Source code for ihm.source

"""Classes for describing the source of an entity.

[docs] class Source(object): """Base class to describe the source of an :class:`ihm.Entity`. See :class:`Manipulated`, :class:`Natural` and :class:`Synthetic`. """ src_method = None
[docs] class Details(object): """Identifying information for an entity source. See :class:`Manipulated`, :class:`Natural` or :class:`Synthetic`. :param ncbi_taxonomy_id: NCBI taxonomy identifier, e.g. "469008" :param scientific_name: Scientific name, e.g. "Escherichia coli" :param common_name: Common name :param strain: Strain, e.g. "BL21(DE3)PLYSS" """ def __init__(self, ncbi_taxonomy_id=None, scientific_name=None, common_name=None, strain=None): self.ncbi_taxonomy_id = ncbi_taxonomy_id self.scientific_name = scientific_name self.common_name = common_name self.strain = strain
[docs] class Manipulated(Source): """An entity isolated from a genetically manipulated source. See :class:`Entity`. :param gene: Details about the gene source. :type gene: :class:`Details` :param host: Details about the host organism. :type host: :class:`Details` """ src_method = 'man' def __init__(self, gene=None, host=None): self.gene, = gene, host
[docs] class Natural(Source, Details): """An entity isolated from a natural source. See :class:`Entity`. See :class:`Details` for a description of the parameters.""" src_method = 'nat'
[docs] class Synthetic(Source, Details): """An entity obtained synthetically. See :class:`Entity`. See :class:`Details` for a description of the parameters.""" src_method = 'syn'