import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
import java.awt.Color;
-import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
public class PDBChain
{
+ public static final String RESNUM_FEATURE = "RESNUM";
+
/**
* SequenceFeature group for PDB File features added to sequences
*/
public String id;
- public Vector bonds = new Vector();
+ public Vector<Bond> bonds = new Vector<Bond>();
- public Vector atoms = new Vector();
+ public Vector<Atom> atoms = new Vector<Atom>();
- public Vector residues = new Vector();
+ public Vector<Residue> residues = new Vector<Residue>();
public int offset;
public PDBChain(String pdbid, String id)
{
- this.pdbid = pdbid.toLowerCase();
+ this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
this.id = id;
}
public String print()
{
- String tmp = "";
+ StringBuilder tmp = new StringBuilder(256);
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
- + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
- + newline;
+ tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
+ .append(" ").append(offset).append(newline);
}
- return tmp;
+ return tmp.toString();
}
/**
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
// first clear out any old alignmentMapping values:
- for (Atom atom : (Vector<Atom>) atoms)
+ for (Atom atom : atoms)
{
atom.alignmentMapping = -1;
}
pdbpos++;
}
- if (as.astr1.charAt(i) == as.astr2.charAt(i))
+ boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
+ as.astr2.charAt(i), false);
+ if (sameResidue)
{
- Residue res = (Residue) residues.elementAt(pdbpos);
- Enumeration en = res.atoms.elements();
- while (en.hasMoreElements())
+ if (pdbpos >= residues.size())
+ {
+ continue;
+ }
+ Residue res = residues.elementAt(pdbpos);
+ for (Atom atom : res.atoms)
{
- Atom atom = (Atom) en.nextElement();
atom.alignmentMapping = alignpos;
}
}
status = PDBChain.IEASTATUS;
}
SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features == null)
+ {
+ return null;
+ }
for (int i = 0; i < features.length; i++)
{
- if (features[i].getFeatureGroup().equals(pdbid))
+ if (features[i].getFeatureGroup() != null
+ && features[i].getFeatureGroup().equals(pdbid))
{
SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1 + ((Atom) ((Residue) residues.elementAt(tx.getBegin()
- - offset)).atoms.elementAt(0)).alignmentMapping);
- tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
- - offset)).atoms.elementAt(0)).alignmentMapping);
+ tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping);
+ tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping);
tx.setStatus(status
- + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+ + ((tx.getStatus() == null || tx.getStatus().length() == 0)
+ ? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
{
return features;
}
+ /**
+ * Traverses the list of residues and constructs bonds where CA-to-CA atoms or
+ * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of
+ * residues contain a P not a CA.
+ */
public void makeCaBondList()
{
boolean na = false;
int numNa = 0;
for (int i = 0; i < (residues.size() - 1); i++)
{
- Residue tmpres = (Residue) residues.elementAt(i);
- Residue tmpres2 = (Residue) residues.elementAt(i + 1);
+ Residue tmpres = residues.elementAt(i);
+ Residue tmpres2 = residues.elementAt(i + 1);
Atom at1 = tmpres.findAtom("CA");
Atom at2 = tmpres2.findAtom("CA");
na = false;
System.out.println("not found " + i);
}
}
- if (numNa > 0 && ((numNa / residues.size()) > 0.99))
+
+ /*
+ * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
+ * residue
+ */
+ if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
{
isNa = true;
}
}
+ /**
+ * Construct a bond from atom1 to atom2 and add it to the list of bonds for
+ * this chain
+ *
+ * @param at1
+ * @param at2
+ */
public void makeBond(Atom at1, Atom at2)
{
- float[] start = new float[3];
- float[] end = new float[3];
-
- start[0] = at1.x;
- start[1] = at1.y;
- start[2] = at1.z;
-
- end[0] = at2.x;
- end[1] = at2.y;
- end[2] = at2.z;
-
- bonds.addElement(new Bond(start, end, at1, at2));
+ bonds.addElement(new Bond(at1, at2));
}
+ /**
+ * Traverses the list of atoms and
+ * <ul>
+ * <li>constructs a list of Residues, each containing all the atoms that share
+ * the same residue number</li>
+ * <li>adds a RESNUM sequence feature for each position</li>
+ * <li>creates the sequence string</li>
+ * <li>determines if nucleotide</li>
+ * <li>saves the residue number of the first atom as 'offset'</li>
+ * <li>adds temp factor annotation if the flag is set to do so</li>
+ * </ul>
+ *
+ * @param visibleChainAnnotation
+ */
public void makeResidueList(boolean visibleChainAnnotation)
{
int count = 0;
Object symbol;
boolean deoxyn = false;
boolean nucleotide = false;
- StringBuffer seq = new StringBuffer();
- Vector resFeatures = new Vector();
- Vector resAnnotation = new Vector();
+ StringBuilder seq = new StringBuilder(256);
+ Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
+ Vector<Annotation> resAnnotation = new Vector<Annotation>();
int i, iSize = atoms.size() - 1;
int resNumber = -1;
+ char insCode = ' ';
for (i = 0; i <= iSize; i++)
{
- Atom tmp = (Atom) atoms.elementAt(i);
+ Atom tmp = atoms.elementAt(i);
resNumber = tmp.resNumber;
+ insCode = tmp.insCode;
+
int res = resNumber;
+ char ins = insCode;
if (i == 0)
{
offset = resNumber;
}
- Vector resAtoms = new Vector();
+ Vector<Atom> resAtoms = new Vector<Atom>();
// Add atoms to a vector while the residue number
// remains the same as the first atom's resNumber (res)
- while ((resNumber == res) && (i < atoms.size()))
+ while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
{
- resAtoms.addElement(atoms.elementAt(i));
+ resAtoms.add(atoms.elementAt(i));
i++;
if (i < atoms.size())
{
- resNumber = ((Atom) atoms.elementAt(i)).resNumber;
+ resNumber = atoms.elementAt(i).resNumber;
+ insCode = atoms.elementAt(i).insCode;
}
else
{
// We need this to keep in step with the outer for i = loop
i--;
- // Make a new Residue object with the new atoms vector
- residues.addElement(new Residue(resAtoms, resNumber - 1, count));
-
- Residue tmpres = (Residue) residues.lastElement();
- Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
- // Make A new SequenceFeature for the current residue numbering
- SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
- + count, offset + count, pdbid);
- // MCview.PDBChain.PDBFILEFEATURE);
- resFeatures.addElement(sf);
- resAnnotation.addElement(new Annotation(tmpat.tfactor));
- // Keep totting up the sequence
- if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+ // Add inserted residues as features to the base residue
+ Atom currAtom = resAtoms.get(0);
+ if (currAtom.insCode != ' ' && !residues.isEmpty()
+ && residues.lastElement().atoms
+ .get(0).resNumber == currAtom.resNumber)
{
- String nucname = tmpat.resName.trim();
- // use the aaIndex rather than call 'toLower' - which would take a bit
- // more time.
- deoxyn = nucname.length() == 2
- && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
- if (tmpat.name.equalsIgnoreCase("CA")
- || ResidueProperties.nucleotideIndex[nucname
- .charAt((deoxyn ? 1 : 0))] == -1)
- {
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
- }
- else
- {
- // nucleotide flag
- nucleotide = true;
- seq.append(nucname.charAt((deoxyn ? 1 : 0)));
- }
+ SequenceFeature sf = new SequenceFeature("INSERTION",
+ currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
+ + id,
+ "", offset + count - 1, offset + count - 1, "PDB_INS");
+ resFeatures.addElement(sf);
+ residues.lastElement().atoms.addAll(resAtoms);
}
else
{
- if (nucleotide)
+
+ // Make a new Residue object with the new atoms vector
+ residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+
+ Residue tmpres = residues.lastElement();
+ Atom tmpat = tmpres.atoms.get(0);
+ // Make A new SequenceFeature for the current residue numbering
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE,
+ tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id,
+ "", offset + count, offset + count, pdbid);
+ resFeatures.addElement(sf);
+ resAnnotation.addElement(new Annotation(tmpat.tfactor));
+ // Keep totting up the sequence
+
+ if ((symbol = ResidueProperties.getAA3Hash()
+ .get(tmpat.resName)) == null)
{
- System.err
- .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ String nucname = tmpat.resName.trim();
+ // use the aaIndex rather than call 'toLower' - which would take a bit
+ // more time.
+ deoxyn = nucname.length() == 2
+ && ResidueProperties.aaIndex[nucname
+ .charAt(0)] == ResidueProperties.aaIndex['D'];
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname
+ .charAt((deoxyn ? 1 : 0))] == -1)
+ {
+ char r = ResidueProperties.getSingleCharacterCode(
+ ResidueProperties.getCanonicalAminoAcid(tmpat.resName));
+ seq.append(r == '0' ? 'X' : r);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+ }
}
- seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
+ else
+ {
+ if (nucleotide)
+ {
+ System.err.println(
+ "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ }
+ seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
+ }
+ count++;
}
- count++;
}
if (id.length() < 1)
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
- for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+
+ if (StructureImportSettings.isShowSeqFeatures())
{
- sequence.addSequenceFeature((SequenceFeature) resFeatures
- .elementAt(i));
- resFeatures.setElementAt(null, i);
+ for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+ {
+ sequence.addSequenceFeature(resFeatures.elementAt(i));
+ resFeatures.setElementAt(null, i);
+ }
}
if (visibleChainAnnotation)
{
float max = 0;
for (i = 0, iSize = annots.length; i < iSize; i++)
{
- annots[i] = (Annotation) resAnnotation.elementAt(i);
+ annots[i] = resAnnotation.elementAt(i);
if (annots[i].value > max)
{
max = annots[i].value;
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
"Temperature Factor", "Temperature Factor for " + pdbid + id,
- annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
+ annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
}
+ /**
+ * Colour start/end of bonds by charge
+ * <ul>
+ * <li>ASP and GLU red</li>
+ * <li>LYS and ARG blue</li>
+ * <li>CYS yellow</li>
+ * <li>others light gray</li>
+ * </ul>
+ */
public void setChargeColours()
{
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- try
+ if (b.at1 != null && b.at2 != null)
{
- Bond b = (Bond) bonds.elementAt(i);
-
- if (b.at1.resName.equalsIgnoreCase("ASP")
- || b.at1.resName.equalsIgnoreCase("GLU"))
- {
- b.startCol = Color.red;
- }
- else if (b.at1.resName.equalsIgnoreCase("LYS")
- || b.at1.resName.equalsIgnoreCase("ARG"))
- {
- b.startCol = Color.blue;
- }
- else if (b.at1.resName.equalsIgnoreCase("CYS"))
- {
- b.startCol = Color.yellow;
- }
- else
- {
- b.startCol = Color.lightGray;
- }
-
- if (b.at2.resName.equalsIgnoreCase("ASP")
- || b.at2.resName.equalsIgnoreCase("GLU"))
- {
- b.endCol = Color.red;
- }
- else if (b.at2.resName.equalsIgnoreCase("LYS")
- || b.at2.resName.equalsIgnoreCase("ARG"))
- {
- b.endCol = Color.blue;
- }
- else if (b.at2.resName.equalsIgnoreCase("CYS"))
- {
- b.endCol = Color.yellow;
- }
- else
- {
- b.endCol = Color.lightGray;
- }
- } catch (Exception e)
+ b.startCol = getChargeColour(b.at1.resName);
+ b.endCol = getChargeColour(b.at2.resName);
+ }
+ else
{
- Bond b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
b.endCol = Color.gray;
}
}
}
- public void setChainColours(jalview.schemes.ColourSchemeI cs)
+ public static Color getChargeColour(String resName)
+ {
+ Color result = Color.lightGray;
+ if ("ASP".equals(resName) || "GLU".equals(resName))
+ {
+ result = Color.red;
+ }
+ else if ("LYS".equals(resName) || "ARG".equals(resName))
+ {
+ result = Color.blue;
+ }
+ else if ("CYS".equals(resName))
+ {
+ result = Color.yellow;
+ }
+ return result;
+ }
+
+ /**
+ * Sets the start/end colours of bonds to those of the start/end atoms
+ * according to the specified colour scheme. Note: currently only works for
+ * peptide residues.
+ *
+ * @param cs
+ */
+ public void setChainColours(ColourSchemeI cs)
{
- Bond b;
int index;
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
try
{
- b = (Bond) bonds.elementAt(i);
-
- index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
- .intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
+ b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
- index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
- .intValue();
- b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
+ b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
} catch (Exception e)
{
- b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
b.endCol = Color.gray;
}
public void setChainColours(Color col)
{
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- Bond tmp = (Bond) bonds.elementAt(i);
- tmp.startCol = col;
- tmp.endCol = col;
+ b.startCol = col;
+ b.endCol = col;
}
}
* @param sqmpping
* - mapping between destination sequence and local chain
*/
- public void transferResidueAnnotation(
- StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
+ public void transferResidueAnnotation(StructureMapping mapping,
+ jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
- ana.getCalcId(), ana.label);
+ List<AlignmentAnnotation> transfer = sq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq
+ List<AlignmentAnnotation> transfer = dsq
.getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
// mapping.transfer(ana);
}
else
// Useful for debugging mappings - adds annotation for mapped position
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
- for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+ for (int i = sq.getStart(), j = sq
+ .getEnd(), k = 0; i <= j; i++, k++)
{
int prn = mapping.getPDBResNum(k + 1);
git://source.jalview.org / jalview.git / blobdiff