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sblivensbliven
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Adding long-running ECOD test. Must be run manually.
Also moves EcodInstallationTest to the right package
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biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/domain/EcodInstallationTest.java renamed to biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java

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* http://www.biojava.org/
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*/
2020

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package org.biojava.nbio.structure.test.domain;
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package org.biojava.nbio.structure.test.ecod;
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import static org.junit.Assert.*;
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java‎

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package org.biojava.nbio.structure.test.ecod;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.AtomPositionMap;
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import org.biojava.nbio.structure.Group;
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import org.biojava.nbio.structure.ResidueRange;
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import org.biojava.nbio.structure.ResidueRangeAndLength;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureTools;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.ecod.EcodDatabase;
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import org.biojava.nbio.structure.ecod.EcodDomain;
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import org.biojava.nbio.structure.ecod.EcodFactory;
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import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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* This is not a unit test.
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*
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* It is a long-running parsing test, which sequentially parses all ECOD domains.
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*
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* The most common warning is caused by residue ranges with missing terminal CA atoms,
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* which cause a warning to print.
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*
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* develop83 and earlier versions also had a number of invalid ranges, which cause
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* error messages to print.
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*
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* Filtering log4j messages to the 'error' level will filter all but the most
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* grevious errors.
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*
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* @author blivens
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*
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*/
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public class EcodParseTest {
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private static final Logger logger = LoggerFactory.getLogger(EcodParseTest.class);
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public static void main(String[] args) throws IOException {
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String ecodVersion = "develop83";
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EcodDatabase ecod = EcodFactory.getEcodDatabase(ecodVersion);
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AtomCache cache = new AtomCache();
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cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
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List<EcodDomain> domains = ecod.getAllDomains();
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// domains = Arrays.asList(ecod.getDomainsById("e1yfbB2"));
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// domains = Arrays.asList(ecod.getDomainsById("e1w50A2"));
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domains = Arrays.asList(ecod.getDomainsById("e2ftlE1"));
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int errors = 0;
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for(EcodDomain d : domains) {
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Atom[] ca1;
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Structure struct;
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try {
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struct = cache.getStructure(d.getPdbId());
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ca1 = StructureTools.getRepresentativeAtomArray(struct);
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} catch (IOException e) {
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logger.error("Error getting structure for "+d.getDomainId(),e);
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errors++;
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continue;
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} catch (StructureException e) {
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logger.error("Error getting structure for "+d.getDomainId(),e);
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errors++;
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continue;
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}
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// Test that the ranges can be parsed
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String rangeStr = d.getRange();
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AtomPositionMap map = new AtomPositionMap(ca1);
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List<? extends ResidueRange> ranges;
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try {
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// Parses range given in domain
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ranges = ResidueRange.parseMultiple(rangeStr);
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} catch(Exception e) {
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logger.error("Error parsing "+d.getPdbId()+"_"+d.getRange(),e);
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errors++;
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continue;
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}
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boolean clean = true;
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for(ResidueRange r : ranges) {
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if( r == null ) {
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clean = false;
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}
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}
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if( ! clean ) {
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logger.error("Empty range for {}_{}",d.getPdbId(),d.getRange());
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errors++;
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continue;
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}
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// Check that the ranges are valid (or at least that they have a group)
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for(ResidueRange range : ranges) {
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try {
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Integer start = map.getPosition(range.getStart());
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if(start == null) {
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Group g = struct.getChainByPDB(range.getStart().getChainId()).getGroupByPDB(range.getStart());
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if(g!=null) {
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logger.warn("No CA atom for starting residue "+d.getDomainId()+"_"+range);
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clean = false;
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} else {
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logger.error("Start doesn't exist for "+d.getDomainId()+"_"+range.toString());
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clean = false;
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}
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}
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} catch(Exception e) {
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logger.error("Start doesn't exist for "+d.getDomainId()+"_"+range.toString(),e);
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clean = false;
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}
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try {
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Integer end = map.getPosition(range.getEnd());
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if(end == null) {
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Group g = null;
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try {
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g = struct.getChainByPDB(range.getEnd().getChainId()).getGroupByPDB(range.getEnd());
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} catch(StructureException e ) {}
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if(g!=null) {
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logger.warn("No CA atom for ending residue "+d.getDomainId()+"_"+range);
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clean = false;
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} else {
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logger.error("End doesn't exist for "+d.getDomainId()+"_"+range.toString());
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clean = false;
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}
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}
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} catch(Exception e) {
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logger.error("End doesn't exist for "+d.getDomainId()+"_"+range.toString(),e);
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clean = false;
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}
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}
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// Try to recover from missing residues by trimming them to the residue range
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try {
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// Parses more flexibly, giving only a warning for missing residues
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ranges = ResidueRangeAndLength.parseMultiple(rangeStr,map);
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} catch(Exception e) {
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logger.error("Error parsing "+d.getPdbId()+"_"+d.getRange(),e);
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errors++;
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continue;
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}
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clean = true;
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for(ResidueRange r : ranges) {
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if( r == null ) {
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clean = false;
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}
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}
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if( ! clean ) {
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logger.error("Empty range for {}_{}",d.getPdbId(),d.getRange());
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errors++;
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continue;
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}
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// Test whether we can use it to get a structure
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String pdbRangeStr = String.format("%s.%s",d.getPdbId(),d.getRange());
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try {
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cache.getStructure(pdbRangeStr);
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} catch(Exception e) {
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logger.error("Can't get range "+pdbRangeStr,e);
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errors++;
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continue;
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}
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//All test passed
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logger.info("OK "+d.getDomainId());
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}
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logger.info("Done. {} errors.",errors);
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}
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}

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