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()

See also

Building

class samson.SBAtom(*args, **kwargs)#

Bases: SBStructuralNode

This class describes an atom in a structural model.

Overloaded function.

  1. __init__(self: samson.SBAtom) -> None

Constructs an atom of with the element type samson.SBElement.Unknown and the default position (0, 0, 0)

  1. __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

  1. __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:

  1. __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:
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:

samson.SBNodeIndexer

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:

samson.SBBond

getBondedAtoms(*args, **kwargs)#

Overloaded function.

  1. getBondedAtoms(self: samson.SBAtom) -> samson.SBNodeIndexer

Returns an indexer with all bonded atoms.

Returns:

The indexer of atoms bonded to this atom

Return type:

samson.SBNodeIndexer

  1. 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:

samson.SBNodeIndexer

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:

samson.SBNodeIndexer

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:

samson.SBColor

getComment(self: samson.SBAtom) → str#

Returns the atom’s comment

getConnectedComponent(*args, **kwargs)#

Overloaded function.

  1. 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:

samson.SBNodeIndexer

  1. 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:

samson.SBNodeIndexer

getMolecule(self: samson.SBAtom) → SBMStructuralModelNodeMolecule#

Returns a molecule in which the atom is

getNumberOfBondedAtoms(*args, **kwargs)#

Overloaded function.

  1. getNumberOfBondedAtoms(self: samson.SBAtom) -> int

Returns the number of bonded atoms

  1. 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.

  1. setCoarseGrainedMass(self: samson.SBAtom, mass: samson.SBQuantity.unitsSI) -> None

Set the coarse-grained atom’s mass

  1. 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