public static void main(String[] args) {
Point3d[] pts = SecondaryStructTools.obtain(NAME);
if (smooth) pts = CS.getSmoothedPoints(pts);
SecondaryStruct s = new SecondaryStruct(pts, smooth);
File f = new File("data/smooth_" + NAME + ".pdb");
Chain c = new ChainImpl();
c.setChainID(NAME.split("\\.")[1]);
try (PrintWriter pw = new PrintWriter(f)) {
for (int i = 0; i < pts.length; i++) {
Atom a = new AtomImpl();
a = new AtomImpl();
a.setName(CA_NAME);
a.setAltLoc(' ');
Group g = new AminoAcidImpl();
g.setPDBName(GROUP_NAME);
g.addAtom(a);
g.setResidueNumber(chainID, i + 1, null);
c.addGroup(g);
a.setX(pts[i].x);
a.setY(pts[i].y);
a.setZ(pts[i].z);
pw.print(a.toPDB());
}
} catch (FileNotFoundException e) {
e.printStackTrace();
}
// SecondaryStructureSequenceFeature sf = s.getSequenceFeature();
System.out.println("Start");
System.out.println(NAME);
System.out.println(s.getAlphaLength());
try (Scanner scan = new Scanner(System.in)) {
String in;
while (!(in = scan.next()).equals("X")) {
if (in.equals("g")) {
int st = scan.nextInt();
System.out.println(
SecondaryStructTools.distsToString(s.getRange(st - 1, scan.nextInt()), st));
} else if (in.equals("a")) s.printHelices();
else if (in.equals("b")) s.printStrands();
else if (in.equals("l")) System.out.println(s.length());
else if (in.equals("c")) s.printPoints();
// else if (in.equals("sf"))
// for (int i = 0; i < s.length(); i++)
// System.out.println((i + 1) + ":\t" + sf.toString(i));
else if (in.equals("test")) s.printVectors(s.getAlpha().getFeatures());
else if (in.equals("test1"))
System.out.println("=(0,0,0)\t=" + s.normP + "*50\t=" + s.normX + "*50");
else if (in.equals("test2"))
SecondaryStruct.printProjection(s.getAlphaNormProjection((byte) 0b00000000));
}
}
// sc.close();
}
/**
* Makes dummy CA atoms at 1A intervals. Only the x coordinate increments by one at each
* consecutive Atom.
*/
private Atom[] makeDummyCA(int len) {
Atom[] ca1;
Chain chain1 = new ChainImpl();
ca1 = new Atom[len];
for (int i = 0; i < len; i++) {
ca1[i] = new AtomImpl();
ca1[i].setName("CA");
ca1[i].setCoords(new double[] {i, 0, 0});
Group aa = new AminoAcidImpl();
aa.setPDBName("GLY");
aa.setResidueNumber(ResidueNumber.fromString(i + ""));
aa.addAtom(ca1[i]);
chain1.addGroup(aa);
}
return ca1;
}
/**
* Returns a {@link Structure} corresponding to the CATH identifier supplied in {@code
* structureName}, using the specified {@link CathDatabase}.
*/
public Structure getStructureForCathDomain(StructureName structureName, CathDatabase cathInstall)
throws IOException, StructureException {
CathDomain cathDomain = cathInstall.getDomainByCathId(structureName.getIdentifier());
Structure s = getStructureForPdbId(cathDomain.getIdentifier());
Structure n = cathDomain.reduce(s);
// add the ligands of the chain...
Chain newChain = n.getChainByPDB(structureName.getChainId());
Chain origChain = s.getChainByPDB(structureName.getChainId());
List<Group> ligands = origChain.getAtomLigands();
for (Group g : ligands) {
if (!newChain.getAtomGroups().contains(g)) {
newChain.addGroup(g);
}
}
return n;
}
/**
* Returns the representation of a {@link ScopDomain} as a BioJava {@link Structure} object.
*
* @param domain a SCOP domain
* @param scopDatabase A {@link ScopDatabase} to use
* @param strictLigandHandling If set to false, hetero-atoms are included if and only if they
* belong to a chain to which the SCOP domain belongs; if set to true, hetero-atoms are
* included if and only if they are strictly within the definition (residue numbers) of the
* SCOP domain
* @return a Structure object
* @throws IOException
* @throws StructureException
*/
public Structure getStructureForDomain(
ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)
throws IOException, StructureException {
String pdbId = domain.getPdbId();
Structure fullStructure = getStructureForPdbId(pdbId);
Structure structure = domain.reduce(fullStructure);
// TODO It would be better to move all of this into the reduce method,
// but that would require ligand handling properties in StructureIdentifiers
// because ligands sometimes occur after TER records in PDB files, we may need to add some
// ligands back in
// specifically, we add a ligand if and only if it occurs within the domain
AtomPositionMap map = null;
List<ResidueRangeAndLength> rrs = null;
if (strictLigandHandling) {
map =
new AtomPositionMap(
StructureTools.getAllAtomArray(fullStructure), AtomPositionMap.ANYTHING_MATCHER);
rrs = ResidueRangeAndLength.parseMultiple(domain.getRanges(), map);
}
for (Chain chain : fullStructure.getChains()) {
if (!structure.hasChain(chain.getChainID())) {
continue; // we can't do anything with a chain our domain
}
// doesn't contain
Chain newChain = structure.getChainByPDB(chain.getChainID());
List<Group> ligands = StructureTools.filterLigands(chain.getAtomGroups());
for (Group group : ligands) {
boolean shouldContain = true;
if (strictLigandHandling) {
shouldContain = false; // whether the ligand occurs within the domain
for (ResidueRange rr : rrs) {
if (rr.contains(group.getResidueNumber(), map)) {
shouldContain = true;
}
}
}
boolean alreadyContains =
newChain.getAtomGroups().contains(group); // we don't want to add duplicate
// ligands
if (shouldContain && !alreadyContains) {
newChain.addGroup(group);
}
}
}
// build a more meaningful description for the new structure
StringBuilder header = new StringBuilder();
header.append(domain.getClassificationId());
if (scopDatabase != null) {
int sf = domain.getSuperfamilyId();
ScopDescription description = scopDatabase.getScopDescriptionBySunid(sf);
if (description != null) {
header.append(" | ");
header.append(description.getDescription());
}
}
structure.getPDBHeader().setDescription(header.toString());
return structure;
}