morfeus.buried_volume module#

Buried volume code.

class morfeus.buried_volume.BuriedVolume(elements, coordinates, metal_index, excluded_atoms=None, radii=None, include_hs=False, radius=3.5, radii_type='bondi', radii_scale=1.17, density=0.001, z_axis_atoms=None, xz_plane_atoms=None)[source]#

Bases: object

Performs and stores the results of a buried volume calculation.

Algorithm similar as to described in Organometallics 2016, 35, 2286.

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)

  • excluded_atoms (Sequence[int] | None) – Indices of atoms to exclude (1-indexed). Metal atom is always excluded and does not have to be given here.

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

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

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

  • radii_type (str) – Type of radii to use: ‘alvarez’, ‘bondi’, ‘crc’ or ‘truhlar’

  • radii_scale (float) – Scaling factor for radii

  • density (float) – Volume per point in the sphere (ų)

  • z_axis_atoms (Sequence[int] | None) – Atom indices for deciding orientation of z axis (1-indexed)

  • xz_plane_atoms (Sequence[int] | None) – Atom indices for deciding orientation of xz plane (1-indexed)

buried_volume#

Buried volume of sphere (ų)

Type:

float

distal_volume#

Distal volume of ligand (ų)

Type:

float

fraction_buried_volume#

Fraction buried volume of sphere

Type:

float

free_volume#

Free volume of sphere (ų)

Type:

float

octants#

Results for octant analysis

Type:

dict[str, dict[int, float]]

quadrants#

Results for quadrant analysis

Type:

dict[str, dict[int, float]]

compute_distal_volume(method='sasa', octants=False, sasa_density=0.01)[source]#

Computes the distal volume.

Uses either SASA or Buried volume with large radius to calculate the molecular volume.

Parameters:

  • method (str) – Method to get total volume: ‘buried_volume’ or ‘sasa’

  • octants (bool) – Whether to compute distal volume for quadrants and octants. Requires method=’buried_volume’

  • sasa_density (float) – Density of points on SASA surface. Ignored unless method=’sasa’

Returns:

Self

Return type:

self

Raises:

ValueError – When method is not specified correctly.

octant_analysis()[source]#

Perform octant analysis of the buried volume.

Return type:

BuriedVolume

property percent_buried_volume: float#

Deprecated attribute. Use ‘fraction_buried_volume’ instead.

print_report()[source]#

Prints a report of the buried volume.

Return type:

None

morfeus.buried_volume.OCTANT_SIGNS: dict[int, str] = {0: '+,+,+', 1: '-,+,+', 2: '-,-,+', 3: '+,-,+', 4: '+,-,-', 5: '-,-,-', 6: '-,+,-', 7: '+,+,-'}#

Conventional signs for octants.

morfeus.buried_volume.QUADRANT_NAMES: dict[int, str] = {1: 'NE', 2: 'NW', 3: 'SW', 4: 'SE'}#

Conventional names for quadrants.

morfeus.buried_volume.QUADRANT_OCTANT_MAP: dict[int, tuple[int, int]] = {1: (0, 7), 2: (1, 6), 3: (2, 5), 4: (3, 4)}#

Map from quadrants to octants.

morfeus.buried_volume.QUADRANT_SIGNS: dict[int, str] = {1: '+,+', 2: '-,+', 3: '-,-', 4: '+,-'}#

Coventional signs for quadrants.

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

CLI for buried volume.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any