Package chemaxon.marvin.util

Class CleanUtil

java.lang.Object
chemaxon.marvin.util.CleanUtil
All Implemented Interfaces:
HybridizationStateConsts
@PublicAPI public class CleanUtil extends Object implements HybridizationStateConsts
Utility methods for cleaning.
Since:
Marvin 4.1, 01/31/2006

  • Constructor Details

    • CleanUtil

      public CleanUtil()

  • Method Details

    • 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 boolean 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:

    • 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:

    • 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: