/**
* Adds 3D coordinates for singly-bonded ligands of a reference atom (A). Initially designed for
* hydrogens. The ligands of refAtom are identified and those with 3D coordinates used to generate
* the new points. (This allows structures with partially known 3D coordinates to be used, as when
* groups are added.) "Bent" and "non-planar" groups can be formed by taking a subset of the
* calculated points. Thus R-NH2 could use 2 of the 3 points calculated from (1,iii) nomenclature:
* A is point to which new ones are "attached". A may have ligands B, C... B may have ligands J,
* K.. points X1, X2... are returned The cases (see individual routines, which use idealised
* geometry by default): (0) zero ligands of refAtom. The resultant points are randomly oriented:
* (i) 1 points required; +x,0,0 (ii) 2 points: use +x,0,0 and -x,0,0 (iii) 3 points: equilateral
* triangle in xy plane (iv) 4 points x,x,x, x,-x,-x, -x,x,-x, -x,-x,x (1a) 1 ligand(B) of refAtom
* which itself has a ligand (J) (i) 1 points required; vector along AB vector (ii) 2 points: 2
* vectors in ABJ plane, staggered and eclipsed wrt J (iii) 3 points: 1 staggered wrt J, the
* others +- gauche wrt J (1b) 1 ligand(B) of refAtom which has no other ligands. A random J is
* generated and (1a) applied (2) 2 ligands(B, C) of refAtom A (i) 1 points required; vector in
* ABC plane bisecting AB, AC. If ABC is linear, no points (ii) 2 points: 2 vectors at angle ang,
* whose resultant is 2i (3) 3 ligands(B, C, D) of refAtom A (i) 1 points required; if A, B, C, D
* coplanar, no points. else vector is resultant of BA, CA, DA
*
* <p>fails if atom itself has no coordinates or >4 ligands
*
* @param atomContainer describing the ligands of refAtom. It could be the whole molecule, or
* could be a selected subset of ligands
* @param refAtom (A) to which new ligands coordinates could be added
* @param length A-X length
* @param angle B-A-X angle (used in certain cases)
* @return Point3D[] points calculated. If request could not be fulfilled (e.g. too many atoms, or
* strange geometry, returns empty array (zero length, not null)
* @cdk.keyword coordinate generation
*/
public static Point3d[] calculate3DCoordinatesForLigands(
AtomContainer atomContainer, IAtom refAtom, int nwanted, double length, double angle) {
Point3d newPoints[] = new Point3d[0];
Point3d aPoint = refAtom.getPoint3d();
// get ligands
List connectedAtoms = atomContainer.getConnectedAtomsList(refAtom);
if (connectedAtoms == null) {
return newPoints;
}
int nligands = connectedAtoms.size();
AtomContainer ligandsWithCoords = new AtomContainer();
for (int i = 0; i < nligands; i++) {
Atom ligand = (Atom) connectedAtoms.get(i);
if (ligand.getPoint3d() != null) {
ligandsWithCoords.addAtom(ligand);
}
}
int nwithCoords = ligandsWithCoords.getAtomCount();
// too many ligands at present
if (nwithCoords > 3) {
return newPoints;
}
if (nwithCoords == 0) {
newPoints = calculate3DCoordinates0(refAtom.getPoint3d(), nwanted, length);
} else if (nwithCoords == 1) {
// ligand on A
IAtom bAtom = ligandsWithCoords.getAtom(0);
connectedAtoms = ligandsWithCoords.getConnectedAtomsList(bAtom);
// does B have a ligand (other than A)
Atom jAtom = null;
for (int i = 0; i < connectedAtoms.size(); i++) {
Atom connectedAtom = (Atom) connectedAtoms.get(i);
if (!connectedAtom.equals(refAtom)) {
jAtom = connectedAtom;
break;
}
}
newPoints =
calculate3DCoordinates1(
aPoint,
bAtom.getPoint3d(),
(jAtom != null) ? jAtom.getPoint3d() : null,
nwanted,
length,
angle);
} else if (nwithCoords == 2) {
Point3d bPoint = ligandsWithCoords.getAtom(0).getPoint3d();
Point3d cPoint = ligandsWithCoords.getAtom(1).getPoint3d();
newPoints = calculate3DCoordinates2(aPoint, bPoint, cPoint, nwanted, length, angle);
} else if (nwithCoords == 3) {
Point3d bPoint = ligandsWithCoords.getAtom(0).getPoint3d();
Point3d cPoint = ligandsWithCoords.getAtom(1).getPoint3d();
Point3d dPoint = ligandsWithCoords.getAtom(2).getPoint3d();
newPoints = new Point3d[1];
newPoints[0] = calculate3DCoordinates3(aPoint, bPoint, cPoint, dPoint, length);
}
return newPoints;
}
public void remove(IAtomContainer atomContainer) {
logger.debug("Removing atom container: ", atomContainer);
super.remove(atomContainer);
}
/**
* Create a benzene molecule with 2 residues and 2 charge groups
*
* @return
*/
public MDMolecule makeMDBenzene() {
MDMolecule mol = new MDMolecule();
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addAtom(new Atom("C")); // 2
mol.addAtom(new Atom("C")); // 3
mol.addAtom(new Atom("C")); // 4
mol.addAtom(new Atom("C")); // 5
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
mol.addBond(1, 2, IBond.Order.DOUBLE); // 2
mol.addBond(2, 3, IBond.Order.SINGLE); // 3
mol.addBond(3, 4, IBond.Order.DOUBLE); // 4
mol.addBond(4, 5, IBond.Order.SINGLE); // 5
mol.addBond(5, 0, IBond.Order.DOUBLE); // 6
// Create 2 residues
AtomContainer ac = new AtomContainer();
ac.addAtom(mol.getAtom(0));
ac.addAtom(mol.getAtom(1));
ac.addAtom(mol.getAtom(2));
Residue res1 = new Residue(ac, 0, mol);
res1.setName("myResidue1");
mol.addResidue(res1);
AtomContainer ac2 = new AtomContainer();
ac2.addAtom(mol.getAtom(3));
ac2.addAtom(mol.getAtom(4));
ac2.addAtom(mol.getAtom(5));
Residue res2 = new Residue(ac2, 1, mol);
res2.setName("myResidue2");
mol.addResidue(res2);
// Create 2 chargegroups
AtomContainer ac3 = new AtomContainer();
ac3.addAtom(mol.getAtom(0));
ac3.addAtom(mol.getAtom(1));
ChargeGroup chg1 = new ChargeGroup(ac3, 2, mol);
chg1.setSwitchingAtom(mol.getAtom(1));
mol.addChargeGroup(chg1);
AtomContainer ac4 = new AtomContainer();
ac4.addAtom(mol.getAtom(2));
ac4.addAtom(mol.getAtom(3));
ac4.addAtom(mol.getAtom(4));
ac4.addAtom(mol.getAtom(5));
ChargeGroup chg2 = new ChargeGroup(ac4, 3, mol);
chg2.setSwitchingAtom(mol.getAtom(4));
mol.addChargeGroup(chg2);
return mol;
}
public void setAtoms(IAtom[] atoms) {
logger.debug("Setting atoms: ", atoms.length);
super.setAtoms(atoms);
}
public void setFlags(boolean[] flagsNew) {
logger.debug("Setting flags:", flagsNew.length);
super.setFlags(flagsNew);
}
public void setFlag(int flag_type, boolean flag_value) {
logger.debug("Setting flag: ", flag_type + "=" + flag_value);
super.setFlag(flag_type, flag_value);
}
public void removeProperty(Object description) {
logger.debug("Removing property: ", description);
super.removeProperty(description);
}
public void notifyChanged(IChemObjectChangeEvent evt) {
logger.debug("Notifying changed event: ", evt);
super.notifyChanged(evt);
}
public void removeAtomAndConnectedElectronContainers(IAtom atom) {
logger.debug("Removing atom and connected electron containers: ", atom);
super.removeAtomAndConnectedElectronContainers(atom);
}
public void removeSingleElectron(ISingleElectron ec) {
logger.debug("Removing bond=" + ec);
super.removeSingleElectron(ec);
}
public void removeLonePair(ILonePair ec) {
logger.debug("Removing bond=" + ec);
super.removeLonePair(ec);
}
public void removeBond(IBond bond) {
logger.debug("Removing bond=" + bond);
super.removeBond(bond);
}
public void removeAtom(IAtom atom) {
logger.debug("Removing atom: ", atom);
super.removeAtom(atom);
}
public void removeAtom(int position) {
logger.debug("Removing atom: ", position);
super.removeAtom(position);
}
public void removeElectronContainer(IElectronContainer electronContainer) {
logger.debug("Removing electron container: ", electronContainer);
super.removeElectronContainer(electronContainer);
}
public void removeListener(IChemObjectListener col) {
logger.debug("Removing listener: ", col);
super.removeListener(col);
}
public void notifyChanged() {
logger.debug("Notifying changed");
super.notifyChanged();
}
public void removeAllElements() {
logger.debug("Removing all elements");
super.removeAllElements();
}
public void setProperty(Object description, Object property) {
logger.debug("Setting property: ", description + "=" + property);
super.setProperty(description, property);
}
public void removeAllElectronContainers() {
logger.debug("Removing all electron containers");
super.removeAllElectronContainers();
}
public void setID(String identifier) {
logger.debug("Setting ID: ", identifier);
super.setID(identifier);
}
public void removeAllBonds() {
logger.debug("Removing all bonds");
super.removeAllBonds();
}
public void setProperties(Map<Object, Object> properties) {
logger.debug("Setting properties: ", properties);
super.setProperties(properties);
}
public void addBond(int atom1, int atom2, IBond.Order order) {
logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
super.addBond(atom1, atom2, order);
}
public void addAtomParity(IAtomParity parity) {
logger.debug("Adding atom parity: ", parity);
super.addAtomParity(parity);
}
public void addLonePair(int atomID) {
logger.debug("Adding lone pair: ", atomID);
super.addLonePair(atomID);
}
public void setAtom(int number, IAtom atom) {
logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
super.setAtom(number, atom);
}
public void addSingleElectron(int atomID) {
logger.debug("Adding single electron: ", atomID);
super.addSingleElectron(atomID);
}
/** Test an MDMolecule with residues and charge groups */
@Test
public void testMDMolecule() {
MDMolecule mol = new MDMolecule();
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addAtom(new Atom("C")); // 2
mol.addAtom(new Atom("C")); // 3
mol.addAtom(new Atom("C")); // 4
mol.addAtom(new Atom("C")); // 5
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
mol.addBond(1, 2, IBond.Order.DOUBLE); // 2
mol.addBond(2, 3, IBond.Order.SINGLE); // 3
mol.addBond(3, 4, IBond.Order.DOUBLE); // 4
mol.addBond(4, 5, IBond.Order.SINGLE); // 5
mol.addBond(5, 0, IBond.Order.DOUBLE); // 6
// Create 2 residues
AtomContainer ac = new AtomContainer();
ac.addAtom(mol.getAtom(0));
ac.addAtom(mol.getAtom(1));
ac.addAtom(mol.getAtom(2));
Residue res1 = new Residue(ac, 0, mol);
res1.setName("myResidue1");
mol.addResidue(res1);
AtomContainer ac2 = new AtomContainer();
ac2.addAtom(mol.getAtom(3));
ac2.addAtom(mol.getAtom(4));
ac2.addAtom(mol.getAtom(5));
Residue res2 = new Residue(ac2, 1, mol);
res2.setName("myResidue2");
mol.addResidue(res2);
// Test residue creation
Assert.assertEquals(res1.getParentMolecule(), mol);
Assert.assertEquals(res2.getParentMolecule(), mol);
Assert.assertEquals(res1.getAtomCount(), 3);
Assert.assertEquals(res2.getAtomCount(), 3);
Assert.assertEquals(res1.getName(), "myResidue1");
Assert.assertEquals(res2.getName(), "myResidue2");
Assert.assertNotNull(mol.getResidues());
Assert.assertEquals(mol.getResidues().size(), 2);
Assert.assertEquals(mol.getResidues().get(0), res1);
Assert.assertEquals(mol.getResidues().get(1), res2);
// Create 2 chargegroups
AtomContainer ac3 = new AtomContainer();
ac3.addAtom(mol.getAtom(0));
ac3.addAtom(mol.getAtom(1));
ChargeGroup chg1 = new ChargeGroup(ac3, 0, mol);
mol.addChargeGroup(chg1);
AtomContainer ac4 = new AtomContainer();
ac4.addAtom(mol.getAtom(2));
ac4.addAtom(mol.getAtom(3));
ac4.addAtom(mol.getAtom(4));
ac4.addAtom(mol.getAtom(5));
ChargeGroup chg2 = new ChargeGroup(ac4, 1, mol);
mol.addChargeGroup(chg2);
// Test chargegroup creation
Assert.assertEquals(chg1.getParentMolecule(), mol);
Assert.assertEquals(chg2.getParentMolecule(), mol);
Assert.assertEquals(chg1.getAtomCount(), 2);
Assert.assertEquals(chg2.getAtomCount(), 4);
Assert.assertNotNull(mol.getChargeGroups());
Assert.assertEquals(mol.getChargeGroups().size(), 2);
Assert.assertEquals(mol.getChargeGroups().get(0), chg1);
Assert.assertEquals(mol.getChargeGroups().get(1), chg2);
}
public void addListener(IChemObjectListener col) {
logger.debug("Adding listener: ", col);
super.addListener(col);
}