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; 
                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_score 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; 
                                        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));

                                                if (j_num>cnum) { // we are over central residue  
                                                        if (!overx) {
                                                                nn+="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 
                                                                        nn+=j_res.toUpperCase()+"%"; // it is included
                                                                        nb+=j_res.toUpperCase()+"%";
                                                                } else { // BB dominated 
                                                                        nn+=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) nn+=j_res.toUpperCase()+"%"; // SC dominated 
                                                                else nn+=xlateSS(j_sec)+"%";
                                                                plus  = j_num; 
                                                                pres  = j_res; 
                                                                pss   = j_sec; 
                                                                pcn   = j_cnsize;  
                                                        } // end if 
                        
                                                } // end if 1st/2nd shell
                                                
                                        } // 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_score 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_score 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);";
                                                        
                                        // 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:	298
Committed:	Wed Aug 22 14:55:01 2007 UTC (17 years, 6 months ago) by lappe
File size:	10102 byte(s)
Log Message:	only one out of both BB/SC insertion per moves based on sc/bb domin. out of temp shell
Line	User	Rev	File contents
1	lappe	273	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	lappe	293	static String backgrndDB = "CASP_decoys";
19	lappe	273	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	lappe	293	System.out.println("Writing Target neighborhoods v.0.2. (SC&BB)");
34	lappe	273	// retrieve node_id \| cid \| res \| sstype defined by graph_id, num
35	lappe	294	// 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	lappe	273	mstmt = conn.createStatement();
38			mrsst = mstmt.executeQuery(sql);
39			while (mrsst.next()) {
40			// this is the central node -> get type and secondary structure
41	lappe	294	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	lappe	273	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	lappe	294	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	lappe	273	int minus, mcn, plus, pcn;
65	lappe	293	String sql, j_res, j_sec, mres, mss, pres, pss, nn, nb;
66	lappe	273	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	lappe	294	// 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	lappe	273	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	lappe	294	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	lappe	273	// 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	lappe	294	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	lappe	273	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	lappe	294	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	lappe	273	} // end while
121
122			System.out.println("\|1st shell\|="+n1+" \tx\t \|2nd shell\|="+n2);
123			mst = conn.createStatement();
124			sql = "delete from target_score 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	lappe	293	nb="%";
148	lappe	273	ni=0; nj=0;
149			rsst.beforeFirst();
150	lappe	294
151	lappe	273	while (rsst.next()) {
152			j_num = rsst.getInt(1);
153			j_res = rsst.getString(2);
154	lappe	293	j_sec = rsst.getString(3);
155	lappe	273	j_shell = rsst.getInt(4);
156			j_cnsize = rsst.getInt(5);
157	lappe	294	j_bb = rsst.getInt(6);
158			j_sc = rsst.getInt(7);
159			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));
160	lappe	293
161	lappe	273	if (j_num>cnum) { // we are over central residue
162			if (!overx) {
163	lappe	293	nn+="x%";
164			nb+="x%";
165	lappe	273	overx=true;
166			} // end if over x
167			} // END IF J > X
168
169			if (j_shell==1) { // a direct 1st shell neighbour
170			ni++;
171	lappe	293	if (ni!=i) {// if this is NOT the one direct nb 2B dropped
172	lappe	294	if (j_sc>=j_bb) { // SC dominated
173			nn+=j_res.toUpperCase()+"%"; // it is included
174			nb+=j_res.toUpperCase()+"%";
175			} else { // BB dominated
176			nn+=xlateSS( j_sec)+"%"; // it is included
177			nb+=xlateSS( j_sec)+"%";
178			} // end if SC/BB domin.
179	lappe	273	} else { // this one IS dropped
180			minus = j_num;
181			mres = j_res;
182			mss = j_sec;
183			mcn = j_cnsize;
184			} // end if ni!=i
185
186			} else { // 2nd shell neighbour
187			nj++;
188			if (nj==j) { // this is the 2nd shell nb 2B included
189	lappe	298	if (j_sc>=j_bb) nn+=j_res.toUpperCase()+"%"; // SC dominated
190			else nn+=xlateSS(j_sec)+"%";
191	lappe	273	plus = j_num;
192			pres = j_res;
193			pss = j_sec;
194			pcn = j_cnsize;
195			} // end if
196
197			} // end if 1st/2nd shell
198
199			} // end while through the entire nbhood
200			if (!overx) { // in case x is the very last we haven't seen it yet
201	lappe	293	nn+="x%"; // add it in the end
202			nb+="x%";
203	lappe	273	overx=true;
204			} // end if over x
205			if (VL>=1) {
206	lappe	293	System.out.print("("+nn+")\t("+nb+")\t");
207	lappe	273	}
208
209	lappe	293	// Store the resulting moves (nn for +SC, nb for +BB contact)
210	lappe	273	// insert into target_score values ( 1, 2, 'C', 0, 'A', 'H', 1, 2, 112, 'V', 'H', 3, 123, 'P', 'O', 2, 'TESTIT', 283, 12, 0, 0.00);
211	lappe	294	// SC move into resulting table
212	lappe	273	mst = conn.createStatement();
213			sql = "insert into target_score values ( "+cgraph_id+", "+cnode_id+", '"+ccid+"', "+cnum+"," +
214			" '"+cres+"', '"+csstype+"', "+i+", "+j+", "+
215			minus+", '"+mres+"', '"+mss+"', "+mcn+", "+
216	lappe	298	plus +", '"+pres+"', '"+pss+"', "+pcn+", "+
217	lappe	273	"'"+nn+"', 0, 0, 0, 0.00);";
218
219			// System.out.println(">"+sql);
220			mst.executeUpdate( sql);
221	lappe	293	mst.close();
222	lappe	298
223	lappe	273	} // close inner loop (i)
224			if (VL>=1) {
225			System.out.println(".");
226			} else {
227			System.out.print(".");
228			}
229			} // next outerloop (j)
230
231			rsst.close();
232			stmt.close();
233
234			} catch (SQLException e) {
235			e.printStackTrace();
236			System.err.println("SQLException: " + e.getMessage());
237			System.err.println("SQLState: " + e.getSQLState());
238			} // end try/catch
239
240			} // end writeMoves
241
242	lappe	293	public static String xlateSS( String sstype) { // xlate SecSTructure-Symbol
243			String SSymbol = "o";
244			sstype=sstype.toUpperCase();
245			if (sstype.equals("H")) SSymbol="z"; // Helix
246			if (sstype.equals("S")) SSymbol="b"; // beta strand
247			return SSymbol;
248			} // end xlateSS
249
250	lappe	273	} // end class
251
252
253			/*
254			drop table target_score;
255			CREATE TABLE `target_score` (
256			`graph_id` int(10) unsigned NOT NULL,
257			`node_id` int(10) unsigned DEFAULT NULL,
258			`cid` varchar(6) COLLATE latin1_general_cs NOT NULL,
259			`num` int(10) unsigned NOT NULL,
260			`res` char(1) COLLATE latin1_general_cs DEFAULT NULL,
261			`sstype` char(1) COLLATE latin1_general_cs DEFAULT NULL,
262			`i` int(2) NOT NULL DEFAULT '0',
263			`j` int(2) NOT NULL DEFAULT '0',
264			`minus` int(2) NOT NULL DEFAULT '0',
265			`mres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
266			`mss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
267			`mcn` int(2) NOT NULL DEFAULT '0',
268			`plus` int(2) NOT NULL DEFAULT '0',
269			`pres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
270			`pss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
271			`pcn` int(2) NOT NULL DEFAULT '0',
272			`nn` varchar(50) COLLATE latin1_general_cs,
273			`total` int(8) NOT NULL DEFAULT '0',
274			`rank` int(3) NOT NULL DEFAULT '0',
275			`deltarank` int(3) NOT NULL DEFAULT '0',
276			`score` decimal(6,2) NOT NULL DEFAULT '0.00'
277			) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_general_cs;
278
279
280			*/