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A

add3DCoordinatesForSinglyBondedLigands(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Generate coordinates for all atoms which are singly bonded and have no coordinates.

allHeavyAtomsPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

True is all the atoms in the given AtomContainer have been placed.

AtomPlacer3D - Class in org.openscience.cdk.modeling.builder3d

Place aliphatic chains with Z matrix method.

AtomTetrahedralLigandPlacer3D - Class in org.openscience.cdk.modeling.builder3d

A set of static utility classes for geometric calculations on Atoms.

C

calculate3DCoordinates0(Point3d, int, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculates substituent points.

calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculate new point(s) X in a B-A system to form B-A-X.

calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X system.

calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculate new point X in a B-A(-D)-C system.

calculate3DCoordinatesSP2_1(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculate new point in B-A-C system.

calculate3DCoordinatesSP2_2(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculate two new points in B-A system.

D

DEFAULT_BOND_LENGTH_H - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

F

findHeavyAtomsInChain(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Count and find first heavy atom(s) (non Hydrogens) in a chain.

G

generate3DCoordinates(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

Generate 3D coordinates with force field information.

geometricCenterAllPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Calculates the geometric center of all placed atoms in the atomcontainer.

get3DCoordinatesForLigands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Adds 3D coordinates for singly-bonded ligands of a reference atom (A).

get3DCoordinatesForSP2Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Main method for the calculation of the ligand coordinates for sp2 atoms.

get3DCoordinatesForSP3Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Main method for the calculation of the ligand coordinates for sp3 atoms.

get3DCoordinatesForSPLigands(IAtom, IAtomContainer, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the angleKey attribute of the AtomPlacer3D object.

getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets the angleKey attribute of the AtomPlacer3D object.

getBitSetFromFile(StringTokenizer) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

getBondLengthValue(String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the distanceValue attribute of the parameter set.

getFarthestAtom(Point3d, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the farthestAtom attribute of the AtomPlacer3D object.

getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

Gives a list of possible force field types.

getInstance() - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

getInstance(TemplateHandler3D, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

getLargestRingSet(List<IRingSet>) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Returns the largest (number of atoms) ring set in a molecule.

getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.

getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.

getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.

getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets all placed neighbouring atoms of a atom.

getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Returns a placed atom connected to a given atom.

getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the first placed Heavy Atom around atomA which is not atomB.

getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Returns a placed neighbouring atom of a central atom atomA, which is not atomB.

getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the placed Heavy Atoms connected to an atom.

getSpatproduct(Vector3d, Vector3d, Vector3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets the spatproduct of three vectors.

getTemplateAt(int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Gets the templateAt attribute of the TemplateHandler object.

getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

Returns the number of loaded templates.

getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Gets the templateCount attribute of the TemplateHandler object.

getTorsionAngle(Point3d, Point3d, Point3d, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Calculates the torsionAngle of a-b-c-d.

getUnplacedRingHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.

getUnsetAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.

H

hasUnsetNeighbour(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

I

initilize(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Initialize the atomPlacer class.

M

makeStereocenter(Point3d, IBond, Point3d, Point3d, Point3d[]) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

set Atoms in respect to stereoinformation.

mapTemplates(IAtomContainer, double) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Deprecated.

Use TemplateHandler3D.mapTemplates(org.openscience.cdk.interfaces.IAtomContainer, int)

mapTemplates(IAtomContainer, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Checks if one of the loaded templates is a substructure in the given Molecule.

markPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Mark all atoms in chain as placed.

ModelBuilder3D - Class in org.openscience.cdk.modeling.builder3d

The main class to generate the 3D coordinates of a molecule ModelBuilder3D.

N

numberOfUnplacedHeavyAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)

O

org.openscience.cdk.modeling.builder3d - package org.openscience.cdk.modeling.builder3d

P

placeAliphaticHeavyChain(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.

R

rescaleBondLength(IAtom, IAtom, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Rescales Point2 so that length 1-2 is sum of covalent radii.

rotate(Vector3d, Vector3d, double) - Static method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Rotates a vector around an axis.

S

setParameterSet(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Constructor for the setParameterSet object.

T

TEMPLATE_PATH - Static variable in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

TemplateHandler3D - Class in org.openscience.cdk.modeling.builder3d

Helper class for ModelBuilder3D.

TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Z

zmatrixChainToCartesian(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Takes the given Z Matrix coordinates and converts them to cartesian coordinates.

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