Package com.actelion.research.chem

Class ExtendedMoleculeFunctions

  • public class ExtendedMoleculeFunctions
extends java.lang.Object
    ExtendedMoleculeFunctions

    Copyright: Actelion Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.

    Version:
    1.0 2005 MvK: Start implementation
    Author:
    Modest von Korff

    • Field Detail

      • COLOR_FOR_CENTER_SELECTION

        public static final int COLOR_FOR_CENTER_SELECTION
        See Also:
        Constant Field Values

      • arrRGroupsAtomicNo

        public static final int[] arrRGroupsAtomicNo

      • arrRGroupsSymbol

        public static final java.lang.String[] arrRGroupsSymbol

    • Constructor Detail

      • ExtendedMoleculeFunctions

        public ExtendedMoleculeFunctions()

    • Method Detail

      • makeSkeleton

        public static void makeSkeleton​(StereoMolecule mol)

      • analyzeMolecule

        public static void analyzeMolecule​(StereoMolecule mol)

      • getColorVal2String

        public static java.lang.String getColorVal2String​(Molecule mol,
                                                  int indexAtom)

      • getcAtomColor2String

        public static java.lang.String getcAtomColor2String​(int cAtomColor)
        Parameters:
        cAtomColor - atom color value from Molecule.
        Returns:

      • getColorRecord

        public static java.lang.String getColorRecord​(Molecule mol,
                                              java.util.Collection<java.lang.Integer> liIndexAtom,
                                              int cAtomColor)
        Parameters:
        mol -
        liIndexAtom -
        cAtomColor - atom color value from Molecule.
        Returns:

      • getNumQueryAtoms

        public static int getNumQueryAtoms​(ExtendedMolecule mol,
                                   int[] arrAtomicNoQuery)

      • getNumCarbonAtoms

        public static int getNumCarbonAtoms​(ExtendedMolecule mol)

      • getNumHeteroAtoms

        public static int getNumHeteroAtoms​(ExtendedMolecule mol)

      • isHetero

        public static boolean isHetero​(ExtendedMolecule mol,
                               int indexAtom)

      • getNumNitroGroupN

        public static int getNumNitroGroupN​(StereoMolecule mol)

      • getNumCarboxy

        public static int getNumCarboxy​(StereoMolecule mol)

      • getNumAcidicOxygen

        public static int getNumAcidicOxygen​(StereoMolecule mol)

      • getNumBasicNitrogen

        public static int getNumBasicNitrogen​(StereoMolecule mol)

      • getNumAliphaticRingAtoms

        public static int getNumAliphaticRingAtoms​(ExtendedMolecule mol,
                                           int atomicNoQuery)

      • getNumHeavyAtoms

        public static int getNumHeavyAtoms​(ExtendedMolecule mol)
        Parameters:
        mol -
        Returns:
        number of atoms which are not hydrogen.

      • getNumAromaticAtoms

        public static int getNumAromaticAtoms​(ExtendedMolecule mol)

      • getNumArylAmine

        public static int getNumArylAmine​(StereoMolecule mol)

      • getNumHeteroAromaticAtoms

        public static int getNumHeteroAromaticAtoms​(ExtendedMolecule mol)

      • getNumSubstructure

        public static int getNumSubstructure​(StereoMolecule mol,
                                     java.lang.String idcodeFragment)

      • getBondNo

        public static int getBondNo​(ExtendedMolecule mol,
                            int atm1,
                            int atm2)

      • getBondOrder

        public static int getBondOrder​(ExtendedMolecule mol,
                               int atm1,
                               int atm2)

      • getBondType

        public static int getBondType​(ExtendedMolecule mol,
                              int atm1,
                              int atm2)

      • getBondParity

        public static int getBondParity​(ExtendedMolecule mol,
                                int atm1,
                                int atm2)

      • deleteBond

        public static boolean deleteBond​(ExtendedMolecule mol,
                                 int atm1,
                                 int atm2)

      • getBiggestFragmentIDCode

        public static java.lang.String getBiggestFragmentIDCode​(java.lang.String idCode)

      • getConverted2CarbonSkeleton

        public static StereoMolecule getConverted2CarbonSkeleton​(StereoMolecule m)
        Replaces all hetero-atoms, except hydrogen, with carbon.
        Parameters:
        m -
        Returns:

      • getComparatorAtomsBonds

        public static java.util.Comparator<StereoMolecule> getComparatorAtomsBonds()

      • checkBiggestFragmentForUnwanted

        public static boolean checkBiggestFragmentForUnwanted​(StereoMolecule mol,
                                                      java.util.List<java.lang.Integer> liAtomicNo)

      • containsAtLeastOneAtomicNumbersFromHashSet

        public static boolean containsAtLeastOneAtomicNumbersFromHashSet​(ExtendedMolecule mol,
                                                                 java.util.HashSet<java.lang.Integer> hsAtomicNo)
        Parameters:
        mol -
        hsAtomicNo -
        Returns:
        true if an atomic number from the hash set is found.

      • containsHeteroAtom

        public static boolean containsHeteroAtom​(ExtendedMolecule mol,
                                         int[] arrIndexAt)

      • containsSolelyAtomicNumbersFromHashSet

        public static boolean containsSolelyAtomicNumbersFromHashSet​(ExtendedMolecule mol,
                                                             java.util.HashSet<java.lang.Integer> hsAtomicNo)
        Parameters:
        mol -
        hsAtomicNo -
        Returns:
        true if the molecule contains an atomic number that is not in the hash set.

      • atomAtomSubStrucMatch

        public static final boolean atomAtomSubStrucMatch​(StereoMolecule molecule,
                                                  int at,
                                                  StereoMolecule fragment)
        Parameters:
        molecule -
        at - index to specify atom in molecule
        fragment - one atom must have the color: COLOR_FOR_CENTER_SELECTION.
        Returns:
        true if the specified atom in molecule equals the colored atom in fragment.

      • getDistanceArray

        public static double[][] getDistanceArray​(ExtendedMolecule mol)

      • getTopologicalDistance

        public static final int getTopologicalDistance​(ExtendedMolecule mol,
                                               int at1,
                                               int at2)

      • getTopologicalDistanceMatrix

        public static final int[][] getTopologicalDistanceMatrix​(StereoMolecule mol)

      • getNumberOfBondsBetweenAtoms

        public static int[][] getNumberOfBondsBetweenAtoms​(StereoMolecule mol,
                                                   int maxBonds,
                                                   int[][] dist)
        From Joel Freyss developed for the FFMolecule Computes a matrix of distances between all the atoms in the graph. Complexity: O(m*n*maxBonds) m = number of bonds, n = number of atoms
        Parameters:
        mol -
        maxBonds -
        Returns:
        an array A[i][j] = nBonds if i and j are connected by less than maxBonds or -1 otherwise

      • isAliphaticAtom

        public static boolean isAliphaticAtom​(StereoMolecule mol,
                                      int atm)
        Parameters:
        mol -
        atm - index of atom
        Returns:
        false if atom is not C or if one of the neighbours is N, O, F, S, P or Cl.

      • isAcceptor

        public static boolean isAcceptor​(StereoMolecule mol,
                                 int atom)

      • isDonor

        public static boolean isDonor​(StereoMolecule mol,
                              int atom)

      • isCarbonTwoValencesMinimum

        public static boolean isCarbonTwoValencesMinimum​(StereoMolecule mol)

      • isCarbonOnlyConnected2Hetero

        public static boolean isCarbonOnlyConnected2Hetero​(StereoMolecule mol)

      • isCarbonConnected2Hetero

        public static boolean isCarbonConnected2Hetero​(StereoMolecule mol,
                                               int atomIndex)
        Parameters:
        mol -
        atomIndex -
        Returns:
        true if at least one neighbour is a hetero atom.

      • isConnected2Hetero

        public static boolean isConnected2Hetero​(StereoMolecule mol,
                                         int[] arrAtomIndex)
        Parameters:
        mol -
        arrAtomIndex -
        Returns:
        true if one of the atoms from arrAtomIndex is connected to a hetero atom.

      • isRingInMolecule

        public static boolean isRingInMolecule​(StereoMolecule mol)

      • isRingExclusively

        public static boolean isRingExclusively​(StereoMolecule mol)
        Parameters:
        mol -
        Returns:
        true if all atoms are in a ring.

      • isCyanoN

        public static boolean isCyanoN​(StereoMolecule mol,
                               int atom)
        Parameters:
        mol -
        atom -
        Returns:
        true for cyano and iso-cyano.

      • isThioEther

        public static boolean isThioEther​(StereoMolecule mol,
                                  int atom)

      • isWildcard

        public static boolean isWildcard​(StereoMolecule mol,
                                 int atom)

      • isSulfoxyGroup

        public static boolean isSulfoxyGroup​(StereoMolecule mol,
                                     int atom)
        Parameters:
        mol -
        atom -
        Returns:
        true if atom is S and at let one attached atom is O.

      • isIsolatedCarbon

        public static boolean isIsolatedCarbon​(StereoMolecule mol,
                                       int indexAtCentral,
                                       int[] arrIndexAt)
        Parameters:
        mol -
        indexAtCentral -
        arrIndexAt -
        Returns:
        true if no connected carbon atom is in arrIndexAt

      • extractAromaticRing

        public static int[] extractAromaticRing​(StereoMolecule mol,
                                        int[] arrIndexAt)

      • getNumCyanoGroups

        public static int getNumCyanoGroups​(StereoMolecule mol)
        Counts cyano and iso-cyano
        Parameters:
        mol -
        Returns:

      • getNumAlcoholicOxygen

        public static int getNumAlcoholicOxygen​(StereoMolecule mol)

      • getNumThioEther

        public static int getNumThioEther​(StereoMolecule mol)

      • getNumSulfOxyGroups

        public static int getNumSulfOxyGroups​(StereoMolecule mol)

      • getNumWildcards

        public static int getNumWildcards​(StereoMolecule mol)

      • isAlcoholicOxygen

        public static boolean isAlcoholicOxygen​(StereoMolecule mol,
                                        int atom)

      • isEtherOxygenAtAromatic

        public static boolean isEtherOxygenAtAromatic​(StereoMolecule mol,
                                              int atom)

      • isCarboxyC

        public static boolean isCarboxyC​(StereoMolecule mol,
                                 int atom)

      • replaceAtoms

        public static int replaceAtoms​(ExtendedMolecule[] arr,
                               int atnoOrig,
                               int atnoRpl)

      • replaceAtoms

        public static int replaceAtoms​(ExtendedMolecule mol,
                               int atnoOrig,
                               int atnoRpl)

      • removeSubStructures

        public static final java.util.LinkedList<StereoMolecule> removeSubStructures​(java.util.List<StereoMolecule> liInput)
        Removes all molecules that are a substructure of one of the molecules in the input list.
        Parameters:
        liInput -
        Returns:

      • removeSubstructuresFromMolecule

        public static StereoMolecule removeSubstructuresFromMolecule​(StereoMolecule mol,
                                                             java.util.List<StereoMolecule> liFragment)
        Deletes the substructures, if found, in the molecule. Starts with the first structure in the list. Helper arrays are ensured.
        Parameters:
        mol -
        liFragment -
        Returns:

      • setColorMolecule

        public static void setColorMolecule​(StereoMolecule mol,
                                    int[] arrIndexMatch)

      • setColorMoleculeFromBondIndex

        public static void setColorMoleculeFromBondIndex​(StereoMolecule mol,
                                                 int[] arrIndexBonds,
                                                 int color)
        Parameters:
        mol -
        arrIndexBonds -
        color - i.e. Molecule.cAtomColorBlue

      • setCoordinatesNull

        public static void setCoordinatesNull​(StereoMolecule mol)

      • getColorVectorSubstructure

        public static java.lang.String getColorVectorSubstructure​(StereoMolecule mol,
                                                          StereoMolecule frag,
                                                          int atomColor)
        Returns the colors vector for the substructure in mol.
        Parameters:
        mol -
        frag -
        atomColor - Molecule.cAtomColor
        Returns:

      • getAtomicNoRGroup

        public static int getAtomicNoRGroup​(int r)
        Starts with 1 and goes until 16
        Returns: