rmgpy.molecule.Atom

class rmgpy.molecule.Atom

An atom. The attributes are:

Attribute	Type	Description
atomtype	AtomType	The atom type
element	Element	The chemical element the atom represents
radical_electrons	short	The number of radical electrons
charge	short	The formal charge of the atom
label	str	A string label that can be used to tag individual atoms
coords	numpy array	The (x,y,z) coordinates in Angstrom
lone_pairs	short	The number of lone electron pairs
id	int	Number assignment for atom tracking purposes
bonds	dict	Dictionary of bond objects with keys being neighboring atoms
props	dict	Dictionary for storing additional atom properties
mass	int	atomic mass of element (read only)
number	int	atomic number of element (read only)
symbol	str	atomic symbol of element (read only)
site	str	type of adsorption site
morphology	str	morphology of the adsorption site

Additionally, the mass, number, and symbol attributes of the atom’s element can be read (but not written) directly from the atom object, e.g. atom.symbol instead of atom.element.symbol.

apply_action(action)

Update the atom pattern as a result of applying action, a tuple containing the name of the reaction recipe action along with any required parameters. The available actions can be found here.

copy()

Generate a deep copy of the current atom. Modifying the attributes of the copy will not affect the original.

decrement_charge()

Update the atom pattern as a result of applying a LOSE_CHARGE action

decrement_lone_pairs()

Update the lone electron pairs pattern as a result of applying a LOSE_PAIR action.

decrement_radical()

Update the atom pattern as a result of applying a LOSE_RADICAL action, where radical specifies the number of radical electrons to remove.

equivalent(other, strict=True)

Return True if other is indistinguishable from this atom, or False otherwise. If other is an Atom object, then all attributes except label and ‘ID’ must match exactly. If other is an GroupAtom object, then the atom must match any of the combinations in the atom pattern. If strict is False, then only the element is compared and electrons are ignored.

get_total_bond_order()

This helper function is to help calculate total bond orders for an input atom.

Some special consideration for the order B bond. For atoms having three B bonds, the order for each is 4/3.0, while for atoms having other than three B bonds, the order for each is 3/2.0

increment_charge()

Update the atom pattern as a result of applying a GAIN_CHARGE action

increment_lone_pairs()

Update the lone electron pairs pattern as a result of applying a GAIN_PAIR action.

increment_radical()

Update the atom pattern as a result of applying a GAIN_RADICAL action, where radical specifies the number of radical electrons to add.

is_bonded_to_halogen()

Return True if the atom is bonded to at least one halogen (F, Cl, Br, or I) False if it is not

is_bonded_to_surface()

Return True if the atom is bonded to a surface atom X False if it is not

is_bromine()

Return True if the atom represents a bromine atom or False if not.

is_carbon()

Return True if the atom represents a carbon atom or False if not.

is_chlorine()

Return True if the atom represents a chlorine atom or False if not.

is_electron()

Return True if the atom represents an electron or False if not.

is_fluorine()

Return True if the atom represents a fluorine atom or False if not.

is_halogen()

Return True if the atom represents a halogen atom (F, Cl, Br, I) False if it does.

is_hydrogen()

Return True if the atom represents a hydrogen atom or False if not.

is_iodine()

Return True if the atom represents an iodine atom or False if not.

is_lithium()

Return True if the atom represents a hydrogen atom or False if not.

is_nitrogen()

Return True if the atom represents a nitrogen atom or False if not.

is_non_hydrogen()

Return True if the atom does not represent a hydrogen atom or False if it does.

is_nos()

Return True if the atom represent either nitrogen, sulfur, or oxygen False if it does not.

is_oxygen()

Return True if the atom represents an oxygen atom or False if not.

is_phosphorus()

Return True if the atom represents a phosphorus atom or False if not.

is_proton()

Return True if the atom represents a proton or False if not.

is_silicon()

Return True if the atom represents a silicon atom or False if not.

is_specific_case_of(other)

Return True if self is a specific case of other, or False otherwise. If other is an Atom object, then this is the same as the equivalent() method. If other is an GroupAtom object, then the atom must match or be more specific than any of the combinations in the atom pattern.

is_sulfur()

Return True if the atom represents a sulfur atom or False if not.

is_surface_site()

Return True if the atom represents a surface site or False if not.

reset_connectivity_values()

Reset the cached structure information for this vertex.

set_lone_pairs(lone_pairs)

Set the number of lone electron pairs.

sorting_key

Returns a sorting key for comparing Atom objects. Read-only

update_charge()

Update self.charge, according to the valence, and the number and types of bonds, radicals, and lone pairs.