Package org.openscience.cdk.modeling.builder3d

Class AtomPlacer3D

  • public class AtomPlacer3D
extends Object
    Place aliphatic chains with Z matrix method. Please use ModelBuilder3D to place general molecules.
    Author:
    chhoppe
    See Also:
    ModelBuilder3D
    Source code:
    main
    Belongs to CDK module:
    builder3d
    Keywords:
    AtomPlacer3D
    Created on:
    2004-10-8

    • Method Detail

      • initilize

        public void initilize​(Map parameterSet)
        Initialize the atomPlacer class.
        Parameters:
        parameterSet - Force Field parameter as Hashtable

      • findHeavyAtomsInChain

        public int[] findHeavyAtomsInChain​(IAtomContainer molecule,
                                   IAtomContainer chain)
        Count and find first heavy atom(s) (non Hydrogens) in a chain.
        Parameters:
        molecule - the reference molecule for searching the chain
        chain - chain to be searched
        Returns:
        the atom number of the first heavy atom the number of heavy atoms in the chain

      • markPlaced

        public IAtomContainer markPlaced​(IAtomContainer ac)
        Mark all atoms in chain as placed. (CDKConstant ISPLACED)
        Parameters:
        ac - chain
        Returns:
        chain all atoms marked as placed

      • placeAliphaticHeavyChain

        public void placeAliphaticHeavyChain​(IAtomContainer molecule,
                                     IAtomContainer chain)
                              throws CDKException
        Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.
        Parameters:
        molecule - the reference molecule for the chain
        chain - the atoms to be assigned, must be connected
        Throws:
        CDKException - the 'chain' was not a chain

      • zmatrixChainToCartesian

        public void zmatrixChainToCartesian​(IAtomContainer molecule,
                                    boolean flagBranched)
        Takes the given Z Matrix coordinates and converts them to cartesian coordinates. The first Atom end up in the origin, the second on on the x axis, and the third one in the XY plane. The rest is added by applying the Zmatrix distances, angles and dihedrals. Assign coordinates directly to the atoms.
        Parameters:
        molecule - the molecule to be placed in 3D
        flagBranched - marks branched chain author: egonw,cho

      • getBondLengthValue

        public double getBondLengthValue​(String id1,
                                 String id2)
        Gets the distanceValue attribute of the parameter set.
        Parameters:
        id1 - atom1 id
        id2 - atom2 id
        Returns:
        The distanceValue value from the force field parameter set

      • getAngleValue

        public double getAngleValue​(String id1,
                            String id2,
                            String id3)
        Gets the angleKey attribute of the AtomPlacer3D object.
        Parameters:
        id1 - Description of the Parameter
        id2 - Description of the Parameter
        id3 - Description of the Parameter
        Returns:
        The angleKey value

      • getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour

        public IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour​(IAtomContainer molecule)
        Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
        Parameters:
        molecule -
        Returns:
        The nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour value author: steinbeck,cho

      • getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour

        public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour​(IAtomContainer molecule)
        Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
        Parameters:
        molecule -
        Returns:
        The nextUnplacedHeavyAtomWithUnplacedAliphaticNeigbor author: steinbeck,cho

      • getNextPlacedHeavyAtomWithUnplacedRingNeighbour

        public IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour​(IAtomContainer molecule)
        Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
        Parameters:
        molecule - The atom container under consideration
        Returns:
        The nextPlacedHeavyAtomWithUnplacedRingNeighbour value

      • getFarthestAtom

        public IAtom getFarthestAtom​(javax.vecmath.Point3d refAtomPoint,
                             IAtomContainer ac)
        Gets the farthestAtom attribute of the AtomPlacer3D object.
        Parameters:
        refAtomPoint - Description of the Parameter
        ac - Description of the Parameter
        Returns:
        The farthestAtom value

      • getUnplacedRingHeavyAtom

        public IAtom getUnplacedRingHeavyAtom​(IAtomContainer molecule,
                                      IAtom atom)
        Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
        Parameters:
        molecule -
        atom - Description of the Parameter
        Returns:
        The unplacedRingHeavyAtom value

      • geometricCenterAllPlacedAtoms

        public javax.vecmath.Point3d geometricCenterAllPlacedAtoms​(IAtomContainer molecule)
        Calculates the geometric center of all placed atoms in the atomcontainer.
        Parameters:
        molecule -
        Returns:
        Point3d the geometric center

      • getPlacedHeavyAtom

        public IAtom getPlacedHeavyAtom​(IAtomContainer molecule,
                                IAtom atom)
        Returns a placed atom connected to a given atom.
        Parameters:
        molecule -
        atom - The Atom whose placed bonding partners are to be returned
        Returns:
        a placed heavy atom connected to a given atom author: steinbeck

      • getPlacedHeavyAtom

        public IAtom getPlacedHeavyAtom​(IAtomContainer molecule,
                                IAtom atomA,
                                IAtom atomB)
        Gets the first placed Heavy Atom around atomA which is not atomB.
        Parameters:
        molecule -
        atomA - Description of the Parameter
        atomB - Description of the Parameter
        Returns:
        The placedHeavyAtom value

      • getPlacedHeavyAtoms

        public IAtomContainer getPlacedHeavyAtoms​(IAtomContainer molecule,
                                          IAtom atom)
        Gets the placed Heavy Atoms connected to an atom.
        Parameters:
        molecule -
        atom - The atom the atoms must be connected to.
        Returns:
        The placed heavy atoms.

      • numberOfUnplacedHeavyAtoms

        public int numberOfUnplacedHeavyAtoms​(IAtomContainer ac)
        Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
        Parameters:
        ac - AtomContainer
        Returns:
        #UnplacedAtoms

      • allHeavyAtomsPlaced

        public boolean allHeavyAtomsPlaced​(IAtomContainer ac)
        True is all the atoms in the given AtomContainer have been placed.
        Parameters:
        ac - The AtomContainer to be searched
        Returns:
        True is all the atoms in the given AtomContainer have been placed