/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * * created at Apr 26, 2008 */ package org.biojava.bio.structure; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.util.List; import org.biojava.bio.structure.io.PDBFileParser; import org.biojava.bio.structure.io.mmcif.MMcifParser; import org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer; import org.biojava.bio.structure.io.mmcif.SimpleMMcifParser; import junit.framework.TestCase; public class MMcifTest extends TestCase { public void testLoad(){ // test a simple protein comparePDB2cif("5pti","A"); // test a protein with modified residues comparePDB2cif("1a4w","L"); comparePDB2cif("1a4w","H"); comparePDB2cif("1a4w","I"); // test a DNA binding protein comparePDB2cif("1j59","A"); comparePDB2cif("1j59","B"); comparePDB2cif("1j59","C"); comparePDB2cif("1j59","D"); comparePDB2cif("1j59","E"); comparePDB2cif("1j59","F"); // test a NMR protein comparePDB2cif("2kc9","A"); } private void comparePDB2cif(String id, String chainId){ String fileName = "/files/"+id+".cif"; InputStream inStream = this.getClass().getResourceAsStream(fileName); assertNotNull(inStream); MMcifParser parser = new SimpleMMcifParser(); SimpleMMcifConsumer consumer = new SimpleMMcifConsumer(); parser.addMMcifConsumer(consumer); try { parser.parse(new BufferedReader(new InputStreamReader(inStream))); } catch (IOException e){ fail(e.getMessage()); } Structure cifStructure = consumer.getStructure(); assertNotNull(cifStructure); // load the PDB file via the PDB parser Structure pdbStructure = null; InputStream pinStream = this.getClass().getResourceAsStream("/files/"+id+".pdb"); assertNotNull(inStream); PDBFileParser pdbpars = new PDBFileParser(); try { pdbStructure = pdbpars.parsePDBFile(pinStream) ; } catch (IOException e) { e.printStackTrace(); } assertNotNull(pdbStructure); //System.out.println(pdbStructure.toPDB()); //System.out.println(cifStructure.toPDB()); // now compare the results try { // chech NMR data assertEquals("the isNMR flag is not the same!", pdbStructure.isNmr(), cifStructure.isNmr()); if ( pdbStructure.isNmr()){ assertEquals("the nr of NMR models is not the same!", pdbStructure.nrModels(), pdbStructure.nrModels()); checkNMR(pdbStructure); checkNMR(cifStructure); } //System.out.println(pdbStructure); //System.out.println(cifStructure); // compare amino acids in chain 1: Chain a_pdb = pdbStructure.getChainByPDB(chainId); Chain a_cif = cifStructure.getChainByPDB(chainId); //System.out.println(a_pdb.getAtomGroups()); //System.out.println(a_cif.getAtomGroups()); //for (Group g: a_cif.getAtomGroups()){ // System.out.println(g); //} //System.out.println("--"); String pdb_SEQseq = a_pdb.getSeqResSequence(); String cif_SEQseq = a_cif.getSeqResSequence(); assertEquals("the SEQRES sequences don;t match!", pdb_SEQseq,cif_SEQseq); // actually this check not necessarily works, since there can be waters in PDB that we don;t deal with yet in cif... //assertEquals("the nr of ATOM record groups is not the same!" , a_pdb.getAtomLength(),a_cif.getAtomLength()); for (int i = 0 ; i < a_pdb.getAtomGroups(GroupType.AMINOACID).size(); i++){ Group gp = a_pdb.getAtomGroups(GroupType.AMINOACID).get(i); Group gc = a_cif.getAtomGroups(GroupType.AMINOACID).get(i); checkGroups(gp,gc); } String pdb_seq = a_pdb.getAtomSequence(); String cif_seq = a_cif.getAtomSequence(); //System.out.println(pdb_seq); //System.out.println(cif_seq); assertEquals("the sequences obtained from PDB and mmCif don't match!",pdb_seq, cif_seq); List pdb_dbrefs= pdbStructure.getDBRefs(); List cif_dbrefs= cifStructure.getDBRefs(); assertEquals("nr of DBrefs found does not match!", pdb_dbrefs.size(),cif_dbrefs.size()); DBRef p = pdb_dbrefs.get(0); DBRef c = cif_dbrefs.get(0); //System.out.println(p.toPDB()); //System.out.println(c.toPDB()); String pdb_dbref = p.toPDB(); String cif_dbref = c.toPDB(); assertEquals("DBRef is not equal",pdb_dbref,cif_dbref); PDBHeader h1 = pdbStructure.getPDBHeader(); PDBHeader h2 = cifStructure.getPDBHeader(); //compareString(h1.toPDB() ,h2.toPDB()); //System.out.println(h1.toPDB()); //System.out.println(h2.toPDB()); assertEquals("the PDBHeader.toPDB representation is not equivalent", h1.toPDB().toUpperCase(),h2.toPDB().toUpperCase()); // and the ultimate test! // but we are not there yet... // TODO: still need to parse SSBOND equivalent info from cif files... //assertEquals("the Structure.toPDB representation is not equivalent", pdbStructure.toPDB(),cifStructure.toPDB()); } catch (StructureException ex){ fail(ex.getMessage() + " for PDB: " + id); } } private void checkGroups(Group g1, Group g2){ //System.out.println("comparing " +g1 + " " + g2); assertEquals(g1.getType(),g2.getType()); assertEquals(g1.getPDBCode(),g2.getPDBCode()); assertEquals(g1.getPDBName(),g2.getPDBName()); assertEquals(g1.has3D(),g2.has3D()); assertEquals(g1.getAtoms().size(), g2.getAtoms().size()); if ( g1.has3D()){ try { Atom a1 = g1.getAtom(0); Atom a2 = g2.getAtom(0); assertEquals(a1.getX(),a2.getX()); assertEquals(a1.getOccupancy(),a2.getOccupancy()); assertEquals(a1.getTempFactor(),a2.getTempFactor()); assertEquals(a1.getFullName(),a2.getFullName()); } catch (StructureException e){ fail(e.getMessage()); } } } private void checkNMR(Structure s){ assertTrue(s.isNmr()); int models = s.nrModels(); assertTrue(models > 0); List model0 = s.getModel(0); // compare with all others for (int i = 1 ; i < models; i++){ List modelX = s.getModel(i); assertEquals(model0.size(),modelX.size()); // compare lengths: for (int j=0 ; j< model0.size();j++){ Chain c1 = model0.get(j); Chain cx = modelX.get(j); assertEquals(c1.getAtomLength(),cx.getAtomLength()); // can;t compare seq res, since this is only done for 1st... //assertEquals("c1.getSeqResLength(),cx.getSeqResLength()); assertEquals(c1.getAtomSequence(),cx.getAtomSequence()); assertEquals(c1.getLengthAminos(),cx.getLengthAminos()); assertEquals(c1.getAtomGroups(GroupType.AMINOACID).size(),cx.getAtomGroups(GroupType.AMINOACID).size()); assertEquals(c1.getAtomGroups(GroupType.NUCLEOTIDE).size(),cx.getAtomGroups(GroupType.NUCLEOTIDE).size()); assertEquals(c1.getAtomGroups(GroupType.HETATM).size(),cx.getAtomGroups(GroupType.HETATM).size()); } } } private void compareString(String t, String pdb){ for (int i =0 ; i < t.length() ; i++){ System.out.println(">"+t.charAt(i)+":"+ pdb.charAt(i)+"<"); if ( Character.toUpperCase(t.charAt(i)) != Character.toUpperCase(pdb.charAt(i))){ break; } } } }