owl/trunk/writeTargetMoves.java

import tools.MySQLConnection;

import java.sql.SQLException;
import java.sql.Statement;
import java.sql.ResultSet;

public class writeTargetMoves {

        /**
         * writes all the moves for a given residue for later scoring. 
         * @author lappe
         */
        static int maxRank = 21; // value to replace for non-existence of central redue in the resultvector (rank=0) 
        // higher values should penalize non-existence more
        static int VL=1; // Verbosity Level 
        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        static String backgrndDB = "CASP_decoys"; 
        static String targetNodes = "single_model_node";
        static String targetEdges = "single_model_edge";
        static String targetScore = "single_model_score";
        static int cn1[], cn2[]; 

        public static void main(String[] args) {
                int graph_id=0, num=0, node_id=0; 
                String cid="", res="", sstype=""; 
                String sql;  
                Statement mstmt;  
                ResultSet mrsst; 
                
                try {
                        conn = new MySQLConnection("white",user,"nieve", backgrndDB); // the UPPERCASE DB!  
                        System.out.println("Writing Target neighborhoods v.0.2. (SC&BB)"); 
                        // retrieve node_id   | cid  | res  | sstype defined by graph_id, num  
                        // sql = "select node_id, cid, num, res, sstype from "+targetNodes+" where graph_id="+graph_id+" limit 3;"; 
                        sql = "select graph_id, node_id, cid, num, res, sstype from "+targetNodes+";"; //  +" limit 1;"; 
                        mstmt = conn.createStatement();
                        mrsst = mstmt.executeQuery(sql); 
                        while (mrsst.next()) {
                            // this is the central node -> get type and secondary structure
                                graph_id = mrsst.getInt( 1); 
                                node_id = mrsst.getInt( 2); 
                                cid = mrsst.getString( 3);
                                num = mrsst.getInt( 4); 
                                res = mrsst.getString( 5).toUpperCase();
                                sstype= mrsst.getString( 6).toUpperCase();
                                System.out.println("GraphID "+graph_id+" Chain "+cid+", Central residue ("+node_id+") "+res+":"+num+":"+sstype); 
                                writeMoves( graph_id, node_id, cid, num, res, sstype);          
                        } // end if central residue
                        mrsst.close();
                        mstmt.close();                  
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                } // end try/catch 
                System.out.println("fin."); 
        }       // end main 


        public static void writeMoves( int cgraph_id, int cnode_id, String ccid, int cnum, String cres, String csstype) {
                int n1=0, n2=0, ni=0, nj=0, i=0, j=0, j_num=0, j_shell=0, j_cnsize=0, j_bb, j_sc;
                int minus, mcn, plus, pcn; 
                String sql, j_res, j_sec, mres, mss, pres, pss, nn, nb, nextn, lastn="", iks; 
                boolean overx = false;
                Statement stmt, mst;  
                ResultSet rsst;
                
                try {
                        
                        // retrieve the original nbhood into orig_shell
                        System.out.println("retrieving first shell ... "); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("drop table if exists temp_shell;"); 
                        stmt.close(); 
        
                        stmt = conn.createStatement();
                        // stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from "+targetEdges+" where graph_id="+cgraph_id+" and i_num="+cnum+";");
                        stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell, weight_bb as BB, weight_SC as SC " +
                                        "from "+targetEdges+" where graph_id="+cgraph_id+" and i_cid='"+ccid+"' and i_num="+cnum+";"); 
                        stmt.close(); 
        
                        System.out.println("adding the 2nd shell ...");  
                        sql = "select j_num from temp_shell where shell=1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        i=0; 
                        while (rsst.next()) {
                                i++; 
                                j_num = rsst.getInt(1);
                                System.out.println(i+":"+j_num); 
                                mst = conn.createStatement();
                                sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell, weight_bb as BB, weight_SC as SC " +
                                                "from "+targetEdges+" where graph_id="+cgraph_id+" and i_cid='"+ccid+"' and i_num="+j_num+";";
                                // System.out.println(">"+sql); 
                                mst.executeUpdate( sql); 
                                mst.close(); 
                        } // end while 
                        rsst.close(); 
                        stmt.close(); 

                        System.out.println("retrieving the entire nbhood (1st and 2nd shell)");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn, max(BB) as BB, max(SC) as SC " +
                                        "from temp_shell where j_num!="+cnum+" group by j_num order by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        n1=0; 
                        n2=0;           
                        while (rsst.next()) {
                                if ( rsst.getInt( 4)==1) { // count 1st shell entry 
                                        n1++;
                                        System.out.print("1#"+n1);
                                } // end if 2st shell 
                                if ( rsst.getInt( 4)==2) { // count 2nd shell entry 
                                        n2++;
                                        System.out.print("2#"+n2);
                                } // end if 2nd shell 
                                System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)+"\t"+rsst.getInt( 6)+"\t"+rsst.getInt( 7)); 
                        } // end while
                        
                        System.out.println("|1st shell|="+n1+" \tx\t |2nd shell|="+n2);
                        mst = conn.createStatement();
                        sql = "delete from target_short where graph_id="+cgraph_id+" and node_id="+cnode_id+" and cid='"+ccid+"' and num="+cnum+";"; 
                        System.out.println(">"+sql); 
                        mst.executeUpdate( sql); 
                        mst.close(); 
                        
                        cn1 = new int[n1+1]; 
                        cn2 = new int[n2+1]; 
                        // minus | mres | mss  | mcn | plus | pres | pss  | pcn | nn
                        for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
                                for (i=0; i<=n1; i++) { // inner loop through all direct contacts
                                        overx = false;
                                        if (VL>=1) {
                                                System.out.print("("+i+","+j+")\t");
                                        }
                                        minus = 0; 
                                        mres  = ""; 
                                        mss   = ""; 
                                        mcn   = n1;  
                                        plus  = 0; 
                                        pres  = ""; 
                                        pss   = ""; 
                                        pcn   = n1;
                                        nn="%";
                                        nb="%";
                                        ni=0; nj=0;
                                        lastn="??";
                                        nextn=""; 
                                        iks=""; 
                                        rsst.beforeFirst();
                                        
                                        while (rsst.next()) {
                                                j_num = rsst.getInt(1); 
                                                j_res = rsst.getString(2);
                                                j_sec = rsst.getString(3); 
                                                j_shell = rsst.getInt(4);
                                                j_cnsize = rsst.getInt(5);
                                                j_bb = rsst.getInt(6);
                                                j_sc = rsst.getInt(7);
                                                
                                                if (VL>=2) System.out.print("\n"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)+"\t"+rsst.getInt( 6)+"\t"+rsst.getInt( 7));

                                                iks="";
                                                if (j_num>cnum) { // we are over central residue  
                                                        if (!overx) {
                                                                iks="x%";
                                                                nb+="x%";
                                                                overx=true; 
                                                        } // end if over x 
                                                } // END IF J > X
                                                
                                                if (j_shell==1) { // a direct 1st shell neighbour 
                                                        ni++;
                                                        if (ni!=i) {// if this is NOT the one direct nb 2B dropped
                                                                if (j_sc>=j_bb) { // SC dominated 
                                                                        nextn=j_res.toUpperCase()+"%"; // it is included
                                                                        nb+=j_res.toUpperCase()+"%";
                                                                } else { // BB dominated 
                                                                        nextn=xlateSS( j_sec)+"%"; // it is included
                                                                        nb+=xlateSS( j_sec)+"%";
                                                                } // end if SC/BB domin. 
                                                        } else { // this one IS dropped
                                                                minus = j_num; 
                                                                mres  = j_res; 
                                                                mss   = j_sec; 
                                                                mcn   = j_cnsize;  
                                                        } // end if ni!=i 
                                                        
                                                } else { // 2nd shell neighbour 
                                                        nj++; 
                                                        if (nj==j) { // this is the 2nd shell nb 2B included
                                                                if (j_sc>=j_bb) {
                                                                        nextn=j_res.toUpperCase()+"%"; // SC dominated
                                                                        nb += j_res.toUpperCase()+"%";
                                                                }
                                                                else {
                                                                        nextn=xlateSS(j_sec)+"%";
                                                                        nb+=xlateSS( j_sec)+"%";
                                                                }
                                                                plus  = j_num; 
                                                                pres  = j_res; 
                                                                pss   = j_sec; 
                                                                pcn   = j_cnsize;  
                                                        } // end if 
                        
                                                } // end if 1st/2nd shell
                                                nn+=iks; 
                                                if (!lastn.equals( nextn)) { 
                                                   nn+=nextn;  
                                                }
                                                lastn = nextn;
                                                nextn=""; 
                                        } // end while through the entire nbhood
                                        if (!overx) { // in case x is the very last we haven't seen it yet  
                                                nn+="x%"; // add it in the end
                                                nb+="x%"; 
                                                overx=true; 
                                        } // end if over x
                                        
                                        if (VL>=1) {
                                                System.out.print("("+nn+")\t("+nb+")\t");
                                        }
                                        
                                        // Store the resulting moves (nn for +SC, nb for +BB contact) 
                                        // insert into target_short values ( 1, 2, 'C', 0, 'A', 'H', 1, 2, 112, 'V', 'H', 3, 123, 'P', 'O', 2, 'TESTIT', 283, 12, 0, 0.00);
                                        // SC move into resulting table 
                                        mst = conn.createStatement();
                                        sql = "insert into target_short values ( "+cgraph_id+", "+cnode_id+", '"+ccid+"', "+cnum+"," +
                                                        " '"+cres+"', '"+csstype+"', "+i+", "+j+", "+
                                                        minus+", '"+mres+"', '"+mss+"', "+mcn+", "+
                                                        plus +", '"+pres+"', '"+pss+"', "+pcn+", "+
                                                        "'"+nn+"', 0, 0, 0, 0.00);";
                                                        
                                        if (VL>=2) System.out.println(">"+sql); 
                                        mst.executeUpdate( sql); 
                                        mst.close();
                                        
                                } // close inner loop (i)
                                if (VL>=1) {
                                   System.out.println(".");
                                } else {
                                        System.out.print(".");
                                } 
                        } // next outerloop (j)
                        
                        rsst.close(); 
                        stmt.close(); 
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                } // end try/catch 

        }       // end writeMoves 
        
        public static String xlateSS( String sstype) { // xlate SecSTructure-Symbol 
                String SSymbol = "o";
                sstype=sstype.toUpperCase(); 
                if (sstype.equals("H")) SSymbol="z"; // Helix 
                if (sstype.equals("S")) SSymbol="b"; // beta strand 
                return SSymbol; 
        } // end xlateSS

} // end class 


/*
drop table target_score;
CREATE TABLE `target_score` (
  `graph_id` int(10) unsigned NOT NULL,
  `node_id` int(10) unsigned DEFAULT NULL,
  `cid` varchar(6) COLLATE latin1_general_cs NOT NULL,
  `num` int(10) unsigned NOT NULL,
  `res` char(1) COLLATE latin1_general_cs DEFAULT NULL,
  `sstype` char(1) COLLATE latin1_general_cs DEFAULT NULL,
  `i` int(2) NOT NULL DEFAULT '0',
  `j` int(2) NOT NULL DEFAULT '0',
  `minus` int(2) NOT NULL DEFAULT '0',
  `mres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
  `mss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
  `mcn` int(2) NOT NULL DEFAULT '0',
  `plus` int(2) NOT NULL DEFAULT '0',
  `pres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
  `pss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
  `pcn` int(2) NOT NULL DEFAULT '0',
  `nn` varchar(50) COLLATE latin1_general_cs,
  `total` int(8) NOT NULL DEFAULT '0',
  `rank` int(3) NOT NULL DEFAULT '0',
  `deltarank` int(3) NOT NULL DEFAULT '0',
  `score` decimal(6,2) NOT NULL DEFAULT '0.00'
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_general_cs;


*/ 
Revision:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 10 months ago) by duarte
File size:	10441 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
Line	File contents
1	import tools.MySQLConnection;
2
3	import java.sql.SQLException;
4	import java.sql.Statement;
5	import java.sql.ResultSet;
6
7	public class writeTargetMoves {
8
9	/**
10	* writes all the moves for a given residue for later scoring.
11	* @author lappe
12	*/
13	static int maxRank = 21; // value to replace for non-existence of central redue in the resultvector (rank=0)
14	// higher values should penalize non-existence more
15	static int VL=1; // Verbosity Level
16	static String user = "lappe" ; // change user name!!
17	static MySQLConnection conn;
18	static String backgrndDB = "CASP_decoys";
19	static String targetNodes = "single_model_node";
20	static String targetEdges = "single_model_edge";
21	static String targetScore = "single_model_score";
22	static int cn1[], cn2[];
23
24	public static void main(String[] args) {
25	int graph_id=0, num=0, node_id=0;
26	String cid="", res="", sstype="";
27	String sql;
28	Statement mstmt;
29	ResultSet mrsst;
30
31	try {
32	conn = new MySQLConnection("white",user,"nieve", backgrndDB); // the UPPERCASE DB!
33	System.out.println("Writing Target neighborhoods v.0.2. (SC&BB)");
34	// retrieve node_id \| cid \| res \| sstype defined by graph_id, num
35	// sql = "select node_id, cid, num, res, sstype from "+targetNodes+" where graph_id="+graph_id+" limit 3;";
36	sql = "select graph_id, node_id, cid, num, res, sstype from "+targetNodes+";"; // +" limit 1;";
37	mstmt = conn.createStatement();
38	mrsst = mstmt.executeQuery(sql);
39	while (mrsst.next()) {
40	// this is the central node -> get type and secondary structure
41	graph_id = mrsst.getInt( 1);
42	node_id = mrsst.getInt( 2);
43	cid = mrsst.getString( 3);
44	num = mrsst.getInt( 4);
45	res = mrsst.getString( 5).toUpperCase();
46	sstype= mrsst.getString( 6).toUpperCase();
47	System.out.println("GraphID "+graph_id+" Chain "+cid+", Central residue ("+node_id+") "+res+":"+num+":"+sstype);
48	writeMoves( graph_id, node_id, cid, num, res, sstype);
49	} // end if central residue
50	mrsst.close();
51	mstmt.close();
52	} catch (SQLException e) {
53	e.printStackTrace();
54	System.err.println("SQLException: " + e.getMessage());
55	System.err.println("SQLState: " + e.getSQLState());
56	} // end try/catch
57	System.out.println("fin.");
58	} // end main
59
60
61
62	public static void writeMoves( int cgraph_id, int cnode_id, String ccid, int cnum, String cres, String csstype) {
63	int n1=0, n2=0, ni=0, nj=0, i=0, j=0, j_num=0, j_shell=0, j_cnsize=0, j_bb, j_sc;
64	int minus, mcn, plus, pcn;
65	String sql, j_res, j_sec, mres, mss, pres, pss, nn, nb, nextn, lastn="", iks;
66	boolean overx = false;
67	Statement stmt, mst;
68	ResultSet rsst;
69
70	try {
71
72	// retrieve the original nbhood into orig_shell
73	System.out.println("retrieving first shell ... ");
74	stmt = conn.createStatement();
75	stmt.executeUpdate("drop table if exists temp_shell;");
76	stmt.close();
77
78	stmt = conn.createStatement();
79	// stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from "+targetEdges+" where graph_id="+cgraph_id+" and i_num="+cnum+";");
80	stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell, weight_bb as BB, weight_SC as SC " +
81	"from "+targetEdges+" where graph_id="+cgraph_id+" and i_cid='"+ccid+"' and i_num="+cnum+";");
82	stmt.close();
83
84	System.out.println("adding the 2nd shell ...");
85	sql = "select j_num from temp_shell where shell=1;";
86	stmt = conn.createStatement();
87	rsst = stmt.executeQuery(sql);
88	i=0;
89	while (rsst.next()) {
90	i++;
91	j_num = rsst.getInt(1);
92	System.out.println(i+":"+j_num);
93	mst = conn.createStatement();
94	sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell, weight_bb as BB, weight_SC as SC " +
95	"from "+targetEdges+" where graph_id="+cgraph_id+" and i_cid='"+ccid+"' and i_num="+j_num+";";
96	// System.out.println(">"+sql);
97	mst.executeUpdate( sql);
98	mst.close();
99	} // end while
100	rsst.close();
101	stmt.close();
102
103	System.out.println("retrieving the entire nbhood (1st and 2nd shell)");
104	sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn, max(BB) as BB, max(SC) as SC " +
105	"from temp_shell where j_num!="+cnum+" group by j_num order by j_num;";
106	stmt = conn.createStatement();
107	rsst = stmt.executeQuery(sql);
108	n1=0;
109	n2=0;
110	while (rsst.next()) {
111	if ( rsst.getInt( 4)==1) { // count 1st shell entry
112	n1++;
113	System.out.print("1#"+n1);
114	} // end if 2st shell
115	if ( rsst.getInt( 4)==2) { // count 2nd shell entry
116	n2++;
117	System.out.print("2#"+n2);
118	} // end if 2nd shell
119	System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)+"\t"+rsst.getInt( 6)+"\t"+rsst.getInt( 7));
120	} // end while
121
122	System.out.println("\|1st shell\|="+n1+" \tx\t \|2nd shell\|="+n2);
123	mst = conn.createStatement();
124	sql = "delete from target_short where graph_id="+cgraph_id+" and node_id="+cnode_id+" and cid='"+ccid+"' and num="+cnum+";";
125	System.out.println(">"+sql);
126	mst.executeUpdate( sql);
127	mst.close();
128
129	cn1 = new int[n1+1];
130	cn2 = new int[n2+1];
131	// minus \| mres \| mss \| mcn \| plus \| pres \| pss \| pcn \| nn
132	for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
133	for (i=0; i<=n1; i++) { // inner loop through all direct contacts
134	overx = false;
135	if (VL>=1) {
136	System.out.print("("+i+","+j+")\t");
137	}
138	minus = 0;
139	mres = "";
140	mss = "";
141	mcn = n1;
142	plus = 0;
143	pres = "";
144	pss = "";
145	pcn = n1;
146	nn="%";
147	nb="%";
148	ni=0; nj=0;
149	lastn="??";
150	nextn="";
151	iks="";
152	rsst.beforeFirst();
153
154	while (rsst.next()) {
155	j_num = rsst.getInt(1);
156	j_res = rsst.getString(2);
157	j_sec = rsst.getString(3);
158	j_shell = rsst.getInt(4);
159	j_cnsize = rsst.getInt(5);
160	j_bb = rsst.getInt(6);
161	j_sc = rsst.getInt(7);
162
163	if (VL>=2) System.out.print("\n"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)+"\t"+rsst.getInt( 6)+"\t"+rsst.getInt( 7));
164
165	iks="";
166	if (j_num>cnum) { // we are over central residue
167	if (!overx) {
168	iks="x%";
169	nb+="x%";
170	overx=true;
171	} // end if over x
172	} // END IF J > X
173
174	if (j_shell==1) { // a direct 1st shell neighbour
175	ni++;
176	if (ni!=i) {// if this is NOT the one direct nb 2B dropped
177	if (j_sc>=j_bb) { // SC dominated
178	nextn=j_res.toUpperCase()+"%"; // it is included
179	nb+=j_res.toUpperCase()+"%";
180	} else { // BB dominated
181	nextn=xlateSS( j_sec)+"%"; // it is included
182	nb+=xlateSS( j_sec)+"%";
183	} // end if SC/BB domin.
184	} else { // this one IS dropped
185	minus = j_num;
186	mres = j_res;
187	mss = j_sec;
188	mcn = j_cnsize;
189	} // end if ni!=i
190
191	} else { // 2nd shell neighbour
192	nj++;
193	if (nj==j) { // this is the 2nd shell nb 2B included
194	if (j_sc>=j_bb) {
195	nextn=j_res.toUpperCase()+"%"; // SC dominated
196	nb += j_res.toUpperCase()+"%";
197	}
198	else {
199	nextn=xlateSS(j_sec)+"%";
200	nb+=xlateSS( j_sec)+"%";
201	}
202	plus = j_num;
203	pres = j_res;
204	pss = j_sec;
205	pcn = j_cnsize;
206	} // end if
207
208	} // end if 1st/2nd shell
209	nn+=iks;
210	if (!lastn.equals( nextn)) {
211	nn+=nextn;
212	}
213	lastn = nextn;
214	nextn="";
215	} // end while through the entire nbhood
216	if (!overx) { // in case x is the very last we haven't seen it yet
217	nn+="x%"; // add it in the end
218	nb+="x%";
219	overx=true;
220	} // end if over x
221
222	if (VL>=1) {
223	System.out.print("("+nn+")\t("+nb+")\t");
224	}
225
226	// Store the resulting moves (nn for +SC, nb for +BB contact)
227	// insert into target_short values ( 1, 2, 'C', 0, 'A', 'H', 1, 2, 112, 'V', 'H', 3, 123, 'P', 'O', 2, 'TESTIT', 283, 12, 0, 0.00);
228	// SC move into resulting table
229	mst = conn.createStatement();
230	sql = "insert into target_short values ( "+cgraph_id+", "+cnode_id+", '"+ccid+"', "+cnum+"," +
231	" '"+cres+"', '"+csstype+"', "+i+", "+j+", "+
232	minus+", '"+mres+"', '"+mss+"', "+mcn+", "+
233	plus +", '"+pres+"', '"+pss+"', "+pcn+", "+
234	"'"+nn+"', 0, 0, 0, 0.00);";
235
236	if (VL>=2) System.out.println(">"+sql);
237	mst.executeUpdate( sql);
238	mst.close();
239
240	} // close inner loop (i)
241	if (VL>=1) {
242	System.out.println(".");
243	} else {
244	System.out.print(".");
245	}
246	} // next outerloop (j)
247
248	rsst.close();
249	stmt.close();
250
251	} catch (SQLException e) {
252	e.printStackTrace();
253	System.err.println("SQLException: " + e.getMessage());
254	System.err.println("SQLState: " + e.getSQLState());
255	} // end try/catch
256
257	} // end writeMoves
258
259	public static String xlateSS( String sstype) { // xlate SecSTructure-Symbol
260	String SSymbol = "o";
261	sstype=sstype.toUpperCase();
262	if (sstype.equals("H")) SSymbol="z"; // Helix
263	if (sstype.equals("S")) SSymbol="b"; // beta strand
264	return SSymbol;
265	} // end xlateSS
266
267	} // end class
268
269
270	/*
271	drop table target_score;
272	CREATE TABLE `target_score` (
273	`graph_id` int(10) unsigned NOT NULL,
274	`node_id` int(10) unsigned DEFAULT NULL,
275	`cid` varchar(6) COLLATE latin1_general_cs NOT NULL,
276	`num` int(10) unsigned NOT NULL,
277	`res` char(1) COLLATE latin1_general_cs DEFAULT NULL,
278	`sstype` char(1) COLLATE latin1_general_cs DEFAULT NULL,
279	`i` int(2) NOT NULL DEFAULT '0',
280	`j` int(2) NOT NULL DEFAULT '0',
281	`minus` int(2) NOT NULL DEFAULT '0',
282	`mres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
283	`mss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
284	`mcn` int(2) NOT NULL DEFAULT '0',
285	`plus` int(2) NOT NULL DEFAULT '0',
286	`pres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
287	`pss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
288	`pcn` int(2) NOT NULL DEFAULT '0',
289	`nn` varchar(50) COLLATE latin1_general_cs,
290	`total` int(8) NOT NULL DEFAULT '0',
291	`rank` int(3) NOT NULL DEFAULT '0',
292	`deltarank` int(3) NOT NULL DEFAULT '0',
293	`score` decimal(6,2) NOT NULL DEFAULT '0.00'
294	) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_general_cs;
295
296
297	*/