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# 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) Constructed number positions.
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 Positions of O and OXT atoms.
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) Position of atom D 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 Position of C-beta atom 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 Transformation matrix 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 Rotation matrix 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. 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

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