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OpenStructure
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OpenStructure
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Public Member Functions | |
| def | __init__ |
| def | URLForID |
| def | Get |
| def | Load |
Data Fields | |
| name | |
| url_pattern | |
| type | |
| id_transform | |
A remote repository represents a structural database accessible through the
internet, e.g. the PDB or SWISS-MODEL template library.
:param name: Name of the repository
:param url_pattern: URL pattern for repository. Required format is described
in :func:`URLForID`
:param type: Data format to expect at resolved URL must be in
('pdb', 'cif')
:param id_transform: Transformation to apply to ID before resolving URL
in :func:`URLForID`. Must be in ('lower', 'upper')
:type name: :class:`str`
:type url_pattern: :class:`str`
:type type: :class:`str`
:type id_transform: :class:`str`
| def __init__ | ( | self, | |
| name, | |||
| url_pattern, | |||
| type, | |||
id_transform = 'upper' |
|||
| ) |
| def Get | ( | self, | |
| id | |||
| ) |
| def Load | ( | self, | |
| id | |||
| ) |
Resolves URL with :func:`URLForID` and directly loads/returns the according :class:`ost.mol.EntityHandle`. Loading invokes the :func:`ost.io.LoadPDB`/:func:`ost.io.LoadMMCIF` with default parameterization. If you need custom settings, you might want to consider to call :func:`Get` and do the loading manually. :param id: ID to resolve :type id: :class:`str`
| def URLForID | ( | self, | |
| id | |||
| ) |
Resolves URL given *url_pattern* and *id_transform* provided at object initialization. The *url_pattern* must contain substring '$ID'. Given *id*, the URL to the structure gets constructed by applying *id_transform* and inserting it at the location of '$ID'. e.g. 'https://files.rcsb.org/view/$ID.pdb' given 1ake as *id* and 'upper' as *id_transform* resolves to: 'https://files.rcsb.org/view/1AKE.pdb'
1.8.5