Module smiles

A module for generating SMILES and unique SMILES strings.

Provides python access to the classes in the canvaslibs_ext directory.

Classes

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SmilesGenerator
A class to generate a SMILES string from a Structure object.

Functions

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get_property_name(stereo)
Return the default m2io property name for the unique SMILES string with the type of stereochemistry given in 'stereo'.

_determine_stereo_option(struct, safe=True)
Look for mmstereo properties in the provide Structure.

remove_stereo_annotation(struct)
There is no current option in the SmilesGenerator that can be used to determine stereochemical information from the 3d geometry only.

_translate_stereo_enum(stereo, safe=True)
This function translates a module sterechemistry constant into its ChmMmctAdaptor enum equivalent.

_get_salt_list()
Returns a list of known salt SMILES strings.

_keep_largest_molecule(smi)

desalt_smiles(smiles_pattern)
Removes salts (if present) from the specified SMILES pattern.

Variables

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_stereo_enums = set([ChmMmctAdaptor.StereoFromGeometry, ChmMmc...

unique_smiles_prop_name = 's_canvas_Unique_SMILES'

unique_smiles_stereo_prop_name = 's_canvas_Unique_SMILES_Stereo'

_mmstereo_re = re.compile("^s_st_(Chirality|EZ|PM|AtomNumChira...

_canvas_license = canvasutils.get_license(canvasutils.LICENSE_...

Function Details

[hide private]

get_property_name(stereo)

Return the default m2io property name for the unique SMILES string with the type of stereochemistry given in 'stereo'.

Parameters:

stereo - Any of the module level variables NO_STEREO, STEREO_FROM_GEOMETRY, STEREO_FROM_ANNOTATION, or STEREO_FROM_ANNOTATION_AND_GEOM, or values from the actual enum in the ChmMmctAdaptor class.

_determine_stereo_option(struct, safe=True)

Look for mmstereo properties in the provide Structure.

If mmstereo properties are found, return the type of stereo determination to use as ChmMmctAdaptor.StereoFromAnnotation. Otherwise, return ChmMmctAdaptor.StereoFromGeometry.

Note: the stereo annotations can be stale.

remove_stereo_annotation(struct)

There is no current option in the SmilesGenerator that can be used to determine stereochemical information from the 3d geometry only. The STEREO_FROM_3D option does not override any stereochemical annotations that are already present in a structure.

If you want the stereochemistry to be determined by the 3d geometry only, use this function to remove any existing stereochemical annotations.

This is a recognized issue that will be addressed in future releases in a backwards compatible way.

desalt_smiles(smiles_pattern)

Removes salts (if present) from the specified SMILES pattern. Will raise a ValueError of the specified compound only contains salts.

Variables Details

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_stereo_enums

Value:

set([ChmMmctAdaptor.StereoFromGeometry, ChmMmctAdaptor.StereoFromGeome
try_Safe, ChmMmctAdaptor.StereoFromAnnotation, ChmMmctAdaptor.StereoFr
omAnnotation_Safe, ChmMmctAdaptor.StereoFromAnnotationAndGeometry, Chm
MmctAdaptor.StereoFromAnnotationAndGeometry_Safe, STEREO_FROM_GEOMETRY
, STEREO_FROM_ANNOTATION, STEREO_FROM_ANNOTATION_AND_GEOM, STEREO_FROM
_3D,])

_mmstereo_re

Value:

re.compile("^s_st_(Chirality|EZ|PM|AtomNumChirality)_")

_canvas_license

Value:

canvasutils.get_license(canvasutils.LICENSE_SHARED)