Modifier and Type | Field and Description |
---|---|
static double |
DEFAULT_BOND_LENGTH_H |
static double |
TETRAHEDRAL_ANGLE |
Modifier and Type | Method and Description |
---|---|
void |
add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have no
coordinates.
|
javax.vecmath.Point3d[] |
calculate3DCoordinates0(javax.vecmath.Point3d aPoint,
int nwanted,
double length)
Calculates substituent points.
|
javax.vecmath.Point3d[] |
calculate3DCoordinates1(javax.vecmath.Point3d aPoint,
javax.vecmath.Point3d bPoint,
javax.vecmath.Point3d cPoint,
int nwanted,
double length,
double angle)
Calculate new point(s) X in a B-A system to form B-A-X.
|
javax.vecmath.Point3d[] |
calculate3DCoordinates2(javax.vecmath.Point3d aPoint,
javax.vecmath.Point3d bPoint,
javax.vecmath.Point3d cPoint,
int nwanted,
double length,
double angle)
Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X
system.
|
javax.vecmath.Point3d |
calculate3DCoordinates3(javax.vecmath.Point3d aPoint,
javax.vecmath.Point3d bPoint,
javax.vecmath.Point3d cPoint,
javax.vecmath.Point3d dPoint,
double length)
Calculate new point X in a B-A(-D)-C system.
|
javax.vecmath.Point3d |
calculate3DCoordinatesSP2_1(javax.vecmath.Point3d aPoint,
javax.vecmath.Point3d bPoint,
javax.vecmath.Point3d cPoint,
double length,
double angle)
Calculate new point in B-A-C system.
|
javax.vecmath.Point3d[] |
calculate3DCoordinatesSP2_2(javax.vecmath.Point3d aPoint,
javax.vecmath.Point3d bPoint,
javax.vecmath.Point3d cPoint,
double length,
double angle)
Calculate two new points in B-A system.
|
javax.vecmath.Point3d[] |
get3DCoordinatesForLigands(IAtom refAtom,
IAtomContainer noCoords,
IAtomContainer withCoords,
IAtom atomC,
int nwanted,
double length,
double angle)
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
|
javax.vecmath.Point3d[] |
get3DCoordinatesForSP2Ligands(IAtom refAtom,
IAtomContainer noCoords,
IAtomContainer withCoords,
IAtom atomC,
double length,
double angle)
Main method for the calculation of the ligand coordinates for sp2 atoms.
|
javax.vecmath.Point3d[] |
get3DCoordinatesForSP3Ligands(IAtom refAtom,
IAtomContainer noCoords,
IAtomContainer withCoords,
IAtom atomC,
int nwanted,
double length,
double angle)
Main method for the calculation of the ligand coordinates for sp3 atoms.
|
javax.vecmath.Point3d |
get3DCoordinatesForSPLigands(IAtom refAtom,
IAtomContainer withCoords,
double length,
double angle) |
double |
getAngleValue(String id1,
String id2,
String id3)
Gets the angleKey attribute of the AtomPlacer3D object.
|
IAtomContainer |
getPlacedAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets all placed neighbouring atoms of a atom.
|
IAtom |
getPlacedHeavyAtomInAtomContainer(IAtom atomA,
IAtom atomB,
IAtomContainer ac)
Returns a placed neighbouring atom of a central atom atomA, which is not
atomB.
|
double |
getSpatproduct(javax.vecmath.Vector3d a,
javax.vecmath.Vector3d b,
javax.vecmath.Vector3d c)
Gets the spatproduct of three vectors.
|
double |
getTorsionAngle(javax.vecmath.Point3d a,
javax.vecmath.Point3d b,
javax.vecmath.Point3d c,
javax.vecmath.Point3d d)
Calculates the torsionAngle of a-b-c-d.
|
IAtomContainer |
getUnsetAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets the unsetAtomsInAtomContainer attribute of the
AtomTetrahedralLigandPlacer3D object.
|
boolean |
hasUnsetNeighbour(IAtom atom,
IAtomContainer ac) |
int |
makeStereocenter(javax.vecmath.Point3d atomA,
IBond ax,
javax.vecmath.Point3d atomB,
javax.vecmath.Point3d atomC,
javax.vecmath.Point3d[] branchPoints)
set Atoms in respect to stereoinformation.
|
javax.vecmath.Point3d |
rescaleBondLength(IAtom atom1,
IAtom atom2,
javax.vecmath.Point3d point2)
Rescales Point2 so that length 1-2 is sum of covalent radii.
|
static javax.vecmath.Vector3d |
rotate(javax.vecmath.Vector3d vector,
javax.vecmath.Vector3d axis,
double angle)
Rotates a vector around an axis.
|
void |
setParameterSet(Map moleculeParameter)
Constructor for the setParameterSet object.
|
public static final double DEFAULT_BOND_LENGTH_H
public static final double TETRAHEDRAL_ANGLE
public void setParameterSet(Map moleculeParameter)
moleculeParameter
- Description of the Parameterpublic void add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer) throws CDKException
atomContainer
- the set of atoms involvedCDKException
public javax.vecmath.Point3d rescaleBondLength(IAtom atom1, IAtom atom2, javax.vecmath.Point3d point2)
atom1
- stationary atomatom2
- movable atompoint2
- coordinates for atom 2public javax.vecmath.Point3d[] get3DCoordinatesForLigands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle) throws CDKException
refAtom
- (A) to which new ligands coordinates could be addedlength
- A-X lengthangle
- B-A-X angle (used in certain cases)nwanted
- Description of the ParameternoCoords
- Description of the ParameterwithCoords
- Description of the ParameteratomC
- Description of the ParameterCDKException
public javax.vecmath.Point3d get3DCoordinatesForSPLigands(IAtom refAtom, IAtomContainer withCoords, double length, double angle)
public javax.vecmath.Point3d[] get3DCoordinatesForSP2Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, double length, double angle)
refAtom
- central atom (Atom)noCoords
- Description of the ParameterwithCoords
- Description of the ParameteratomC
- Description of the Parameterlength
- Description of the Parameterangle
- Description of the Parameterpublic javax.vecmath.Point3d[] get3DCoordinatesForSP3Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle)
refAtom
- central atom (Atom)nwanted
- how many ligands should be createdlength
- bond lengthangle
- angle in a B-A-(X) system; a=central atom;
x=ligand with unknown coordinatesnoCoords
- Description of the ParameterwithCoords
- Description of the ParameteratomC
- Description of the Parameterpublic javax.vecmath.Point3d[] calculate3DCoordinates0(javax.vecmath.Point3d aPoint, int nwanted, double length)
aPoint
- to which substituents are addednwanted
- number of points to calculate (1-4)length
- from aPointpublic javax.vecmath.Point3d[] calculate3DCoordinates1(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, int nwanted, double length, double angle)
aPoint
- to which substituents are addednwanted
- number of points to calculate (1-3)length
- A-X lengthangle
- B-A-X anglebPoint
- Description of the ParametercPoint
- Description of the Parameterpublic javax.vecmath.Point3d[] calculate3DCoordinates2(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, int nwanted, double length, double angle)
aPoint
- to which substituents are addedbPoint
- first ligand of AcPoint
- second ligand of Anwanted
- number of points to calculate (1-2)length
- A-X lengthangle
- B-A-X anglepublic javax.vecmath.Point3d calculate3DCoordinates3(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, javax.vecmath.Point3d dPoint, double length)
aPoint
- to which substituents are addedbPoint
- first ligand of AcPoint
- second ligand of AdPoint
- third ligand of Alength
- A-X lengthpublic javax.vecmath.Point3d calculate3DCoordinatesSP2_1(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, double length, double angle)
aPoint
- central point A (Point3d)bPoint
- B (Point3d)cPoint
- C (Point3d)length
- bond lengthangle
- angle between B(C)-A-Xpublic javax.vecmath.Point3d[] calculate3DCoordinatesSP2_2(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, double length, double angle)
aPoint
- central point A (Point3d)bPoint
- B (Point3d)cPoint
- C (Point3d)length
- bond lengthangle
- angle between B(C)-A-Xpublic static javax.vecmath.Vector3d rotate(javax.vecmath.Vector3d vector, javax.vecmath.Vector3d axis, double angle)
vector
- vector to be rotated around axisaxis
- axis of rotationangle
- angle to vector rotate aroundpublic double getAngleValue(String id1, String id2, String id3)
id1
- Description of the Parameterid2
- Description of the Parameterid3
- Description of the Parameterpublic int makeStereocenter(javax.vecmath.Point3d atomA, IBond ax, javax.vecmath.Point3d atomB, javax.vecmath.Point3d atomC, javax.vecmath.Point3d[] branchPoints)
atomA
- placed Atom - stereocenterax
- bond between stereocenter and unplaced atomatomB
- neighbour of atomA (in plane created by atomA, atomB and atomC)atomC
- neighbour of atomAbranchPoints
- the two possible placement points for unplaced atom (up and down)public double getSpatproduct(javax.vecmath.Vector3d a, javax.vecmath.Vector3d b, javax.vecmath.Vector3d c)
a
- vector ab
- vector bc
- vector cpublic double getTorsionAngle(javax.vecmath.Point3d a, javax.vecmath.Point3d b, javax.vecmath.Point3d c, javax.vecmath.Point3d d)
a
- Point3db
- Point3dc
- Point3dd
- Point3dpublic IAtomContainer getPlacedAtomsInAtomContainer(IAtom atom, IAtomContainer ac)
atom
- central atom (Atom)ac
- the moleculepublic IAtomContainer getUnsetAtomsInAtomContainer(IAtom atom, IAtomContainer ac)
atom
- Description of the Parameterac
- Description of the Parameterpublic boolean hasUnsetNeighbour(IAtom atom, IAtomContainer ac)
public IAtom getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac)
atomA
- central atom (Atom)atomB
- atom connected to atomA (Atom)ac
- moleculeCopyright © 2021. All rights reserved.