definitions
XML handling for biomolecular residue topology definitions.
Code author: Jens Erik Nielsen
Code author: Todd Dolinsky
Code author: Yong Huang
- class pdb2pqr.definitions.Definition(aa_file, na_file, patch_file)[source]
Force field topology definitions.
The Definition class contains the structured definitions found in the files and several mappings for easy access to the information.
- class pdb2pqr.definitions.DefinitionAtom(name=None, x=None, y=None, z=None)[source]
Store force field atom topology definitions.
- __init__(name=None, x=None, y=None, z=None)[source]
Initialize class.
- Parameters
name (str) – atom name
x (float) – x-coordinate
y (float) – y-coordinate
z (float) – z-coordinate
- property is_backbone
Identify whether atom is in backbone.
- Returns
true if atom name is in backbone, otherwise false
- Return type
bool
- class pdb2pqr.definitions.DefinitionHandler[source]
Handle definition XML file content.