Python class Notation of the CurlySMILES software package

Notation is the core class for managing a CurlySMILES notation in a Python program. It has been implemented in module file notation.py. This class contains methods that convert a user-given notation into a work notation, parse the work notation, and provide access to the evaluated data and parameters derived from the CurlySMILES-encoded material or molecular structure.

Assuming that modules csm_notation and csm_dataface have been imported and the variable sNotation has been assigned with a string containing a CurlySMILES notation, then a Notation object is created as follows:

___ oDataFace = csm_dataface.Dataface()
___ oNotation = csm_notation.Notation(oDataFace)
___ oNotation.parse(sNotation)

The object oDataFace needs to be created only once and can be used as a singleton while generating further Notation object. Once method parse has been called, other methods can access atom, molecule, and notation data.

Atom list methods apply to CurlySMILES components encoded as SMILES or annotated SMILES. They return a list containing an attribute value for each atom node in the encoded molecular graph. These values occur in the returned list in the same as order as the associated atomic symbols occur in the component notation. Component methods return component-related data of various types. The following table includes links to the detailed description and examples of usage for individual methods of class Notation:

Atom list methods Component methods Miscellaneous methods
atf0_compnt
atoms_aromat_compnt
atoms_charge_compnt
atoms_hcount_compnt
atoms_label_compnt
atoms_nbors_compnt
atoms_nvbors_compnt
atoms_numb_compnt
atoms_symb_compnt
aaa_entries_compnt
aaa_indices_compnt
aaa_indices_iu_compnt
atpair_bond_compnt
caa_entries_compnt
deloc_charge_compnt
dmat_compnt
mf_compnt
numof_atoms_compnt
numof_rings_compnt
rings_compnt
rings_iu_compnt
msgs_acc
msgs_err
mf_total
numof_components
numof_composite_parts
set_client_ali
set_client_ann
set_user_notation
type_components
type_composite_parts
work_notation



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