Geometry functions¶
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promod3.core.EvaluateGromacsPosRule(rule, number, anchors)¶ Constructs number positions with the given Gromacs rule and anchor positions (see Gromacs manual for details).
Parameters: Returns: Constructed number positions.
Return type: listofVec3
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promod3.core.ConstructCTerminalOxygens(c_pos, ca_pos, n_pos)¶ Constructs positions of O and OXT atoms for C terminal.
Parameters: Returns: Positions of O and OXT atoms.
Return type: tupleofVec3
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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: Returns: Position of atom D
Return type:
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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: Returns: Position of C-beta atom
Return type:
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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: Returns: Transformation matrix
Return type:
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promod3.core.RotationAroundLine(axis, angle) Creates a 3x3 matrix for a rotation by a specified angle around an axis going through the origin.
Parameters: Returns: Rotation matrix
Return type:
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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: RuntimeErrorif res does not contain N, CA and C atoms.
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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.
- n_stem (