branches/aglappe-jung/testGetChains.java

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.sql.SQLException;

import proteinstructure.CiffilePdb;
//import proteinstructure.MsdsdPdb;
import proteinstructure.Pdb;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbLoadError;
import proteinstructure.PdbasePdb;
import proteinstructure.PdbfilePdb;
import tools.MySQLConnection;


public class testGetChains {

        public static void main(String[] args) throws IOException, SQLException{
                
                String pdbFilesDir = "/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/pdb";
                String cifFilesDir = "/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF";
                MySQLConnection conn = new MySQLConnection("white","duarte","nieve");
                
                //String[] pdbCodes = {"12as", "3eca", "1bxy"} ;
                
                String listFile = "/project/StruPPi/jose/workspace/aglappe-jung/pdbcodes.testset";
                BufferedReader fpdb = new BufferedReader(new FileReader(listFile));
                String  line;
                while ((line=fpdb.readLine())!=null) {
                        String pdbCode = line.split("\t")[0].toLowerCase();
                
                        System.out.println("pdb "+pdbCode);
                        
                        try {
                                Pdb pdbasepdb = new PdbasePdb(pdbCode, "pdbase", conn);
                                String[] pdbasechains = pdbasepdb.getChains();
                                Integer[] pdbasemodels = pdbasepdb.getModels();
                                pdbasepdb.load(pdbasechains[0]);


//                              Pdb msdsdpdb = new MsdsdPdb(pdbCode,"msdsd_00_07_a",conn);
//                              String[] msdsdchains = msdsdpdb.getChains();
//                              Integer[] msdsdmodels = msdsdpdb.getModels();
//                              msdsdpdb.load(msdsdchains[0]);

                                Pdb ciffilepdb = new CiffilePdb(new File(cifFilesDir,pdbCode+".cif"));
                                String[] ciffilechains = ciffilepdb.getChains();
                                Integer[] ciffilemodels = ciffilepdb.getModels();
                                ciffilepdb.load(ciffilechains[0]);


                                Pdb pdbfilepdb = new PdbfilePdb(pdbFilesDir+"/pdb"+pdbCode+".ent");
                                String[] pdbfilechains = pdbfilepdb.getChains();
                                Integer[] pdbfilemodels = pdbfilepdb.getModels();
                                pdbfilepdb.load(pdbfilechains[0]);
                                

//                      System.out.println("online cif file...");
//                      pdb = new CiffilePdb(pdbCode);
//                      allChains = pdb.getChains();
//                      System.out.print("pdb: "+pdbCode+", chains: ");
//                      for (String chain:allChains) {
//                              System.out.print(chain+ " ");
//                      }
//                      System.out.println();
//                      pdb.load("A");
//                      System.out.println("length:" + pdb.getFullLength());

                                boolean chainsmatch = true;
                                boolean modelsmatch = true;
                                if (pdbasechains.length != ciffilechains.length || pdbasechains.length!= pdbfilechains.length ) { //|| pdbasechains.length!=msdsdchains.length) {
                                        System.out.println("different number of chains");
                                        chainsmatch=false;
                                }
                                else {
                                        for (int i=0; i<pdbasechains.length;i++) {
                                                if (!pdbasechains[i].equals(ciffilechains[i]) || !pdbasechains[i].equals(pdbfilechains[i]) ){ // || !pdbasechains[i].equals(msdsdchains[i])){
                                                        System.out.println("chain differs: pdbase "+pdbasechains[i]+", ciffile "+ciffilechains[i]+", pdbfile "+pdbfilechains[i]);//+", msdsd "+msdsdchains[i]);
                                                        chainsmatch=false;
                                                }
                                        }
                                }
                                
                                if (chainsmatch) {
                                        for (String chain:pdbfilechains) {
                                                System.out.print(chain+ " ");
                                        }
                                        System.out.println();

                                        if (pdbasepdb.getFullLength()!=ciffilepdb.getFullLength() || pdbasepdb.getFullLength()!=pdbfilepdb.getFullLength()){ // || pdbasepdb.getFullLength()!=msdsdpdb.getFullLength()) {
                                                System.out.println("length for chain "+pdbfilechains[0]+" differs");
                                        }
                                }
                                
                                if (pdbasemodels.length != ciffilemodels.length || pdbasemodels.length != pdbfilemodels.length ) {//|| pdbasemodels.length != msdsdmodels.length) {
                                        System.out.println("different number of models");
                                        modelsmatch = false;
                                } else {
                                        for (int i=0;i<pdbasemodels.length;i++){
                                                if (pdbasemodels[i]!=ciffilemodels[i] || pdbasemodels[i]!=pdbfilemodels[i] ){ //|| pdbasemodels[i]!=msdsdmodels[i]){
                                                        System.out.println("model differs: pdbase "+pdbasemodels[i]+", ciffile "+ciffilemodels[i]+", pdbfile "+pdbfilemodels[i]);//+", msdsd "+msdsdmodels[i]);
                                                        modelsmatch = false;
                                                }
                                        }
                                }
                                if (modelsmatch) {
                                        for (int model:pdbasemodels) {
                                                System.out.print(model+" ");
                                        }
                                        System.out.println();
                                }
                                
                                
                        } catch (PdbCodeNotFoundError e) {
                                System.err.println("pdb code was not found in pdbase");
                        } catch (PdbLoadError e) {
                                System.err.println("couldn't load pdb data, specific error: "+e.getMessage());
                        }
                }
                fpdb.close();
                
                
        }

}
Revision:	441
Committed:	Thu Nov 29 15:19:37 2007 UTC (16 years, 10 months ago) by duarte
File size:	4542 byte(s)
Log Message:	Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
Line	User	Rev	File contents
1	duarte	441	import java.io.BufferedReader;
2			import java.io.File;
3			import java.io.FileReader;
4			import java.io.IOException;
5			import java.sql.SQLException;
6
7			import proteinstructure.CiffilePdb;
8			//import proteinstructure.MsdsdPdb;
9			import proteinstructure.Pdb;
10			import proteinstructure.PdbCodeNotFoundError;
11			import proteinstructure.PdbLoadError;
12			import proteinstructure.PdbasePdb;
13			import proteinstructure.PdbfilePdb;
14			import tools.MySQLConnection;
15
16
17			public class testGetChains {
18
19			public static void main(String[] args) throws IOException, SQLException{
20
21			String pdbFilesDir = "/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/pdb";
22			String cifFilesDir = "/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF";
23			MySQLConnection conn = new MySQLConnection("white","duarte","nieve");
24
25			//String[] pdbCodes = {"12as", "3eca", "1bxy"} ;
26
27			String listFile = "/project/StruPPi/jose/workspace/aglappe-jung/pdbcodes.testset";
28			BufferedReader fpdb = new BufferedReader(new FileReader(listFile));
29			String line;
30			while ((line=fpdb.readLine())!=null) {
31			String pdbCode = line.split("\t")[0].toLowerCase();
32
33			System.out.println("pdb "+pdbCode);
34
35			try {
36			Pdb pdbasepdb = new PdbasePdb(pdbCode, "pdbase", conn);
37			String[] pdbasechains = pdbasepdb.getChains();
38			Integer[] pdbasemodels = pdbasepdb.getModels();
39			pdbasepdb.load(pdbasechains[0]);
40
41
42			// Pdb msdsdpdb = new MsdsdPdb(pdbCode,"msdsd_00_07_a",conn);
43			// String[] msdsdchains = msdsdpdb.getChains();
44			// Integer[] msdsdmodels = msdsdpdb.getModels();
45			// msdsdpdb.load(msdsdchains[0]);
46
47			Pdb ciffilepdb = new CiffilePdb(new File(cifFilesDir,pdbCode+".cif"));
48			String[] ciffilechains = ciffilepdb.getChains();
49			Integer[] ciffilemodels = ciffilepdb.getModels();
50			ciffilepdb.load(ciffilechains[0]);
51
52
53			Pdb pdbfilepdb = new PdbfilePdb(pdbFilesDir+"/pdb"+pdbCode+".ent");
54			String[] pdbfilechains = pdbfilepdb.getChains();
55			Integer[] pdbfilemodels = pdbfilepdb.getModels();
56			pdbfilepdb.load(pdbfilechains[0]);
57
58
59			// System.out.println("online cif file...");
60			// pdb = new CiffilePdb(pdbCode);
61			// allChains = pdb.getChains();
62			// System.out.print("pdb: "+pdbCode+", chains: ");
63			// for (String chain:allChains) {
64			// System.out.print(chain+ " ");
65			// }
66			// System.out.println();
67			// pdb.load("A");
68			// System.out.println("length:" + pdb.getFullLength());
69
70			boolean chainsmatch = true;
71			boolean modelsmatch = true;
72			if (pdbasechains.length != ciffilechains.length \|\| pdbasechains.length!= pdbfilechains.length ) { //\|\| pdbasechains.length!=msdsdchains.length) {
73			System.out.println("different number of chains");
74			chainsmatch=false;
75			}
76			else {
77			for (int i=0; i<pdbasechains.length;i++) {
78			if (!pdbasechains[i].equals(ciffilechains[i]) \|\| !pdbasechains[i].equals(pdbfilechains[i]) ){ // \|\| !pdbasechains[i].equals(msdsdchains[i])){
79			System.out.println("chain differs: pdbase "+pdbasechains[i]+", ciffile "+ciffilechains[i]+", pdbfile "+pdbfilechains[i]);//+", msdsd "+msdsdchains[i]);
80			chainsmatch=false;
81			}
82			}
83			}
84
85			if (chainsmatch) {
86			for (String chain:pdbfilechains) {
87			System.out.print(chain+ " ");
88			}
89			System.out.println();
90
91			if (pdbasepdb.getFullLength()!=ciffilepdb.getFullLength() \|\| pdbasepdb.getFullLength()!=pdbfilepdb.getFullLength()){ // \|\| pdbasepdb.getFullLength()!=msdsdpdb.getFullLength()) {
92			System.out.println("length for chain "+pdbfilechains[0]+" differs");
93			}
94			}
95
96			if (pdbasemodels.length != ciffilemodels.length \|\| pdbasemodels.length != pdbfilemodels.length ) {//\|\| pdbasemodels.length != msdsdmodels.length) {
97			System.out.println("different number of models");
98			modelsmatch = false;
99			} else {
100			for (int i=0;i<pdbasemodels.length;i++){
101			if (pdbasemodels[i]!=ciffilemodels[i] \|\| pdbasemodels[i]!=pdbfilemodels[i] ){ //\|\| pdbasemodels[i]!=msdsdmodels[i]){
102			System.out.println("model differs: pdbase "+pdbasemodels[i]+", ciffile "+ciffilemodels[i]+", pdbfile "+pdbfilemodels[i]);//+", msdsd "+msdsdmodels[i]);
103			modelsmatch = false;
104			}
105			}
106			}
107			if (modelsmatch) {
108			for (int model:pdbasemodels) {
109			System.out.print(model+" ");
110			}
111			System.out.println();
112			}
113
114
115			} catch (PdbCodeNotFoundError e) {
116			System.err.println("pdb code was not found in pdbase");
117			} catch (PdbLoadError e) {
118			System.err.println("couldn't load pdb data, specific error: "+e.getMessage());
119			}
120			}
121			fpdb.close();
122
123
124
125
126
127
128			}
129
130			}