tqchem.puckering¶

Classes¶

PuckeringFrame

Pucker coordinate frame.

Functions¶

`reference_coordinate_system`(→ tuple[numpy.array, ...)	Obtain x0, y0, z0 from the current geometry
`puckering_to_xyz`(→ tqchem.molgraph.MolecularSystem)	Transform puckering coordinates to xyz coordinates.
`xyz_to_puckering`(→ PuckeringFrame)	Transform xyz coordinates to puckering coordinates.
`pucker_coordinate_5ring`(→ list[PuckeringFrame])	Generate sets of values representing the most relevant conformers of a 5 ring
`pucker_coordinate_6ring_smart`(→ list[PuckeringFrame])	Selected generation of puckering points for 6 rings.
`pucker_coordinate_6ring`(→ list[PuckeringFrame])	Generate sets of values representing the most relevant conformers of a 5 ring
`planar_conformer`(→ PuckeringFrame)	Returns planar ring conformer
`is_planar_ring`(→ bool)

Module Contents¶

class tqchem.puckering.PuckeringFrame(x=..., y=..., q=..., phi=..., batframe=..., cycle=..., planar_only=...)¶

Pucker coordinate frame.

This class represents a frame in puckering coordinates.

Puckering is implemented according to: D. Cremer, J. Pople, https://doi.org/10.1021/ja00839a011

x¶

in-plane x-coordinates of each atom

Type:: np.ndarray

y¶

in-plane y-coordinates of each atom

Type:: np.ndarray

q¶

(n_atoms - 3) out-of-plane amplitudes

Type:: np.ndarray

phi¶

(n_atoms - 3) out-of-plane angles

Type:: np.ndarray

batframe¶

BATFrame connecting the ring to the rest of the molecule

Type:: BATFrame

cycle¶

list of atoms in the cycle

Type:: list[int]

planar_only¶

Should only the planar conformation be used?

Type:: bool

x: numpy.ndarray = Ellipsis¶

y: numpy.ndarray = Ellipsis¶

q: numpy.ndarray = Ellipsis¶

phi: numpy.ndarray = Ellipsis¶

batframe: tqchem.batframe.BATFrame = Ellipsis¶

cycle: list = Ellipsis¶

planar_only: bool = Ellipsis¶

update(frame) → None¶

variable_coordinates(molecule: tqchem.molgraph.MolecularSystem, **kwargs) → PuckeringFrame¶

Select coordinates for optimization of conformers.

This includes the all puckering coordinates and a batframe connecting it to possible other parts of the molecule described using BAT coordinates.

constant_coordinates(molecule: tqchem.molgraph.MolecularSystem) → PuckeringFrame¶

Get subset of coordinates which need to stay constant during conformer search

Only coordinates of the batframe which are not variable are added

grid = Ellipsis¶

make_grid(graph: networkx.Graph = None, shift_by_reference: bool = False)¶: Discretize coordinates of puckering frame for optimization.

evaluate_grid(indices: list[int])¶

Evaluate the puckering frame at a given grid index.

The first parameter in i will be used for the puckering frame and the remaining ones for the BAT frame.

grid_range()¶: Obtain ranges for each of the coordinates.

closest_gridpoint(molecule: tqchem.molgraph.MolecularSystem) → list[int]¶: Return the gridpoint most similar to the provided molecule

tqchem.puckering.reference_coordinate_system(mol: tqchem.molgraph.MolecularSystem, cycle: tuple[int, Ellipsis]) → tuple[numpy.array, numpy.array, numpy.array, numpy.array]¶: Obtain x0, y0, z0 from the current geometry

tqchem.puckering.puckering_to_xyz(mol: tqchem.molgraph.MolecularSystem, frame: PuckeringFrame) → tqchem.molgraph.MolecularSystem¶: Transform puckering coordinates to xyz coordinates.

tqchem.puckering.xyz_to_puckering(mol: tqchem.molgraph.MolecularSystem, cycle: tuple[int, Ellipsis]) → PuckeringFrame¶: Transform xyz coordinates to puckering coordinates.

tqchem.puckering.pucker_coordinate_5ring(reference: PuckeringFrame, amplitude: float = 0.8, n_phi: int = 12) → list[PuckeringFrame]¶

Generate sets of values representing the most relevant conformers of a 5 ring

As shown in Figure 1 of https://s3.smu.edu/dedman/catco/ring-puckering.html

By default, it creates 13 frames that generate all usual conformers, where each edge of the ring points up and down once and it includes a planar geometry

Parameters:

reference (PuckeringFrame) – reference frame to build the different ring conformers from
amplitude (float) – amplitude of the out-of-plane displacement
n_phi (int) – number of non-planar conformers created Specifies the discretization of the pseudorotational cycle shown in figure 1

tqchem.puckering.pucker_coordinate_6ring_smart(ref: PuckeringFrame, amplitude: float = 0.7, n_phi: float = 12, equatorial: bool = False, tropical: bool = False, planar: bool = True, axial: bool = True) → list[PuckeringFrame]¶

Selected generation of puckering points for 6 rings.

Select which parts of the puckering sphere should be included by setting the flags. Please see Fig. 2 of https://s3.smu.edu/dedman/catco/ring-puckering.html for reference.

axial: include 2 chair conformations planar: include planar conformation equatorial: include Boat conformation tropical: include envelope conformation

tqchem.puckering.pucker_coordinate_6ring(reference: PuckeringFrame, amplitude: float = 0.7, n_phi: int = 12, n_theta: int = 5) → list[PuckeringFrame]¶

Generate sets of values representing the most relevant conformers of a 5 ring

As shown in Figure 2 of https://s3.smu.edu/dedman/catco/ring-puckering.html

By default, it creates 39 frames that generate all usual conformers, including planar geometry, chair, twist, and boat conformations.

tqchem.puckering.planar_conformer(reference: PuckeringFrame) → PuckeringFrame¶: Returns planar ring conformer

tqchem.puckering.is_planar_ring(cycle: list[int], graph: networkx.Graph) → bool¶