Package com.actelion.research.chem.mmp
Class MMPFragmenter
- java.lang.Object
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- com.actelion.research.chem.mmp.MMPFragmenter
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public class MMPFragmenter extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MMPFragmenter.MoleculeIndexID
class
MMPFragmenter.MoleculeIndexIDByte
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Field Summary
Fields Modifier and Type Field Description static int
FRAGMENT_ATOMIC_NO
static java.lang.String
FRAGMENT_DELIMITER
static java.lang.Integer
KEYS_MIN_ATOMS
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Constructor Summary
Constructors Constructor Description MMPFragmenter(StereoMolecule mol)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static java.lang.String
createR1HMoleculeID()
Generates the idCode for the R-[H] moleculevoid
fragmentMolecule()
void
fragmentMolecule(boolean generateWholeMoleculeVariations)
Fragments one StereoMolecule into keys-value pairs of StereoMolecules;
- for single cuts, keys is an array containing one fragment
('constant' part of the molecule), value the 'variable' part;
- for double cuts, keys in an array containing two fragments
(constant parts of the molecule, i.e.void
generateWholeMoleculeVariations()
Generates all variations of Hydrogen replacements on the whole molecule;
fragments are added to the moleculeIndexesID.StereoMolecule
getMol()
java.util.List<java.lang.String[]>
getMoleculeFragmentsID()
Returns an ArrayList of {R-group, "clean" (without R-groups)}
fragmentsID used for Hydrogen replacements.java.util.List<MMPFragmenter.MoleculeIndexID>
getMoleculeIndexesID()
java.util.List<MMPFragmenter.MoleculeIndexID>
getMoleculeIndexesID(boolean generateWholeMoleculeVariations)
Returns an ArrayList of MoleculeIndexID containing
IDCodes of keys and values of single and double cuts.java.util.List<MMPFragmenter.MoleculeIndexIDByte>
getMoleculeIndexesIDByte()
java.util.List<MMPFragmenter.MoleculeIndexIDByte>
getMoleculeIndexesIDByte(boolean generateWholeMoleculeVariations)
Returns an ArrayList of MoleculeIndexIDByte containing bytes of IDCodes of keys and values of single and double cuts.java.util.ArrayList<java.lang.Integer>
getRotBondsIndex()
Returns the indexes of the rotatable bonds
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Field Detail
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KEYS_MIN_ATOMS
public static final java.lang.Integer KEYS_MIN_ATOMS
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FRAGMENT_DELIMITER
public static final java.lang.String FRAGMENT_DELIMITER
- See Also:
- Constant Field Values
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FRAGMENT_ATOMIC_NO
public static final int FRAGMENT_ATOMIC_NO
- See Also:
- Constant Field Values
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Constructor Detail
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MMPFragmenter
public MMPFragmenter(StereoMolecule mol)
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Method Detail
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createR1HMoleculeID
public static java.lang.String createR1HMoleculeID()
Generates the idCode for the R-[H] molecule- Returns:
- idCode String
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getMoleculeIndexesID
public java.util.List<MMPFragmenter.MoleculeIndexID> getMoleculeIndexesID()
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getMoleculeIndexesID
public java.util.List<MMPFragmenter.MoleculeIndexID> getMoleculeIndexesID(boolean generateWholeMoleculeVariations)
Returns an ArrayList of MoleculeIndexID containing
IDCodes of keys and values of single and double cuts.- Parameters:
generateWholeMoleculeVariations
- true/false to generate whole molecule variations, used for identification of H-replacements
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getMoleculeFragmentsID
public java.util.List<java.lang.String[]> getMoleculeFragmentsID()
Returns an ArrayList of {R-group, "clean" (without R-groups)}
fragmentsID used for Hydrogen replacements.
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getMoleculeIndexesIDByte
public java.util.List<MMPFragmenter.MoleculeIndexIDByte> getMoleculeIndexesIDByte()
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getMoleculeIndexesIDByte
public java.util.List<MMPFragmenter.MoleculeIndexIDByte> getMoleculeIndexesIDByte(boolean generateWholeMoleculeVariations)
Returns an ArrayList of MoleculeIndexIDByte containing bytes of IDCodes of keys and values of single and double cuts.- Parameters:
generateWholeMoleculeVariations
- true/false to generate whole molecule variations, used for identification of H-replacements
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getRotBondsIndex
public java.util.ArrayList<java.lang.Integer> getRotBondsIndex()
Returns the indexes of the rotatable bonds- Returns:
- Array of integers
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fragmentMolecule
public void fragmentMolecule()
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fragmentMolecule
public void fragmentMolecule(boolean generateWholeMoleculeVariations)
Fragments one StereoMolecule into keys-value pairs of StereoMolecules;
- for single cuts, keys is an array containing one fragment
('constant' part of the molecule), value the 'variable' part;
- for double cuts, keys in an array containing two fragments
(constant parts of the molecule, i.e. 'left' and 'right' part), value the 'middle' part.
An array containing all 'single cut' fragments is available for Hydrogen replacements.- Parameters:
generateWholeMoleculeVariations
- true/false to generate whole molecule variations, used for identification of H-replacements
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generateWholeMoleculeVariations
public void generateWholeMoleculeVariations()
Generates all variations of Hydrogen replacements on the whole molecule;
fragments are added to the moleculeIndexesID.
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getMol
public StereoMolecule getMol()
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