morfeus.sterimol module#

Sterimol code.

class morfeus.sterimol.Sterimol(elements, coordinates, dummy_index, attached_index, radii=None, radii_type='crc', n_rot_vectors=3600, excluded_atoms=None, calculate=True)[source]#

Bases: object

Performs and stores results of Sterimol calculation.

Parameters:

  • elements (Iterable[int] | Iterable[str]) – Elements as atomic symbols or numbers

  • coordinates (ArrayLike2D) – Coordinates (Å)

  • dummy_index (int) – Index of dummy atom (1-indexed)

  • attached_index (int | Iterable[int]) – Index of attached atom of substituent (1-indexed). For a list of indices, a dummy atom is created at their geometric center

  • radii (ArrayLike1D | None) – List of radii (Å)

  • radii_type (str) – vdW radii type: ‘alvarez’, ‘bondi’, ‘crc’ or ‘truhlar’

  • n_rot_vectors (int) – Number of rotational vectors for determining B₁ and B₅

  • excluded_atoms (Sequence[int] | None) – Atom indices to exclude from the calculation

  • calculate (bool) – Whether to calculate the Sterimol parameters directly

B_1_value#

Sterimol B₁ value (Å)

Type:

float

B_1#

Sterimol B₁ vector (Å)

Type:

Any

B_5_value#

Sterimol B_5 value (Å)

Type:

float

B_5#

Sterimol B₅ vector (Å)

Type:

Any

bond_length#

Bond length between atom 1 and atom 2 (Å)

Type:

float

L_value_uncorrected#

Sterimol L value minus 0.40 (Å)

Type:

float

L_value#

Sterimol L value (Å)

Type:

float

L#

Sterimol L vector (Å)

Type:

Any

bury(sphere_radius=5.5, method='delete', radii_scale=0.5, density=0.01)[source]#

Do a Buried Sterimol calculation.

There are three available schemes based on deletion, truncation or slicing.

Parameters:

  • sphere_radius (float) – Radius of sphere (Å)

  • method (str) – Method for burying: ‘delete’, ‘slice’ or ‘truncate’

  • radii_scale (float) – Scale radii for metohd=’delete’ calculation

  • density (float) – Area per point on surface (Ų)

Returns:

Self

Return type:

self

Raises:

  • ValueError – When method is not specified correctly

  • Exception – When using method=’truncate’ and sphere is too small

calculate()[source]#

Calculate Sterimol parameters.

Return type:

Sterimol

print_report(verbose=False)[source]#

Prints the values of the Sterimol parameters.

Parameters:

verbose (bool) – Whether to print uncorrected L_value and bond length

Return type:

None

set_points(points, shift=True)[source]#

Set points for calculation of Sterimol.

Parameters:

  • points (Sequence[Sequence[float]]) – Points (Å)

  • shift (bool) – Whether to shift the points to have origin at dummy atom.

Returns:

Self

Return type:

self

surface_from_radii(density=0.01)[source]#

Create surface points from vdW surface.

Parameters:

density (float) – Area per point on surface (Ų)

Returns:

Self

Return type:

self

morfeus.sterimol.cli(file)[source]#

CLI for Sterimol.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any