Modifier and Type | Field and Description |
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static double |
TETRAHEDRAL_ANGLE |
Constructor and Description |
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AtomTools() |
Modifier and Type | Method and Description |
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static void |
add3DCoordinates1(IAtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have
no coordinates.
|
static javax.vecmath.Point3d[] |
calculate3DCoordinates0(javax.vecmath.Point3d aPoint,
int nwanted,
double length)
Calculates substituent points.
|
static 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.
|
static 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.
|
static 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.
|
static javax.vecmath.Point3d[] |
calculate3DCoordinatesForLigands(IAtomContainer atomContainer,
IAtom refAtom,
int nwanted,
double length,
double angle)
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
|
static javax.vecmath.Point3d |
rescaleBondLength(IAtom atom1,
IAtom atom2,
javax.vecmath.Point3d point2)
Rescales Point2 so that length 1-2 is sum of covalent radii.
|
public static void add3DCoordinates1(IAtomContainer atomContainer)
atomContainer
- the set of atoms involvedpublic static javax.vecmath.Point3d rescaleBondLength(IAtom atom1, IAtom atom2, javax.vecmath.Point3d point2)
atom1
- stationary atomatom2
- movable atompoint2
- coordinates for atom 2public static javax.vecmath.Point3d[] calculate3DCoordinatesForLigands(IAtomContainer atomContainer, IAtom refAtom, int nwanted, double length, double angle)
atomContainer
- describing the ligands of refAtom. It could be the
whole molecule, or could be a selected subset of ligandsrefAtom
- (A) to which new ligands coordinates could be addedlength
- A-X lengthangle
- B-A-X angle (used in certain cases)public static 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 static 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 anglepublic static 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 static 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 lengthCopyright © 2017. All Rights Reserved.