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