SBAtom#
This class describes an atom in a structural model.
You can get a number of atom’s parameters on its topology (bonds), identity (type, element name and symbol, atomic weight, etc), and other properties (chain, occupancy, serial number, formal charge, temperature factor, etc), for example:
# get the bond list of an atom
atom.getBondList
# atom's element name
atom.elementName
# atom's element symbol
atom.elementSymbol
# atom's atomic weight
atom.atomicWeight
# atom's occupancy
atom.occupancy
# atom's temperature factor
if atom.hasTemperatureFactor:
atom.temperatureFactor
# atom's water flag
if atom.hasWaterFlag:
atom.waterFlag
# the name of a residue to which atom belongs
if atom.isInResidue:
atom.residueName
Note
Parameters which are owned by an atom are accessible as properties (e.g., atom.partialCharge
), but due to some limitations some parameters which are owned by atom’s parent nodes are accessible via getter and setter functions (if setter functions are available for a parameter).
There is a number of constructors for an atom node, for example:
# construct a Carbon atom at (0, 0, 0) position
atom1 = SBAtom(SBElement.Carbon)
atom1.setPosition(SBPosition3(SBQuantity.nm(1), SBQuantity.nm(-1.5), SBQuantity.nm(0)))
print(atom1)
# construct a Carbon atom at (0, 0, 0) position
atom2 = SBAtom(SBElement.Carbon, SBPosition3(SBQuantity.nm(1), SBQuantity.nm(-1.5), SBQuantity.nm(0)))
print(atom2)
You can further add an atom to e.g. a structural model, chain, backbone, or sidechain:
# turn the undo system on
SAMSON.beginHolding("Add new atom")
# hold the atom instance
SAMSON.hold(atom)
# create the atom
atom.create()
# add the atom to a chain
chain.addChild(atom)
# turn the undo system off
SAMSON.endHolding()
- class samson.SBAtom(*args, **kwargs)#
Bases:
SBStructuralNode
This class describes an atom in a structural model.
Overloaded function.
__init__(self: samson.SBAtom) -> None
Constructs an atom of with the element type samson.SBElement.Unknown and the default position (0, 0, 0)
__init__(self: samson.SBAtom, element: samson.SBElement.ElementType) -> None
Constructs an atom of the given element type and the default position (0, 0, 0).
- Parameters:
element (samson.SBElement.ElementType) – The element type
__init__(self: samson.SBAtom, element: samson.SBElement.ElementType, x: samson.SBQuantity.unitsSI, y: samson.SBQuantity.unitsSI, z: samson.SBQuantity.unitsSI) -> None
Constructs an atom of the given element type at position = (x, y, z).
- Parameters:
element (samson.SBElement.ElementType) – The element type
x (samson.SBQuantity.unitsSI) – The x-coordinate
y (samson.SBQuantity.unitsSI) – The y-coordinate
z (samson.SBQuantity.unitsSI) – The z-coordinate
__init__(self: samson.SBAtom, element: samson.SBElement.ElementType, position: samson.SBPhysicalVector3) -> None
Constructs an atom of the given element type at the given position.
- Parameters:
element (samson.SBElement.ElementType) – The element type
position (samson.SBPosition3) – The position
- class Geometry(self: samson.SBAtom.Geometry, value: int)#
Bases:
pybind11_object
Members:
Undefined
Linear
Bent
TrigonalPlanar
TrigonalPyramidal
TShaped
Tetrahedral
SquarePlanar
Seesaw
TrigonalBipyramidal
SquarePyramidal
PentagonalPlanar
Octahedral
TrigonalPrismatic
PentagonalPyramidal
PentagonalBipyramidal
CappedOctahedral
CappedTrigonalPrismatic
SquareAntiprismatic
Dodecahedral
BicappedTrigonalPrismatic
TricappedTrigonalPrismatic
CappedSquareAntiprismatic
- Bent = <Geometry.Bent: 22>#
- BicappedTrigonalPrismatic = <Geometry.BicappedTrigonalPrismatic: 83>#
- CappedOctahedral = <Geometry.CappedOctahedral: 72>#
- CappedSquareAntiprismatic = <Geometry.CappedSquareAntiprismatic: 92>#
- CappedTrigonalPrismatic = <Geometry.CappedTrigonalPrismatic: 73>#
- Dodecahedral = <Geometry.Dodecahedral: 82>#
- Linear = <Geometry.Linear: 21>#
- Octahedral = <Geometry.Octahedral: 61>#
- PentagonalBipyramidal = <Geometry.PentagonalBipyramidal: 71>#
- PentagonalPlanar = <Geometry.PentagonalPlanar: 53>#
- PentagonalPyramidal = <Geometry.PentagonalPyramidal: 63>#
- Seesaw = <Geometry.Seesaw: 43>#
- SquareAntiprismatic = <Geometry.SquareAntiprismatic: 81>#
- SquarePlanar = <Geometry.SquarePlanar: 42>#
- SquarePyramidal = <Geometry.SquarePyramidal: 52>#
- TShaped = <Geometry.TShaped: 33>#
- Tetrahedral = <Geometry.Tetrahedral: 41>#
- TricappedTrigonalPrismatic = <Geometry.TricappedTrigonalPrismatic: 91>#
- TrigonalBipyramidal = <Geometry.TrigonalBipyramidal: 51>#
- TrigonalPlanar = <Geometry.TrigonalPlanar: 31>#
- TrigonalPrismatic = <Geometry.TrigonalPrismatic: 62>#
- TrigonalPyramidal = <Geometry.TrigonalPyramidal: 32>#
- Undefined = <Geometry.Undefined: 0>#
- property name#
- property value#
- class Hybridization(self: samson.SBAtom.Hybridization, value: int)#
Bases:
pybind11_object
Members:
NoHybridization : No hybridization
SP : Hybridization of an s-orbital and one p-orbital
SP2 : Hybridization of an s-orbital and two p-orbitals
SP3 : Hybridization of an s-orbital and three p-orbitals
SP3D : Hybridization of an s-orbital, three p-orbitals, and a d-orbital
SP3D2 : Hybridization of an s-orbital, three p-orbitals, and two d-orbital
Unknown : Hybridization is unknown
- NoHybridization = <Hybridization.NoHybridization: 0>#
- SP = <Hybridization.SP: 1>#
- SP2 = <Hybridization.SP2: 2>#
- SP3 = <Hybridization.SP3: 3>#
- SP3D = <Hybridization.SP3D: 4>#
- SP3D2 = <Hybridization.SP3D2: 5>#
- Unknown = <Hybridization.Unknown: 6>#
- property name#
- property value#
- addHydrogens(self: samson.SBAtom) int #
Adds hydrogens and returns the number of added hydrogens
- clearAltLocation(self: samson.SBAtom) None #
Clears the atom’s alternate location
- clearAnisotropicTFactors(self: samson.SBAtom) None #
Clears the atom’s anisotropic temperature factors
- clearAromaticity(self: samson.SBAtom) None #
Clears the atom’s aromaticity
- clearComment(self: samson.SBAtom) None #
Clears the atom’s comment
- clearCustomType(self: samson.SBAtom) None #
Clears the atom’s custom type
- clearFormalCharge(self: samson.SBAtom) None #
Clears the atom’s formal charge
- clearGeometry(self: samson.SBAtom) None #
Clears the atom’s geometry
- clearHybridization(self: samson.SBAtom) None #
Clears the atom’s hybridization
- clearInsertionCode(self: samson.SBAtom) None #
Clears the atom’s insertion code
- clearName(self: samson.SBAtom) None #
Clears the atom’s full name
- clearOccupancy(self: samson.SBAtom) None #
Clears the atom’s occupancy
- clearOxidationState(self: samson.SBAtom) None #
Clears the atom’s oxidation state
- clearPartialCharge(self: samson.SBAtom) None #
Clears the atom’s partial charge
- clearRecordType(self: samson.SBAtom) None #
Clears the atom’s record type
- clearResonance(self: samson.SBAtom) None #
Clears the atom’s resonance
- clearSYBYLType(self: samson.SBAtom) None #
Clears the atom’s SYBYL type
- clearSerialNumber(self: samson.SBAtom) None #
Clears the atom’s serial number
- clearStatusBit(self: samson.SBAtom) None #
Clears the atom’s status bit
- clearTemperatureFactor(self: samson.SBAtom) None #
Clears the atom’s temperature factor
- clearWaterFlag(self: samson.SBAtom) None #
Clears the atom’s water flag
- getBackbone(self: samson.SBAtom) SBMStructuralModelNodeBackbone #
Returns a pointer to the backbone
- getBondList(self: samson.SBAtom) samson.SBNodeIndexer #
Returns the bond indexer.
- Returns:
The indexer of bonds to the atom
- Return type:
- getBondTo(self: samson.SBAtom, atom: samson.SBAtom) SBMStructuralModelNodeBond #
Returns the bond to the given atom (None if no bond).
- Parameters:
atom (samson.SBAtom) – An atom
- Returns:
The bond between this atom and the given atom atom
- Return type:
- getBondedAtoms(*args, **kwargs)#
Overloaded function.
getBondedAtoms(self: samson.SBAtom) -> samson.SBNodeIndexer
Returns an indexer with all bonded atoms.
- Returns:
The indexer of atoms bonded to this atom
- Return type:
getBondedAtoms(self: samson.SBAtom, element: samson.SBElement.ElementType) -> samson.SBNodeIndexer
Returns an indexer with all bonded atoms of type element.
- Parameters:
element (samson.SBElement.ElementType) – The element type
- Returns:
The indexer of atoms of type element bonded to this atom
- Return type:
- getBondedHeavyAtoms(self: samson.SBAtom) samson.SBNodeIndexer #
Returns an indexer with all bonded heavy atoms (non-Hydrogens).
- Returns:
The indexer of heavy atoms bonded to this atom
- Return type:
- getChain(self: samson.SBAtom) SBMStructuralModelNodeChain #
Returns the atom’s chain
- getCoarseGrainedColor(self: samson.SBAtom) samson.SBColor #
Get the coarse-grained atom’s color
- getCoarseGrainedMass(self: samson.SBAtom) samson.SBQuantity.unitsSI #
Get the coarse-grained atom’s mass
- getCoarseGrainedRadius(self: samson.SBAtom) samson.SBQuantity.unitsSI #
Get the coarse-grained atom’s radius
- getCoarseGrainedType(self: samson.SBAtom) str #
Get the coarse-grained atom’s type
- getColor(self: samson.SBAtom) samson.SBColor #
Returns the atom’s element color (CPK or coarse grained).
- Returns:
The color
- Return type:
- getComment(self: samson.SBAtom) str #
Returns the atom’s comment
- getConnectedComponent(*args, **kwargs)#
Overloaded function.
getConnectedComponent(self: samson.SBAtom) -> samson.SBNodeIndexer
Gets all atoms in the connected component containing the atom.
- Returns:
The indexer with atoms in the connected component
- Return type:
getConnectedComponent(self: samson.SBAtom, maximumNumberOfAtoms: int) -> tuple
Gets atoms in the connected component containing the atom and stops once maximumNumberOfAtoms is reached.
- Parameters:
maximumNumberOfAtoms (int) – The maximum number of atoms in the connected component after reaching which the algorithm should stop.
- Returns:
- A tuple with a first element being a boolean showing whether the whole connected component has no more than maximumNumberOfAtoms atoms
and the second element being the indexer with atoms in the connected component.
- Return type:
Tuple(bool, samson.SBNodeIndexer)
- static getGeometryString(geometry: SBMStructuralModelNodeAtom::Geometry) str #
Returns the geometry as a string
- static getHybridizationString(hybridization: SBMStructuralModelNodeAtom::Hybridization) str #
Returns the hybridization as a string
- getHydrogens(self: samson.SBAtom) samson.SBNodeIndexer #
Returns an indexer with all bonded hydrogens.
- Returns:
The indexer of hydrogen atoms bonded to this atom
- Return type:
- getMolecule(self: samson.SBAtom) SBMStructuralModelNodeMolecule #
Returns a molecule in which the atom is
- getNumberOfBondedAtoms(*args, **kwargs)#
Overloaded function.
getNumberOfBondedAtoms(self: samson.SBAtom) -> int
Returns the number of bonded atoms
getNumberOfBondedAtoms(self: samson.SBAtom, element: samson.SBElement.ElementType) -> int
Returns the number of bonded atoms with element type element.
- Parameters:
element (samson.SBElement.ElementType) – The element type
- Returns:
The number of atoms of type element bonded to this atom
- Return type:
int
- getNumberOfBondedCarbons(self: samson.SBAtom) int #
Returns the number of bonded carbons
- getNumberOfBondedHeavyAtoms(self: samson.SBAtom) int #
Returns the number of bonded heavy atoms
- getNumberOfBondedHydrogens(self: samson.SBAtom) int #
Returns the number of bonded hydrogens
- getNumberOfBondedNitrogens(self: samson.SBAtom) int #
Returns the number of bonded nitrogens
- getNumberOfBondedOxygens(self: samson.SBAtom) int #
Returns the number of bonded oxygens
- getNumberOfBondedSulfurs(self: samson.SBAtom) int #
Returns the number of bonded sulfurs
- getNumberOfBonds(self: samson.SBAtom) int #
The number of bonds without taking into account the bond order. Note that a double bond is considered as one bond.
- getPosition(self: samson.SBAtom) samson.SBPhysicalVector3 #
Returns the position
- getRecordType(self: samson.SBAtom) str #
Returns the atom’s record type
- getResidue(self: samson.SBAtom) SBMStructuralModelNodeResidue #
Returns a residue in which the atom is
- getSYBYLType(self: samson.SBAtom) str #
Returns the atom’s SYBYL type
- getSegment(self: samson.SBAtom) SBMStructuralModelNodeSegment #
Returns the segment in which the atom is
- getSideChain(self: samson.SBAtom) SBMStructuralModelNodeSideChain #
Returns a pointer to the side chain
- getStatusBit(self: samson.SBAtom) str #
Returns the atom’s status bit
- getSubstructure(self: samson.SBAtom) samson.SBStructuralGroup #
Returns a substructure in which the atom is
- getX(self: samson.SBAtom) samson.SBQuantity.unitsSI #
Returns the x-coordinate
- getY(self: samson.SBAtom) samson.SBQuantity.unitsSI #
Returns the y-coordinate
- getZ(self: samson.SBAtom) samson.SBQuantity.unitsSI #
Returns the z-coordinate
- isAttachedToHydrogenBondDonor(self: samson.SBAtom) bool #
Returns True if the atom is connected to an H-Bond donor
- isCarbon(self: samson.SBAtom) bool #
Returns True when the atom is a carbon atom
- isCarboxylOxygen(self: samson.SBAtom) bool #
Returns True for an Oxygen atom in a carboxyl group (C(=O)OH)
- isCoarseGrained(self: samson.SBAtom) bool #
Returns True if the atom is coarse grained
- isDonorBorneHydrogen(self: samson.SBAtom) bool #
Returns True if the atom is a hydrogen connected to an H-Bond donor
- isHydrogen(self: samson.SBAtom) bool #
Returns True when the atom is a hydrogen atom
- isHydrogenBondAcceptor(self: samson.SBAtom) bool #
Returns True if the atom is an H-Bond acceptor (N, O, S, F)
- isHydrogenBondDonor(self: samson.SBAtom) bool #
Returns True if the atom is an H-Bond donor (N, O, S, F)
- isNitroOxygen(self: samson.SBAtom) bool #
Returns True for an Oxygen atom in a nitro group (-NO2)
- isNitrogen(self: samson.SBAtom) bool #
Returns True when the atom is a nitrogen atom
- isOxygen(self: samson.SBAtom) bool #
Returns True when the atom is an oxygen atom
- isPlanar(self: samson.SBAtom) bool #
Returns True if the atom with atoms bonded to it are in the same plane
- isSulfoneOxygen(self: samson.SBAtom) bool #
Returns True for an Oxygen atom in a sulfone (R1-SO2-R2)
- isSulfur(self: samson.SBAtom) bool #
Returns True when the atom is a sulfur atom
- isThiocarboxylOxygen(self: samson.SBAtom) bool #
Returns True for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH)
- isUnknown(self: samson.SBAtom) bool #
Returns True when the atom is an unknown atom
- removeHydrogens(self: samson.SBAtom) int #
Removes the hydrogens bonded to the atom and returns the number of removed hydrogens
- setCoarseGrainedColor(self: samson.SBAtom, color: samson.SBColor) None #
Set the coarse-grained atom’s color
- setCoarseGrainedMass(*args, **kwargs)#
Overloaded function.
setCoarseGrainedMass(self: samson.SBAtom, mass: samson.SBQuantity.unitsSI) -> None
Set the coarse-grained atom’s mass
setCoarseGrainedMass(self: samson.SBAtom, mass: samson.SBQuantity.unitsDalton) -> None
Set the coarse-grained atom’s mass
- setCoarseGrainedRadius(self: samson.SBAtom, radius: samson.SBQuantity.unitsSI) None #
Set the coarse-grained atom’s radius
- setCoarseGrainedType(self: samson.SBAtom, type: str) None #
Set the coarse-grained atom’s type
- setComment(self: samson.SBAtom, comment: str) None #
Set the atom’s comment
- setPosition(self: samson.SBAtom, position: samson.SBPhysicalVector3) None #
Sets the position
- setPositionOnTetrahedron(self: samson.SBAtom, center: samson.SBPhysicalVector3, vertex1: samson.SBPhysicalVector3, vertex2: samson.SBPhysicalVector3, vertex3: samson.SBPhysicalVector3, distanceFromCenter: samson.SBQuantity.unitsSI) None #
Sets the particle’s position on a tetrahedron vertex based on the center position, the distance from the center distanceFromCenter, and positions of other 3 vertices vertex1, vertex2, and vertex3.
- setRecordType(self: samson.SBAtom, recordType: str) None #
Set the atom’s recordType
- setSYBYLType(self: samson.SBAtom, type: str) None #
Set the atom’s SYBYL type
- setStatusBit(self: samson.SBAtom, statusBit: str) None #
Set the atom’s status bit
- setX(self: samson.SBAtom, x: samson.SBQuantity.unitsSI) None #
Sets the x-coordinate
- setY(self: samson.SBAtom, y: samson.SBQuantity.unitsSI) None #
Sets the y-coordinate
- setZ(self: samson.SBAtom, z: samson.SBQuantity.unitsSI) None #
Sets the z-coordinate
- Bent = <Geometry.Bent: 22>#
- BicappedTrigonalPrismatic = <Geometry.BicappedTrigonalPrismatic: 83>#
- CappedOctahedral = <Geometry.CappedOctahedral: 72>#
- CappedSquareAntiprismatic = <Geometry.CappedSquareAntiprismatic: 92>#
- CappedTrigonalPrismatic = <Geometry.CappedTrigonalPrismatic: 73>#
- Dodecahedral = <Geometry.Dodecahedral: 82>#
- Linear = <Geometry.Linear: 21>#
- NoHybridization = <Hybridization.NoHybridization: 0>#
- Octahedral = <Geometry.Octahedral: 61>#
- PentagonalBipyramidal = <Geometry.PentagonalBipyramidal: 71>#
- PentagonalPlanar = <Geometry.PentagonalPlanar: 53>#
- PentagonalPyramidal = <Geometry.PentagonalPyramidal: 63>#
- SP = <Hybridization.SP: 1>#
- SP2 = <Hybridization.SP2: 2>#
- SP3 = <Hybridization.SP3: 3>#
- SP3D = <Hybridization.SP3D: 4>#
- SP3D2 = <Hybridization.SP3D2: 5>#
- Seesaw = <Geometry.Seesaw: 43>#
- SquareAntiprismatic = <Geometry.SquareAntiprismatic: 81>#
- SquarePlanar = <Geometry.SquarePlanar: 42>#
- SquarePyramidal = <Geometry.SquarePyramidal: 52>#
- TShaped = <Geometry.TShaped: 33>#
- Tetrahedral = <Geometry.Tetrahedral: 41>#
- TricappedTrigonalPrismatic = <Geometry.TricappedTrigonalPrismatic: 91>#
- TrigonalBipyramidal = <Geometry.TrigonalBipyramidal: 51>#
- TrigonalPlanar = <Geometry.TrigonalPlanar: 31>#
- TrigonalPrismatic = <Geometry.TrigonalPrismatic: 62>#
- TrigonalPyramidal = <Geometry.TrigonalPyramidal: 32>#
- Undefined = <Geometry.Undefined: 0>#
- Unknown = <Hybridization.Unknown: 6>#
- property alternateLocation#
The atom’s alternate location
- property anisotropicTFactors#
The atom’s anisotropic temperature factors
- property aromaticity#
The atom’s aromaticity
- property atomicNumber#
The atom’s atomic number
- property atomicWeight#
The atom’s atomic weight
- property block#
The atom’s block
- property chainID#
Returns the ID of a chain in which the atom is
- property chainIDString#
Returns the ID (as a string) of a chain in which the atom is
- property chainName#
Returns the atom’s chain name
- property covalentRadius#
The atom’s covalent radius
- property currentValence#
The current valence, i.e. the sum of the orders of the bonds connected to the atom.
- Returns:
The current valence
- Return type:
samson.SBQuantity
- property customType#
The atom’s custom type
- property electronegativity#
The atom’s electronegativity
- property elementName#
The atom’s element name
- property elementSymbol#
The atom’s element symbol
- property elementType#
The atom’s element type
- property expectedValence#
The expected valence of the atom based on its formal charge and its number of bonds (based on the MDL valence model).
- Returns:
The expected valence
- Return type:
samson.SBQuantity
- property fixedFlag#
The atom’s fixed flag
- property formalCharge#
The atom’s formal charge
- property geometry#
The atom’s geometry
- property geometryString#
Returns the geometry as a string
- property group#
The atom’s group
- property hasAltLocation#
Returns True when the atom’s alternate location is set
- property hasAminoAcidBackboneAtomName#
Returns True when the atom’s name corresponds to one of the amino acid backbone atoms
- property hasAnisotropicTFactors#
Returns True when the atom’s anisotropic temperature factors are set
- property hasAromaticity#
Returns True when the atom’s aromaticity is set
- property hasChainID#
Returns True when the atom is in a chain and the chain’s ID is set
- property hasComment#
Returns True when the atom’s comment is set
- property hasCustomType#
Returns True when the atom’s custom type is set
- property hasFormalCharge#
Returns True when the atom’s formal charge is set
- property hasGeometry#
Returns True when the atom’s geometry is set
- property hasHybridization#
Returns True when the atom’s hybridization is set
- property hasInsertionCode#
Returns True when the atom’s insertion code is set
- property hasName#
Returns True when the atom’s name is set
- property hasNucleicAcidBackboneAtomName#
Returns True when the atom’s name corresponds to one of the nucleic acid backbone atoms
- property hasOccupancy#
Returns True when the atom’s occupancy is set
- property hasOxidationState#
Returns True when the atom’s oxidation state is set
- property hasPartialCharge#
Returns True when the atom’s partial charge is set
- property hasRecordType#
Returns True when the atom’s record type is set
- property hasResidueSequenceNumber#
Returns True when the atom is in a residue and the chain’s ID is set
- property hasResonance#
Returns True when the atom’s resonance is set
- property hasSYBYLType#
Returns True when the atom’s SYBYL type is set
- property hasSerialNumber#
Returns True when the atom’s serial number is set
- property hasStatusBit#
Returns True when the atom’s status bit is set
- property hasSubstructureSequenceNumber#
Returns True when the atom is in a substructure and the chain’s ID is set
- property hasTemperatureFactor#
Returns True when the atom’s temperature factor is set
- property hasWaterFlag#
Returns True when the atom’s water flag is set
- property hybridization#
The atom’s hybridization
- property hybridizationString#
Returns the hybridization as a string
- property insertionCode#
The atom’s insertion code
- property isActinide#
Returns True if the atom is actinide metal
- property isAlkaliMetal#
Returns True if the atom is alkali metal
- property isAlkalineEarthMetal#
Returns True if the atom is alkaline earth metal
- property isDiatomicNonmetal#
Returns True if the atom is diatomic nonmetal
- property isFixed#
Returns whether the node is fixed (opposite of mobile)
- property isFromAminoAcidBackbone#
Returns True when the atom is from an amino acid backbone
- property isFromNucleicAcidBackbone#
Returns True when the atom is from a nucleic acid backbone
- property isHalogen#
Returns True if the atom is halogen
- property isInAminoAcid#
Returns True when the atom is in an amino acid residue
- property isInBackbone#
Returns True when the atom is in a backbone
- property isInChain#
Returns True when the atom is in a chain
- property isInMolecule#
Returns True when the atom is in a molecule
- property isInNucleicAcid#
Returns True when the atom is in a nucleic acid residue
- property isInResidue#
Returns True when the atom is in a residue group
- property isInSegment#
Returns True when the atom is in segment
- property isInSideChain#
Returns True when the atom is in a side chain
- property isInSubstructure#
Returns True when the atom is in a substructure group
- property isLanthanide#
Returns True if the atom is lanthanide metal
- property isMetal#
Returns True if the atom is metal
- property isMetalloid#
Returns True if the atom is metalloid
- property isNobleGas#
Returns True if the atom is noble gas
- property isPolyatomicNonmetal#
Returns True if the atom is polyatomic nonmetal
- property isPostTransitionMetal#
Returns True if the atom is post-transition metal
- property isReactiveNonmetal#
Returns True if the atom is reactive nonmetal
- property isTransitionMetal#
Returns True if the atom is transition metal
- property metalSubcategory#
Returns the atom’s subcategory type in the metal–metalloid–nonmetal trend
- property metalSubcategoryString#
Returns the string representation of the atom’s subcategory type in the metal–metalloid–nonmetal trend
- property mobilityFlag#
The atom’s mobility flag. Please note that this attribute has been marked as deprecated and will be removed in future versions of the software. We recommend that you update your code to use the recommended alternative attribute instead, which is fixedFlag
- property moleculeName#
Returns the name of a molecule in which the atom is
- property name#
The atom’s full name
- property occupancy#
The atom’s occupancy
- property oxidationState#
The atom’s oxidation state
- property partialCharge#
The atom’s partial charge
- property period#
The atom’s period
- property residueName#
Returns the name of a residue in which the atom is
- property residueSequenceNumber#
Returns the sequence number of a residue in which the atom is
- property residueSequenceNumberString#
Returns the sequence number (as a string) of a residue in which the atom is
- property residueTypeString#
Returns the name of a residue in which the atom is
- property resonance#
The atom’s resonance
- property segmentName#
Returns the name of a segment in which the atom is
- property serialNumber#
The atom’s serial number
- property substructureName#
Returns the name of a substructure in which the atom is
- property substructureSequenceNumber#
Returns the sequence number of a substructure in which the atom is
- property substructureSequenceNumberString#
Returns the sequence number (as a string) of a substructure in which the atom is
- property temperatureFactor#
The atom’s temperature factor
- property vanDerWaalsRadius#
The atom’s van der Waals radius
- property waterFlag#
The atom’s water flag