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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)
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:
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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