/**
* identify additional groups that are not directly attached to amino acids.
*
* @param mc {@link ModifiedCompound}.
* @param chain a {@link Chain}.
* @return a list of added groups.
*/
private void identifyAdditionalAttachments(
ModifiedCompound mc, List<Group> ligands, Map<String, Chain> mapChainIdChain) {
if (ligands.isEmpty()) {
return;
}
// TODO: should the additional groups only be allowed to the identified
// ligands or both amino acids and ligands? Currently only on ligands
// ligands to amino acid bonds for same modification of unknown category
// will be combined in mergeModComps()
// TODO: how about chain-chain links?
List<Group> identifiedGroups = new ArrayList<Group>();
for (StructureGroup num : mc.getGroups(false)) {
Group group;
try {
// String numIns = "" + num.getResidueNumber();
// if (num.getInsCode() != null) {
// numIns += num.getInsCode();
// }
ResidueNumber resNum = new ResidueNumber();
resNum.setChainId(num.getChainId());
resNum.setSeqNum(num.getResidueNumber());
resNum.setInsCode(num.getInsCode());
// group = chain.getGroupByPDB(numIns);
group = mapChainIdChain.get(num.getChainId()).getGroupByPDB(resNum);
} catch (StructureException e) {
e.printStackTrace();
// should not happen
continue;
}
identifiedGroups.add(group);
}
int start = 0;
int n = identifiedGroups.size();
while (n > start) {
for (Group group1 : ligands) {
for (int i = start; i < n; i++) {
Group group2 = identifiedGroups.get(i);
if (!identifiedGroups.contains(group1)) {
List<Atom[]> linkedAtoms =
StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
if (!linkedAtoms.isEmpty()) {
for (Atom[] atoms : linkedAtoms) {
mc.addAtomLinkage(
StructureUtil.getStructureAtomLinkage(atoms[0], false, atoms[1], false));
}
identifiedGroups.add(group1);
break;
}
}
}
}
start = n;
n = identifiedGroups.size();
}
}
private void updateJmolDisplay() {
if (jmol == null) return;
int size = afpChain.getAlnLength();
StringBuffer cmd = new StringBuffer("select ");
int nrSelected = 0;
try {
for (int i = 0; i < size; i++) {
if (selection.get(i)) {
Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, i, ca1, false);
Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, i, ca2, false);
String select1 = "";
if (a1 != null) select1 = JmolTools.getPdbInfo(a1);
String select2 = "";
if (a2 != null) select2 = JmolTools.getPdbInfo(a2);
// nothing to display
if (select1.equals("") && select2.equals("")) continue;
if (nrSelected > 0) cmd.append(", ");
cmd.append(select1);
cmd.append(", ");
cmd.append(select2);
nrSelected++;
}
}
} catch (StructureException e) {
e.printStackTrace();
}
if (nrSelected == 0) cmd.append(" none;");
else cmd.append("; set display selected;");
jmol.evalString(cmd.toString());
}
@Override
public double calculate(
MultipleAlignment reference,
AFPChain align,
Atom[] ca1,
Atom[] ca2,
Map<String, Object> metaData) {
try {
List<Atom[]> structures = new ArrayList<Atom[]>(2);
structures.add(ca1);
structures.add(ca2);
int[][] optAln = reference.getAlignmentMatrix(structures);
// Create new arrays for the subset of atoms in the alignment.
Atom[] ca1aligned = new Atom[reference.size()];
Atom[] ca2aligned = new Atom[reference.size()];
int pos = 0;
for (int i = 0; i < optAln[0].length; i++) {
ca1aligned[pos] = ca1[optAln[0][pos]];
ca2aligned[pos] = (Atom) ca2[optAln[1][pos]].clone();
pos++;
}
// Superimpose
SVDSuperimposer svd = new SVDSuperimposer(ca1aligned, ca2aligned);
Matrix matrix = svd.getRotation();
Atom shift = svd.getTranslation();
for (Atom a : ca2aligned) {
Calc.rotate(a, matrix);
Calc.shift(a, shift);
}
return SVDSuperimposer.getTMScore(ca1aligned, ca2aligned, ca1.length, ca2.length);
} catch (StructureException e) {
e.printStackTrace();
return Double.NaN;
}
}
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2D = (Graphics2D) g;
g2D.setRenderingHint(
RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
// only draw within the ranges of the Clip
// Rectangle drawHere = g2D.getClipBounds();
// int startpos = coordManager.getSeqPos(0,drawHere.x);
// int endpos = coordManager.getSeqPos(0,drawHere.x+drawHere.width-2);
char[] seq1 = afpChain.getAlnseq1();
char[] seq2 = afpChain.getAlnseq2();
char[] symb = afpChain.getAlnsymb();
int startpos = 0;
int endpos = afpChain.getAlnLength();
String summary = afpChain.toString();
g2D.drawString(summary, 20, coordManager.getSummaryPos());
Color significantCol = Color.red;
if (afpChain.isSignificantResult()) significantCol = Color.green;
g2D.setPaint(significantCol);
// draw a darker backgroun
Rectangle sig = new Rectangle(10, 10, 10, 10);
g2D.fill(sig);
boolean isFATCAT = false;
if (afpChain.getAlgorithmName().startsWith("jFatCat")) {
isFATCAT = true;
}
for (int i = startpos; ((i <= endpos) && (i < afpChain.getAlnLength())); i++) {
// TODO:
// color amino acids by hydrophobicity
char c1 = seq1[i];
char c2 = seq2[i];
boolean isGapped = false;
g2D.setFont(seqFont);
List<Integer> alignedPos = null;
if (colorByAlignmentBlock) {
alignedPos = DisplayAFP.getEQRAlignmentPos(afpChain);
}
if (isFATCAT) {
char s = symb[i];
if (s != ' ') {
isGapped = false;
g2D.setFont(eqFont);
} else isGapped = true;
} else {
if (c1 != '-' && c2 != '-') {
// no gap
g2D.setFont(eqFont);
} else {
isGapped = true;
}
}
Point p1 = coordManager.getPanelPos(0, i);
int xpos1 = p1.x;
int ypos1 = p1.y;
Point p2 = coordManager.getPanelPos(1, i);
int xpos2 = p2.x;
int ypos2 = p2.y;
int blockNum = afpChain.getBlockNum();
if (!isGapped) {
Color bg = Color.white;
Color bg2 = Color.white;
Color end1 = ColorUtils.rotateHue(ColorUtils.orange, (1.0f / 24.0f) * blockNum);
Color end2 = ColorUtils.rotateHue(ColorUtils.cyan, (1.0f / 24.0f) * (blockNum + 1));
if (colorByAlignmentBlock) {
if (!alignedPos.contains(i)) {
// unaligned!
bg = Color.white;
bg2 = Color.white;
} else {
int colorPos = 0;
if (isFATCAT) {
int block = 0;
char s = symb[i];
try {
block = Integer.parseInt(s + "") - 1;
bg = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, block);
bg2 = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, block);
// bg = ColorUtils.rotateHue(ColorUtils.orange, (1.0f / 24.0f) * block );
// bg2 = ColorUtils.rotateHue(ColorUtils.cyan, (1.0f / 16.0f) * block );
} catch (Exception e) {
}
if (colorPos > ColorUtils.colorWheel.length) {
colorPos = ColorUtils.colorWheel.length % colorPos;
}
} else {
colorPos = DisplayAFP.getBlockNrForAlignPos(afpChain, i);
bg = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, colorPos);
bg2 = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, colorPos);
// bg = ColorUtils.rotateHue(ColorUtils.orange, (1.0f / 24.0f) * colorPos );
// bg2 = ColorUtils.rotateHue(ColorUtils.cyan, (1.0f / 16.0f) * colorPos);
}
}
} else {
bg = Color.LIGHT_GRAY;
bg2 = Color.LIGHT_GRAY;
}
// draw a darker background
g2D.setPaint(bg);
Rectangle rec = new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 1);
g2D.fill(rec);
g2D.setPaint(bg2);
Rectangle rec2 = new Rectangle(p1.x - 1, p1.y + 4, (p2.x - p1.x) + 12, (p2.y - p1.y) - 3);
g2D.fill(rec2);
// g2D.setPaint(Color.black);
// g2D.draw(rec);
}
if (colorBySimilarity) {
if (c1 == c2) {
Color bg = Color.red;
g2D.setPaint(bg);
Rectangle rec =
new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 12);
g2D.fill(rec);
} else if (AFPAlignmentDisplay.aaScore(c1, c2) > 0) {
Color bg = Color.orange;
g2D.setPaint(bg);
Rectangle rec =
new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 12);
g2D.fill(rec);
}
}
// if ( selectionStart != null && selectionEnd != null){
// if ( i >= selectionStart.getPos1() && i <= selectionEnd.getPos1()) {
if (isSelected(i)) {
// draw selection
Color bg = Color.YELLOW;
g2D.setPaint(bg);
// draw a darker backgroun
Rectangle rec = new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 12);
g2D.fill(rec);
// }
}
// draw the AA sequence
g2D.setColor(Color.black);
g2D.drawString(c1 + "", xpos1, ypos1);
g2D.drawString(c2 + "", xpos2, ypos2);
// System.out.println(seq1[i] + " " + xpos1 + " " + ypos1 + " " + seq2[i] + xpos2 + " " +
// ypos2);
}
int nrLines = (afpChain.getAlnLength() - 1) / AFPChainCoordManager.DEFAULT_LINE_LENGTH;
for (int i = 0; i <= nrLines; i++) {
try {
// draw legend at i
Point p1 = coordManager.getLegendPosition(i, 0);
Point p2 = coordManager.getLegendPosition(i, 1);
int aligPos = i * AFPChainCoordManager.DEFAULT_LINE_LENGTH;
Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, aligPos, ca1, false);
Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, aligPos, ca2, false);
String label1 = JmolTools.getPdbInfo(a1, false);
String label2 = JmolTools.getPdbInfo(a2, false);
g2D.drawString(label1, p1.x, p1.y);
g2D.drawString(label2, p2.x, p2.y);
Point p3 = coordManager.getEndLegendPosition(i, 0);
Point p4 = coordManager.getEndLegendPosition(i, 1);
aligPos =
i * AFPChainCoordManager.DEFAULT_LINE_LENGTH
+ AFPChainCoordManager.DEFAULT_LINE_LENGTH
- 1;
if (aligPos > afpChain.getAlnLength()) aligPos = afpChain.getAlnLength() - 1;
Atom a3 = DisplayAFP.getAtomForAligPos(afpChain, 0, aligPos, ca1, true);
Atom a4 = DisplayAFP.getAtomForAligPos(afpChain, 1, aligPos, ca2, true);
String label3 = JmolTools.getPdbInfo(a3, false);
String label4 = JmolTools.getPdbInfo(a4, false);
g2D.drawString(label3, p3.x, p3.y);
g2D.drawString(label4, p4.x, p4.y);
} catch (StructureException e) {
e.printStackTrace();
}
}
}