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) {
                
            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, jrs;
                
                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; 
                int num; 
                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:	174
Committed:	Fri May 25 15:07:55 2007 UTC (17 years, 5 months ago) by lappe
File size:	8710 byte(s)
Log Message:	original version to be saved ...
Line	User	Rev	File contents
1	lappe	171	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7	lappe	174	public class iterateNbs {
8	lappe	171
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) {
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, jrs;
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			int num;
174			try {
175			sql = "select count(*) from single_model_node where n like '"+nbs+"';";
176			// System.out.println( sql);
177			stmt = conn.createStatement();
178			rsst = stmt.executeQuery(sql);
179			if (rsst.next()) lastTotal = rsst.getInt( 1);
180			rsst.close();
181			stmt.close();
182
183			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;";
184			stmt = conn.createStatement();
185			rsst = stmt.executeQuery(sql);
186			// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
187			int rank = 0;
188			boolean seenCentRes = false;
189			lastAUC = 0.0;
190			lastRank = 0;
191			lastFreq = 0.0;
192			lastavgk = 0.0;
193			lastdevk = 0.0;
194			while (rsst.next()) {
195			rank ++;
196			res = rsst.getString(1); // 1st column -- res
197			num = rsst.getInt(2); // 2nd column -- num
198			p = rsst.getDouble(3); // 3rd: fraction p
199			// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
200			logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
201			// System.out.print(" : " + logp);
202			plogp = -1.0 * p * logp;
203			// System.out.print(" : " + plogp);
204			plogpsum += plogp;
205			psum += p;
206
207			if (res.equals(centRes)) {
208			// System.out.print(" <==" + centRes);
209			seenCentRes = true;
210			lastFreq = p;
211			lastRank = rank;
212			lastavgk = rsst.getDouble(4);
213			lastdevk = rsst.getDouble(5);
214			}
215			if (seenCentRes) lastAUC += p;
216			// System.out.println("");
217			}
218			// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
219			rsst.close();
220			stmt.close();
221			lastEntropy = plogpsum;
222
223			} catch (SQLException e) {
224			e.printStackTrace();
225			System.err.println("SQLException: " + e.getMessage());
226			System.err.println("SQLState: " + e.getSQLState());
227			}
228
229			} // end of getEntropy
230
231			} // end class