definitions
¶
XML handling for biomolecular residue topology definitions.
Code author: Jens Erik Nielsen
Code author: Todd Dolinsky
Code author: Yong Huang
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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.
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class
pdb2pqr.definitions.
DefinitionAtom
(name=None, x=None, y=None, z=None)[source]¶ Store force field atom topology definitions.
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class
pdb2pqr.definitions.
DefinitionHandler
[source]¶ Handle definition XML file content.
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endElement
(name)[source]¶ End XML element parsing.
Parameters: name (str) – element name
Raises: - KeyError – for invalid atom or residue names
- RuntimeError – for unexpected XML features or format
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