@PublicAPI public class MolFragLoader extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
MolFragLoader.RgroupAttachmentCountFilter
Molecule filter which accepts molecules with a specified number of R-group attachments.
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Modifier and Type | Field and Description |
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static MolFilter |
FILTER_ONE_ATTACHMENT
Filter object for accepting fragments with one attachment point.
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static MolFilter |
FILTER_TWO_ATTACHMENTS
Filter object for accepting fragments with two attachment points.
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Constructor and Description |
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MolFragLoader()
Constructor.
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MolFragLoader(MoleculeIterator iterator)
Constructor: sets the molecule fragment iterator.
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MolFragLoader(MolImporter importer)
Constructor: sets the molecule fragment iterator
from the specified importer.
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Modifier and Type | Method and Description |
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void |
arrangeRgroupMembers(RgMolecule mol)
Arranges R-group definition member coordinates.
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Molecule |
loadFrags()
Loads fragments, fuses them and returns the resulting molecule.
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Molecule |
loadFrags(boolean arrange)
Loads fragments, fuses them and returns the resulting molecule.
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void |
loadFrags(MoleculeGraph mol,
boolean arrange)
Loads fragments, fuses them to the specified molecule.
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void |
loadFrags(MoleculeGraph mol,
int dim,
boolean arrange)
Loads fragments, fuses them to the specified molecule.
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void |
loadRgroupMembers(RgMolecule mol,
int rgroupID)
Loads fragments and adds them as R-group definition members in the specified molecule.
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void |
setFilter(MolFilter filter)
Sets the fragment filter.
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void |
setImporter(MolImporter importer)
Sets the fragment iterator from the specified importer.
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void |
setIterator(MoleculeIterator iterator)
Sets the fragment iterator.
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void |
setRange(chemaxon.common.util.IntRange range)
Sets the (1-based) fragment index range to be loaded.
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public static MolFilter FILTER_ONE_ATTACHMENT
public static MolFilter FILTER_TWO_ATTACHMENTS
public MolFragLoader()
public MolFragLoader(MolImporter importer)
importer
- the fragment importerpublic MolFragLoader(MoleculeIterator iterator)
iterator
- the fragment iteratorpublic void setImporter(MolImporter importer)
importer
- the fragment importerpublic void setIterator(MoleculeIterator iterator)
iterator
- the fragment iteratorpublic void setRange(chemaxon.common.util.IntRange range)
range
- the fragment index rangepublic void setFilter(MolFilter filter)
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.)filter
- the fragment filterFILTER_ONE_ATTACHMENT
,
FILTER_TWO_ATTACHMENTS
public Molecule loadFrags()
RgMolecule
then its root structure
(structure without R-definitions) is used.
Arranges fragments if needed.public Molecule loadFrags(boolean arrange)
RgMolecule
then its root structure
(structure without R-definitions) is used.arrange
- is true
if fragment coordinates should be shifted
to avoid overlappingspublic void loadFrags(MoleculeGraph mol, boolean arrange)
RgMolecule
then its root structure
(structure without R-definitions) is used.mol
- the base moleculearrange
- is true
if fragment coordinates should be shifted
to avoid overlappingspublic void loadFrags(MoleculeGraph mol, int dim, boolean arrange)
RgMolecule
then its root structure
(structure without R-definitions) is used.mol
- the base moleculedim
- the cleaning dim, -1
for automatic (dim of first fragment)arrange
- is true
if fragment coordinates should be shifted
to avoid overlappingspublic void loadRgroupMembers(RgMolecule mol, int rgroupID)
RgMolecule
then its root structure
(structure without R-definitions) is used.mol
- the base moleculergroupID
- the R-group ID, 0
for unnumbered R-grouppublic void arrangeRgroupMembers(RgMolecule mol)
loadRgroupMembers(chemaxon.struc.RgMolecule, int)
.mol
- the molecule