chemaxon.calculations.clean

Class Cleaner

java.lang.Object

chemaxon.calculations.clean.Cleaner

public class Cleaner
extends Object

Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.

Author:

Janos Kendi

Constructor Summary

Constructors

Constructor and Description
Cleaner()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	clean(MoleculeGraph mg, int dim) Calculates atom coordinates.
static boolean	clean(MoleculeGraph mg, int dim, String opts) Calculates atom coordinates.
static boolean	clean(MoleculeGraph mg, int dim, String opts, MProgressMonitor pmon) Calculates atom coordinates.
static boolean	partialClean(MoleculeGraph mg, int dim, int[] fixed, String opts) Calculates atom coordinates by using fixed atoms.
static boolean	partialClean(MoleculeGraph mg, MoleculeGraph template, int[] map, String opts) Calculates atom coordinates by using the given template molecule.
static boolean	partialClean(Molecule m, Molecule[] template, String opts) Calculates atom coordinates by using the given template molecule array.
static boolean	partialCleanWithStereo(MoleculeGraph mg, int dim, int[] fixed, String opts) Calculates atom coordinates by using fixed atoms.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Cleaner

public Cleaner()

Method Detail

clean

public static boolean clean(MoleculeGraph mg,
            int dim,
            String opts,
            MProgressMonitor pmon)

Calculates atom coordinates. In a 3D it works only for Molecules (not for MoleculeGraphs).

Parameters:

mg - MoleculeGraph to clean.

dim - dimensions

opts - cleaning options

pmon - progress monitor or null

Returns:

true for success, false if an error occured (for example 3D case for MoleculeGraphs).

Since:

Marvin 5.7, 07/22/2011

clean

public static boolean clean(MoleculeGraph mg,
            int dim,
            String opts)

Calculates atom coordinates. In a 3D it works only for Molecules (not for MoleculeGraphs).

Parameters:

mg - MoleculeGraph to clean.

dim - dimensions

opts - cleaning options

Returns:

true for success, false if an error occurred (for example 3D case for MoleculeGraphs).

Since:

Marvin 5.7, 07/22/2011

clean

public static boolean clean(MoleculeGraph mg,
            int dim)

Calculates atom coordinates. In a 3D it works only for Molecules (not for MoleculeGraphs). Simple function to clean molecule if we don't want to give option for the clean.

Parameters:

mg - MoleculeGraph to clean.

dim - dimensions

Returns:

true for success, false if an error occurred (for example 3D case for MoleculeGraphs).

Since:

Marvin 6.1, 05/27/2013

See Also:

clean(MoleculeGraph, int, String)

partialClean

public static boolean partialClean(MoleculeGraph mg,
                   MoleculeGraph template,
                   int[] map,
                   String opts)

Calculates atom coordinates by using the given template molecule. Works only in 2D. Set the x and y coordinates of the molecule from the given template using the given mapping. Partially clean the rest atoms. Map length should be equal the atomcount of the template. If the template has no wedges, try to keep the wedges of the original molecule. Otherwise try to keep the template wedge settings.

Parameters:

mg - MoleculeGraph to clean.

template - template molecule (substructure of the target)

map - hit list which describes the atom mapping (the size equals to the number of atoms in the template, contains target atom indexes or -1 to exclude)

opts - cleaning options

Returns:

true for success, false if an error occurred

Since:

Marvin 5.7, 07/19/2011

partialClean

public static boolean partialClean(MoleculeGraph mg,
                   int dim,
                   int[] fixed,
                   String opts)

Calculates atom coordinates by using fixed atoms. Works only in 2D. For stereoisomers, the expected parity information should be stored in the atomflags and the CIS/TRANS information in the bondflags.

Parameters:

mg - MoleculeGraph to clean.

dim - dimensions

fixed - fixed atom indexes, which are already cleaned

opts - cleaning options

Returns:

true for success, false if an error occurred

Since:

Marvin 5.7, 07/22/2011

partialCleanWithStereo

public static boolean partialCleanWithStereo(MoleculeGraph mg,
                             int dim,
                             int[] fixed,
                             String opts)

Calculates atom coordinates by using fixed atoms. The arrangement is based on the parity and CIS/TRANS information of the original molecule if it was 2D or 3D. Otherwise this information will be read from the atomflags and bondflags (see partialClean(MoleculeGraph, int, int[], String)

Parameters:

mg - MoleculeGraph to clean.

dim - dimensions

fixed - fixed atom indexes, which are already cleaned

opts - cleaning options

Returns:

true for success, false if an error occurred

Since:

Marvin 6.0, Mar 22, 2013

partialClean

public static boolean partialClean(Molecule m,
                   Molecule[] template,
                   String opts)

Calculates atom coordinates by using the given template molecule array. Works only in 2D. Set the x and y coordinates for the substructure of this molecule which first match a molecule from template molecule array. Partially clean the rest atoms. Remark, that only the first matching template molecule is used despite any later match in the template molecules. If the template has no wedges, try to keep the wedges of the original molecule. Otherwise try to keep the template wedge settings.

Parameters:

m - Molecule to clean.

template - template molecule array (substructure of the target)

opts - cleaning options

Returns:

true for success, false if no template match found or an error occurred

Since:

Marvin 5.7, 07/19/2011