet<String> chains = new TreeSet<String>();
123	try {
124	String sql = "SELECT DISTINCT pdb_strand_id FROM "+db+".pdbx_poly_seq_scheme WHERE entry_key="+entrykey;
125	Statement stmt = conn.createStatement();
126	ResultSet rsst = stmt.executeQuery(sql);
127	while (rsst.next()) {
128	chains.add(rsst.getString(1));
129	}
130	rsst.close();
131	stmt.close();
132	} catch (SQLException e) {
133	throw new PdbLoadError(e);
134	}
135
136	if (chains.isEmpty()) return null;
137
138	String[] chainsArray = new String[chains.size()];
139	chains.toArray(chainsArray);
140	return chainsArray;
141	}
142
143	public Integer[] getModels() throws PdbLoadError {
144	TreeSet<Integer> models = new TreeSet<Integer>();
145	try {
146	String sql = "SELECT DISTINCT model_num FROM "+db+".atom_site WHERE entry_key="+entrykey;
147	Statement stmt = conn.createStatement();
148	ResultSet rsst = stmt.executeQuery(sql);
149	while (rsst.next()) {
150	models.add(rsst.getInt(1));
151	}
152	rsst.close();
153	stmt.close();
154
155	} catch (SQLException e) {
156	throw new PdbLoadError(e);
157	}
158
159	if (models.isEmpty()) return null;
160	Integer[] modelsArray = new Integer[models.size()];
161	models.toArray(modelsArray);
162	return modelsArray;
163	}
164
165	private int get_entry_key() throws PdbCodeNotFoundError, SQLException {
166	String sql="SELECT entry_key FROM "+db+".struct WHERE entry_id='"+pdbCode.toUpperCase()+"'";
167	Statement stmt = conn.createStatement();
168	ResultSet rsst = stmt.executeQuery(sql);
169	if (rsst.next()) {
170	entrykey = rsst.getInt(1);
171	if (! rsst.isLast()) {
172	//System.err.println("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
173	throw new PdbCodeNotFoundError("More than 1 entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
174	}
175	} else {
176	//System.err.println("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
177	throw new PdbCodeNotFoundError("No entry_key match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode);
178	}
179	rsst.close();
180	stmt.close();
181	return entrykey;
182	}
183
184	private String get_asym_id() throws PdbChainCodeNotFoundError, SQLException {
185	String pdbstrandid=pdbChainCode;
186	if (pdbChainCode.equals(NULL_CHAIN_CODE)){
187	pdbstrandid="A";
188	}
189	// NOTE: 'limit 1' not really needed since there can be only one asym_id
190	// per entry_key,pdb_strand_id combination (pdb_strand_id case sensitive!)
191	String sql="SELECT asym_id " +
192	" FROM "+db+".pdbx_poly_seq_scheme " +
193	" WHERE entry_key=" + entrykey +
194	" AND pdb_strand_id='"+pdbstrandid+"' " +
195	" LIMIT 1";
196
197	Statement stmt = conn.createStatement();
198	ResultSet rsst = stmt.executeQuery(sql);
199	if (rsst.next()) {
200	asymid = rsst.getString(1);
201	} else {
202	//System.err.println("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
203	throw new PdbChainCodeNotFoundError("No asym_id match for entry_key="+entrykey+", pdb_strand_id="+pdbChainCode);
204	}
205	rsst.close();
206	stmt.close();
207	// we set the internal chain identifier chainCode from asymid
208	chainCode = asymid;
209	return asymid;
210	}
211
212	// NOTE: Entity key not really needed since there can be only one entity_key
213	// per entry_key,asym_id combination
214	private int get_entity_key() throws PdbaseInconsistencyError, SQLException {
215	String sql="SELECT entity_key " +
216	" FROM "+db+".struct_asym " +
217	" WHERE entry_key="+ entrykey +
218	" AND id='"+asymid+"'";
219
220	Statement stmt = conn.createStatement();
221	ResultSet rsst = stmt.executeQuery(sql);
222	if (rsst.next()) {
223	entitykey = rsst.getInt(1);
224	if (! rsst.isLast()) {
225	//System.err.println("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
226	throw new PdbaseInconsistencyError("More than 1 entity_key match for entry_key="+entrykey+", asym_id="+asymid);
227	}
228	} else {
229	//System.err.println("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
230	throw new PdbaseInconsistencyError("No entity_key match for entry_key="+entrykey+", asym_id="+asymid);
231	}
232	rsst.close();
233	stmt.close();
234	return entitykey;
235	}
236
237	private String get_atom_alt_locs() throws PdbaseInconsistencyError, SQLException{
238	ArrayList<String> alt_ids = new ArrayList<String>();
239	HashMap<String,Integer> alt_ids2keys = new HashMap<String,Integer>();
240	String alt_loc_field="label_alt_key";
241	String sql="SELECT id, atom_sites_alt_key FROM "+db+".atom_sites_alt WHERE entry_key="+entrykey;
242
243	Statement stmt = conn.createStatement();
244	ResultSet rsst = stmt.executeQuery(sql);
245	int count=0;
246	while (rsst.next()) {
247	count++;
248	alt_ids.add(rsst.getString(1));
249	alt_ids2keys.put(rsst.getString(1), rsst.getInt(2));
250	}
251	if (count!=0){
252	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
253	//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!");
254	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!");
255	}
256	alt_ids.remove(".");
257	Collections.sort(alt_ids);
258	String lowest_alt_id = alt_ids.get(0);
259	alt_locs_sql_str = "("+alt_loc_field+"="+alt_ids2keys.get(".")+" OR "+alt_loc_field+"="+alt_ids2keys.get(lowest_alt_id)+")";
260	} else {
261	alt_locs_sql_str=alt_loc_field+" IS NULL";
262	}
263
264	rsst.close();
265	stmt.close();
266
267	return alt_locs_sql_str;
268	}
269
270	private void read_atomData() throws PdbaseInconsistencyError, SQLException{
271	resser_atom2atomserial = new HashMap<String,Integer>();
272	resser2restype = new HashMap<Integer,String>();
273	atomser2coord = new HashMap<Integer,Point3d>();
274	atomser2resser = new HashMap<Integer,Integer>();
275
276	// NOTE: label_entity_key not really needed since there can be only one entity_key
277	// per entry_key,asym_id combination
278	String sql = "SELECT id, label_atom_id, label_comp_id, label_seq_id, Cartn_x, Cartn_y, Cartn_z " +
279	" FROM "+db+".atom_site " +
280	" WHERE entry_key="+entrykey +
281	" AND label_asym_id='"+asymid+"' " +
282	" AND label_entity_key="+ entitykey +
283	" AND model_num="+ model +
284	" AND "+alt_locs_sql_str;
285
286	Statement stmt = conn.createStatement();
287	ResultSet rsst = stmt.executeQuery(sql);
288	int count=0;
289	while (rsst.next()){
290	count++;
291
292	int atomserial = rsst.getInt(1); // atomserial
293	String atom = rsst.getString(2).trim(); // atom
294	String res_type = rsst.getString(3).trim(); // res_type
295	int res_serial = rsst.getInt(4); // res_serial
296	double x = rsst.getDouble(5); // x
297	double y = rsst.getDouble(6); // y
298	double z = rsst.getDouble(7); // z
299	Point3d coords = new Point3d(x, y, z);
300	if (AAinfo.isValidAA(res_type)) {
301	atomser2coord.put(atomserial, coords);
302	atomser2resser.put(atomserial, res_serial);
303	resser2restype.put(res_serial, res_type);
304	if (AAinfo.isValidAtomWithOXT(res_type,atom)){
305	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
306	}
307	}
308
309	}
310	if (count==0){
311	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+"'");
312	}
313	rsst.close();
314	stmt.close();
315	}
316
317	private String read_seq() throws PdbaseInconsistencyError, SQLException{
318	String sequence="";
319
320	// we use seq_id+0 (implicitly converts to int) in ORDER BY because seq_id is varchar!!
321	String sql="SELECT mon_id" +
322	" FROM "+db+".pdbx_poly_seq_scheme " +
323	" WHERE entry_key=" + entrykey +
324	" AND asym_id='"+asymid+"' " +
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	String res_type = rsst.getString(1);
333	if (AAinfo.isValidAA(res_type)){
334	sequence+=AAinfo.threeletter2oneletter(res_type);
335	} else {
336	sequence+=NONSTANDARD_AA_LETTER;
337	}
338	}
339	if (count==0) {
340	//System.err.println("No sequence data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
341	throw new PdbaseInconsistencyError("No sequence data match for entry_key="+entrykey+", asym_id="+asymid);
342	}
343	rsst.close();
344	stmt.close();
345
346	return sequence;
347	}
348
349	private HashMap<String,Integer> get_ressers_mapping() throws PdbaseInconsistencyError, SQLException{
350	String pdbstrandid=pdbChainCode;
351	if (pdbChainCode.equals(NULL_CHAIN_CODE)){
352	pdbstrandid="A";
353	}
354
355	HashMap<String,Integer> map = new HashMap<String, Integer>();
356	String sql="SELECT seq_id, concat(pdb_seq_num,IF(pdb_ins_code='.','',pdb_ins_code))" +
357	" FROM "+db+".pdbx_poly_seq_scheme " +
358	" WHERE entry_key=" + entrykey +
359	" AND asym_id='"+asymid+"' " +
360	" AND pdb_strand_id='"+pdbstrandid+"' " +
361	" ORDER BY seq_id+0";
362
363	Statement stmt = conn.createStatement();
364	ResultSet rsst = stmt.executeQuery(sql);
365	int count=0;
366	while (rsst.next()) {
367	count++;
368	int resser = Integer.parseInt(rsst.getString(1));
369	String pdbresser = rsst.getString(2);
370	map.put(pdbresser, resser);
371	}
372	if (count==0) {
373	//System.err.println("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
374	throw new PdbaseInconsistencyError("No residue serials mapping data match for entry_key="+entrykey+", asym_id="+asymid+", pdb_strand_id="+pdbstrandid);
375	}
376	rsst.close();
377	stmt.close();
378
379	return map;
380	}
381
382	private void readSecStructure() throws SQLException {
383	this.secondaryStructure = new SecondaryStructure();
384
385	// HELIX AND TURN -- struct_conf table
386	String sql = "SELECT id,beg_label_seq_id,end_label_seq_id " +
387	" FROM "+db+".struct_conf " +
388	" WHERE entry_key="+entrykey+
389	" AND beg_label_asym_id='"+asymid+"'";
390	Statement stmt = conn.createStatement();
391	ResultSet rsst = stmt.executeQuery(sql);
392	int count=0;
393	while (rsst.next()) {
394	count++;
395	String id = rsst.getString(1).trim(); // id is either HELIX_Pnn or TURN_Pnn
396	Pattern p = Pattern.compile("^(\\w).+_P(\\d)+$");
397	Matcher m = p.matcher(id);
398	String ssId="Unknown";
399	if (m.find()){
400	ssId = m.group(1)+m.group(2); // e.g.: Hnn (helices) or Tnn (turns)
401	}
402	int beg = rsst.getInt(2);
403	int end =rsst.getInt(3);
404	char ssType = SecStrucElement.OTHER;
405	if(id.startsWith("H")) {
406	ssType = SecStrucElement.HELIX;
407	} else if(id.startsWith("T")) {
408	ssType = SecStrucElement.TURN;
409	} else {
410	System.err.println("Unknown secondary structure type " + id + " encountered when reading from Pdbase. Skipping.");
411	}
412	if(ssType != SecStrucElement.OTHER) {
413	SecStrucElement ssElem = new SecStrucElement(ssType, beg, end, ssId);
414	secondaryStructure.add(ssElem);
415	}
416	}
417	rsst.close();
418	stmt.close();
419
420	// SHEET -- struct_sheet_range table
421	sql = "SELECT sheet_id, id, beg_label_seq_id, end_label_seq_id " +
422	" FROM "+db+".struct_sheet_range " +
423	" WHERE entry_key="+entrykey+
424	" AND beg_label_asym_id='"+asymid+"'";
425	stmt = conn.createStatement();
426	rsst = stmt.executeQuery(sql);
427	count=0;
428	while (rsst.next()) {
429	count++;
430	String sheetid = rsst.getString(1).trim();
431	int id = rsst.getInt(2);
432	int beg = rsst.getInt(3);
433	int end =rsst.getInt(4);
434	String ssId=SecStrucElement.STRAND+sheetid+id; // e.g.: SA1, SA2..., SB1, SB2,...
435	SecStrucElement ssElem = new SecStrucElement(SecStrucElement.STRAND, beg, end, ssId);
436	secondaryStructure.add(ssElem);
437	}
438	rsst.close();
439	stmt.close();
440
441	}
442	}