morfeus.visible_volume module#

Visible volume code.

class morfeus.visible_volume.VisibleVolume(elements, coordinates, metal_index, include_hs=True, radii=None, radii_type='pyykko', radius=3.5, density=0.01)[source]#

Bases: object

Calculates and stores visible volume and area.

Parameters:

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

  • coordinates (ArrayLike2D) – Coordinates (Å)

  • metal_index (int) – Index of metal atom (1-indexed)

  • include_hs (bool) – Whether to include H atoms in the calculation

  • radii (ArrayLike1D | None) – Atomic radii (Å)

  • radii_type (str) – Radii type: ‘alvarez’, ‘bondi’, ‘crc’, ‘pyykko’, ‘rahm’ or ‘truhlar’

  • radius (float) – Radius of sphere to divide proximal and distal (Å)

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

distal_area#

Distal area (Ų)

Type:

float

distal_visible_area#

Distal visible area (Ų)

Type:

float

distal_visible_volume#

Distal visible volume (ų)

Type:

float

distal_volume#

Distal volume (ų)

Type:

float

invisible_area#

Invisible area (Ų)

Type:

float

invisible_volume#

Invisible volume (ų)

Type:

float

proximal_area#

Proximal area (Ų)

Type:

float

proximal_visible_area#

Proximal visible area (Ų)

Type:

float

proximal_visible_volume#

Proximal visible volume (ų)

Type:

float

proximal_volume#

Proximal volume (ų)

Type:

float

total_area#

Total area (Ų)

Type:

float

total_volume#

Total volume (ų)

Type:

float

visible_area#

Visible area (Ų)

Type:

float

visible_volume#

Visible volume (ų)

Type:

float

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

CLI for visible volume.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any