java.lang.Object

chemaxon.calculations.hydrogenize.Hydrogenize

All Implemented Interfaces:: StereoConstants

@PublicApi public class Hydrogenize extends Object implements StereoConstants

Addition and removal of explicit hydrogens or lone pairs.

Since:: Marvin 2.4, 04/24/2000

Field Summary

Fields inherited from interface chemaxon.struc.StereoConstants
ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS
Constructor Summary

Constructors

Constructor

Description

Hydrogenize()
Method Summary

Modifier and Type

Method

Description

static boolean

addHAtoms(MoleculeGraph m)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertImplicitHToExplicit(MoleculeGraph) instead

static boolean

addHAtoms(MoleculeGraph m, MolAtom[] atoms)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead

static boolean

addHAtoms(MoleculeGraph m, MolAtom[] atoms, int flags)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) instead

static boolean

addLonePairs(MoleculeGraph m, MolAtom[] atoms)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) instead

static boolean

convertExplicitHToImplicit(MoleculeGraph m)

Converts explicit Hydrogen atoms of the molecule to implicit.

static boolean

convertExplicitHToImplicit(MoleculeGraph m, int flags)

Converts explicit Hydrogen atoms of the molecule to implicit.

static boolean

convertExplicitHToImplicit(MoleculeGraph m, MolAtom[] atoms, int flags)

Converts explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.

static boolean

convertExplicitHToImplicit(MoleculeGraph m, MolAtom[] atoms, int flags, boolean check)

Converts explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.

static boolean

convertExplicitLonePairsToImplicit(MoleculeGraph m)

Converts explicit lone pairs from a molecule to implicit.

static boolean

convertImplicitHToExplicit(MoleculeGraph m)

Converts implicit Hydrogen atoms of the molecule to explicit.

static boolean

convertImplicitHToExplicit(MoleculeGraph m, MolAtom[] atoms)

Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

static boolean

convertImplicitHToExplicit(MoleculeGraph m, MolAtom[] atoms, int flags)

Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

static boolean

convertImplicitLonePairsToExplicit(MoleculeGraph m, MolAtom[] atoms)

Convert implicit lone pairs of the atoms of a molecule to explicit.

static boolean[]

getImplicitizableHList(Molecule m, int flags)

Gets which atom is an implicitizable hydrogen.

static boolean

isBridgeHeadAtom(MoleculeGraph mol, int atom)

Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.11.1, replaced by TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)

static boolean

removeHAtoms(MoleculeGraph m)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph) instead

static boolean

removeHAtoms(MoleculeGraph m, int flags)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph, int) instead

static boolean

removeHAtoms(MoleculeGraph m, MolAtom[] atoms, int flags)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) instead

static boolean

removeHAtoms(MoleculeGraph m, MolAtom[] atoms, int flags, boolean check)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) instead

static boolean

removeLonePairs(MoleculeGraph m)

Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.11, use convertExplicitLonePairsToImplicit(MoleculeGraph) instead

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

Constructor Details
- Hydrogenize
  
  public Hydrogenize()
Method Details
- addHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean addHAtoms(MoleculeGraph m, MolAtom[] atoms)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead
  
  Adds Hydrogen atoms to specified atoms in a molecule. Same as convertImplicitHToExplicit(m, atoms).
  
  Parameters:
  
  m - the molecule to add Hydrogen atoms to.
  
  atoms - the atoms to add Hydrogen atoms to, null for all
  
  Returns:
  
  true if Hydrogen atoms were successfully added
- convertImplicitHToExplicit
  
  public static boolean convertImplicitHToExplicit(MoleculeGraph m, MolAtom[] atoms)
  
  Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit. Same as convertImplicitHToExplicit(m, atoms, 0).
  
  Parameters:
  
  m - the molecule to add Hydrogen atoms to.
  
  atoms - the atoms to add Hydrogen atoms to, null for all
  
  Returns:
  
  true if Hydrogen atoms were successfully added
- addHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean addHAtoms(MoleculeGraph m)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertImplicitHToExplicit(MoleculeGraph) instead
  
  Adds Hydrogen atoms to all atoms in a molecule. Same as convertImplicitHToExplicit(m).
  
  Parameters:
  
  m - the molecule to add Hydrogen atoms to.
  
  Returns:
  
  true if Hydrogen atoms were successfully added
- convertImplicitHToExplicit
  
  public static boolean convertImplicitHToExplicit(MoleculeGraph m)
  
  Converts implicit Hydrogen atoms of the molecule to explicit. Same as convertImplicitHToExplicit(m, null, 0).
  
  Parameters:
  
  m - the molecule to add Hydrogen atoms to.
  
  Returns:
  
  true if Hydrogen atoms were successfully added
- addHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean addHAtoms(MoleculeGraph m, MolAtom[] atoms, int flags)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) instead
  
  Adds Hydrogen atoms to specified atoms in a molecule. Same as convertImplicitHToExplicit(m, atoms, flags).
  
  Parameters:
  
  m - the molecule to add Hydrogen atoms to.
  
  atoms - the atoms to add Hydrogen atoms to, null for all
  
  flags - set this flag to MoleculeGraph.OMIT_POSTCLEAN to include partial clean after Hydrogen atom addition.
  
  Returns:
  
  true if Hydrogen atoms were successfully added
- convertImplicitHToExplicit
  
  public static boolean convertImplicitHToExplicit(MoleculeGraph m, MolAtom[] atoms, int flags)
  
  Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
  
  Parameters:
  
  m - the molecule to add Hydrogen atoms to.
  
  atoms - the atoms to add Hydrogen atoms to, null for all
  
  flags - set this flag to MoleculeGraph.OMIT_POSTCLEAN to exclude partial clean after Hydrogen atom addition.
  
  Returns:
  
  true if Hydrogen atoms were successfully added
- removeHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean removeHAtoms(MoleculeGraph m, int flags)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph, int) instead
  
  Removes Hydrogen atoms from atoms in a molecule.
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  flags - to use special removal conditions set
  
  Returns:
  
  true if specified Hydrogen atoms were successfully removed.
  
  See Also:
  
  convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)
- convertExplicitHToImplicit
  
  public static boolean convertExplicitHToImplicit(MoleculeGraph m, int flags)
  
  Converts explicit Hydrogen atoms of the molecule to implicit.
  
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  flags - the flags to specify special removal conditions, see convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) for the details.
  
  Returns:
  
  true if specified Hydrogen atoms were successfully removed.
- removeHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean removeHAtoms(MoleculeGraph m)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph) instead
  
  Removes Hydrogen atoms from a molecule. Besides lonely and wedged H atoms, bound (to non-Hydrogen atom and without Hydrogen bond), non-isotope, neutral, non-radical, non-mapped H atoms are also removed.
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  Returns:
  
  true if Hydrogen atoms were successfully removed.
  
  See Also:
  
  MolAtom.isImplicitizableH(int)
- convertExplicitHToImplicit
  
  public static boolean convertExplicitHToImplicit(MoleculeGraph m)
  
  Converts explicit Hydrogen atoms of the molecule to implicit. Same as convertExplicitHToImplicit(m, MolAtom.LONELY_H | MolAtom.WEDGED_H | MolAtom.METALCONNECTED_H). Besides lonely and wedged H atoms, bound (to non-Hydrogen atom and without Hydrogen bond), non-isotope, neutral, non-radical, non-mapped H atoms are also removed.
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  Returns:
  
  true if Hydrogen atoms were successfully removed.
  
  See Also:
  
  MolAtom.isImplicitizableH(int)
- removeHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean removeHAtoms(MoleculeGraph m, MolAtom[] atoms, int flags)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) instead
  
  Removes Hydrogen atoms from specified atoms of a molecule.
  
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  atoms - the subset of atoms to include or null for all
  
  flags - to use special removal conditions
- convertExplicitHToImplicit
  
  public static boolean convertExplicitHToImplicit(MoleculeGraph m, MolAtom[] atoms, int flags)
  
  Converts explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.
  
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  atoms - the subset of atoms to include or null for all
  
  flags - the flags to specify special removal conditions, see convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) for the details.
- convertExplicitHToImplicit
  
  public static boolean convertExplicitHToImplicit(MoleculeGraph m, MolAtom[] atoms, int flags, boolean check)
  
  Converts explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  atoms - the subset of atoms to include or null for all
  
  flags - the flags to specify special removal conditions:
  
  MolAtom.ALL_H for including any Hydrogen atom for removal.
  
  MolAtom.LONELY_H for including lonely Hydrogen atom(s) for removal. Hydrogen atoms with only Hydrogen bonds counted as lonely.
  
  MolAtom.ISOTOPE_H for including Hydrogen isotope(s) for removal.
  
  MolAtom.CHARGED_H for including charged Hydrogen atom(s) for removal.
  
  MolAtom.RADICAL_H for including radical Hydrogen atom(s) for removal.
  
  MolAtom.MAPPED_H for including mapped Hydrogen atom(s) for removal.
  
  MolAtom.WEDGED_H for including Hydrogen atom(s) with wedge bonds for removal.
  
  MolAtom.HCONNECTED_H for including Hydrogen atom(s) connected to another Hydrogen atom only for removal.
  
  MolAtom.METALCONNECTED_H for including Hydrogen atom(s) connected to metal atoms.
  
  MolAtom.HBONDED_H for including Hydrogen atom(s) having a Hydrogen bond connected to them for removal.
  
  MolAtom.CTSPECIFIC_H for including to remove the Hydrogen atom(s) connecting alone to one side of a double bond with specified CIS or TRANS stereo information.
  
  MolAtom.POLYMERENDGROUP_H for including Hydrogen atom(s) which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup).
  
  MolAtom.SGROUPEND_H for including Hydrogen atom(s) which have a neighbor that is in SuperatomSgroup.
  
  MolAtom.VALENCEERROR_H for including Hydrogen atom(s) connected to an atom with valence error.
  
  MolAtom.SGROUP_H for including Hydrogen atom(s) which are in one element Sgroups.
  
  MolAtom.BRIDGEHEAD_H for including Hydrogen atom which is connected to a bridgehead atom.
  
  check - checks if the given atoms belong to the given molecule.
  
  Returns:
  
  true if specified Hydrogen atoms were successfully removed.
  
  See Also:
  
  MolAtom.ALL_H
  
  MolAtom.LONELY_H
  
  MolAtom.ISOTOPE_H
  
  MolAtom.CHARGED_H
  
  MolAtom.RADICAL_H
  
  MolAtom.MAPPED_H
  
  MolAtom.WEDGED_H
  
  MolAtom.HCONNECTED_H
  
  MolAtom.METALCONNECTED_H
  
  MolAtom.HBONDED_H
  
  MolAtom.CTSPECIFIC_H
  
  MolAtom.POLYMERENDGROUP_H
  
  MolAtom.SGROUPEND_H
  
  MolAtom.VALENCEERROR_H
  
  MolAtom.SGROUP_H
  
  MolAtom.BRIDGEHEAD_H
- removeHAtoms
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean removeHAtoms(MoleculeGraph m, MolAtom[] atoms, int flags, boolean check)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) instead
  
  Removes Hydrogen atoms from specified atoms of a molecule.
  Parameters:
  
  m - the molecule to remove Hydrogen atoms from.
  
  atoms - the subset of atoms to include or null for all
  
  flags - to use special removal conditions set this flag to:
  
  MolAtom.ALL_H for including any Hydrogen atom for removal.
  
  MolAtom.LONELY_H for including lonely Hydrogen atom(s) for removal. Hydrogen atoms with only Hydrogen bonds counted as lonely.
  
  MolAtom.ISOTOPE_H for including Hydrogen isotope(s) for removal.
  
  MolAtom.CHARGED_H for including charged Hydrogen atom(s) for removal.
  
  MolAtom.RADICAL_H for including radical Hydrogen atom(s) for removal.
  
  MolAtom.MAPPED_H for including mapped Hydrogen atom(s) for removal.
  
  MolAtom.WEDGED_H for including Hydrogen atom(s) with wedge bonds for removal.
  
  MolAtom.HCONNECTED_H for including Hydrogen atom(s) connected to another Hydrogen atom only for removal.
  
  MolAtom.CTSPECIFIC_H for including to remove the Hydrogen atom(s) connecting alone to one side of a double bond with specified CIS or TRANS stereo information.
  
  MolAtom.POLYMERENDGROUP_H for including Hydrogen atom(s) which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup).
  
  MolAtom.SGROUPEND_H for including Hydrogen atom(s) which have a neighbor that is in SuperatomSgroup.
  
  MolAtom.VALENCEERROR_H for including Hydrogen atom(s) connected to an atom with valence error.
  
  MolAtom.SGROUP_H for including Hydrogen atom(s) which are in one element Sgroups.
  
  MolAtom.BRIDGEHEAD_H for including Hydrogen atom which is connected to a bridgehead atom.
  
  check - checks if the given atoms belong to the given molecule.
  
  Returns:
  
  true if specified Hydrogen atoms were successfully removed.
  
  See Also:
  
  MolAtom.ALL_H
  
  MolAtom.LONELY_H
  
  MolAtom.ISOTOPE_H
  
  MolAtom.CHARGED_H
  
  MolAtom.RADICAL_H
  
  MolAtom.MAPPED_H
  
  MolAtom.WEDGED_H
  
  MolAtom.HCONNECTED_H
  
  MolAtom.CTSPECIFIC_H
  
  MolAtom.POLYMERENDGROUP_H
  
  MolAtom.SGROUPEND_H
  
  MolAtom.VALENCEERROR_H
  
  MolAtom.SGROUP_H
  
  MolAtom.BRIDGEHEAD_H
- convertImplicitLonePairsToExplicit
  
  public static boolean convertImplicitLonePairsToExplicit(MoleculeGraph m, MolAtom[] atoms)
  
  Convert implicit lone pairs of the atoms of a molecule to explicit.
  
  Parameters:
  
  m - the molecule to add lone pairs to.
  
  atoms - the atoms to include for lone pair addition, null for all
  
  Returns:
  
  true if lone pairs were successfully added false otherwise
- addLonePairs
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean addLonePairs(MoleculeGraph m, MolAtom[] atoms)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) instead
  
  Adds lone pairs to atoms of a molecule.
  
  Parameters:
  
  m - the molecule to add lone pairs to.
  
  atoms - the atoms to include for lone pair addition, null for all
  
  Returns:
  
  true if lone pairs were successfully added false otherwise
- convertExplicitLonePairsToImplicit
  
  public static boolean convertExplicitLonePairsToImplicit(MoleculeGraph m)
  
  Converts explicit lone pairs from a molecule to implicit.
  
  Parameters:
  
  m - the molecule to remove lone pairs from.
  
  Returns:
  
  true if lone pairs were successfully removed false otherwise.
- removeLonePairs
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean removeLonePairs(MoleculeGraph m)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  since Marvin 5.11, use convertExplicitLonePairsToImplicit(MoleculeGraph) instead
  
  Removes lone pairs from a molecule.
  
  Parameters:
  
  m - the molecule to remove lone pairs from.
  
  Returns:
  
  true if lone pairs were successfully removed false otherwise.
- isBridgeHeadAtom
  
  @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean isBridgeHeadAtom(MoleculeGraph mol, int atom)
  
  Deprecated, for removal: This API element is subject to removal in a future version.
  as of Marvin 5.11.1, replaced by TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)
  
  Test whether the given atom is bridgehead.
  
  Parameters:
  
  mol - molecule
  
  atom - atom to check
  
  Returns:
  
  true if the given atom is bridgehead else false
- getImplicitizableHList
  
  public static boolean[] getImplicitizableHList(Molecule m, int flags)
  
  Gets which atom is an implicitizable hydrogen.
  
  Returns:
  
  a boolean array. The i-th element of the array is true if the i-th atom of the molecule is an implicitizable hydrogen.

Class Hydrogenize

Field Summary

Fields inherited from interface chemaxon.struc.StereoConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

Hydrogenize

Method Details

addHAtoms

convertImplicitHToExplicit

addHAtoms

convertImplicitHToExplicit

addHAtoms

convertImplicitHToExplicit

removeHAtoms

convertExplicitHToImplicit

removeHAtoms

convertExplicitHToImplicit

removeHAtoms

convertExplicitHToImplicit

convertExplicitHToImplicit

removeHAtoms

convertImplicitLonePairsToExplicit

addLonePairs

convertExplicitLonePairsToImplicit

removeLonePairs

isBridgeHeadAtom

getImplicitizableHList