MolHandler (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

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.
Author:

Ferenc Csizmadia, Andras Volford, Szilard Dorant

Field Summary

Fields
Modifier and Type Field and Description

protected boolean molAlignerSet
- Fields inherited from class chemaxon.util.MolHandlerBase
  mol, queryMode
- Fields inherited from class chemaxon.util.ErrorHandler
  CLASS_NOT_FOUND_ERROR, DATABASE_SEARCH_ERROR, exception, ILLEGAL_ACCESS_ERROR, INSTANTIATION_ERROR, IO_ERROR, MAX_SEARCH_FREQUENCY_EXCEEDED_ERROR, MOL_FORMAT_ERROR, NO_ERROR, SQL_ERROR, UNIDENTIFIED_ERROR

Fields
Modifier and Type	Field and Description
`protected boolean`	`molAlignerSet`

Constructor Summary

Constructors
Constructor and Description
`MolHandler()` Creates an uninitialized MolHandler object.
`MolHandler(byte[] molecule)` Creates a MolHandler object from a byte array.
`MolHandler(byte[] molecule, boolean queryMode)` Creates a MolHandler object from a byte array.
`MolHandler(Molecule mol)` Creates a MolHandler object from a Molecule.
`MolHandler(java.lang.String molecule)` Creates a MolHandler object from a String.
`MolHandler(java.lang.String molecule, boolean queryMode)` Creates a MolHandler object from a String.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addHydrogens()` Adds explicit H atoms instead of the current implicit ones.
`void`	`addHydrogensToAromaticHeteroAtoms()` Adds the implicit Hydrogen atoms to heteroatoms in aromatic rings.
`double`	`align(Molecule mol, int[] indexes)` Alignes (rotates) a specified molecule realtive to the contained molecule according to the specified atom pairs.
`void`	`aromatize()` Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.
`void`	`aromatize(int method)` Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.
`java.lang.String`	`calcMolFormula()` Calculates the molecular formula of the molecule.
`float`	`calcMolWeight()` Calculates the molecular weight of the molecule.
`double`	`calcMolWeightInDouble()` Calculates the molecular weight of the molecule.
`void`	`clean(boolean always, java.lang.String options)` Calculates 2D coordinates.
`boolean`	`containsHydrogens()` True if the molecule contains explicit Hydrogen atoms, false otherwise.
`byte[]`	`generateFingerprintInBytes(int numberOfInts, int numberOfOnes, int numberOfBonds)` Generates chemical hashed fingerprint for the molecule and returns it in `byte` units.
`int[]`	`generateFingerprintInInts(int numberOfInts, int numberOfOnes, int numberOfBonds)` Generates chemical hashed fingerprint for the molecule and returns it in `int` units.
`int`	`getAtomCount()` Retrieves the number of atoms in the Molecule stored in the MolHandler object.
`int`	`getHeavyAtomCount()` Retrieves the number of non-hydrogen atoms in the Molecule stored in the MolHandler object.
`int`	`getImplicitHCount()` Counts the number of implicit hydrogens on the molecule
`boolean`	`getQueryMode()` Gets query mode.
`static boolean`	`isPlainH(MolAtom atom)` Decides if atom is a plain H atom.
`static void`	`main(java.lang.String[] args)`
`void`	`removeHydrogens()` Removes all hydrogen atoms.
`void`	`removeHydrogensFromCarbons()` Removes Hydrogen atoms attached to Carbon atoms.
`void`	`setMolecule(byte[] molecule)` Initializes a MolHandler object from a byte array.
`void`	`setMolecule(Molecule molecule)` Initializes a MolHandler object from a Molecule.
`void`	`setMolecule(java.lang.String molecule)` Sets the molecule.
`byte[]`	`toBinFormat(java.lang.String format)` Converts the molecule to the specified binary format.
`java.lang.String`	`toFormat(java.lang.String format)` Converts the molecule to the specified text format.

Methods inherited from class chemaxon.util.MolHandlerBase
getMolecule, importMol, setQueryMode

Methods inherited from class chemaxon.util.ErrorHandler
checkError, checkException, getError, getErrorMessage, getException, getStackTrace

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - molAlignerSet
```
protected boolean molAlignerSet
```
- Constructor Detail
  - 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(java.lang.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(java.lang.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 Detail
  - 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(java.lang.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:
    
    MoleculeGraph.AROM_GENERAL - Chemaxon aromatization
    
    MoleculeGraph.AROM_BASIC - Daylight aromatization (modified Huckel rule)
    See Also:
    
    MoleculeGraph.AROM_GENERAL, MoleculeGraph.AROM_BASIC, Aromata
  - 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 java.lang.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,
                  java.lang.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:
    
    MoleculeGraph.clean(int,java.lang.String)
  - toFormat
```
public java.lang.String toFormat(java.lang.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(java.lang.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(int, int, int)
  - 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:
    
    generateFingerprintInInts(int, int, int)
  - 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 java.lang.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:
    
    java.lang.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
  - main
```
public static void main(java.lang.String[] args)
                 throws MolFormatException,
                        java.io.IOException
```
    Throws:
    
    MolFormatException
    
    java.io.IOException

Class MolHandler

Field Summary

Fields inherited from class chemaxon.util.MolHandlerBase

Fields inherited from class chemaxon.util.ErrorHandler

Constructor Summary

Method Summary

Methods inherited from class chemaxon.util.MolHandlerBase

Methods inherited from class chemaxon.util.ErrorHandler

Methods inherited from class java.lang.Object

Field Detail

molAlignerSet

Constructor Detail

MolHandler

MolHandler

MolHandler

MolHandler

MolHandler

MolHandler

Method Detail

setMolecule

setMolecule

setMolecule

getAtomCount

getHeavyAtomCount

addHydrogens

addHydrogensToAromaticHeteroAtoms

removeHydrogens

removeHydrogensFromCarbons

containsHydrogens

aromatize

aromatize

calcMolWeight

calcMolWeightInDouble

calcMolFormula

clean

toFormat

toBinFormat

generateFingerprintInInts

generateFingerprintInBytes

getImplicitHCount

align

getQueryMode

isPlainH

main