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 = "test_targets"; 
        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; 
                
            if (args.length<1){
                        System.err.println("The graph_id needs to be given .... i.e. 7");
                        System.exit(1);
                }               
                graph_id = Integer.parseInt( args[0]);
                try {
                        conn = new MySQLConnection("white",user,"nieve", backgrndDB); // the UPPERCASE DB!  
                        System.out.println("Writing Target neighborhoods v.0.1. "); 
                        // 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+";"; 
                        mstmt = conn.createStatement();
                        mrsst = mstmt.executeQuery(sql); 
                        while (mrsst.next()) {
                            // this is the central node -> get type and secondary structure
                                node_id = mrsst.getInt( 1); 
                                cid = mrsst.getString( 2);
                                num = mrsst.getInt( 3); 
                                res = mrsst.getString( 4).toUpperCase();
                                sstype = ""; 
                                // sstype= mrsst.getString( 5).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;
                int minus, mcn, plus, pcn; 
                String sql, j_res, j_sec, mres, mss, pres, pss, nn; 
                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, '' as j_sstype, 1 as shell from "+targetEdges+" where graph_id="+cgraph_id+" 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 from "+targetEdges+" where graph_id="+cgraph_id+" and i_num="+j_num+";";
                                sql = "insert into temp_shell select i_num, i_res, j_num, j_res, '', 2 as shell from "+targetEdges+" where graph_id="+cgraph_id+" 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 from temp_shell where j_num!="+cnum+" group by j_num order by j_num;";
                        sql = "select j_num, j_res, '' as jsstype, min(shell) as shell, count(*) as cn 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)); 
                        } // 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="%";
                                        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_sec=""; 
                                                j_shell = rsst.getInt(4);
                                                j_cnsize = rsst.getInt(5);
                                                
                                                if (j_num>cnum) { // we are over central residue  
                                                        if (!overx) {
                                                                nn+="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 
                                                                nn+=j_res.toUpperCase()+"%"; // it is included
                                                        } 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
                                                                nn+=j_res.toUpperCase()+"%";
                                                                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 
                                                overx=true; 
                                        } // end if over x
                                        if (VL>=1) {
                                                System.out.print("("+nn+")\t");
                                        }
                                        
                                        // Store the resulting move/nn 
                                        // 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);
                                        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 
        
        
} // 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:	273
Committed:	Tue Aug 14 09:13:07 2007 UTC (17 years, 2 months ago) by lappe
File size:	9293 byte(s)
Log Message:
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 = "test_targets";
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	if (args.length<1){
32	System.err.println("The graph_id needs to be given .... i.e. 7");
33	System.exit(1);
34	}
35	graph_id = Integer.parseInt( args[0]);
36	try {
37	conn = new MySQLConnection("white",user,"nieve", backgrndDB); // the UPPERCASE DB!
38	System.out.println("Writing Target neighborhoods v.0.1. ");
39	// retrieve node_id \| cid \| res \| sstype defined by graph_id, num
40	sql = "select node_id, cid, num, res, sstype from "+targetNodes+" where graph_id="+graph_id+";";
41	mstmt = conn.createStatement();
42	mrsst = mstmt.executeQuery(sql);
43	while (mrsst.next()) {
44	// this is the central node -> get type and secondary structure
45	node_id = mrsst.getInt( 1);
46	cid = mrsst.getString( 2);
47	num = mrsst.getInt( 3);
48	res = mrsst.getString( 4).toUpperCase();
49	sstype = "";
50	// sstype= mrsst.getString( 5).toUpperCase();
51	System.out.println("GraphID "+graph_id+" Chain "+cid+", Central residue ("+node_id+") "+res+":"+num+":"+sstype);
52	writeMoves( graph_id, node_id, cid, num, res, sstype);
53	} // end if central residue
54	mrsst.close();
55	mstmt.close();
56	} catch (SQLException e) {
57	e.printStackTrace();
58	System.err.println("SQLException: " + e.getMessage());
59	System.err.println("SQLState: " + e.getSQLState());
60	} // end try/catch
61	System.out.println("fin.");
62	} // end main
63
64
65
66	public static void writeMoves( int cgraph_id, int cnode_id, String ccid, int cnum, String cres, String csstype) {
67	int n1=0, n2=0, ni=0, nj=0, i=0, j=0, j_num=0, j_shell=0, j_cnsize=0;
68	int minus, mcn, plus, pcn;
69	String sql, j_res, j_sec, mres, mss, pres, pss, nn;
70	boolean overx = false;
71	Statement stmt, mst;
72	ResultSet rsst;
73
74	try {
75
76	// retrieve the original nbhood into orig_shell
77	System.out.println("retrieving first shell ... ");
78	stmt = conn.createStatement();
79	stmt.executeUpdate("drop table if exists temp_shell;");
80	stmt.close();
81
82	stmt = conn.createStatement();
83	//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+";");
84	stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, '' as j_sstype, 1 as shell from "+targetEdges+" where graph_id="+cgraph_id+" and i_num="+cnum+";");
85	stmt.close();
86
87	System.out.println("adding the 2nd shell ...");
88	sql = "select j_num from temp_shell where shell=1;";
89	stmt = conn.createStatement();
90	rsst = stmt.executeQuery(sql);
91	i=0;
92	while (rsst.next()) {
93	i++;
94	j_num = rsst.getInt(1);
95	System.out.println(i+":"+j_num);
96	mst = conn.createStatement();
97	// sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from "+targetEdges+" where graph_id="+cgraph_id+" and i_num="+j_num+";";
98	sql = "insert into temp_shell select i_num, i_res, j_num, j_res, '', 2 as shell from "+targetEdges+" where graph_id="+cgraph_id+" and i_num="+j_num+";";
99	// System.out.println(">"+sql);
100	mst.executeUpdate( sql);
101	mst.close();
102	} // end while
103	rsst.close();
104	stmt.close();
105
106	System.out.println("retrieving the entire nbhood (1st and 2nd shell)");
107	// sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell where j_num!="+cnum+" group by j_num order by j_num;";
108	sql = "select j_num, j_res, '' as jsstype, min(shell) as shell, count(*) as cn from temp_shell where j_num!="+cnum+" group by j_num order by j_num;";
109	stmt = conn.createStatement();
110	rsst = stmt.executeQuery(sql);
111	n1=0;
112	n2=0;
113	while (rsst.next()) {
114	if ( rsst.getInt( 4)==1) { // count 1st shell entry
115	n1++;
116	System.out.print("1#"+n1);
117	} // end if 2st shell
118	if ( rsst.getInt( 4)==2) { // count 2nd shell entry
119	n2++;
120	System.out.print("2#"+n2);
121	} // end if 2nd shell
122	System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
123	} // end while
124
125	System.out.println("\|1st shell\|="+n1+" \tx\t \|2nd shell\|="+n2);
126	mst = conn.createStatement();
127	sql = "delete from target_score where graph_id="+cgraph_id+" and node_id="+cnode_id+" and cid='"+ccid+"' and num="+cnum+";";
128	System.out.println(">"+sql);
129	mst.executeUpdate( sql);
130	mst.close();
131
132	cn1 = new int[n1+1];
133	cn2 = new int[n2+1];
134	// minus \| mres \| mss \| mcn \| plus \| pres \| pss \| pcn \| nn
135	for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
136	for (i=0; i<=n1; i++) { // inner loop through all direct contacts
137	overx = false;
138	if (VL>=1) {
139	System.out.print("("+i+","+j+")\t");
140	}
141	minus = 0;
142	mres = "";
143	mss = "";
144	mcn = n1;
145	plus = 0;
146	pres = "";
147	pss = "";
148	pcn = n1;
149	nn="%";
150	ni=0; nj=0;
151	rsst.beforeFirst();
152	while (rsst.next()) {
153	j_num = rsst.getInt(1);
154	j_res = rsst.getString(2);
155	//j_sec = rsst.getString(3);
156	j_sec="";
157	j_shell = rsst.getInt(4);
158	j_cnsize = rsst.getInt(5);
159
160	if (j_num>cnum) { // we are over central residue
161	if (!overx) {
162	nn+="x%";
163	overx=true;
164	} // end if over x
165	} // END IF J > X
166
167	if (j_shell==1) { // a direct 1st shell neighbour
168	ni++;
169	if (ni!=i) {// if this is NOT the one direct nb 2B dropped
170	nn+=j_res.toUpperCase()+"%"; // it is included
171	} else { // this one IS dropped
172	minus = j_num;
173	mres = j_res;
174	mss = j_sec;
175	mcn = j_cnsize;
176	} // end if ni!=i
177
178	} else { // 2nd shell neighbour
179	nj++;
180	if (nj==j) { // this is the 2nd shell nb 2B included
181	nn+=j_res.toUpperCase()+"%";
182	plus = j_num;
183	pres = j_res;
184	pss = j_sec;
185	pcn = j_cnsize;
186	} // end if
187
188	} // end if 1st/2nd shell
189
190	} // end while through the entire nbhood
191	if (!overx) { // in case x is the very last we haven't seen it yet
192	nn+="x%"; // add it in the end
193	overx=true;
194	} // end if over x
195	if (VL>=1) {
196	System.out.print("("+nn+")\t");
197	}
198
199	// Store the resulting move/nn
200	// 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);
201	mst = conn.createStatement();
202
203	sql = "insert into target_score values ( "+cgraph_id+", "+cnode_id+", '"+ccid+"', "+cnum+"," +
204	" '"+cres+"', '"+csstype+"', "+i+", "+j+", "+
205	minus+", '"+mres+"', '"+mss+"', "+mcn+", "+
206	plus +", '"+pres+"', '"+pss+"', "+pcn+", "+
207	"'"+nn+"', 0, 0, 0, 0.00);";
208
209	// System.out.println(">"+sql);
210	mst.executeUpdate( sql);
211	mst.close();
212
213	} // close inner loop (i)
214	if (VL>=1) {
215	System.out.println(".");
216	} else {
217	System.out.print(".");
218	}
219	} // next outerloop (j)
220
221	rsst.close();
222	stmt.close();
223
224	} catch (SQLException e) {
225	e.printStackTrace();
226	System.err.println("SQLException: " + e.getMessage());
227	System.err.println("SQLState: " + e.getSQLState());
228	} // end try/catch
229
230	} // end writeMoves
231
232
233	} // end class
234
235
236	/*
237	drop table target_score;
238	CREATE TABLE `target_score` (
239	`graph_id` int(10) unsigned NOT NULL,
240	`node_id` int(10) unsigned DEFAULT NULL,
241	`cid` varchar(6) COLLATE latin1_general_cs NOT NULL,
242	`num` int(10) unsigned NOT NULL,
243	`res` char(1) COLLATE latin1_general_cs DEFAULT NULL,
244	`sstype` char(1) COLLATE latin1_general_cs DEFAULT NULL,
245	`i` int(2) NOT NULL DEFAULT '0',
246	`j` int(2) NOT NULL DEFAULT '0',
247	`minus` int(2) NOT NULL DEFAULT '0',
248	`mres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
249	`mss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
250	`mcn` int(2) NOT NULL DEFAULT '0',
251	`plus` int(2) NOT NULL DEFAULT '0',
252	`pres` char(1) COLLATE latin1_general_cs DEFAULT NULL,
253	`pss` char(1) COLLATE latin1_general_cs DEFAULT NULL,
254	`pcn` int(2) NOT NULL DEFAULT '0',
255	`nn` varchar(50) COLLATE latin1_general_cs,
256	`total` int(8) NOT NULL DEFAULT '0',
257	`rank` int(3) NOT NULL DEFAULT '0',
258	`deltarank` int(3) NOT NULL DEFAULT '0',
259	`score` decimal(6,2) NOT NULL DEFAULT '0.00'
260	) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_general_cs;
261
262
263	*/