/**
* Fundamentally, an alignment is just a list of aligned residues in each protein. This method
* converts two lists of ResidueNumbers into an AFPChain.
*
* <p>Parameters are filled with defaults (often null) or sometimes calculated.
*
* <p>For a way to modify the alignment of an existing AFPChain, see {@link
* AlignmentTools#replaceOptAln(AFPChain, Atom[], Atom[], Map)}
*
* @param ca1 CA atoms of the first protein
* @param ca2 CA atoms of the second protein
* @param aligned1 A list of aligned residues from the first protein
* @param aligned2 A list of aligned residues from the second protein. Must be the same length as
* aligned1.
* @return An AFPChain representing the alignment. Many properties may be null or another default.
* @throws StructureException if an error occured during superposition
* @throws IllegalArgumentException if aligned1 and aligned2 have different lengths
* @see AlignmentTools#replaceOptAln(AFPChain, Atom[], Atom[], Map)
*/
public static AFPChain createAFPChain(
Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2)
throws StructureException {
// input validation
int alnLen = aligned1.length;
if (alnLen != aligned2.length) {
throw new IllegalArgumentException("Alignment lengths are not equal");
}
AFPChain a = new AFPChain(AFPChain.UNKNOWN_ALGORITHM);
try {
a.setName1(ca1[0].getGroup().getChain().getStructure().getName());
if (ca2[0].getGroup().getChain().getStructure() != null) {
// common case for cloned ca2
a.setName2(ca2[0].getGroup().getChain().getStructure().getName());
}
} catch (Exception e) {
// One of the structures wasn't fully created. Ignore
}
a.setBlockNum(1);
a.setCa1Length(ca1.length);
a.setCa2Length(ca2.length);
a.setOptLength(alnLen);
a.setOptLen(new int[] {alnLen});
Matrix[] ms = new Matrix[a.getBlockNum()];
a.setBlockRotationMatrix(ms);
Atom[] blockShiftVector = new Atom[a.getBlockNum()];
a.setBlockShiftVector(blockShiftVector);
String[][][] pdbAln = new String[1][2][alnLen];
for (int i = 0; i < alnLen; i++) {
pdbAln[0][0][i] = aligned1[i].getChainId() + ":" + aligned1[i];
pdbAln[0][1][i] = aligned2[i].getChainId() + ":" + aligned2[i];
}
a.setPdbAln(pdbAln);
// convert pdbAln to optAln, and fill in some other basic parameters
AFPChainXMLParser.rebuildAFPChain(a, ca1, ca2);
return a;
// Currently a single block. Split into several blocks by sequence if needed
// return AlignmentTools.splitBlocksByTopology(a,ca1,ca2);
}
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);
}