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import java.io.BufferedReader; |
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import java.io.File; |
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import java.io.FileReader; |
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import java.io.IOException; |
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import java.sql.SQLException; |
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import actionTools.GetterError; |
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import proteinstructure.CiffilePdb; |
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//import proteinstructure.MsdsdPdb; |
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import proteinstructure.Pdb; |
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import proteinstructure.PdbCodeNotFoundError; |
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import proteinstructure.PdbLoadError; |
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import proteinstructure.PdbasePdb; |
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import proteinstructure.PdbfilePdb; |
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import tools.MySQLConnection; |
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public class testGetChains { |
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duarte |
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public static void main(String[] args) throws IOException, SQLException, GetterError{ |
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String pdbFilesDir = "/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/pdb"; |
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String cifFilesDir = "/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF"; |
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MySQLConnection conn = new MySQLConnection("white","duarte","nieve"); |
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//String[] pdbCodes = {"12as", "3eca", "1bxy"} ; |
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String listFile = "/project/StruPPi/jose/workspace/aglappe-jung/pdbcodes.testset"; |
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BufferedReader fpdb = new BufferedReader(new FileReader(listFile)); |
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String line; |
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while ((line=fpdb.readLine())!=null) { |
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String pdbCode = line.split("\t")[0].toLowerCase(); |
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System.out.println("pdb "+pdbCode); |
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try { |
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Pdb pdbasepdb = new PdbasePdb(pdbCode, "pdbase", conn); |
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String[] pdbasechains = pdbasepdb.getChains(); |
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Integer[] pdbasemodels = pdbasepdb.getModels(); |
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pdbasepdb.load(pdbasechains[0]); |
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// Pdb msdsdpdb = new MsdsdPdb(pdbCode,"msdsd_00_07_a",conn); |
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// String[] msdsdchains = msdsdpdb.getChains(); |
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// Integer[] msdsdmodels = msdsdpdb.getModels(); |
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// msdsdpdb.load(msdsdchains[0]); |
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Pdb ciffilepdb = new CiffilePdb(new File(cifFilesDir,pdbCode+".cif")); |
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String[] ciffilechains = ciffilepdb.getChains(); |
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Integer[] ciffilemodels = ciffilepdb.getModels(); |
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ciffilepdb.load(ciffilechains[0]); |
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Pdb pdbfilepdb = new PdbfilePdb(pdbFilesDir+"/pdb"+pdbCode+".ent"); |
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String[] pdbfilechains = pdbfilepdb.getChains(); |
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Integer[] pdbfilemodels = pdbfilepdb.getModels(); |
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pdbfilepdb.load(pdbfilechains[0]); |
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// System.out.println("online cif file..."); |
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// pdb = new CiffilePdb(pdbCode); |
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// allChains = pdb.getChains(); |
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// System.out.print("pdb: "+pdbCode+", chains: "); |
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// for (String chain:allChains) { |
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// System.out.print(chain+ " "); |
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// } |
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// System.out.println(); |
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// pdb.load("A"); |
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// System.out.println("length:" + pdb.getFullLength()); |
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boolean chainsmatch = true; |
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boolean modelsmatch = true; |
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if (pdbasechains.length != ciffilechains.length || pdbasechains.length!= pdbfilechains.length ) { //|| pdbasechains.length!=msdsdchains.length) { |
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System.out.println("different number of chains"); |
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chainsmatch=false; |
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} |
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else { |
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for (int i=0; i<pdbasechains.length;i++) { |
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if (!pdbasechains[i].equals(ciffilechains[i]) || !pdbasechains[i].equals(pdbfilechains[i]) ){ // || !pdbasechains[i].equals(msdsdchains[i])){ |
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System.out.println("chain differs: pdbase "+pdbasechains[i]+", ciffile "+ciffilechains[i]+", pdbfile "+pdbfilechains[i]);//+", msdsd "+msdsdchains[i]); |
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chainsmatch=false; |
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} |
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} |
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} |
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if (chainsmatch) { |
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for (String chain:pdbfilechains) { |
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System.out.print(chain+ " "); |
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} |
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System.out.println(); |
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if (pdbasepdb.getFullLength()!=ciffilepdb.getFullLength() || pdbasepdb.getFullLength()!=pdbfilepdb.getFullLength()){ // || pdbasepdb.getFullLength()!=msdsdpdb.getFullLength()) { |
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System.out.println("length for chain "+pdbfilechains[0]+" differs"); |
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} |
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} |
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if (pdbasemodels.length != ciffilemodels.length || pdbasemodels.length != pdbfilemodels.length ) {//|| pdbasemodels.length != msdsdmodels.length) { |
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System.out.println("different number of models"); |
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modelsmatch = false; |
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} else { |
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for (int i=0;i<pdbasemodels.length;i++){ |
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if (pdbasemodels[i]!=ciffilemodels[i] || pdbasemodels[i]!=pdbfilemodels[i] ){ //|| pdbasemodels[i]!=msdsdmodels[i]){ |
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System.out.println("model differs: pdbase "+pdbasemodels[i]+", ciffile "+ciffilemodels[i]+", pdbfile "+pdbfilemodels[i]);//+", msdsd "+msdsdmodels[i]); |
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modelsmatch = false; |
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} |
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} |
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} |
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if (modelsmatch) { |
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for (int model:pdbasemodels) { |
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System.out.print(model+" "); |
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} |
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System.out.println(); |
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} |
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} catch (PdbCodeNotFoundError e) { |
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System.err.println("pdb code was not found in pdbase"); |
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} catch (PdbLoadError e) { |
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System.err.println("couldn't load pdb data, specific error: "+e.getMessage()); |
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} |
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} |
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fpdb.close(); |
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} |
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} |
