001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 * created at Sep 18, 2013 021 * Author: ap3 022 */ 023 024package demo; 025 026import org.biojava.nbio.structure.Structure; 027import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol; 028import org.biojava.nbio.structure.StructureIO; 029import org.biojava.nbio.structure.validation.*; 030 031import javax.xml.bind.JAXBContext; 032import javax.xml.bind.Unmarshaller; 033import java.io.InputStream; 034import java.math.BigDecimal; 035import java.math.BigInteger; 036import java.util.List; 037import java.util.zip.GZIPInputStream; 038 039public class DemoShowValidationResults { 040 041 public static void main(String[] args){ 042 //String pdbId ="3zjr"; 043 String pdbId ="3vtq"; 044 showPdbValidation(pdbId); 045 } 046 047 private static void showPdbValidation(String pdbId) { 048 try { 049 JAXBContext ctx = JAXBContext.newInstance(new Class[] {WwPDBValidationInformation.class}); 050 051 Unmarshaller um = ctx.createUnmarshaller(); 052 053 InputStream inStream = new GZIPInputStream(DemoShowValidationResults.class.getResourceAsStream("/"+pdbId+"-valdata.xml.gz")); 054 055 WwPDBValidationInformation validationReport = (WwPDBValidationInformation) um.unmarshal(inStream); 056 057 Entry entry = validationReport.getEntry(); 058 059 System.out.println(pdbId + " " + entry.getPDBRevisionNumber() + 060 "\t Rfree: " + entry.getDCCRfree() + 061 "\t Clashscore " + entry.getClashscore() + 062 "\t % Ramachandran outliers: " + entry.getPercentRamaOutliers() + 063 "\t % RSRC outliers: " + entry.getPercentRSRZOutliers() ); 064 065 066 StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol(); 067 068 Structure s = StructureIO.getStructure(pdbId); 069 070 jmolPanel.setStructure(s); 071 072 jmolPanel.evalString("select *; color grey ; cartoon off ; "); 073 074 for (ModelledSubgroup subgroup: validationReport.getModelledSubgroup()) { 075 076 List<Clash> clashes = subgroup.getClash(); 077 078 String chainId = subgroup.getChain(); 079 //String resname = subgroup.getResname(); 080 String iCode = subgroup.getIcode(); 081 BigInteger resnum = subgroup.getResnum(); 082 //String altcode = subgroup.getAltcode(); 083 084 085 String pos = resnum.toString() ; 086 if ( iCode !=null && iCode.length()>0 && (! iCode.equals(" "))) 087 pos +="^" + iCode; 088 pos +=":" + chainId; 089 090 BigDecimal base = new BigDecimal(0.5); 091 092 for (Clash clash : clashes){ 093 String clashatom = clash.getAtom(); 094 BigDecimal clashmag = clash.getClashmag(); 095 // pos1 icode A chain X should become: 096 // 1^A:X 097 // [MET]508:A.CA/1 #3918 098 // insertion code: [ASP]1^A:A.CA/1 #2 099 100 String clashj = pos + "." + clashatom; 101 String jmols = " select " + clashj + "; color red; spacefill " + (base.add(clashmag)) + ";" ; 102 System.out.println(jmols + " " + clashmag); 103 jmolPanel.evalString(jmols); 104 } 105 106 107 for (AngleOutlier angleout : subgroup.getAngleOutlier()) { 108 String atom0 = angleout.getAtom0(); 109 String atom1 = angleout.getAtom1(); 110 String atom2 = angleout.getAtom2(); 111 112 String anglej = "select " + pos + "." + atom0+"," +pos+"." + atom1 +"," + pos +"." + atom2+"; color wireframe blue; wireframe 0.5;"; 113 //System.out.println(anglej); 114 jmolPanel.evalString(anglej); 115 } 116 117 for (BondOutlier bondout : subgroup.getBondOutlier()){ 118 String atom0 = bondout.getAtom0(); 119 String atom1 = bondout.getAtom1(); 120 String bondj = "select " + pos + "." + atom0+"," +pos+"." + atom1 +"; color wireframe green; wireframe 0.5;"; 121 jmolPanel.evalString(bondj); 122 123 } 124 } 125 126 127 } catch (Exception e){ 128 e.printStackTrace(); 129 130 } 131 132 } 133 134}