Interface MoleculeWithValence<AtomReference>
- Type Parameters:
AtomReference
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- All Known Implementing Classes:
Molecule
,MoleculeGraph
,RgMolecule
,RxnMolecule
,SelectionMolecule
Interface for molecule object for which valence calculations can be performed.
This interface is intended for internal use only (e.g. in Marvin JS).
- Since:
- Marvin 5.9
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Method Summary
Modifier and TypeMethodDescriptionatoms()
Returns list for the atom references in the molecule.int
getAtomicNumber
(AtomReference atom) Gets the atomic number of the given atom.int
getCharge
(AtomReference atom) Gets the charge of the given atom.int
Returns the number of the free attachment points for the given atom.int
Gets the number of implicit hydrogens attached to the given atom.getLigand
(AtomReference atom, int n) Gets the n-th ligand of the given atom.int
getLigandAtno
(AtomReference atom, int n) Gets the atomic number of the n-th ligand of the given atom.getLigandBondType
(AtomReference atom, int n) Gets the type of the n-th ligand bond of the given atom.int
getLigandCount
(AtomReference atom) Gets the number of ligands of the given atom.int
getRadicalCount
(AtomReference atom) Gets the number of free electrons of the given atom.int
Gets the valence property of the given atom.boolean
Check if the ligand is a special atom which changes the ring atom column number with -1boolean
isAtomInRing
(AtomReference atom) Checks whether the atom is in ring.
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Method Details
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atoms
List<AtomReference> atoms()Returns list for the atom references in the molecule.- Returns:
- the iterator
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getLigandCount
Gets the number of ligands of the given atom.- Parameters:
atom
- the atom- Returns:
- number of ligands
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getLigand
Gets the n-th ligand of the given atom.- Parameters:
atom
- the atomn
- index- Returns:
- the n-th ligand
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getLigandBondType
Gets the type of the n-th ligand bond of the given atom.- Parameters:
atom
- the atomn
- index- Returns:
- the bond type
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getLigandAtno
Gets the atomic number of the n-th ligand of the given atom.- Parameters:
atom
- the atomn
- index- Returns:
- the atomic number
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getCharge
Gets the charge of the given atom.- Parameters:
atom
- the atom- Returns:
- the charge
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getAtomicNumber
Gets the atomic number of the given atom.- Parameters:
atom
- the atom- Returns:
- the atomic number
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getRadicalCount
Gets the number of free electrons of the given atom.- Parameters:
atom
- the atom- Returns:
- the number of free electrons
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getValenceProperty
Gets the valence property of the given atom.- Parameters:
atom
- the atom- Returns:
- the valence or -1 if not set
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getImplicitHCount
Gets the number of implicit hydrogens attached to the given atom.- Parameters:
atom
- the atom- Returns:
- the number of implicit hydrogens
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getFreeAttachmentPoints
Returns the number of the free attachment points for the given atom.- Parameters:
atom
- the atom- Returns:
- the number of the free attachment points or
0
if the atom is not located in any SuperatomSgroup
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isAtomInRing
Checks whether the atom is in ring.- Parameters:
atom
- the atom reference- Returns:
- true if the atom is in ring, false otherwise
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isAcceptedSpecialLigand
Check if the ligand is a special atom which changes the ring atom column number with -1- Parameters:
atom
- ligand- Returns:
- true if the ligand modifies the reference atom column number with -1 else false.
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