chemaxon.marvin.util

Class MolFragLoader

java.lang.Object

chemaxon.marvin.util.MolFragLoader

@PublicAPI
public class MolFragLoader
extends java.lang.Object

Molecule fragment loader. Fragments can be added to the root structure or to R-group definitions as members.

Since:

Marvin 5.2

Author:

Nora Mate

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MolFragLoader.RgroupAttachmentCountFilter Molecule filter which accepts molecules with a specified number of R-group attachments.

Field Summary

Fields

Modifier and Type	Field and Description
static MolFilter	FILTER_ONE_ATTACHMENT Filter object for accepting fragments with one attachment point.
static MolFilter	FILTER_TWO_ATTACHMENTS Filter object for accepting fragments with two attachment points.

Constructor Summary

Constructors

Constructor and Description
MolFragLoader() Constructor.
MolFragLoader(MoleculeIterator iterator) Constructor: sets the molecule fragment iterator.
MolFragLoader(MolImporter importer) Constructor: sets the molecule fragment iterator from the specified importer.

Method Summary

Modifier and Type	Method and Description
void	arrangeRgroupMembers(RgMolecule mol) Arranges R-group definition member coordinates.
Molecule	loadFrags() Loads fragments, fuses them and returns the resulting molecule.
Molecule	loadFrags(boolean arrange) Loads fragments, fuses them and returns the resulting molecule.
void	loadFrags(MoleculeGraph mol, boolean arrange) Loads fragments, fuses them to the specified molecule.
void	loadFrags(MoleculeGraph mol, int dim, boolean arrange) Loads fragments, fuses them to the specified molecule.
void	loadRgroupMembers(RgMolecule mol, int rgroupID) Loads fragments and adds them as R-group definition members in the specified molecule.
void	setFilter(MolFilter filter) Sets the fragment filter.
void	setImporter(MolImporter importer) Sets the fragment iterator from the specified importer.
void	setIterator(MoleculeIterator iterator) Sets the fragment iterator.
void	setRange(chemaxon.common.util.IntRange range) Sets the (1-based) fragment index range to be loaded.

Methods inherited from class java.lang.Object

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

Field Detail

FILTER_ONE_ATTACHMENT

public static MolFilter FILTER_ONE_ATTACHMENT

Filter object for accepting fragments with one attachment point.

FILTER_TWO_ATTACHMENTS

public static MolFilter FILTER_TWO_ATTACHMENTS

Filter object for accepting fragments with two attachment points.

Constructor Detail

MolFragLoader

public MolFragLoader()

Constructor.

MolFragLoader

public MolFragLoader(MolImporter importer)

Constructor: sets the molecule fragment iterator from the specified importer.

Parameters:

importer - the fragment importer

MolFragLoader

public MolFragLoader(MoleculeIterator iterator)

Constructor: sets the molecule fragment iterator.

Parameters:

iterator - the fragment iterator

Since:

Marvin 5.4

Method Detail

setImporter

public void setImporter(MolImporter importer)

Sets the fragment iterator from the specified importer.

Parameters:

importer - the fragment importer

setIterator

public void setIterator(MoleculeIterator iterator)

Sets the fragment iterator.

Parameters:

iterator - the fragment iterator

Since:

Marvin 5.4

setRange

public void setRange(chemaxon.common.util.IntRange range)

Sets the (1-based) fragment index range to be loaded. The range is assumed to be sorted in ascending order.

Parameters:

range - the fragment index range

setFilter

public void setFilter(MolFilter filter)

Sets the fragment filter. Only those fragments will be added which pass this filter. For example, the filter may accept only structures with one R-group attachment point (FILTER_ONE_ATTACHMENT), or structures with two R-group attachment points (FILTER_TWO_ATTACHMENTS), checking attachment point types. (By default, all loaded fragments will be added.)

Parameters:

filter - the fragment filter

See Also:

FILTER_ONE_ATTACHMENT, FILTER_TWO_ATTACHMENTS

loadFrags

public Molecule loadFrags()

Loads fragments, fuses them and returns the resulting molecule. If a fragment is an RgMolecule then its root structure (structure without R-definitions) is used. Arranges fragments if needed.

Returns:

the resulting molecule

Since:

Marvin 5.3

loadFrags

public Molecule loadFrags(boolean arrange)

Loads fragments, fuses them and returns the resulting molecule. If a fragment is an RgMolecule then its root structure (structure without R-definitions) is used.

Parameters:

arrange - is true if fragment coordinates should be shifted to avoid overlappings

Returns:

the resulting molecule

Since:

Marvin 5.3

loadFrags

public void loadFrags(MoleculeGraph mol,
                      boolean arrange)

Loads fragments, fuses them to the specified molecule. If a fragment is an RgMolecule then its root structure (structure without R-definitions) is used.

Parameters:

mol - the base molecule

arrange - is true if fragment coordinates should be shifted to avoid overlappings

loadFrags

public void loadFrags(MoleculeGraph mol,
                      int dim,
                      boolean arrange)

Loads fragments, fuses them to the specified molecule. If a fragment is an RgMolecule then its root structure (structure without R-definitions) is used.

Parameters:

mol - the base molecule

dim - the cleaning dim, -1 for automatic (dim of first fragment)

arrange - is true if fragment coordinates should be shifted to avoid overlappings

Since:

Marvin 5.3

loadRgroupMembers

public void loadRgroupMembers(RgMolecule mol,
                              int rgroupID)

Loads fragments and adds them as R-group definition members in the specified molecule. If a fragment is an RgMolecule then its root structure (structure without R-definitions) is used.

Parameters:

mol - the base molecule

rgroupID - the R-group ID, 0 for unnumbered R-group

arrangeRgroupMembers

public void arrangeRgroupMembers(RgMolecule mol)

Arranges R-group definition member coordinates. Shifts members to avoid overlappings after one or more invokation of loadRgroupMembers(chemaxon.struc.RgMolecule, int).

Parameters:

mol - the molecule