morfeus.geometry module#

Help classes and functions related to geometry.

class morfeus.geometry.Angle(atom_1, atom_2, atom_3)[source]#

Bases: object

Bond internal coordinate.

Code adapted from pyberny: https://github.com/jhrmnn/pyberny.

Parameters:

  • atom_1 (int) – Index of atom 1 (1-indexed)

  • atom_2 (int) – Index of atom 2 (1-indexed)

  • atom_3 (int) – Index of atom 3 (1-indexed)

i#

Index of atom 1 (1-indexed)

Type:

int

j#

Index of atom 2 (1-indexed)

Type:

int

k#

Index of atom 3 (1-indexed)

Type:

int

get_b_vector(coordinates)[source]#

Calculate vector of B matrix for internal coordinate.

Code adapted from pyberny: https://github.com/jhrmnn/pyberny.

Parameters:

coordinates (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Coordinates (Å)

Returns:

Vector of B matrix (a.u.)

Return type:

b_vector

class morfeus.geometry.Atom(element, coordinates, radius, index)[source]#

Bases: object

Atom common for morfeus calculations.

Parameters:

  • element (int) – Atomic number (starting from 1)

  • coordinates (Any) – Coordinates (Å)

  • radius (float) – vdW radius (Å)

  • index (int) – Atom index (starting from 1)

accessible_mask#

Boolean mask for accessible points

Type:

Any

accessible_points#

Points accessible to solvent (Å)

Type:

Any

area#

Solvent-accessible surface area (Ų)

Type:

float

cone#

Cone tangent to atom

Type:

morfeus.geometry.Cone

coordinates#

Coordinates (Å)

Type:

Any

coordination_number#

Coordination number

Type:

float

element#

Atomic number (1-indexed)

Type:

int

index#

Atom index (1-indexed)

Type:

int

invisible_mask#

Boolean mask for invisible points

Type:

Any

occluded_mask#

Boolean mask for occluded points

Type:

Any

occluded_points#

Points occluded by other atoms (Å)

Type:

Any

p_values#

P values

Type:

Any

point_areas#

Point areas (Ų)

Type:

Any

point_volumes#

Point volumes (ų)

Type:

Any

point#

Points (Å)

proximal_mask#

Boolean mask for proximal points

Type:

Any

radius#

vdW radius (Å)

Type:

float

volume#

Volume inside solvent-accessible surface area (ų)

Type:

float

get_cone()[source]#

Construct cone for atom.

Return type:

None

class morfeus.geometry.Bond(atom_1, atom_2)[source]#

Bases: object

Bond internal coordinate.

Parameters:

  • atom_1 (int) – Index of atom 1 (1-indexed)

  • atom_2 (int) – Index of atom 2 (1-indexed)

i#

Index of atom 1 (1-indexed)

Type:

int

j#

Index of atom 2 (1-indexed)

Type:

int

get_b_vector(coordinates)[source]#

Calculate vector of B matrix for internal coordinate.

Code adapted from pyberny: https://github.com/jhrmnn/pyberny.

Parameters:

coordinates (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Coordinates (Å)

Returns:

Vector of B matrix (a.u.)

Return type:

b_vector

class morfeus.geometry.Cone(angle, atoms, normal)[source]#

Bases: object

Cone used in cone angle calculations.

Parameters:

  • angle (float) – Cone angle (rad)

  • atoms (list[Atom]) – Atoms that are tangent to cone (1-indexed)

  • normal (Any) – Normal vector of cone

angle#

Cone angle (rad)

Type:

float

atoms#

Atoms that are tangent to cone (1-indexed)

Type:

list[morfeus.geometry.Atom]

normal#

Normal vector of cone

Type:

Any

is_inside(atom)[source]#

Tests if atom lies inside the cone.

Parameters:

atom (Atom) – Atom to test.

Returns:

True if inside, False if outside.

Return type:

bool

is_inside_points(points, method='cross')[source]#

Test if points are inside cone of atom.

Parameters:

  • points (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Points to check (Å)

  • method (str) – Method for testing: ‘angle’, ‘cross’ or ‘dot’

Returns:

Boolean array with points marked as inside

Return type:

is_inside

Raises:

ValueError – When method not supported

class morfeus.geometry.Dihedral(atom_1, atom_2, atom_3, atom_4)[source]#

Bases: object

Bond internal coordinate.

Code adapted from pyberny: https://github.com/jhrmnn/pyberny.

Parameters:

  • atom_1 (int) – Index of atom 1 (1-indexed)

  • atom_2 (int) – Index of atom 2 (1-indexed)

  • atom_3 (int) – Index of atom 3 (1-indexed)

  • atom_4 (int) – Index of atom 4 (1-indexed)

i#

Index of atom 1 (1-indexed)

Type:

int

j#

Index of atom 2 (1-indexed)

Type:

int

k#

Index of atom 3 (1-indexed)

Type:

int

l#

Index of atom 4 (1-indexed)

Type:

int

get_b_vector(coordinates)[source]#

Calculate vector of B matrix for internal coordinate.

Code adapted from pyberny: https://github.com/jhrmnn/pyberny.

Parameters:

coordinates (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Coordinates (Å)

Returns:

Vector of B matrix (a.u.)

Return type:

b_vector

class morfeus.geometry.InternalCoordinates[source]#

Bases: object

Internal coordinates.

internal_coordinates#

Internal coordinates

Type:

list[Bond | Angle | Dihedral]

add_angle(atom_1, atom_2, atom_3)[source]#

Add angle to internal coordinates.

Parameters:

  • atom_1 (int) – Index of atom 1 (1-indexed)

  • atom_2 (int) – Index of atom 2 (1-indexed)

  • atom_3 (int) – Index of atom 3 (1-indexed)

Return type:

None

add_bond(atom_1, atom_2)[source]#

Add bonds to internal coordinates.

Parameters:

  • atom_1 (int) – Index of atom 1 (1-indexed)

  • atom_2 (int) – Index of atom 2 (1-indexed)

Return type:

None

add_dihedral(atom_1, atom_2, atom_3, atom_4)[source]#

Add dihedral angle to internal coordinates.

Parameters:

  • atom_1 (int) – Index of atom 1 (1-indexed)

  • atom_2 (int) – Index of atom 2 (1-indexed)

  • atom_3 (int) – Index of atom 3 (1-indexed)

  • atom_4 (int) – Index of atom 4 (1-indexed)

Return type:

None

add_internal_coordinate(atoms)[source]#

Add internal coordinate automatically depending on number of atoms.

Parameters:

atoms (Sequence[int]) – Sequence of atom indices (1-index).

Return type:

None

detect_bonds(coordinates, elements, radii=None, radii_type='pyykko', scale_factor=1.2)[source]#

Detect bonds based on covalent radii cutoffs.

Parameters:

  • coordinates (ArrayLike2D) –

  • elements (Iterable[int] | Iterable[str] | None) –

  • radii (ArrayLike1D | None) –

  • radii_type (str) –

  • scale_factor (float) –

Return type:

None

get_B_matrix(coordinates)[source]#

Calculate B matrix for coordinates.

Parameters:

coordinates (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Coordinates (Å)

Returns:

B matrix

Return type:

B_matrix

class morfeus.geometry.Sphere(center, radius, density=0.005, method='fibonacci', filled=False)[source]#

Bases: object

Sphere class for creating and holding points on vdW surface.

Parameters:

  • center (Any) – Coordinates for center (Å)

  • density (float) – Area per point (Ų) for empty sphere and volume per point (ų) for filled sphere.

  • filled (bool) – Whether a sphere with internal points should be constructed (works only with method=’projection’)

  • method (str) – Method for generating points: ‘fibonacci’, ‘polar’ or ‘projection’

  • radius (float) – Radius (Å)

area#

Area (Ų)

Type:

float

center#

Coordinates for sphere center (Å)

Type:

Any

circumference#

Circumference (Å)

Type:

float

density#

Density of points (Ų or ų)

Type:

float

points#

Points in/on sphere (Å)

Type:

Any

radius#

Radius (Å)

Type:

float

volume#

Volume (ų)

Type:

float

morfeus.geometry.kabsch_rotation_matrix(P, Q, center=True)[source]#

Construct Kabsch rotation matrix.

Constructs the rotation matrix that overlays the points in P with the points in Q with minimum RMSD. https://en.wikipedia.org/wiki/Kabsch_algorithm

Parameters:

  • P (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Coordinates to be rotated

  • Q (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Reference coordinates

  • center (bool) – Whether to center P and Q at origin.

Returns:

Rotation matrix

Return type:

R

morfeus.geometry.rotate_coordinates(coordinates, vector, axis)[source]#

Rotates coordinates by the rotation that aligns vector with axis.

Parameters:

  • axis (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Reference vector to align input vector with

  • coordinates (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Coordinates to rotate

  • vector (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Vector to align

Returns:

Rotated coordinates.

Return type:

rotated_coordinates

morfeus.geometry.sphere_line_intersection(vector, center, radius)[source]#

Get points of intersection between line and sphere.

Follows the procedure outlined here: http://paulbourke.net/geometry/circlesphere/.

Parameters:

  • vector (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Vector giving direction of line

  • center (_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]) – Center of sphere

  • radius (float) – Radius of sphere

Returns:

Intersection points

Return type:

intersection_points