public class AtomPlacer3D extends Object
Modifier and Type | Method and Description |
---|---|
boolean |
allHeavyAtomsPlaced(IAtomContainer ac)
True is all the atoms in the given AtomContainer have been placed
|
int[] |
findHeavyAtomsInChain(IAtomContainer molecule,
IAtomContainer chain)
Count and find first heavy atom(s) (non Hydrogens) in a chain.
|
javax.vecmath.Point3d |
geometricCenterAllPlacedAtoms(IAtomContainer molecule)
Calculates the geometric center of all placed atoms in the atomcontainer
|
double |
getAngleValue(String id1,
String id2,
String id3)
Gets the angleKey attribute of the AtomPlacer3D object
|
double |
getBondLengthValue(String id1,
String id2)
Gets the distanceValue attribute of the parameter set
|
IAtom |
getFarthestAtom(javax.vecmath.Point3d refAtomPoint,
IAtomContainer ac)
Gets the farthestAtom attribute of the AtomPlacer3D object
|
IAtom |
getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)
Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule
|
IAtom |
getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)
Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object
|
IAtom |
getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)
Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule
|
IAtom |
getPlacedHeavyAtom(IAtomContainer molecule,
IAtom atom)
Returns a placed atom connected to a given atom
|
IAtom |
getPlacedHeavyAtom(IAtomContainer molecule,
IAtom atomA,
IAtom atomB)
Gets the first placed Heavy Atom around atomA which is not atomB
|
IAtomContainer |
getPlacedHeavyAtoms(IAtomContainer molecule,
IAtom atom)
Gets the placed Heavy Atoms connected to an atom.
|
IAtom |
getUnplacedRingHeavyAtom(IAtomContainer molecule,
IAtom atom)
Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object
|
void |
initilize(Map parameterSet)
Initialize the atomPlacer class.
|
IAtomContainer |
markPlaced(IAtomContainer ac)
Mark all atoms in chain as placed (CDKConstant ISPLACED)
|
int |
numberOfUnplacedHeavyAtoms(IAtomContainer ac)
Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
|
void |
placeAliphaticHeavyChain(IAtomContainer molecule,
IAtomContainer chain)
Method assigns 3Dcoordinates to the heavy atoms in an aliphatic chain
|
void |
zmatrixChainToCartesian(IAtomContainer molecule,
boolean flag_branched)
Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
|
public void initilize(Map parameterSet)
parameterSet
- Force Field parameter as Hashtablepublic int[] findHeavyAtomsInChain(IAtomContainer molecule, IAtomContainer chain)
molecule
- the reference molecule for searching the chainchain
- chain to be searchedpublic IAtomContainer markPlaced(IAtomContainer ac)
ac
- chainpublic void placeAliphaticHeavyChain(IAtomContainer molecule, IAtomContainer chain) throws CDKException
chain
- the atoms to be assigned, must be connectedCDKException
public void zmatrixChainToCartesian(IAtomContainer molecule, boolean flag_branched)
flag_branched
- marks branched chain
author: egonw,chopublic double getBondLengthValue(String id1, String id2)
id1
- atom1 idid2
- atom2 idpublic double getAngleValue(String id1, String id2, String id3)
id1
- Description of the Parameterid2
- Description of the Parameterid3
- Description of the Parameterpublic IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)
public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)
public IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)
public IAtom getFarthestAtom(javax.vecmath.Point3d refAtomPoint, IAtomContainer ac)
refAtomPoint
- Description of the Parameterac
- Description of the Parameterpublic IAtom getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom)
atom
- Description of the Parameterpublic javax.vecmath.Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule)
public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)
atom
- The Atom whose placed bonding partners are to be returnedpublic IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB)
atomA
- Description of the ParameteratomB
- Description of the Parameterpublic IAtomContainer getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom)
atom
- The atom the atoms must be connected to.public int numberOfUnplacedHeavyAtoms(IAtomContainer ac)
ac
- AtomContainerpublic boolean allHeavyAtomsPlaced(IAtomContainer ac)
ac
- The AtomContainer to be searched