Geometry functions¶

promod3.core.EvaluateGromacsPosRule(rule, number, anchors)¶

Constructs number positions with the given Gromacs rule and anchor positions (see Gromacs manual for details).

Parameters:

• rule (int) – Gromacs rule

• number (int) – Desired number of positions (max. 3)

• anchors (list of Vec3) – Anchor positions (max. 4)

Returns:

Constructed number positions.

Return type:

list of Vec3

promod3.core.ConstructCTerminalOxygens(c_pos, ca_pos, n_pos)¶

Constructs positions of O and OXT atoms for C terminal.

Parameters:

• c_pos (Vec3) – Position of C atom

• n_pos (Vec3) – Position of nitrogen atom

• ca_pos (Vec3) – Position of C-alpha atom

Returns:

Positions of O and OXT atoms.

Return type:

tuple of Vec3

promod3.core.ConstructAtomPos(A, B, C, bond_length, angle, dihedral)¶

Constructs position of atom “D” based on bond length (C-D), angle (B-C-D) and dihedral (A-B-C-D).

Parameters:

• A (Vec3) – Position of atom A

• B (Vec3) – Position of atom B

• C (Vec3) – Position of atom C

• bond_length (float) – Bond length (C-D)

• angle (float) – Angle (B-C-D)

• dihedral (float) – Dihedral (A-B-C-D)

Returns:

Position of atom D

Return type:

Vec3

promod3.core.ConstructCBetaPos(n_pos, ca_pos, c_pos)¶

Constructs position of C-beta atom given the positions of the backbone nitrogen, C-alpha and C atoms.

Parameters:

• n_pos (Vec3) – Position of nitrogen atom

• ca_pos (Vec3) – Position of C-alpha atom

• c_pos (Vec3) – Position of C atom

Returns:

Position of C-beta atom

Return type:

Vec3

promod3.core.RotationAroundLine(axis, anchor, angle)¶

Creates a geometric transform leading to a rotation with specified angle around a line defined by axis and anchor.

Parameters:

• axis (Vec3) – Axis of rotation

• anchor (Vec3) – Anchor for rotation

• angle (float) – Angle (in radians in range [-pi,pi]) of rotation

Returns:

Transformation matrix

Return type:

Mat4

promod3.core.RotationAroundLine(axis, angle)¶

Creates a 3x3 matrix for a rotation by a specified angle around an axis going through the origin.

Parameters:

• axis (Vec3) – Axis of rotation

• angle (float) – Angle (in radians in range [-pi,pi]) of rotation

Returns:

Rotation matrix

Return type:

Mat3

class promod3.core.StemCoords¶

class promod3.core.StemCoords(res)

Simple container class to store N, CA and C coordinates.

Parameters:

res (ost.mol.ResidueHandle) – Residue handle from which to extract N, CA and C coordinates.

Raises:

RuntimeError if res does not contain N, CA and C atoms.

n_coord¶

ca_coord¶

c_coord¶

Position of nitrogen / alpha carbon / carbon atom.

Type:

Vec3

class promod3.core.StemPairOrientation¶

class promod3.core.StemPairOrientation(n_stem, c_stem)

Relative orientation of a pair of stems. Can be used to define gaps with four angles and one distance and is used in the fragment database for fast lookups.

Parameters:

• n_stem (StemCoords) – Coordinates of stem A.

• c_stem (StemCoords) – Coordinates of stem B.

distance¶

Distance of C atom of stem A to N atom of stem B.

Type:

float

angle_one¶

angle_two¶

Angles defining relative orientation of stem B with respect to stem A.

Type:

float

angle_three¶

angle_four¶

Angles defining relative orientation of stem A with respect to stem B.

Type:

float