/**
* Generate coordinates for all atoms which are singly bonded and have no coordinates. This is
* useful when hydrogens are present but have no coords. It knows about C, O, N, S only and will
* give tetrahedral or trigonal geometry elsewhere. Bond lengths are computed from covalent radii
* if available. Angles are tetrahedral or trigonal
*
* @param atomContainer the set of atoms involved
* @cdk.keyword coordinate calculation
* @cdk.keyword 3D model
*/
public static void add3DCoordinates1(AtomContainer atomContainer) {
// atoms without coordinates
AtomContainer noCoords = new AtomContainer();
// get vector of possible referenceAtoms?
AtomContainer refAtoms = new AtomContainer();
for (int i = 0; i < atomContainer.getAtomCount(); i++) {
IAtom atom = atomContainer.getAtom(i);
// is this atom without 3D coords, and has only one ligand?
if (atom.getPoint3d() == null) {
java.util.List connectedAtoms = atomContainer.getConnectedAtomsList(atom);
if (connectedAtoms.size() == 1) {
IAtom refAtom = (IAtom) connectedAtoms.get(0);
;
if (refAtom.getPoint3d() != null) {
refAtoms.addAtom(refAtom);
// store atoms with no coords and ref atoms in a
// single container
noCoords.addAtom(atom);
noCoords.addAtom(refAtom);
// bond is required to extract ligands
noCoords.addBond(new Bond(atom, refAtom, CDKConstants.BONDORDER_SINGLE));
}
}
}
}
// now add coordinates to ligands of reference atoms
// use default length of 1.0, which can be adjusted later
double length = 1.0;
double angle = TETRAHEDRAL_ANGLE;
for (int i = 0; i < refAtoms.getAtomCount(); i++) {
IAtom refAtom = refAtoms.getAtom(i);
java.util.List noCoordLigands = noCoords.getConnectedAtomsList(refAtom);
int nLigands = noCoordLigands.size();
int nwanted = nLigands;
String elementType = refAtom.getSymbol();
// try to deal with lone pairs on small hetero
if (elementType.equals("N") || elementType.equals("O") || elementType.equals("S")) {
nwanted = 3;
}
Point3d[] newPoints =
calculate3DCoordinatesForLigands(atomContainer, refAtom, nwanted, length, angle);
for (int j = 0; j < nLigands; j++) {
IAtom ligand = (IAtom) noCoordLigands.get(j);
Point3d newPoint = rescaleBondLength(refAtom, ligand, newPoints[j]);
ligand.setPoint3d(newPoint);
}
}
}
/**
* Adds all atoms and electronContainers of a given atomcontainer to this container.
*
* @param atomContainer The atomcontainer to be added
*/
public void add(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
for (IStereoElement se : atomContainer.stereoElements()) stereoElements.add(se);
notifyChanged();
}
/**
* 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;
}
/**
* 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;
}
/** 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 addAtom(IAtom atom) {
logger.debug("Adding atom: ", atom);
super.addAtom(atom);
}
