Class Substrate

An instance stores required information about a substrate molecule and supplies APIs for later retrieval. At the class level, a record of active objects is kept, and some methods may access this container-like functionality.

Instance Methods

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__init__(self, rules, st, atom_indices, fname, findx, fpos=None)
rules is a JoiningRules object, st a Structure object, attachments an iterable of attachment heavy atoms of the structure, fname the originating file name, findx the index of the st in the file (origin 1), fpos the file offset of the structure.

__del__(self)

Class Methods

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readFile(cls, mae_fname, joining_rules_fname, possible_linker)
Create objects from the structures in mae_fname.

Class Variables

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substrates = []

__nobj = 0
hash(x)

Method Details

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readFile(cls, mae_fname, joining_rules_fname, possible_linker)
Class Method

Create objects from the structures in mae_fname. If possible_linker is False, attachments are all heavy atoms attached to H. If True, attachments are all heavy atoms attached to H labeled with "s_cgch_attachment".

Class Substrate

readFile(cls, mae_fname, joining_rules_fname, possible_linker) Class Method

readFile(cls, mae_fname, joining_rules_fname, possible_linker)
Class Method