Atoms#
- class autode.atoms.Atom(atomic_symbol: str, x: Any = 0.0, y: Any = 0.0, z: Any = 0.0, atom_class: int | None = None, partial_charge: float | None = None)#
- __init__(atomic_symbol: str, x: Any = 0.0, y: Any = 0.0, z: Any = 0.0, atom_class: int | None = None, partial_charge: float | None = None)#
Atom class. Centered at the origin by default. Can be initialised from positional or keyword arguments:
>>> import autode as ade >>> ade.Atom('H') Atom(H, 0.0000, 0.0000, 0.0000) >>> >>> ade.Atom('H', x=1.0, y=1.0, z=1.0) Atom(H, 1.0000, 1.0000, 1.0000) >>> >>> ade.Atom('H', 1.0, 1.0, 1.0) Atom(H, 1.0000, 1.0000, 1.0000)
- Parameters:
y – y coordinate in 3D space (Å)
z – z coordinate in 3D space (Å)
atom_class – Fictitious additional labels to distinguish otherwise identical atoms. Useful in finding bond isomorphisms over identity reactions
partial_charge – Partial atomic charge in units of e, determined by the atomic envrionment. Not an observable property.
- property atomic_number: int#
Atomic numbers are the position in the elements (indexed from zero), plus one. Example:
>>> import autode as ade >>> atom = ade.Atom('C') >>> atom.atomic_number 6
- property atomic_symbol: str#
A more interpretable alias for Atom.label. Should be present in the elements. Example:
>>> import autode as ade >>> atom = ade.Atom('Zn') >>> atom.atomic_symbol 'Zn'
- property coord: Coordinate#
Position of this atom in space. Coordinate has attributes x, y, z for the Cartesian displacements. Example:
>>> import autode as ade >>> atom = ade.Atom('H') >>> atom.coord Coordinate([0. 0. 0.] Å)
To initialise at a different position away from the origin
>>> ade.Atom('H', x=1.0).coord Coordinate([1. 0. 0.] Å) >>> ade.Atom('H', x=1.0).coord.x 1.0
Coordinates are instances of autode.values.ValueArray, so can be converted from the default angstrom units to e.g. Bohr
>>> ade.Atom('H', x=1.0, y=-1.0).coord.to('a0') Coordinate([1.889 -1.889 0. ] bohr)
- property covalent_radius: Distance#
Covalent radius for this atom. Example:
>>> import autode as ade >>> ade.Atom('H').covalent_radius Distance(0.31 Å)
- property group: int#
Group of the periodic table is this atom in. 0 if not found. Example:
>>> import autode as ade >>> ade.Atom('C').group 14
- property is_metal: bool#
Is this atom a metal? Defines metals to be up to and including: Ga, Sn, Bi. Example:
>>> import autode as ade >>> ade.Atom('C').is_metal False >>> ade.Atom('Zn').is_metal True
- is_pi(valency: int) bool#
Determine if this atom is a ‘π-atom’ i.e. is unsaturated. Only approximate! Example:
>>> import autode as ade >>> ade.Atom('C').is_pi(valency=3) True >>> ade.Atom('H').is_pi(valency=1) False
- Return type:
(bool)
- property mass: Mass#
Alias of weight. Returns Atom.weight an so can be converted to different units. For example, to convert the mass to electron masses:
>>> import autode as ade >>> ade.Atom('H').mass.to('me') Mass(1837.36222 m_e)
- property maximal_valance: int#
The maximum/maximal valance that this atom supports in any charge state (most commonly). i.e. for H the maximal_valance=1. Useful for generating molecular graphs
- property period: int#
Period of the periodic table is this atom in. 0 if not found. Example:
>>> import autode as ade >>> ade.Atom('C').period 2
- rotate(axis: ndarray | Sequence, theta: Angle | float, origin: ndarray | Sequence | None = None) None#
Rotate this atom theta radians around an axis given an origin. By default the rotation is applied around the origin with the angle in radians (unless an autode.values.Angle). Rotation is applied in place. To rotate a H atom around the z-axis:
>>> import autode as ade >>> atom = ade.Atom('H', x=1.0) >>> atom.rotate(axis=[0.0, 0.0, 1.0], theta=3.14) >>> atom.coord Coordinate([-1. 0. 0.] Å)
With an origin:
>>> import autode as ade >>> atom = ade.Atom('H') >>> atom.rotate(axis=[0.0, 0.0, 1.0], theta=3.14, origin=[1.0, 0.0, 0.0]) >>> atom.coord Coordinate([2. 0. 0.] Å)
And with an angle not in radians:
>>> import autode as ade >>> from autode.values import Angle >>> >>> atom = ade.Atom('H', x=1.0) >>> atom.rotate(axis=[0.0, 0.0, 1.0], theta=Angle(180, units='deg')) >>> atom.coord Coordinate([-1. 0. 0.] Å)
- Parameters:
origin – Rotate about this origin. shape = (3,) if no origin is specified then the atom is rotated without translation.
- property tm_row: int | None#
Row of transition metals that this element is in. Returns None if this atom is not a metal. Example:
>>> import autode as ade >>> ade.Atom('Zn').tm_row 1
- translate(*args, **kwargs) None#
Translate this atom by a vector in place. Arguments should be coercible into a coordinate (i.e. length 3). Example:
>>> import autode as ade >>> atom = ade.Atom('H') >>> atom.translate(1.0, 0.0, 0.0) >>> atom.coord Coordinate([1. 0. 0.] Å)
Atoms can also be translated using numpy arrays:
>>> import autode as ade >>> import numpy as np >>> >>> atom = ade.Atom('H') >>> atom.translate(np.ones(3)) >>> atom.coord Coordinate([1. 1. 1.] Å) >>> >>> atom.translate(vec=-atom.coord) >>> atom.coord Coordinate([0. 0. 0.] Å)
- Keyword Arguments:
vec (np.ndarray) – Shape = (3,)
- class autode.atoms.AtomCollection(atoms: List[Atom] | Atoms | None = None)#
- __init__(atoms: List[Atom] | Atoms | None = None)#
Collection of atoms, used as a base class for a species, complex or transition state.
- angle(i: int, j: int, k: int) Angle#
Angle between three atoms i-j-k, where the atoms are indexed from zero:
E_i --- E_j \ θ E_k
Example:
>>> from autode import Atom, Molecule >>> h2o = Molecule(atoms=[Atom('H', x=-1), Atom('O'), Atom('H', x=1)]) >>> h2o.angle(0, 1, 2).to('deg') Angle(180.0 °)
- Parameters:
j (int) – — middle
k (int) – — right
- Returns:
Angle
- Return type:
- Raises:
(ValueError) – If any of the atom indexes are not present
- property com: Coordinate | None#
Centre of mass of this atom collection
- Raises:
(ValueError) – If there are no atoms
- property coordinates: Coordinates | None#
Numpy array of coordinates
- dihedral(w: int, x: int, y: int, z: int) Angle#
Dihedral angle between four atoms (x, y, z, w), where the atoms are indexed from zero:
E_w --- E_x \ φ \ E_y ---- E_z
Example:
>>> from autode import Atom, Molecule >>> h2s2 = Molecule(atoms=[Atom('S', 0.1527, 0.9668, -0.9288), ... Atom('S', 2.0024, 0.0443, -0.4227), ... Atom('H', -0.5802, 0.0234, -0.1850), ... Atom('H', 2.1446, 0.8424, 0.7276)]) >>> h2s2.dihedral(2, 0, 1, 3).to('deg') Angle(-90.0 °)
- Parameters:
x (int) – – second –
y (int) – – third –
z (int) – – fourth –
- Returns:
Dihedral angle
- Return type:
- Raises:
(ValueError) – If any of the atom indexes are not present in the molecule
- property moi: MomentOfInertia | None#
Moment of inertia matrix (I)
- property n_atoms: int#
Number of atoms in this collection
- class autode.atoms.Atoms(iterable=(), /)#
- are_linear(angle_tol: ~autode.values.Angle = Angle(1.0 °)) bool#
Are these set of atoms colinear?
- Returns:
Whether the atoms are linear
- Return type:
(bool)
- are_planar(distance_tol: ~autode.values.Distance = Distance(0.001 Å)) bool#
Do all the atoms in this set lie in a single plane?
- Return type:
(bool)
- property com: Coordinate#
Centre of mass of these coordinates
\[\text{COM} = \frac{1}{M} \sum_i m_i R_i\]where M is the total mass, m_i the mass of atom i and R_i it’s coordinate
- property contain_metals: bool#
Do these atoms contain at least a single metal atom?
- property coordinates: Coordinates#
- distance(i: int, j: int) Distance#
Distance between two atoms (Å), indexed from 0.
>>> import autode as ade >>> mol = ade.Molecule(atoms=[ade.Atom('H'), ade.Atom('H', x=1.0)]) >>> mol.distance(0, 1) Distance(1.0 Å)
- Parameters:
j (int) – Atom index of the second atom
- Returns:
Distance
- Return type:
- Raises:
(ValueError) –
- eqm_bond_distance(i: int, j: int) Distance#
Equilibrium distance between two atoms. If known then use the experimental dimer distance, otherwise estimate if from the covalent radii of the two atoms. Example
Example:
>>> import autode as ade >>> mol = ade.Molecule(atoms=[ade.Atom('H'), ade.Atom('H')]) >>> mol.distance(0, 1) Distance(0.0 Å) >>> mol.eqm_bond_distance(0, 1) Distance(0.741 Å)
- idxs_are_present(*args: int) bool#
Are all these indexes present in this set of atoms
- property moi: MomentOfInertia#
Moment of inertia matrix (I):
(I_00 I_01 I_02) I = (I_10 I_11 I_12) (I_20 I_21 I_22)
- Return type:
- nvector(i: int, j: int) ndarray#
Normalised vector from atom i to atom j
- Parameters:
j (int)
- Return type:
(np.ndarray)
- Raises:
(IndexError) – If i or j are not present
- remove_dummy() None#
Remove all the dummy atoms from this list of atoms
- vector(i: int, j: int) ndarray#
Vector from atom i to atom j
- Parameters:
j (int)
- Return type:
(np.ndarray)
- Raises:
(IndexError) – If i or j are not present
- class autode.atoms.DummyAtom(x, y, z)#
- __init__(x, y, z)#
Dummy atom
- Parameters:
y (float) – y
z (float) – z
- property atomic_number#
The atomic number is defined as 0 for a dummy atom
- class autode.atoms.PeriodicTable#
- actinides = array(['Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr'], dtype='<U2')#
- actinoids = array(['Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr'], dtype='<U2')#
- classmethod element(period: int, group: int)#
Element given it’s index in the periodic table, excluding lanthanides and actinides.
- Parameters:
group (int)
- Returns:
Atomic symbol of the element
- Return type:
(str)
- Raises:
(IndexError) – If such an element does not exist
- classmethod group(n: int)#
Group of the periodic table, with 1 being the first period
- Return type:
(np.ndarray(str))
- Raises:
(ValueError) – If n is not valid group index
- lanthanides = array(['La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu'], dtype='<U2')#
- lanthanoids = array(['La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu'], dtype='<U2')#
- classmethod period(n: int)#
Period of the periodic table, with 1 being the first period
- Return type:
(np.ndarray(str))
- Raises:
(ValueError) – If n is not valid period index
- table = array([['H', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', 'He'], ['Li', 'Be', '', '', '', '', '', '', '', '', '', '', 'B', 'C', 'N', 'O', 'F', 'Ne'], ['Na', 'Mg', '', '', '', '', '', '', '', '', '', '', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar'], ['K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr'], ['Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe'], ['Cs', 'Ba', '', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn'], ['Fr', 'Ra', '', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']], dtype='<U2')#
- classmethod transition_metals(row: int)#
Collection of transition metals (TMs) of a defined row. e.g.
row = 1 -> [Sc, Ti .. Zn]
- Return type:
(np.ndarray(str))
- Raises:
(ValueError) – If the row is not valid
- autode.atoms.vdw_radii = {'Ac': 2.47, 'Ag': 2.11, 'Al': 1.84, 'Am': 2.44, 'Ar': 1.88, 'As': 1.85, 'At': 2.02, 'Au': 2.14, 'B': 1.92, 'Ba': 2.68, 'Be': 1.53, 'Bi': 2.07, 'Bk': 2.44, 'Br': 1.85, 'C': 1.7, 'Ca': 2.31, 'Cd': 2.18, 'Ce': 2.42, 'Cf': 2.45, 'Cl': 1.75, 'Cm': 2.45, 'Co': 2.0, 'Cr': 2.06, 'Cs': 3.43, 'Cu': 1.96, 'Dy': 2.31, 'Er': 2.29, 'Es': 2.45, 'Eu': 2.35, 'F': 1.47, 'Fe': 2.04, 'Fm': 2.45, 'Fr': 3.48, 'Ga': 1.87, 'Gd': 2.34, 'Ge': 2.11, 'H': 1.1, 'He': 1.4, 'Hf': 2.23, 'Hg': 2.23, 'Ho': 2.3, 'I': 1.98, 'In': 1.93, 'Ir': 2.13, 'K': 2.75, 'Kr': 2.02, 'La': 2.43, 'Li': 1.82, 'Lr': 2.46, 'Lu': 2.24, 'Md': 2.46, 'Mg': 1.73, 'Mn': 2.05, 'Mo': 2.17, 'N': 1.55, 'Na': 2.27, 'Nb': 2.18, 'Nd': 2.39, 'Ne': 1.54, 'Ni': 1.97, 'No': 2.46, 'Np': 2.39, 'O': 1.52, 'Os': 2.16, 'P': 1.8, 'Pa': 2.43, 'Pb': 2.02, 'Pd': 2.1, 'Pm': 2.38, 'Po': 1.97, 'Pr': 2.4, 'Pt': 2.13, 'Pu': 2.43, 'Ra': 2.83, 'Rb': 3.03, 'Re': 2.16, 'Rh': 2.1, 'Rn': 2.2, 'Ru': 2.13, 'S': 1.8, 'Sb': 2.06, 'Sc': 2.15, 'Se': 1.9, 'Si': 2.1, 'Sm': 2.36, 'Sn': 2.17, 'Sr': 2.49, 'Ta': 2.22, 'Tb': 2.33, 'Tc': 2.16, 'Te': 2.06, 'Th': 2.45, 'Ti': 2.11, 'Tl': 1.96, 'Tm': 2.27, 'U': 2.41, 'V': 2.07, 'W': 2.18, 'Xe': 2.16, 'Y': 2.32, 'Yb': 2.26, 'Zn': 2.01, 'Zr': 2.23}#
Although a π-bond may not be well defined, it is useful to have a notion of a bond about which there is restricted rotation. The below sets are used to define which atoms may be π-bonded to another