/**
* Constructor.
*
* @param atom1 - First protein atom to be connected by the virtual cross-linker.
* @param atom2 - Second protein atom to be connected by the virtual cross-linker.
*/
public CrossLink(final Atom atom1, final Atom atom2) {
this(
atom1,
atom2,
Math.abs(atom1.getRank() - atom2.getRank()),
Mathematics.distance(atom1.getXYZ(), atom2.getXYZ()));
}
/**
* Writes a the shortest paths of a list of virtual cross-links into a PDB formated file.
*
* @param pathFileName - String object holding the path to the PDB file to be written.
* @param crossLinkList - List of cross-link objects holding each the the shortest path
*/
public final void writeSASDpdbFile(final String pathFileName, final CrossLinkList crossLinkList) {
StringBuffer content = new StringBuffer();
for (CrossLink crossLink : crossLinkList) {
if (crossLink.getPath() != null) {
Atom atom1 = crossLink.getPreAtom();
Atom atom2 = crossLink.getPostAtom();
String distName =
crossLink.getIndex()
+ "_"
+ this.decFormat.format(crossLink.getSolventPathDistance())
+ "_"
+ atom1.getResidueName().trim()
+ ""
+ atom1.getResidueNumber()
+ ""
+ atom1.getChainId()
+ "-"
+ atom2.getResidueName().trim()
+ ""
+ atom2.getResidueNumber()
+ ""
+ atom2.getChainId()
+ "_solventPath";
content.append("HEADER " + distName + Constants.LINE_SEPERATOR);
content.append(crossLink.getPath().toString(crossLink.getIndex()));
content.append("END" + Constants.LINE_SEPERATOR);
}
}
WriteFile file = new WriteFile();
file.setFile(pathFileName);
file.write(content.toString());
}
/**
* Sets to all amino acids atoms in a protein their associated XlogP values.
*
* @return float value representing the sum of XlogP values for the protein complex.
*/
private float setAtomicXlogP() {
Hashtable<AminoAcidType, Hashtable<AtomType, Float>> xlogPs =
ParameterReader.getXlogPparameterSet();
float sum = 0;
for (PolyPeptide polyPeptide : this.polyPeptideComplex) {
for (AminoAcid aa : polyPeptide) {
for (Atom atom : aa.getAllAtoms()) {
if (!atom.getElement().getSymbol().equals("H")) {
Hashtable<AtomType, Float> atomicXlogPs = xlogPs.get(aa.getType());
float xlogP = atomicXlogPs.get(atom.getType());
atom.setXlogP(xlogP);
sum += xlogP;
} else {
// hydrogen atoms have always a XlogP value of 0.
atom.setXlogP(0);
}
}
}
}
return sum;
}
/**
* Maps the hydrophobicity property of the protein on a list of atom. Note, that only atoms within
* mm.constants.Constants.PHYSICOCHEMICAL_INFLUENCE_RADIUS will be included in the potential
* calculation.
*
* @param sampleAtoms List of atoms on which potential will be calculated.
*/
public final void mapHydrophobicity(final AtomList sampleAtoms) {
float max = mm.constants.Constants.PHYSICOCHEMICAL_INFLUENCE_RADIUS;
for (Atom sampleAtom : sampleAtoms) {
for (Atom atom : this.polyPeptideComplex.getAllAtoms()) {
float dist = Mathematics.distance(atom.getXYZ(), sampleAtom.getXYZ());
if (dist <= max) {
float h = atom.getXlogP();
double s = Mathematics.sigmoidFunction(dist, max);
sampleAtom.setHes((float) (sampleAtom.getHes() + (h * s)));
}
}
}
}
/**
* Returns a string representation of the PyMol commands to name and place dashes between
* cross-linked amino acids.
*
* @param crossLinkList - CrossLinkList object holding all cross-links found for a protein
* complex.
* @return String object with PyMol commands.
*/
private String getEuclideanDistancePyMolCommands(final CrossLinkList crossLinkList) {
StringBuffer output = new StringBuffer();
String infile = CrossLinkParameter.getParameter(Parameter.INFILE_PATH);
String nl = Constants.LINE_SEPERATOR;
String infileWithoutExtension =
new File(infile).getName().substring(0, new File(infile).getName().lastIndexOf('.'));
for (CrossLink crossLink : crossLinkList) {
Atom atom1 = crossLink.getPreAtom();
Atom atom2 = crossLink.getPostAtom();
if (atom1.getChainId() != '_') {
output.append(
"create chain"
+ atom1.getChainId()
+ ", chain "
+ atom1.getChainId()
+ " and "
+ infileWithoutExtension
+ nl);
}
if (atom2.getChainId() != '_') {
output.append(
"create chain"
+ atom2.getChainId()
+ ", chain "
+ atom2.getChainId()
+ " and "
+ infileWithoutExtension
+ nl);
}
String selection1 =
"resn "
+ atom1.getResidueName().trim()
+ " and resi "
+ atom1.getResidueNumber()
+ " and chain "
+ atom1.getChainId()
+ " and name "
+ atom1.getName().trim()
+ " and "
+ infileWithoutExtension;
if (atom1.getAlternativeLocation() != ' ') {
selection1 += " and alt " + atom1.getAlternativeLocation();
}
String selection2 =
"resn "
+ atom2.getResidueName().trim()
+ " and resi "
+ atom2.getResidueNumber()
+ " and chain "
+ atom2.getChainId()
+ " and name "
+ atom1.getName().trim()
+ " and "
+ infileWithoutExtension;
if (atom2.getAlternativeLocation() != ' ') {
selection2 += " and alt " + atom2.getAlternativeLocation();
}
String distName = crossLink.getIndex() + "_";
if (Boolean.parseBoolean(
CrossLinkParameter.getParameter(Parameter.DO_SOLVENT_PATH_DISTANCE))) {
distName += this.decFormat.format(crossLink.getSolventPathDistance()) + "_";
} else {
distName += this.decFormat.format(crossLink.getEuclideanDistance()) + "_";
}
distName +=
atom1.getResidueName().trim()
+ ""
+ atom1.getResidueNumber()
+ ""
+ atom1.getChainId()
+ atom1.getName().trim();
if (atom1.getAlternativeLocation() != ' ') {
distName += atom1.getAlternativeLocation();
}
distName +=
"-"
+ atom2.getResidueName().trim()
+ ""
+ atom2.getResidueNumber()
+ ""
+ atom2.getChainId()
+ atom2.getName().trim();
if (atom2.getAlternativeLocation() != ' ') {
distName += atom2.getAlternativeLocation();
}
output.append("select pk1, " + selection1 + nl);
output.append("select pk2, " + selection2 + nl);
output.append("show spheres, pk1" + nl);
output.append("show spheres, pk2" + nl);
output.append("distance \"" + distName + "\"" + nl);
// output.append("cmd.color(\"red\", \"" + distName + "\")" + nl);
}
output.append("delete pk1" + nl);
output.append("delete pk2" + nl);
return output.toString();
}
/**
* Returns a String representation of this cross-link in distance file format.
*
* @return String object holding the representation of this cross-link in distance file format.
*/
public final String toString() {
String atomId1 = AminoAcid.getAminoAcidId(preAtom) + "-" + preAtom.getName().trim();
String atomId2 = AminoAcid.getAminoAcidId(postAtom) + "-" + postAtom.getName().trim();
if (preAtom.getAlternativeLocation() != ' ') {
atomId1 += "-" + preAtom.getAlternativeLocation();
}
if (postAtom.getAlternativeLocation() != ' ') {
atomId2 += "-" + postAtom.getAlternativeLocation();
}
StringBuffer output = new StringBuffer();
int maxPeptideLength = xwalk.constants.Constants.MAX_PEPTIDE_LENGTH;
int minPeptideLength = xwalk.constants.Constants.MIN_PEPTIDE_LENGTH;
boolean outputPeptide = false;
if (preAtomPeptide != null && postAtomPeptide != null) {
outputPeptide =
preAtomPeptide.size() <= maxPeptideLength
&& preAtomPeptide.size() >= minPeptideLength
&& postAtomPeptide.size() <= maxPeptideLength
&& postAtomPeptide.size() >= minPeptideLength;
}
output.append(
this.filePath
+ "\t"
+ atomId1
+ "\t"
+ atomId2
+ "\t"
+ this.seqDist
+ "\t"
+ this.getEuclideanDistance()
+ "\t");
if (this.getSolventPathDistance() > -0.1 || this.getSolventPathDistance() < -0.9) {
output.append(this.getSolventPathDistance() + "\t");
} else {
output.append("-\t");
}
if (this.doProbability) {
output.append(this.getEuclideanDistanceProbability() + "\t");
if (this.getSolventPathDistance() > -0.1 || this.getSolventPathDistance() < -0.9) {
output.append(this.getSolventPathDistanceProbability() + "\t");
} else {
output.append("-\t");
}
} else {
output.append("-\t-\t");
}
if (outputPeptide) {
output.append(
this.preAtomPeptide.toStringOneLetterCode()
+ "-"
+ this.postAtomPeptide.toStringOneLetterCode());
} else {
output.append("-");
}
output.append(Constants.LINE_SEPERATOR);
return output.toString();
}
/**
* Checks whether a second cross-link has the same atom identifier, i.e. residue name, residue
* number, chain Id and atom name.
*
* @param crossLink - CrossLink object to be compared to this CrossLink object.
* @return {@code TRUE} if both CrossLink object are equal in all atom identifier, {@code FALSE}
* otherwise.
*/
public final boolean equals(final CrossLink crossLink) {
Atom preAtom1 = this.getPreAtom();
Atom postAtom1 = this.getPostAtom();
Atom preAtom2 = crossLink.getPreAtom();
Atom postAtom2 = crossLink.getPostAtom();
if (this.equalsInHomolog(crossLink)) {
String residueId1 = preAtom1.getChainId() + "#" + preAtom1.getName().trim();
String residueId2 = postAtom1.getChainId() + "#" + postAtom1.getName().trim();
String residueId3 = preAtom2.getChainId() + "#" + preAtom2.getName().trim();
String residueId4 = postAtom2.getChainId() + "#" + postAtom2.getName().trim();
if ((residueId1.equals(residueId3) && residueId2.equals(residueId4))
|| (residueId2.equals(residueId3) && residueId1.equals(residueId4))) {
return true;
}
}
return false;
}