owl/trunk/iterateNbs.java

import tools.MySQLConnection;

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

public class iterateNbs {

        /**
         *  
         * exchange of one neighbor at a time by a common neighbor 
         * @author lappe
         */
        
        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk; 
        static double  orgEntropy=0.0, orgFreq, orgAUC, orgavgk, orgdevk; 
        static int lastRank, lastTotal;  
        static int orgRank, orgTotal;
        
        public static void main(String[] args) throws SQLException {
                
            if (args.length<2){
                        System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
                        System.exit(1);
                }               
                int graphid = Integer.parseInt( args[0]);
                int resnr = Integer.parseInt( args[1]); 
                int n1=0, n2=0, ni=0, nj=0, j_num=0, j_shell, j_cnsize, i, j; 
                conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2_a"); 
                String sql, j_res, j_sec, restype="?", ressec="?", nbs_lo, nbs_up; 
                Statement stmt, jst;  
                ResultSet rsst;
                
                try {
                        System.out.println("getting direct neighborhood ... "); 
                        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 single_model_edge where graph_id="+graphid+" and i_num="+resnr+";");
                        stmt.close(); 
        
                        System.out.println("building the 2nd shell");  
                        sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                n1++; 
                                j_num = rsst.getInt(1);
                                System.out.println(n1+":"+j_num); 
                                jst = conn.createStatement();
                                sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
                                // System.out.println(">"+sql); 
                                jst.executeUpdate( sql); 
                                jst.close(); 
                        } // end while 
                        rsst.close(); 
                        stmt.close(); 
                        
                        System.out.println("retrieving the entire 1st and 2nd shell");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // counting shell2
                        n2=0; 
                        while (rsst.next()) {
                                if ( rsst.getInt( 4)==2) { // count 2nd shell entry 
                                        n2++;
                                        if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure 
                                                restype =  rsst.getString( 2).toUpperCase(); 
                                                ressec  =  rsst.getString( 3).toUpperCase();
                                        } // end if central residue 
                                } // end if 2nds shell 
                                System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); 
                        } // end while 
                        System.out.println("SIZE 1st shell "+n1); 
                        System.out.println("SIZE 2nd shell "+n2);
                        System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); 
                        
                        for (i=0; i<=n1; i++) { // 1st loop through all direct contacts
                                // System.out.print(i+" - "); 
                                for (j=0; j<=n2; j++) { // 2nd loop through all indirect contacts
                                        System.out.print("("+i+","+j+")");
                                        ni = 0; 
                                        nj = 0; 
                                        nbs_lo="%";
                                        nbs_up="%";
                                        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);
                                          
                                                if (j_shell==1) { // a direct 1st shell neighbour 
                                                        ni++;
                                                        if (ni!=i) {// if this is NOT the one direct nb 2B dropped 
                                                                nbs_lo+=j_res+"%";
                                                                nbs_up+=j_res+"%";                                                              
                                                        } else { // this one IS dropped 
                                                                System.out.print("(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"); 
                                                        } // end if ni!=i 
                                                } else { // 2nd shell neighbour 
                                                        nj++; 
                                                        if (j_num==resnr) { // the central residue is part if the 2nd shell
                                                                if (nj!=j) { // drop x if marked for inclusion 
                                                                        nbs_lo +="x%"; 
                                                                        nbs_up +="x%"; 
                                                                } else {
                                                                        System.out.print(" no x ..."); 
                                                                }
                                                        } else { // this is not x 
                                                                if (nj==j) { // this is the 2nd shell nb 2B included
                                                                        nbs_lo+=j_res.toLowerCase()+"%";
                                                                        nbs_up+=j_res.toUpperCase()+"%";
                                                                        System.out.print("(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"); 
                                                                } // end if 
                                                        } // end if this is central residue x 
                                                } // end if 1st/2nd shell
                                        } // end while through the entire nbhood 
                                        
                                        getEntropy( nbs_lo, restype); 
                                        if (i==0 && j==0) { // original nbhoodstring without any insertions/deletions 
                                                orgEntropy = lastEntropy;
                                                orgFreq = lastFreq;
                                                orgAUC  = lastAUC;
                                                orgavgk = lastavgk;
                                                orgdevk = lastdevk; 
                                                orgRank = lastRank;
                                                orgTotal= lastTotal; 
                                        } // end if 0/0 for defining org* 
                                        System.out.println(" t="+orgTotal+" \tentropy = "+String.format("%.5f", orgEntropy)+" \trank#"+String.format("%2d",orgRank)+" \tp("+restype+") = "+String.format("%.5f",orgFreq)+" \t\tAUC = "+String.format("%.5f",orgAUC)+" \t\tavg(k)="+String.format("%.2f",orgavgk)+"\tstddev="+String.format("%.2f",orgdevk));
                                        System.out.print("\tlo "+nbs_lo);
                                        printValues();                          
                                        System.out.print("\tup "+nbs_up);
                                        getEntropy(nbs_up, restype); 
                                        printValues(); 
                                        
                                        // System.out.println(".");
                                } // close for loop 2 (j)
                        } // next loop 1 (i)
                        rsst.close(); 
                        stmt.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 printValues() {
                System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")"); 
                System.out.print( "\t"+String.format("%.5f", lastEntropy) +" ("+String.format("%.5f", lastEntropy-orgEntropy)+")");
                System.out.print( "\t#"+String.format("%2d",lastRank) +" ("+String.format("%2d",(lastRank-orgRank))+")");
                System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
                System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
                System.out.print( "\t"+String.format("%.2f", lastavgk) +" ("+String.format("%.2f", (lastavgk-orgavgk))+")");
                System.out.print( "\t"+String.format("%.2f", lastdevk) +" ("+String.format("%.2f", (lastdevk-orgdevk))+")");
                System.out.println("");
        }
        
        public static void getEntropy( String nbs, String centRes) {
                String sql, res; 
                Statement stmt;  
                ResultSet rsst;
                double p, psum=0.0, logp, plogp, plogpsum=0.0;  
                try {
                        sql = "select count(*) from single_model_node where n like '"+nbs+"';";
                        // System.out.println( sql); 
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) lastTotal = rsst.getInt( 1); 
                        rsst.close(); 
                        stmt.close(); 
                        
                        sql = "select res, count(*) as t, count(*)/"+lastTotal+" as p, avg( k), stddev( k) from single_model_node where n like '"+nbs+"' group by res order by p DESC;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
                        int rank = 0; 
                        boolean seenCentRes = false;  
                        lastAUC = 0.0; 
                        lastRank = 0; 
                        lastFreq = 0.0;
                        lastavgk = 0.0;
                        lastdevk = 0.0;
                        while (rsst.next()) {   
                                rank ++;
                                res = rsst.getString(1); // 1st column -- res
                                //num = rsst.getInt(2); // 2nd column -- num
                                p = rsst.getDouble(3); // 3rd: fraction p 
                                // System.out.print(rank+ " : " + res+"   : "+num+ " : " + p);
                                logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits 
                                // System.out.print(" : " + logp); 
                                plogp = -1.0 * p * logp;  
                                // System.out.print(" : " + plogp);
                                plogpsum += plogp;  
                                psum += p; 
                                
                                if (res.equals(centRes)) { 
                                        // System.out.print(" <==" + centRes);
                                        seenCentRes = true;
                                        lastFreq = p;
                                        lastRank = rank; 
                                        lastavgk = rsst.getDouble(4);
                                        lastdevk = rsst.getDouble(5);
                                }
                                if (seenCentRes) lastAUC += p; 
                                // System.out.println("");
                        }
                        // System.out.println("Sum :"+lastTotal+"       : "+psum+"       : "+plogpsum);
                        rsst.close(); 
                        stmt.close(); 
                        lastEntropy = plogpsum; 
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }
                
        } // end of getEntropy 

} // end class 
Revision:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (17 years, 1 month ago) by duarte
File size:	8716 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 iterateNbs {
8
9	/**
10	*
11	* exchange of one neighbor at a time by a common neighbor
12	* @author lappe
13	*/
14
15	static String user = "lappe" ; // change user name!!
16	static MySQLConnection conn;
17	static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk;
18	static double orgEntropy=0.0, orgFreq, orgAUC, orgavgk, orgdevk;
19	static int lastRank, lastTotal;
20	static int orgRank, orgTotal;
21
22	public static void main(String[] args) throws SQLException {
23
24	if (args.length<2){
25	System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
26	System.exit(1);
27	}
28	int graphid = Integer.parseInt( args[0]);
29	int resnr = Integer.parseInt( args[1]);
30	int n1=0, n2=0, ni=0, nj=0, j_num=0, j_shell, j_cnsize, i, j;
31	conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2_a");
32	String sql, j_res, j_sec, restype="?", ressec="?", nbs_lo, nbs_up;
33	Statement stmt, jst;
34	ResultSet rsst;
35
36	try {
37	System.out.println("getting direct neighborhood ... ");
38	stmt = conn.createStatement();
39	stmt.executeUpdate("drop table if exists temp_shell;");
40	stmt.close();
41
42	stmt = conn.createStatement();
43	stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from single_model_edge where graph_id="+graphid+" and i_num="+resnr+";");
44	stmt.close();
45
46	System.out.println("building the 2nd shell");
47	sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
48	stmt = conn.createStatement();
49	rsst = stmt.executeQuery(sql);
50	while (rsst.next()) {
51	n1++;
52	j_num = rsst.getInt(1);
53	System.out.println(n1+":"+j_num);
54	jst = conn.createStatement();
55	sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
56	// System.out.println(">"+sql);
57	jst.executeUpdate( sql);
58	jst.close();
59	} // end while
60	rsst.close();
61	stmt.close();
62
63	System.out.println("retrieving the entire 1st and 2nd shell");
64	sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num;";
65	stmt = conn.createStatement();
66	rsst = stmt.executeQuery(sql);
67	// counting shell2
68	n2=0;
69	while (rsst.next()) {
70	if ( rsst.getInt( 4)==2) { // count 2nd shell entry
71	n2++;
72	if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure
73	restype = rsst.getString( 2).toUpperCase();
74	ressec = rsst.getString( 3).toUpperCase();
75	} // end if central residue
76	} // end if 2nds shell
77	System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
78	} // end while
79	System.out.println("SIZE 1st shell "+n1);
80	System.out.println("SIZE 2nd shell "+n2);
81	System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec);
82
83	for (i=0; i<=n1; i++) { // 1st loop through all direct contacts
84	// System.out.print(i+" - ");
85	for (j=0; j<=n2; j++) { // 2nd loop through all indirect contacts
86	System.out.print("("+i+","+j+")");
87	ni = 0;
88	nj = 0;
89	nbs_lo="%";
90	nbs_up="%";
91	rsst.beforeFirst();
92	while (rsst.next()) {
93	j_num = rsst.getInt( 1);
94	j_res = rsst.getString(2);
95	j_sec = rsst.getString(3);
96	j_shell = rsst.getInt( 4);
97	j_cnsize = rsst.getInt( 5);
98
99	if (j_shell==1) { // a direct 1st shell neighbour
100	ni++;
101	if (ni!=i) {// if this is NOT the one direct nb 2B dropped
102	nbs_lo+=j_res+"%";
103	nbs_up+=j_res+"%";
104	} else { // this one IS dropped
105	System.out.print("(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")");
106	} // end if ni!=i
107	} else { // 2nd shell neighbour
108	nj++;
109	if (j_num==resnr) { // the central residue is part if the 2nd shell
110	if (nj!=j) { // drop x if marked for inclusion
111	nbs_lo +="x%";
112	nbs_up +="x%";
113	} else {
114	System.out.print(" no x ...");
115	}
116	} else { // this is not x
117	if (nj==j) { // this is the 2nd shell nb 2B included
118	nbs_lo+=j_res.toLowerCase()+"%";
119	nbs_up+=j_res.toUpperCase()+"%";
120	System.out.print("(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")");
121	} // end if
122	} // end if this is central residue x
123	} // end if 1st/2nd shell
124	} // end while through the entire nbhood
125
126	getEntropy( nbs_lo, restype);
127	if (i==0 && j==0) { // original nbhoodstring without any insertions/deletions
128	orgEntropy = lastEntropy;
129	orgFreq = lastFreq;
130	orgAUC = lastAUC;
131	orgavgk = lastavgk;
132	orgdevk = lastdevk;
133	orgRank = lastRank;
134	orgTotal= lastTotal;
135	} // end if 0/0 for defining org*
136	System.out.println(" t="+orgTotal+" \tentropy = "+String.format("%.5f", orgEntropy)+" \trank#"+String.format("%2d",orgRank)+" \tp("+restype+") = "+String.format("%.5f",orgFreq)+" \t\tAUC = "+String.format("%.5f",orgAUC)+" \t\tavg(k)="+String.format("%.2f",orgavgk)+"\tstddev="+String.format("%.2f",orgdevk));
137	System.out.print("\tlo "+nbs_lo);
138	printValues();
139	System.out.print("\tup "+nbs_up);
140	getEntropy(nbs_up, restype);
141	printValues();
142
143	// System.out.println(".");
144	} // close for loop 2 (j)
145	} // next loop 1 (i)
146	rsst.close();
147	stmt.close();
148
149	} catch (SQLException e) {
150	e.printStackTrace();
151	System.err.println("SQLException: " + e.getMessage());
152	System.err.println("SQLState: " + e.getSQLState());
153	} // end try/catch
154	System.out.println("fin.");
155	} // end main
156
157	public static void printValues() {
158	System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")");
159	System.out.print( "\t"+String.format("%.5f", lastEntropy) +" ("+String.format("%.5f", lastEntropy-orgEntropy)+")");
160	System.out.print( "\t#"+String.format("%2d",lastRank) +" ("+String.format("%2d",(lastRank-orgRank))+")");
161	System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
162	System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
163	System.out.print( "\t"+String.format("%.2f", lastavgk) +" ("+String.format("%.2f", (lastavgk-orgavgk))+")");
164	System.out.print( "\t"+String.format("%.2f", lastdevk) +" ("+String.format("%.2f", (lastdevk-orgdevk))+")");
165	System.out.println("");
166	}
167
168	public static void getEntropy( String nbs, String centRes) {
169	String sql, res;
170	Statement stmt;
171	ResultSet rsst;
172	double p, psum=0.0, logp, plogp, plogpsum=0.0;
173	try {
174	sql = "select count(*) from single_model_node where n like '"+nbs+"';";
175	// System.out.println( sql);
176	stmt = conn.createStatement();
177	rsst = stmt.executeQuery(sql);
178	if (rsst.next()) lastTotal = rsst.getInt( 1);
179	rsst.close();
180	stmt.close();
181
182	sql = "select res, count() as t, count()/"+lastTotal+" as p, avg( k), stddev( k) from single_model_node where n like '"+nbs+"' group by res order by p DESC;";
183	stmt = conn.createStatement();
184	rsst = stmt.executeQuery(sql);
185	// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
186	int rank = 0;
187	boolean seenCentRes = false;
188	lastAUC = 0.0;
189	lastRank = 0;
190	lastFreq = 0.0;
191	lastavgk = 0.0;
192	lastdevk = 0.0;
193	while (rsst.next()) {
194	rank ++;
195	res = rsst.getString(1); // 1st column -- res
196	//num = rsst.getInt(2); // 2nd column -- num
197	p = rsst.getDouble(3); // 3rd: fraction p
198	// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
199	logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
200	// System.out.print(" : " + logp);
201	plogp = -1.0 * p * logp;
202	// System.out.print(" : " + plogp);
203	plogpsum += plogp;
204	psum += p;
205
206	if (res.equals(centRes)) {
207	// System.out.print(" <==" + centRes);
208	seenCentRes = true;
209	lastFreq = p;
210	lastRank = rank;
211	lastavgk = rsst.getDouble(4);
212	lastdevk = rsst.getDouble(5);
213	}
214	if (seenCentRes) lastAUC += p;
215	// System.out.println("");
216	}
217	// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
218	rsst.close();
219	stmt.close();
220	lastEntropy = plogpsum;
221
222	} catch (SQLException e) {
223	e.printStackTrace();
224	System.err.println("SQLException: " + e.getMessage());
225	System.err.println("SQLState: " + e.getSQLState());
226	}
227
228	} // end of getEntropy
229
230	} // end class