/**
* Builds an {@link AFPChain} from already-matched arrays of atoms and residues.
*
* @param ca1 An array of atoms in the first structure
* @param ca2 An array of atoms in the second structure
* @param residues1 An array of {@link ResidueNumber ResidueNumbers} in the first structure that
* are aligned. Only null ResidueNumbers are considered to be unaligned
* @param residues2 An array of {@link ResidueNumber ResidueNumbers} in the second structure that
* are aligned. Only null ResidueNumbers are considered to be unaligned
* @throws StructureException
*/
private static AFPChain buildAlignment(
Atom[] ca1, Atom[] ca2, ResidueNumber[] residues1, ResidueNumber[] residues2)
throws StructureException {
// remove any gap
// this includes the ones introduced by the nullifying above
List<ResidueNumber> alignedResiduesList1 = new ArrayList<ResidueNumber>();
List<ResidueNumber> alignedResiduesList2 = new ArrayList<ResidueNumber>();
for (int i = 0; i < residues1.length; i++) {
if (residues1[i] != null && residues2[i] != null) {
alignedResiduesList1.add(residues1[i]);
alignedResiduesList2.add(residues2[i]);
}
}
ResidueNumber[] alignedResidues1 =
alignedResiduesList1.toArray(new ResidueNumber[alignedResiduesList1.size()]);
ResidueNumber[] alignedResidues2 =
alignedResiduesList2.toArray(new ResidueNumber[alignedResiduesList2.size()]);
AFPChain afpChain = AlignmentTools.createAFPChain(ca1, ca2, alignedResidues1, alignedResidues2);
afpChain.setAlgorithmName("unknown");
AlignmentTools.updateSuperposition(afpChain, ca1, ca2);
afpChain.setBlockSize(new int[] {afpChain.getNrEQR()});
afpChain.setBlockRmsd(new double[] {afpChain.getTotalRmsdOpt()});
afpChain.setBlockGap(new int[] {afpChain.getGapLen()});
return afpChain;
}
public void testOldSecOutput() throws Exception {
String fileName = "/ce_1fdo.A_2iv2.X.out";
InputStream inStream = this.getClass().getResourceAsStream(fileName);
assertNotNull("Could not find file " + fileName + " in resource path. Config error?", inStream);
String xml = StringManipulationHelper.convertStreamToString(inStream);
AtomCache cache = new AtomCache();
String name1 = "1FDO.A";
String name2 = "2IV2.X";
Atom[] ca1 = cache.getAtoms(name1);
Atom[] ca2 = cache.getAtoms(name2);
assertEquals(715, ca1.length);
assertEquals(697, ca2.length);
AFPChain afpChainOrig = AFPChainXMLParser.fromXML(xml, ca1, ca2);
assertNotNull("Could not get AfpChain object from flat file!", afpChainOrig);
assertEquals(
"Could not find alignment string for prot 1",
"MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVUHGPSVA-----GLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA",
new String(afpChainOrig.getAlnseq1(), 0, afpChainOrig.getAlnLength()));
assertEquals(
"Could not find alignment string for prot 2",
"MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCAR-----VUHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWW------------------PEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA",
new String(afpChainOrig.getAlnseq2(), 0, afpChainOrig.getAlnLength()));
// calc time is hardware dependent.... overwrite...
afpChainOrig.setCalculationTime(-1);
assertEquals(
"alnLength is wrong! (" + afpChainOrig.getAfpChainLen() + ")",
720,
afpChainOrig.getAlnLength());
assertEquals(
"gapLength is wrong! (" + afpChainOrig.getGapLen() + ")", 28, afpChainOrig.getGapLen());
// identity should be 0.9569
assertTrue(
"alinment ID is < 0.95 ! (" + afpChainOrig.getIdentity() + ")",
afpChainOrig.getIdentity() > 0.95);
assertTrue(
"alignment ID is > 0.96 ! (" + afpChainOrig.getIdentity() + ")",
afpChainOrig.getIdentity() < 0.96);
String xmlComp = AFPChainXMLConverter.toXML(afpChainOrig, ca1, ca2);
FlipAFPChainTest t = new FlipAFPChainTest();
t.printFirstMismatch(xml, xmlComp);
StringManipulationTestsHelper.assertEqualsIgnoreEndline(xml, xmlComp);
StructureAlignment ce = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);
AFPChain afpChainNew = ce.align(ca1, ca2);
afpChainNew.setCalculationTime(-1);
afpChainNew.setName1(name1);
afpChainNew.setName2(name2);
String xmlNew = AFPChainXMLConverter.toXML(afpChainNew, ca1, ca2);
StringManipulationTestsHelper.assertEqualsIgnoreEndline(xml, xmlNew);
}
