com.actelion.research.chem.contrib.HydrogenHandler Maven / Gradle / Ivy
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Open Source Chemistry Library
package com.actelion.research.chem.contrib;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
public class HydrogenHandler {
final static double cos30 = Math.cos(30.0 / 360.0 * Math.PI * 2);
final static double sin30 = Math.sin(30.0 / 360.0 * Math.PI * 2);
final static double cos330 = Math.cos(-30.0 / 360.0 * Math.PI * 2);
final static double sin330 = Math.sin(-30.0 / 360.0 * Math.PI * 2);
final static double cos60 = Math.cos(60.0 / 360.0 * Math.PI * 2);
final static double sin60 = Math.sin(60.0 / 360.0 * Math.PI * 2);
final static double cos300 = Math.cos(-60.0 / 360.0 * Math.PI * 2);
final static double sin300 = Math.sin(-60.0 / 360.0 * Math.PI * 2);
final static double cos45 = Math.cos(45.0 / 360.0 * Math.PI * 2);
final static double sin45 = Math.sin(45.0 / 360.0 * Math.PI * 2);
final static double cos315 = Math.cos(-45.0 / 360.0 * Math.PI * 2);
final static double sin315 = Math.sin(-45.0 / 360.0 * Math.PI * 2);
final static double H_BOND_RATIO=0.7;
// changed from method name from expandHydrogensAtAtom(); TLS 9.Nov.2015
public static void addImplicitHydrogens(StereoMolecule molecule, int iAtom) {
final int atomicNo = 1;
// Following line let crash the "cleanup"
// molecule.setAtomMarker(iAtom, true);
int nHydrogens = molecule.getImplicitHydrogens(iAtom);
double x = molecule.getAtomX(iAtom);
double y = molecule.getAtomY(iAtom);
switch (nHydrogens) {
case 1: {
int nNeighbours = molecule.getConnAtoms(iAtom);
// this is for salts like HCL
double dx, dy;
int iNew;
if (nNeighbours == 0) {
double distMin = Double.MAX_VALUE;
int iMin = -1;
for (int atm = 0; atm < molecule.getAllAtoms(); atm++) {
if (atm == iAtom)
continue;
double deltaX = x - molecule.getAtomX(atm);
double deltaY = y - molecule.getAtomY(atm);
double currDist = Math.sqrt((deltaX * deltaX) + (deltaY * deltaY));
if (distMin > currDist) {
distMin = currDist;
iMin = atm;
}
}
dx = x - molecule.getAtomX(iMin);
dy = y - molecule.getAtomY(iMin);
} else {
dx = x - molecule.getAtomX(molecule.getConnAtom(iAtom, 0));
dy = y - molecule.getAtomY(molecule.getConnAtom(iAtom, 0));
}
if (nNeighbours == 1) {
// rotate by 45
iNew = molecule.addAtom((float)(x + cos45 * dx + sin45 * dy),(float)(y - sin45 * dx + cos45 * dy));
} else if (nNeighbours == 2) {
dx = x - 0.5 * (molecule.getAtomX(molecule.getConnAtom(iAtom, 0)) + molecule.getAtomX(molecule.getConnAtom(iAtom, 1)));
dy = y - 0.5 * (molecule.getAtomY(molecule.getConnAtom(iAtom, 0)) + molecule.getAtomY(molecule.getConnAtom(iAtom, 1)));
iNew = molecule.addAtom((float)(x + dx),(float)(y + dy));
} else if (nNeighbours == 3) { // case of existing 3 atoms. We need to put the hydrogen next to the chiral bond !
// looking for a stereobond ...
int stereoAtom1=molecule.getConnAtom(iAtom, 0);
for (int i=1; i<3; i++) {
int bond=molecule.getConnBond(iAtom, i);
if ((molecule.getBondType(bond)== Molecule.cBondTypeDown) ||
(molecule.getBondType(bond)==Molecule.cBondTypeUp)) {
stereoAtom1=molecule.getConnAtom(iAtom, i);
}
}
// should we put the hydrogen next to the chiral bond ? It depends ot the sum of the 3 vectors
double angle1=Math.abs(Molecule.getAngleDif(
Molecule.getAngle(molecule.getAtomX(iAtom),
molecule.getAtomY(iAtom),
molecule.getAtomX(molecule.getConnAtom(iAtom, 0)),
molecule.getAtomY(molecule.getConnAtom(iAtom, 0))
),
Molecule.getAngle(molecule.getAtomX(iAtom),
molecule.getAtomY(iAtom),
molecule.getAtomX(molecule.getConnAtom(iAtom, 1)),
molecule.getAtomY(molecule.getConnAtom(iAtom, 1))
)
));
double angle2=Math.abs(Molecule.getAngleDif(
Molecule.getAngle(molecule.getAtomX(iAtom),
molecule.getAtomY(iAtom),
molecule.getAtomX(molecule.getConnAtom(iAtom, 0)),
molecule.getAtomY(molecule.getConnAtom(iAtom, 0))
),
Molecule.getAngle(molecule.getAtomX(iAtom),
molecule.getAtomY(iAtom),
molecule.getAtomX(molecule.getConnAtom(iAtom, 2)),
molecule.getAtomY(molecule.getConnAtom(iAtom, 2))
)
));
double angle3=Math.abs(Molecule.getAngleDif(
Molecule.getAngle(molecule.getAtomX(iAtom),
molecule.getAtomY(iAtom),
molecule.getAtomX(molecule.getConnAtom(iAtom, 1)),
molecule.getAtomY(molecule.getConnAtom(iAtom, 1))
),
Molecule.getAngle(molecule.getAtomX(iAtom),
molecule.getAtomY(iAtom),
molecule.getAtomX(molecule.getConnAtom(iAtom, 2)),
molecule.getAtomY(molecule.getConnAtom(iAtom, 2))
)
));
// System.out.println(angle1+" - "+angle2+" - "+angle3);
boolean normal=true;
if ((angle1>angle2) && (angle1>angle3)) {
if ((angle2+angle3) < Math.PI) {
normal=false;
dx = x - 0.5 * (molecule.getAtomX(molecule.getConnAtom(iAtom, 0)) + molecule.getAtomX(molecule.getConnAtom(iAtom, 1)));
dy = y - 0.5 * (molecule.getAtomY(molecule.getConnAtom(iAtom, 0)) + molecule.getAtomY(molecule.getConnAtom(iAtom, 1)));
}
} else if ((angle2>angle1) && (angle2>angle3)) {
if ((angle1+angle3) < Math.PI) {
normal=false;
dx = x - 0.5 * (molecule.getAtomX(molecule.getConnAtom(iAtom, 0)) + molecule.getAtomX(molecule.getConnAtom(iAtom, 2)));
dy = y - 0.5 * (molecule.getAtomY(molecule.getConnAtom(iAtom, 0)) + molecule.getAtomY(molecule.getConnAtom(iAtom, 2)));
}
} else {
if ((angle1+angle2) < Math.PI) {
normal=false;
dx = x - 0.5 * (molecule.getAtomX(molecule.getConnAtom(iAtom, 1)) + molecule.getAtomX(molecule.getConnAtom(iAtom, 2)));
dy = y - 0.5 * (molecule.getAtomY(molecule.getConnAtom(iAtom, 1)) + molecule.getAtomY(molecule.getConnAtom(iAtom, 2)));
}
}
if (normal) {
// what is the closest atom to the atom 1 ?
int stereoAtom2=molecule.getConnAtom(iAtom, 0);
double distance=Double.MAX_VALUE;
for (int i=0; i<3; i++) {
int atom=molecule.getConnAtom(iAtom, i);
if (atom!=stereoAtom1) {
double currentDistance=Math.pow(molecule.getAtomX(iAtom)-molecule.getAtomX(atom),2)+Math.pow(molecule.getAtomY(iAtom)-molecule.getAtomY(atom),2);
if (currentDistance-1) {
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
} else {
molecule.addBond(iAtom, iNew, Molecule.cBondTypeUp);
}
iNew = molecule.addAtom((float)(x + cos330 * dx - sin330 * dy),(float)(y + sin330 * dx + cos330 * dy));
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
/*
iNew = molecule.addAtom(x + dx1, y + dy1);
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeUp);
iNew = molecule.addAtom(x + dx2, y + dy2);
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
*/
} else {
for (int iHydrogen = 0; iHydrogen < nHydrogens; iHydrogen++) {
int iNew = molecule.addAtom((float)x, (float)y);
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
}
}
break;
case 3:
// CH3 and the like
{
int iNew;
double dx = (x - molecule.getAtomX(molecule.getConnAtom(iAtom, 0)))*H_BOND_RATIO;
double dy = (y - molecule.getAtomY(molecule.getConnAtom(iAtom, 0)))*H_BOND_RATIO;
// backwards
iNew = molecule.addAtom((float)(x + dx),(float)(y + dy));
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
// to the left
iNew = molecule.addAtom((float)(x - dy),(float)(y + dx));
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
// to the right
iNew = molecule.addAtom((float)(x + dy),(float)(y - dx));
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
}
break;
default:
//
{
for (int iHydrogen = 0; iHydrogen < nHydrogens; iHydrogen++) {
int iNew = molecule.addAtom((float)x,(float)y);
molecule.setAtomicNo(iNew, atomicNo);
molecule.addBond(iAtom, iNew, Molecule.cBondTypeSingle);
}
break;
}
}
}
// changed from method name from expandHydrogens(); TLS 9.Nov.2015
public static void addImplicitHydrogens(StereoMolecule molecule) {
molecule.ensureHelperArrays(Molecule.cHelperNeighbours);
int nAtomsBefore = molecule.getAtoms();
for (int iAtom = 0; iAtom < nAtomsBefore; iAtom++) {
addImplicitHydrogens(molecule, iAtom);
}
}
/* This seems strange: explicit hydrogens are counted twice.
* I suggest using one of the following two functions: TLS 9.Nov.2015
*
public static int getNumberOfExplicitHydrogens(StereoMolecule molecule) {
molecule.ensureHelperArrays(Molecule.cHelperNeighbours);
return molecule.getAllAtoms() - molecule.getAtoms();
}
public static int getNumberOfAllHydrogens(StereoMolecule molecule) {
molecule.ensureHelperArrays(Molecule.cHelperNeighbours);
int nbHydrogens = 0;
for (int iAtom = 0; iAtom < molecule.getAtoms(); iAtom++)
nbHydrogens += molecule.getAllHydrogens(iAtom);
return nbHydrogens;
}
*/
public static int getNumberOfHydrogens(StereoMolecule molecule) {
molecule.ensureHelperArrays(Molecule.cHelperNeighbours);
int nbHydrogens = 0;
for (int iAtom = 0; iAtom < molecule.getAllAtoms(); iAtom++) {
if (molecule.getAtomicNo(iAtom) == 1)
nbHydrogens++;
else
nbHydrogens += molecule.getPlainHydrogens(iAtom);
}
return nbHydrogens;
}
}
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