// method which calculated distance btw an atom and the middle point of a bond
// and returns distance and coordinates of middle point
private double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond) {
Point3d middlePoint = theBond.get3DCenter();
Point3d protonPoint = proton.getPoint3d();
double[] values = new double[4];
values[0] = middlePoint.distance(protonPoint);
values[1] = middlePoint.x;
values[2] = middlePoint.y;
values[3] = middlePoint.z;
return values;
}
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(
IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset) {
IAtomContainer varAtomContainer;
try {
varAtomContainer = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
int atomPosition = atomContainer.getAtomNumber(atom);
IAtom clonedAtom = varAtomContainer.getAtom(atomPosition);
DoubleArrayResult rdfProtonCalculatedValues = new DoubleArrayResult(gsr_desc_length);
if (!atom.getSymbol().equals("H")) {
return getDummyDescriptorValue(new CDKException("Invalid atom specified"));
}
///////////////////////// FIRST SECTION OF MAIN METHOD: DEFINITION OF MAIN VARIABLES
///////////////////////// AND AROMATICITY AND PI-SYSTEM AND RINGS DETECTION
Molecule mol = new Molecule(varAtomContainer);
if (varAtomContainer != acold) {
acold = varAtomContainer;
// DETECTION OF pi SYSTEMS
varAtomContainerSet = ConjugatedPiSystemsDetector.detect(mol);
if (precalculatedringset == null)
try {
varRingSet = (new AllRingsFinder()).findAllRings(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
else varRingSet = precalculatedringset;
try {
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
} catch (Exception ex1) {
return getDummyDescriptorValue(ex1);
}
}
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(varAtomContainer);
CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
IRingSet rsAtom;
Ring ring;
IRingSet ringsWithThisBond;
// SET ISINRING FLAGS FOR BONDS
Iterator<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
while (bondsInContainer.hasNext()) {
IBond bond = bondsInContainer.next();
ringsWithThisBond = varRingSet.getRings(bond);
if (ringsWithThisBond.getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
// SET ISINRING FLAGS FOR ATOMS
IRingSet ringsWithThisAtom;
for (int w = 0; w < varAtomContainer.getAtomCount(); w++) {
ringsWithThisAtom = varRingSet.getRings(varAtomContainer.getAtom(w));
if (ringsWithThisAtom.getAtomContainerCount() > 0) {
varAtomContainer.getAtom(w).setFlag(CDKConstants.ISINRING, true);
}
}
IAtomContainer detected = varAtomContainerSet.getAtomContainer(0);
// neighboors[0] is the atom joined to the target proton:
List<IAtom> neighboors = mol.getConnectedAtomsList(clonedAtom);
IAtom neighbour0 = neighboors.get(0);
// 2', 3', 4', 5', 6', and 7' atoms up to the target are detected:
List<IAtom> atomsInSecondSphere = mol.getConnectedAtomsList(neighbour0);
List<IAtom> atomsInThirdSphere;
List<IAtom> atomsInFourthSphere;
List<IAtom> atomsInFifthSphere;
List<IAtom> atomsInSixthSphere;
List<IAtom> atomsInSeventhSphere;
// SOME LISTS ARE CREATED FOR STORING OF INTERESTING ATOMS AND BONDS DURING DETECTION
ArrayList<Integer> singles = new ArrayList<Integer>(); // list of any bond not rotatable
ArrayList<Integer> doubles = new ArrayList<Integer>(); // list with only double bonds
ArrayList<Integer> atoms = new ArrayList<Integer>(); // list with all the atoms in spheres
// atoms.add( Integer.valueOf( mol.getAtomNumber(neighboors[0]) ) );
ArrayList<Integer> bondsInCycloex =
new ArrayList<Integer>(); // list for bonds in cycloexane-like rings
// 2', 3', 4', 5', 6', and 7' bonds up to the target are detected:
IBond secondBond; // (remember that first bond is proton bond)
IBond thirdBond; //
IBond fourthBond; //
IBond fifthBond; //
IBond sixthBond; //
IBond seventhBond; //
// definition of some variables used in the main FOR loop for detection of interesting atoms and
// bonds:
boolean theBondIsInA6MemberedRing; // this is like a flag for bonds which are in cycloexane-like
// rings (rings with more than 4 at.)
IBond.Order bondOrder;
int bondNumber;
int sphere;
// THIS MAIN FOR LOOP DETECT RIGID BONDS IN 7 SPHERES:
for (IAtom curAtomSecond : atomsInSecondSphere) {
secondBond = mol.getBond(neighbour0, curAtomSecond);
if (mol.getAtomNumber(curAtomSecond) != atomPosition
&& getIfBondIsNotRotatable(mol, secondBond, detected)) {
sphere = 2;
bondOrder = secondBond.getOrder();
bondNumber = mol.getBondNumber(secondBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSecond),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInThirdSphere = mol.getConnectedAtomsList(curAtomSecond);
if (atomsInThirdSphere.size() > 0) {
for (IAtom curAtomThird : atomsInThirdSphere) {
thirdBond = mol.getBond(curAtomThird, curAtomSecond);
// IF THE ATOMS IS IN THE THIRD SPHERE AND IN A CYCLOEXANE-LIKE RING, IT IS STORED IN
// THE PROPER LIST:
if (mol.getAtomNumber(curAtomThird) != atomPosition
&& getIfBondIsNotRotatable(mol, thirdBond, detected)) {
sphere = 3;
bondOrder = thirdBond.getOrder();
bondNumber = mol.getBondNumber(thirdBond);
theBondIsInA6MemberedRing = false;
// if the bond is in a cyclohexane-like ring (a ring with 5 or more atoms, not
// aromatic)
// the boolean "theBondIsInA6MemberedRing" is set to true
if (!thirdBond.getFlag(CDKConstants.ISAROMATIC)) {
if (!curAtomThird.equals(neighbour0)) {
rsAtom = varRingSet.getRings(thirdBond);
for (int f = 0; f < rsAtom.getAtomContainerCount(); f++) {
ring = (Ring) rsAtom.getAtomContainer(f);
if (ring.getRingSize() > 4 && ring.contains(thirdBond)) {
theBondIsInA6MemberedRing = true;
}
}
}
}
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomThird),
atoms,
sphere,
theBondIsInA6MemberedRing);
theBondIsInA6MemberedRing = false;
atomsInFourthSphere = mol.getConnectedAtomsList(curAtomThird);
if (atomsInFourthSphere.size() > 0) {
for (IAtom curAtomFourth : atomsInFourthSphere) {
fourthBond = mol.getBond(curAtomThird, curAtomFourth);
if (mol.getAtomNumber(curAtomFourth) != atomPosition
&& getIfBondIsNotRotatable(mol, fourthBond, detected)) {
sphere = 4;
bondOrder = fourthBond.getOrder();
bondNumber = mol.getBondNumber(fourthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFourth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInFifthSphere = mol.getConnectedAtomsList(curAtomFourth);
if (atomsInFifthSphere.size() > 0) {
for (IAtom curAtomFifth : atomsInFifthSphere) {
fifthBond = mol.getBond(curAtomFifth, curAtomFourth);
if (mol.getAtomNumber(curAtomFifth) != atomPosition
&& getIfBondIsNotRotatable(mol, fifthBond, detected)) {
sphere = 5;
bondOrder = fifthBond.getOrder();
bondNumber = mol.getBondNumber(fifthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFifth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSixthSphere = mol.getConnectedAtomsList(curAtomFifth);
if (atomsInSixthSphere.size() > 0) {
for (IAtom curAtomSixth : atomsInSixthSphere) {
sixthBond = mol.getBond(curAtomFifth, curAtomSixth);
if (mol.getAtomNumber(curAtomSixth) != atomPosition
&& getIfBondIsNotRotatable(mol, sixthBond, detected)) {
sphere = 6;
bondOrder = sixthBond.getOrder();
bondNumber = mol.getBondNumber(sixthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSixth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSeventhSphere = mol.getConnectedAtomsList(curAtomSixth);
if (atomsInSeventhSphere.size() > 0) {
for (IAtom curAtomSeventh : atomsInSeventhSphere) {
seventhBond = mol.getBond(curAtomSeventh, curAtomSixth);
if (mol.getAtomNumber(curAtomSeventh) != atomPosition
&& getIfBondIsNotRotatable(mol, seventhBond, detected)) {
sphere = 7;
bondOrder = seventhBond.getOrder();
bondNumber = mol.getBondNumber(seventhBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSeventh),
atoms,
sphere,
theBondIsInA6MemberedRing);
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
// Variables
double[] values; // for storage of results of other methods
double distance;
double sum;
double smooth = -20;
double partial;
int position;
double limitInf;
double limitSup;
double step;
//////////////////////// THE FOUTH DESCRIPTOR IS gS(r), WHICH TAKES INTO ACCOUNT SINGLE BONDS IN
// RIGID SYSTEMS
Vector3d a_a = new Vector3d();
Vector3d a_b = new Vector3d();
Vector3d b_a = new Vector3d();
Vector3d b_b = new Vector3d();
Point3d middlePoint = new Point3d();
double angle = 0;
if (singles.size() > 0) {
double dist0;
double dist1;
IAtom singleBondAtom0;
IAtom singleBondAtom1;
distance = 0;
position = 0;
IBond theSingleBond = null;
limitInf = 0;
limitSup = Math.PI / 2;
step = (limitSup - limitInf) / 7;
smooth = -1.15;
int counter = 0;
for (double ghs = 0; ghs < limitSup; ghs = ghs + step) {
sum = 0;
for (int sing = 0; sing < singles.size(); sing++) {
angle = 0;
partial = 0;
Integer thisSingleBond = singles.get(sing);
position = thisSingleBond;
theSingleBond = mol.getBond(position);
middlePoint = theSingleBond.get3DCenter();
singleBondAtom0 = theSingleBond.getAtom(0);
singleBondAtom1 = theSingleBond.getAtom(1);
dist0 = calculateDistanceBetweenTwoAtoms(singleBondAtom0, atom);
dist1 = calculateDistanceBetweenTwoAtoms(singleBondAtom1, atom);
a_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
if (dist1 > dist0)
a_b.set(
singleBondAtom0.getPoint3d().x,
singleBondAtom0.getPoint3d().y,
singleBondAtom0.getPoint3d().z);
else
a_b.set(
singleBondAtom1.getPoint3d().x,
singleBondAtom1.getPoint3d().y,
singleBondAtom1.getPoint3d().z);
b_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
b_b.set(atom.getPoint3d().x, atom.getPoint3d().y, atom.getPoint3d().z);
values = calculateDistanceBetweenAtomAndBond(atom, theSingleBond);
angle = calculateAngleBetweenTwoLines(a_a, a_b, b_a, b_b);
// System.out.println("ANGLe: "+angle+ " "+ mol.getAtomNumber(atomsInSingleBond[0]) +" "
// +mol.getAtomNumber(atomsInSingleBond[1]));
partial =
(1 / (Math.pow(values[0], 2))) * Math.exp(smooth * (Math.pow((ghs - angle), 2)));
sum += partial;
}
// gSr_function.add(new Double(sum));
rdfProtonCalculatedValues.add(sum);
logger.debug("RDF gSr prob.: " + sum + " at distance " + ghs);
counter++;
}
} else {
return getDummyDescriptorValue(new CDKException("Some error occurred. Please report"));
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
rdfProtonCalculatedValues,
getDescriptorNames());
}