Class CleanUtil

    • Constructor Detail

      • CleanUtil

        public CleanUtil()
    • Method Detail

      • arrangeComponents

        public static boolean arrangeComponents​(MoleculeGraph mol)
        Arranges molecule components (reactants, agents, products, R-group definitions) nicely. Also arranges attached data, Sgroup brackets.
        Parameters:
        mol - the molecule
        Returns:
        true if components have been rearranged, false if no components found
      • arrangeComponents

        public static boolean arrangeComponents​(MoleculeGraph mol,
                                                boolean obj)
        Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
        Parameters:
        mol - the molecule
        obj - also arrange other object attached to the molecule (like data, brackets)
        Returns:
        true if components have been rearranged, false if no components found
      • arrangeComponents

        public static boolean arrangeComponents​(MoleculeGraph mol,
                                                boolean obj,
                                                boolean frags)
        Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
        Parameters:
        mol - the molecule
        obj - also arrange other object attached to the molecule (like data, brackets)
        frags - also arrange fragments in root / main molecule
        Returns:
        true if components have been rearranged, false if no components found
        Since:
        Marvin 5.4.1
      • arrangeReaction

        public static void arrangeReaction​(RxnMolecule m)
        Arranges reaction components nicely
        Parameters:
        m - the reaction molecule
      • arrangeMolecules

        public static void arrangeMolecules​(MoleculeGraph[] mo,
                                            int dist,
                                            int col)
        Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice. Also arrange the DataSgroup values close to the atoms if relative arrangement needed.
        Parameters:
        mo - molecules
        dist - use CCLENGTH distance for the molecules
        col - number of colums (if -1 calculate it)
      • arrangeDataSgroupData

        public static void arrangeDataSgroupData​(MoleculeGraph m)
        Arrange data attached to DataSgroup. Set it to the right down corner.
      • arrangeRelativeDataSgroupData

        public static void arrangeRelativeDataSgroupData​(MoleculeGraph m)
        Arrange data attached to DataSgroup. Keeps the position of the data label if it is relative.
        Parameters:
        m - molecule
      • arrangeSgBrackets

        public static void arrangeSgBrackets​(MoleculeGraph m)
        Arrange sgroup brackets in the molecule.
        Parameters:
        m - molecule
      • sumDistanceSquare

        public static double sumDistanceSquare​(MoleculeGraph mol,
                                               DPoint3 p)
        Calculates the sum of the distance square for each atom from a point.
        Parameters:
        mol - the molecule
        p - the point
      • calcBadness

        public static double calcBadness​(MoleculeGraph mol1,
                                         MoleculeGraph mol2,
                                         MolAtom sa,
                                         MolBond[] xbonds)
        Calculates a "badness" value for the atomic coordinates.
        Parameters:
        mol1 - the original molecule
        mol2 - the transformed substructure
        sa - additional transformed atom or null
        xbonds - additional bonds between mol1 and mol2, or null
        Returns:
        the badness
      • createSavedCoordsArray

        public static double[] createSavedCoordsArray​(MoleculeGraph g)
        Creates an empty array for the atomic coordinates of a structure.
        Parameters:
        g - the structure
      • saveCoords

        public static void saveCoords​(MoleculeGraph g,
                                      double[] coords)
        Saves atomic coordinates. This method can be called before trying a coordinate transformation.
        Parameters:
        g - the structure
        coords - array for the coordinates
      • restoreCoords

        public static void restoreCoords​(MoleculeGraph g,
                                         double[] coords)
        Restores atomic coordinates. This method can be called after trying a coordinate transformation.
        Parameters:
        g - the structure
        coords - array containing the coordinates
      • createRotationAboutBond

        public static CTransform3D createRotationAboutBond​(MolBond b,
                                                           double phi)
        Creates a rotation transformation about a bond.
        Parameters:
        b - the bond
        phi - rotation angle
      • setCTWigglyBond

        public static boolean setCTWigglyBond​(MoleculeGraph m)
        Convert crossed double bonds to wiggly type.
        Parameters:
        m - molecule
      • setCTWigglyBond

        public static boolean setCTWigglyBond​(MoleculeGraph m,
                                              int bond)
        Convert crossed double bond to wiggly type. Set wiggly bond to the endpoint of the given double bond.
        Parameters:
        m - a molecule that contains a double bond to convert it to a wiggly represented up-o-down stereo double bond
        bond - the index of the double bond to
        Returns:
        true if the wiggly representation could be set successfully
        Since:
        Marvin 5.2
      • hasWiggly

        public static boolean hasWiggly​(MolAtom a)
        Check if at least one wiggly bond starts from this atom. (The which first atom of the bond should be the given atom.)
        Parameters:
        a - atom
        Returns:
        true if has wiggly bond starting from this atom
      • setCTCrossedBond

        public static void setCTCrossedBond​(MoleculeGraph m)
        Convert wiggly type double bonds to crossed.
        Parameters:
        m - molecule
      • isNonPreferredStereoAtom

        public static boolean[] isNonPreferredStereoAtom​(MoleculeGraph m)
        Check if the atoms in the molecule is in SP2 hybridization state and has wedge whose getAtom1 is the specified atom, but wiggly bonds next to double bonds are allowed.
        Parameters:
        m - molecule
        Returns:
        true for SP2 atom which has wedge with narrow end else false.
        Since:
        Marvin 5.0
      • removeCTflagFromSmallRings

        public static boolean removeCTflagFromSmallRings​(MoleculeGraph m)
        Remove CIS|TRANS flag from bonds in rings smaller than size 8. Remove TRANS flag from bonds in rings smaller than size 8, but give warning. Suppose that the stereo info stored already in the flags.
        Parameters:
        m - molecule
        Returns:
        false if TRANS stereoinformation is removed, otherwise true.
      • setBestLigandPosition

        public static void setBestLigandPosition​(MolAtom atom,
                                                 MolAtom ligand)
        Calculates and sets an optimal position for a ligand atom.
        Parameters:
        atom - the atom whose ligand atom's position is calculated
        ligand - the ligand atom whoose optimal position is calculated
        Since:
        Marvin 5.4
      • setBestLigandPosition

        public static void setBestLigandPosition​(MolAtom atom,
                                                 MolAtom ligand,
                                                 double bondlength)
        Calculates and sets an optimal position for a ligand atom.
        Parameters:
        atom - the atom whose ligand atom's position is calculated
        ligand - the ligand atom whoose optimal position is calculated
        bondlength - the requested bond length between the atom and its ligand, use -1 for automatic bond length determination according atom types.
        Since:
        Marvin 5.4
      • calcBracketEndPoints

        public static DPoint3[] calcBracketEndPoints​(DPoint3[] q,
                                                     DPoint3 p1,
                                                     double c)
        Calculates the bracket endpoints from the base line of the bracket. Another point is neccessary to calculate in the plane where the end points will be.
        Parameters:
        q - endpoints of the base line in the bracket.
        p1 - point to fix the plane in which the bracket endpoints will be.
        c - expected length of the bracket internal segment
        Returns:
        bracket endpoints.
      • calcDividingPoint

        public static DPoint3 calcDividingPoint​(DPoint3 p1,
                                                DPoint3 p2,
                                                double k)
        Calculates the division point of a segment with a given ratio.
        Parameters:
        p1 - the first endpoint of the segment
        p2 - the second endpoint of the segment
        k - the ratio
        Returns:
        the division point
      • calcSimplePolymerBracket

        public static DPoint3[] calcSimplePolymerBracket​(DPoint3 p1,
                                                         DPoint3 p2,
                                                         double ratio)
        Calculates the points of a simple polymer bracket that belongs to a bond.
        Parameters:
        p1 - endpoint of the bond that belongs to the sgroup
        p2 - the other endpoint of the bond
        Returns:
        bracket points
        See Also:
        RepeatingUnitSgroup
      • createBracket

        public static void createBracket​(Sgroup sg,
                                         DPoint3[] q,
                                         int btype)
      • generateBracketCoords

        public static void generateBracketCoords​(Sgroup sg,
                                                 int btype)
        Generates brackets with coordinates for a specified S-group.
        Parameters:
        sg - the S-group to generate the brackets and coordinates for
        btype - the type of the brackets to generate
        See Also:
        MBracket.T_ROUND, MBracket.T_SQUARE
      • generateBracketCoords

        public static void generateBracketCoords​(Sgroup sg,
                                                 int btype,
                                                 boolean extraSpace)
        Generates brackets with coordinates for a specified S-group.
        Parameters:
        sg - the S-group to generate the brackets and coordinates for
        btype - the type of the brackets to generate
        extraSpace - calculate with extra space at atom labels
        See Also:
        MBracket.T_ROUND, MBracket.T_SQUARE