private static AtomCache initializeCache() {
AtomCache cache = new AtomCache();
cache.setUseMmCif(true);
FileParsingParameters params = cache.getFileParsingParams();
params.setStoreEmptySeqRes(true);
params.setAlignSeqRes(true);
// params.setParseCAOnly(true);
params.setLoadChemCompInfo(true);
params.setCreateAtomBonds(false);
cache.setFileParsingParams(params);
ChemCompGroupFactory.setChemCompProvider(new AllChemCompProvider());
// ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
return cache;
}
public static void main(String[] args) throws IOException {
String timeStamp =
new SimpleDateFormat("yyyyMMdd_HHmmss").format(Calendar.getInstance().getTime());
String uri = args[0] + "_" + timeStamp + ".seq";
Set<String> pdbIds = getAll();
StructureIO.setAtomCache(cache);
cache.setPath("/Users/Chris/Documents/RCSB/Data/Protein_chains/cache/");
long start = System.nanoTime();
toSequenceFile(uri, pdbIds, true);
long end = System.nanoTime();
System.out.println("Time: " + (end - start) / 1E9 + " sec.");
}
/**
* Returns the file name of the input structure: if user job it returns the path to the file in
* the job dir, if precomputed it finds the file path in the local atom cache and creates a
* symbolic link to it in the job dir
*
* @param directory Directory to search for the file
* @param inputName either the input file name, or a PDB code
* @param atomCachePath Path for downloaded CIF files
* @return the path to the AU structure file in the job dir
* @throws IOException if file is a user job file and can't be found, or if the input is a pdb id
* and its file can't be found in atom cache
*/
public static File getAuFileName(File directory, String inputName, String atomCachePath)
throws IOException {
// inputName will be the full file name in user jobs and the pdbId for precomputed jobs
File structFile = new File(directory, inputName);
logger.info(
"Trying to find the structure file for input name '{}'. Searching file in {}",
inputName,
structFile.toString());
if (!structFile.exists()) {
if (!inputName.matches("^\\d\\w\\w\\w$")) {
throw new IOException(
String.format(
"Could not find file %s and the inputName '%s' does not look "
+ "like a PDB id. Can't produce the lattice graph page!",
structFile, inputName));
} else {
// it is like a PDB id, leave it to AtomCache
AtomCache atomCache = null;
if (atomCachePath == null) {
atomCache = new AtomCache();
logger.warn(
"Defaulting to downloading structures to {}. Please set the ATOM_CACHE_PATH property.",
atomCache.getCachePath());
} else {
atomCache = new AtomCache(atomCachePath);
}
atomCache.setUseMmCif(true);
structFile = LatticeGUI.getFile(atomCache, inputName);
if (structFile == null || !structFile.exists()) {
logger.error(
"The structure file {} does not exist in atom cache! Will not be able to display lattice graph",
structFile);
throw new IOException("Structure file " + structFile + " does not exist in atom cache");
}
File sLink = new File(directory, structFile.getName());
if (!sLink.exists()) {
// TODO downloading symlinks don't work with current server configuration,
// TODO for now resorting to copy: must fix server config and do it with symlinks!
logger.info("Copying to {} from file {}", sLink.toString(), structFile.toString());
Files.copy(structFile.toPath(), sLink.toPath());
// we create a symbolic link to the file in the atomcache dir
// logger.info("Creating symbolic link {} to file {}", sLink.toString(),
// structFile.toString());
// Files.createSymbolicLink(sLink.toPath(), structFile.toPath());
}
// and finally if no exception is thrown we return the symbolic link
structFile = sLink;
}
}
return structFile;
}
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);
}