Package chemaxon.marvin.util
Class MolFragLoader
java.lang.Object
chemaxon.marvin.util.MolFragLoader
Molecule fragment loader. Fragments can be added to the root structure or
to R-group definitions as members.
- Since:
- Marvin 5.2
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
Molecule filter which accepts molecules with a specified number of R-group attachments. -
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionConstructor.MolFragLoader
(MolImporter importer) Constructor: sets the molecule fragment iterator from the specified importer.MolFragLoader
(MoleculeIterator iterator) Constructor: sets the molecule fragment iterator. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Arranges R-group definition member coordinates.Loads fragments, fuses them and returns the resulting 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
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.
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Field Details
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FILTER_ONE_ATTACHMENT
Filter object for accepting fragments with one attachment point. -
FILTER_TWO_ATTACHMENTS
Filter object for accepting fragments with two attachment points.
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Constructor Details
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MolFragLoader
public MolFragLoader()Constructor. -
MolFragLoader
Constructor: sets the molecule fragment iterator from the specified importer.- Parameters:
importer
- the fragment importer
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MolFragLoader
Constructor: sets the molecule fragment iterator.- Parameters:
iterator
- the fragment iterator- Since:
- Marvin 5.4
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Method Details
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setImporter
Sets the fragment iterator from the specified importer.- Parameters:
importer
- the fragment importer
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setIterator
Sets the fragment iterator.- Parameters:
iterator
- the fragment iterator- Since:
- Marvin 5.4
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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
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setFilter
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:
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loadFrags
Loads fragments, fuses them and returns the resulting molecule. If a fragment is anRgMolecule
then its root structure (structure without R-definitions) is used. Arranges fragments if needed.- Returns:
- the resulting molecule
- Since:
- Marvin 5.3
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loadFrags
Loads fragments, fuses them and returns the resulting molecule. If a fragment is anRgMolecule
then its root structure (structure without R-definitions) is used.- Parameters:
arrange
- istrue
if fragment coordinates should be shifted to avoid overlappings- Returns:
- the resulting molecule
- Since:
- Marvin 5.3
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loadFrags
Loads fragments, fuses them to the specified molecule. If a fragment is anRgMolecule
then its root structure (structure without R-definitions) is used.- Parameters:
mol
- the base moleculearrange
- istrue
if fragment coordinates should be shifted to avoid overlappings
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loadFrags
Loads fragments, fuses them to the specified molecule. If a fragment is anRgMolecule
then its root structure (structure without R-definitions) is used.- Parameters:
mol
- the base moleculedim
- the cleaning dim,-1
for automatic (dim of first fragment)arrange
- istrue
if fragment coordinates should be shifted to avoid overlappings- Since:
- Marvin 5.3
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loadRgroupMembers
Loads fragments and adds them as R-group definition members in the specified molecule. If a fragment is anRgMolecule
then its root structure (structure without R-definitions) is used.- Parameters:
mol
- the base moleculergroupID
- the R-group ID,0
for unnumbered R-group
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arrangeRgroupMembers
Arranges R-group definition member coordinates. Shifts members to avoid overlappings after one or more invokation ofloadRgroupMembers(chemaxon.struc.RgMolecule, int)
.- Parameters:
mol
- the molecule
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