API documentation¶
This part of the documentation is automatically generated from the CIRpy source code and comments.
Resolve¶
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cirpy.resolve(input, representation, resolvers=None, get3d=False, **kwargs)¶ Resolve input to the specified output representation.
Parameters: Returns: Output representation or None
Return type: string or None
Raises: - HTTPError – if CIR returns an error code
- ParseError – if CIR response is uninterpretable
Query¶
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cirpy.query(input, representation, resolvers=None, get3d=False, tautomers=False, **kwargs)¶ Get all results for resolving input to the specified output representation.
Parameters: - input (string) – Chemical identifier to resolve
- representation (string) – Desired output representation
- resolvers (list(string)) – (Optional) Ordered list of resolvers to use
- get3d (bool) – (Optional) Whether to return 3D coordinates (where applicable)
- tautomers (bool) – (Optional) Whether to return all tautomers
Returns: List of resolved results
Return type: list(Result)
Raises: - HTTPError – if CIR returns an error code
- ParseError – if CIR response is uninterpretable
Result¶
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class
cirpy.Result(input, notation, input_format, resolver, representation, value)¶ A single result returned by CIR.
Parameters: - input (string) – Originally supplied input identifier that produced this result
- notation (string) – Identifier matched by the resolver or tautomer ID
- input_format (string) – Format of the input as interpreted by the resolver
- resolver (string) – Resolver used to produce this result
- representation (string) – Requested output representation
- value (string or list(string)) – Actual result value
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to_dict()¶ Return a dictionary containing Result data.
Images¶
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cirpy.resolve_image(input, resolvers=None, fmt=u'png', width=300, height=300, frame=False, crop=None, bgcolor=None, atomcolor=None, hcolor=None, bondcolor=None, framecolor=None, symbolfontsize=11, linewidth=2, hsymbol=u'special', csymbol=u'special', stereolabels=False, stereowedges=True, header=None, footer=None, **kwargs)¶ Resolve input to a 2D image depiction.
Parameters: - input (string) – Chemical identifier to resolve
- resolvers (list(string)) – (Optional) Ordered list of resolvers to use
- fmt (string) – (Optional) gif or png image format (default png)
- width (int) – (Optional) Image width in pixels (default 300)
- height (int) – (Optional) Image height in pixels (default 300)
- frame (bool) – (Optional) Whether to show border frame (default False)
- crop (int) – (Optional) Crop image with specified padding
- symbolfontsize (int) – (Optional) Atom label font size (default 11)
- linewidth (int) – (Optional) Bond line width (default 2)
- bgcolor (string) – (Optional) Background color
- atomcolor (string) – (Optional) Atom label color
- hcolor (string) – (Optional) Hydrogen atom label color
- bondcolor (string) – (Optional) Bond color
- framecolor (string) – (Optional) Border frame color
- hsymbol (bool) – (Optional) Hydrogens: all, special or none (default special)
- csymbol (bool) – (Optional) Carbons: all, special or none (default special)
- stereolabels (bool) – (Optional) Whether to show stereochemistry labels (default False)
- stereowedges (bool) – (Optional) Whether to show wedge/dash bonds (default True)
- header (string) – (Optional) Header text above structure
- footer (string) – (Optional) Footer text below structure
Request¶
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cirpy.request(input, representation, resolvers=None, get3d=False, tautomers=False, **kwargs)¶ Make a request to CIR and return the XML response.
Parameters: - input (string) – Chemical identifier to resolve
- representation (string) – Desired output representation
- resolvers (list(string)) – (Optional) Ordered list of resolvers to use
- get3d (bool) – (Optional) Whether to return 3D coordinates (where applicable)
- tautomers (bool) – (Optional) Whether to return all tautomers
Returns: XML response from CIR
Return type: Element
Raises: - HTTPError – if CIR returns an error code
- ParseError – if CIR response is uninterpretable
Download¶
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cirpy.download(input, filename, representation, overwrite=False, resolvers=None, get3d=False, **kwargs)¶ Convenience function to save a CIR response as a file.
This is just a simple wrapper around the resolve function.
Parameters: - input (string) – Chemical identifier to resolve
- filename (string) – File path to save to
- representation (string) – Desired output representation
- overwrite (bool) – (Optional) Whether to allow overwriting of an existing file
- resolvers (list(string)) – (Optional) Ordered list of resolvers to use
- get3d (bool) – (Optional) Whether to return 3D coordinates (where applicable)
Raises: - HTTPError – if CIR returns an error code
- ParseError – if CIR response is uninterpretable
- IOError – if overwrite is False and file already exists
API URLs¶
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cirpy.construct_api_url(input, representation, resolvers=None, get3d=False, tautomers=False, xml=True, **kwargs)¶ Return the URL for the desired API endpoint.
Parameters: - input (string) – Chemical identifier to resolve
- representation (string) – Desired output representation
- resolvers (list(str)) – (Optional) Ordered list of resolvers to use
- get3d (bool) – (Optional) Whether to return 3D coordinates (where applicable)
- tautomers (bool) – (Optional) Whether to return all tautomers
- xml (bool) – (Optional) Whether to return full XML response
Returns: CIR API URL
Return type:
Molecule¶
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class
cirpy.Molecule(input, resolvers=None, get3d=False, **kwargs)¶ Class to hold and cache the structure information for a given CIR input.
Initialize with a resolver input.
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stdinchi¶ Standard InChI.
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stdinchikey¶ Standard InChIKey.
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inchi¶ Non-standard InChI. (Uses options DONOTADDH W0 FIXEDH RECMET NEWPS SPXYZ SAsXYZ Fb Fnud).
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smiles¶ SMILES string.
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ficts¶ FICTS NCI/CADD hashed structure identifier.
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ficus¶ FICuS NCI/CADD hashed structure identifier.
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uuuuu¶ uuuuu NCI/CADD hashed structure identifier.
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hashisy¶ CACTVS HASHISY identifier.
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sdf¶ SDF file.
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names¶ List of chemical names.
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iupac_name¶ IUPAC approved name.
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cas¶ CAS registry numbers.
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mw¶ Molecular weight.
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formula¶ Molecular formula
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h_bond_donor_count¶ Hydrogen bond donor count.
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h_bond_acceptor_count¶ Hydrogen bond acceptor count.
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h_bond_center_count¶ Hydrogen bond center count.
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rule_of_5_violation_count¶ Rule of 5 violation count.
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rotor_count¶ Rotor count.
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effective_rotor_count¶ Effective rotor count.
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ring_count¶ Ring count.
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ringsys_count¶ Ring system count.
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image¶ 2D image depiction.
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image_url¶ URL of a GIF image.
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twirl_url¶ Url of a TwirlyMol 3D viewer.
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