Package chemaxon.calculations.clean
Class Cleaner
java.lang.Object
chemaxon.calculations.clean.Cleaner
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionstatic 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
(MoleculeGraph mg, MoleculeGraph template, int[] map, String opts, AtomChangeEventListener l) static boolean
partialClean
(Molecule m, Molecule[] template, String opts) Calculates atom coordinates by using the given template molecule array.static boolean
partialClean
(Molecule m, Molecule[] template, String opts, AtomChangeEventListener l) A specific overloading for partial clean.static boolean
partialCleanWithStereo
(MoleculeGraph mg, int dim, int[] fixed, String opts) Calculates atom coordinates by using fixed atoms.
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Constructor Details
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Cleaner
public Cleaner()
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Method Details
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clean
Calculates atom coordinates. In a 3D it works only for Molecules (not for MoleculeGraphs).- Parameters:
mg
- MoleculeGraph to clean.dim
- dimensionsopts
- cleaning optionspmon
- progress monitor ornull
- Returns:
- true for success, false if an error occurred (for example 3D case for MoleculeGraphs).
- Since:
- Marvin 5.7, 07/22/2011
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clean
Calculates atom coordinates. In a 3D it works only for Molecules (not for MoleculeGraphs).- Parameters:
mg
- MoleculeGraph to clean.dim
- dimensionsopts
- cleaning options- Returns:
- true for success, false if an error occurred (for example 3D case for MoleculeGraphs).
- Since:
- Marvin 5.7, 07/22/2011
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clean
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:
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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
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partialClean
public static boolean partialClean(MoleculeGraph mg, MoleculeGraph template, int[] map, String opts, AtomChangeEventListener l) -
partialClean
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
- dimensionsfixed
- fixed atom indexes, which are already cleanedopts
- cleaning options- Returns:
- true for success, false if an error occurred
- Since:
- Marvin 5.7, 07/22/2011
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partialCleanWithStereo
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 (seepartialClean(MoleculeGraph, int, int[], String)
- Parameters:
mg
- MoleculeGraph to clean.dim
- dimensionsfixed
- fixed atom indexes, which are already cleanedopts
- cleaning options- Returns:
- true for success, false if an error occurred
- Since:
- Marvin 6.0, Mar 22, 2013
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partialClean
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
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partialClean
public static boolean partialClean(Molecule m, Molecule[] template, String opts, AtomChangeEventListener l) A specific overloading for partial clean. Events on applying template related changes to atoms are fired for the passed listener.- Parameters:
l
- listener to be fired on changes
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