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 (Å²)

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 (Å²)

Type:: Any

point_volumes¶

Point volumes (Å³)

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 (Å³)

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 (Å²) for empty sphere and volume per point (Å³) 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 (Å²)

Type:: float

center¶

Coordinates for sphere center (Å)

Type:: Any

circumference¶

Circumference (Å)

Type:: float

density¶

Density of points (Å² or Å³)

Type:: float

points¶

Points in/on sphere (Å)

Type:: Any

radius¶

Radius (Å)

Type:: float

volume¶

Volume (Å³)

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:

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