Package chemaxon.util

Class MolHandler

java.lang.Object
chemaxon.util.ErrorHandler
chemaxon.util.MolHandlerBase
chemaxon.util.MolHandler
@PublicAPI public class MolHandler extends chemaxon.util.MolHandlerBase
Class for handling molecules for systems based on ChemAxon's programming interface. A MolHandler object contains the structure of a molecule.
Operations on the object:
  • retrieving the molecule
  • adding and removing Hydrogens
  • replacing bonds in aromatic systems to aromatic bonds
  • calculating molecular weight and formula
  • etc.

  • Field Details

    • molAlignerSet

      protected boolean molAlignerSet

  • Constructor Details

    • MolHandler

      public MolHandler()
      Creates an uninitialized MolHandler object.

    • MolHandler

      public MolHandler(Molecule mol)
      Creates a MolHandler object from a Molecule.
      Parameters:
      mol - a clone of this parameter is stored in the MolHandler object

    • MolHandler

      public MolHandler(String molecule) throws MolFormatException
      Creates a MolHandler object from a String.
      Parameters:
      molecule - the String must contain a molecule in MDL's Molfile or Compressed Molfile or Smiles format.
      Throws:
      MolFormatException - if the importer encounters a problem

    • MolHandler

      public MolHandler(String molecule, boolean queryMode) throws MolFormatException
      Creates a MolHandler object from a String.
      Parameters:
      molecule - the String must contain a molecule in MDL's Molfile or Compressed Molfile or Smiles format.
      queryMode - if set to trueSMILES strings are imported as SMARTS. Default is false.
      Throws:
      MolFormatException - if the importer encounters a problem
      Since:
      2.2

    • MolHandler

      public MolHandler(byte[] molecule) throws MolFormatException
      Creates a MolHandler object from a byte array.
      Parameters:
      molecule - the byte array must contain a molecule in MDL's Molfile or Compressed Molfile or Smiles format.
      Throws:
      MolFormatException - if the importer encounters a problem

    • MolHandler

      public MolHandler(byte[] molecule, boolean queryMode) throws MolFormatException
      Creates a MolHandler object from a byte array.
      Parameters:
      molecule - the byte array must contain a molecule in MDL's Molfile or Compressed Molfile or Smiles format
      queryMode - if set to trueSMILES strings are imported as SMARTS. Default is false.
      Throws:
      MolFormatException - if the importer encounters a problem since 2.2

  • Method Details

    • setMolecule

      public void setMolecule(Molecule molecule)
      Initializes a MolHandler object from a Molecule.
      Parameters:
      molecule - a clone of this parameter is stored in the MolHandler object

    • setMolecule

      public void setMolecule(String molecule) throws MolFormatException
      Sets the molecule.
      Overrides:
      setMolecule in class chemaxon.util.MolHandlerBase
      Parameters:
      molecule - the molecule to load into this molhandler
      Throws:
      MolFormatException - if the importer encounters a problem

    • setMolecule

      public void setMolecule(byte[] molecule) throws MolFormatException
      Initializes a MolHandler object from a byte array.
      Parameters:
      molecule - the byte array must contain a molecule in MDL's Molfile or Compressed Molfile or Smiles format.
      Throws:
      MolFormatException - if the importer encounters a problem

    • getAtomCount

      public int getAtomCount()
      Retrieves the number of atoms in the Molecule stored in the MolHandler object.
      Returns:
      the atomcount of the current molecule

    • getHeavyAtomCount

      public int getHeavyAtomCount()
      Retrieves the number of non-hydrogen atoms in the Molecule stored in the MolHandler object.
      Returns:
      the heavyatomcount of the current molecule

    • addHydrogens

      public void addHydrogens()
      Adds explicit H atoms instead of the current implicit ones.

    • addHydrogensToAromaticHeteroAtoms

      public void addHydrogensToAromaticHeteroAtoms()
      Adds the implicit Hydrogen atoms to heteroatoms in aromatic rings. The coordinates of the H atoms set to 0.

    • removeHydrogens

      public void removeHydrogens()
      Removes all hydrogen atoms.

    • removeHydrogensFromCarbons

      public void removeHydrogensFromCarbons()
      Removes Hydrogen atoms attached to Carbon atoms.

    • containsHydrogens

      public boolean containsHydrogens()
      True if the molecule contains explicit Hydrogen atoms, false otherwise.
      Returns:
      if the molecule contains at least one explicit H

    • aromatize

      public void aromatize()
      Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.

    • aromatize

      public void aromatize(int method)
      Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds. since 2.3
      Parameters:
      method - specifies the algorithm for aromatization. Possible values:
      See Also:

    • calcMolWeight

      public float calcMolWeight()
      Calculates the molecular weight of the molecule. In the case of query structures 0 is returned.
      Returns:
      the molweight

    • calcMolWeightInDouble

      public double calcMolWeightInDouble()
      Calculates the molecular weight of the molecule. Returns a double value.
      Returns:
      the molweight

    • calcMolFormula

      public String calcMolFormula()
      Calculates the molecular formula of the molecule. The symbols are listed in Hill Order: C is listed first, followed by H, followed by the remaining elements in alphabetical order.
      Returns:
      the formula of the molecule

    • clean

      public void clean(boolean always, String options)
      Calculates 2D coordinates. The bond length is set to 0.825. The calculation uses the O1 option of cleaning.
      Parameters:
      always - if false then cleaning will only be performed if the present coordinates are different from zero.
      options - specifies the options used for 2D calculation. (E.g.: "O1e")
      See Also:

    • toFormat

      public String toFormat(String format)
      Converts the molecule to the specified text format.
      Parameters:
      format - "mol", "csmol", "smiles", ...
      The documentation of marvin details all the possible formats.
      Returns:
      the export result

    • toBinFormat

      public byte[] toBinFormat(String format)
      Converts the molecule to the specified binary format.
      Parameters:
      format - "png", "jpeg", "ppm", ...
      The documentation of marvin details all the possible formats.
      Returns:
      the export result
      Since:
      JChem 2.2

    • generateFingerprintInInts

      public int[] generateFingerprintInInts(int numberOfInts, int numberOfOnes, int numberOfBonds)
      Generates chemical hashed fingerprint for the molecule and returns it in int units.
      NOTE: The structure should be standardized (including aromatization) before fingerprint generation.
      Parameters:
      numberOfInts - the length of the binary fingerprint in int (32 bit) units.
      numberOfOnes - the number of bits to switch on for each pattern.
      numberOfBonds - the maximum length of edges in patterns used for generating the fingerprint.
      Returns:
      an int array of the fingerprint
      Since:
      JChem 3.1
      See Also:

    • generateFingerprintInBytes

      public byte[] generateFingerprintInBytes(int numberOfInts, int numberOfOnes, int numberOfBonds)
      Generates chemical hashed fingerprint for the molecule and returns it in byte units.
      NOTE: The structure should be standardized (including aromatization) before fingerprint generation.
      Parameters:
      numberOfInts - the length of the binary fingerprint in int (32 bit) units.
      numberOfOnes - the number of bits to switch on for each pattern.
      numberOfBonds - the maximum length of edges in patterns used for generating the fingerprint.
      Returns:
      an byte array of the fingerprint
      Since:
      JChem 3.1
      See Also:

    • getImplicitHCount

      public int getImplicitHCount()
      Counts the number of implicit hydrogens on the molecule
      Returns:
      the number of implicit hydrogens

    • align

      public double align(Molecule mol, int[] indexes) throws IllegalArgumentException
      Alignes (rotates) a specified molecule realtive to the contained molecule according to the specified atom pairs.
      NOTE: S-groups in the MolHandler contained molecule will be expanded.
      Parameters:
      mol - the molecule to be aligned
      indexes - the atom indexes of the pattern in the order of the atoms of the molecule to be aligned. Negative values are ignored. The size of this array should be at least the number of atoms in the pattern molecule (in case of RgMolecules, the number of non R-group atoms of the root structure). If the size of the array is grater, the excess elements are ignored.
      Returns:
      the error value of the alignment, can be used to try to align multiple hits and choose the best solution.
      Throws:
      IllegalArgumentException - if encountered

    • getQueryMode

      public boolean getQueryMode()
      Gets query mode. SMILES strings are imported as SMARTS if query mode is set.
      Returns:
      query mode
      Since:
      JChem 2.2

    • isPlainH

      public static boolean isPlainH(MolAtom atom)
      Decides if atom is a plain H atom.
      Parameters:
      atom - MolAtom to decide.
      Returns:
      true if atom is an uncharged, nonisotopic hydrogen.
      Since:
      JChem 3.2