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Defaults

Defines various constants and default values related to atomic radii, contact distances, theta angle, contact definitions, and Gemmi supported formats.

Constants

VDW_RADII (dict): A dictionary that defines van der Waals radii for different atom types (currently only H is defined)

CONTACTS_DIST_MAX (float): Maximum distance for contacts.

THETA_REQUIRED (set): set of atom types that require theta for calculation.

CONTACTS (dict): A nested dictionary that defines different types of atom-atom interactions and their geometric parameters. The outer keys are the interaction types and the inner keys are the geometric parameters (distance, angle etc.) with their values.

GEMMI_SUPPRTED_FORMATS (set): set of file formats that are supported by Gemmi library.

CONTACTS_DIST_MAX module-attribute 

CONTACTS_DIST_MAX = 4.5

Type: float: Maximum distance for contacts.

CONTACTS module-attribute 

CONTACTS = {'hbond': {'distance': 3.9, 'polar distance': 3.5, 'angle rad': 1.57, 'angle degree': 90.0}, 'weak hbond': {'distance': 3.6, 'weak polar distance': 3.5, 'angle rad': 2.27, 'angle degree': 130.0, 'cx angle min rad': 0.52, 'cx angle min degree': 30.0, 'cx angle max rad': 2.62, 'cx angle max degree': 150.0}, 'aromatic': {'distance': 4.0, 'centroid_distance': 6.0, 'atom_aromatic_distance': 4.5, 'met_sulphur_aromatic_distance': 6.0}, 'amide': {'centroid_distance': 6.0, 'angle degree': 30.0, 'angle rad': 0.52}, 'xbond': {'catmap distance': 1.85, 'angle theta 1 rad': 2.09, 'angle theta 1 degree': 120.0, 'angle theta 2 min rad': 1.22, 'angle theta 2 max rad': 2.97, 'angle theta 2 min degree': 70.0, 'angle theta 2 max degree': 170.0}, 'ionic': {'distance': 4.0}, 'hydrophobic': {'distance': 4.5}, 'carbonyl': {'distance': 3.6}, 'metal': {'distance': 2.8}}

Type: dict: A nested dictionary that defines different types of atom-atom interactions and their geometric parameters. The outer keys are the interaction types and the inner keys are the geometric parameters (distance, angle etc.) with their values.

GEMMI_SUPPRTED_FORMATS module-attribute 

GEMMI_SUPPRTED_FORMATS = {'cif', 'mmcif', 'cif.gz', 'pdb', 'pdb.gz'}

Type: set: set of file formats that are supported by Gemmi library.