from_smiles_step package

Submodules

from_smiles_step.from_smiles module

a node to create a structure from a SMILES string

class from_smiles_step.from_smiles.FromSMILES(flowchart=None, extension=None)

Bases: Node

description_text(P=None)

Return a short description of this step.

Return a nicely formatted string describing what this step will do.

Keyword Arguments:

P – a dictionary of parameter values, which may be variables or final values. If None, then the parameters values will be used as is.

property git_revision

The git version of this module.

run()

Create 3-D structure from a SMILES string

property version

The semantic version of this module.

from_smiles_step.from_smiles_parameters module

Control parameters for generating a structure from SMILES

class from_smiles_step.from_smiles_parameters.FromSMILESParameters(defaults={}, data=None)

Bases: Parameters

The control parameters for creating a structure from SMILES

parameters = {'notation': {'default': 'perceive', 'default_units': '', 'description': 'Input notation:', 'enumeration': ('perceive', 'SMILES', 'InChI', 'InChIKey', 'name'), 'format_string': 's', 'help_text': 'The line notation used.', 'kind': 'enum'}, 'smiles flavor': {'default': 'rdkit', 'default_units': '', 'description': 'SMILES flavor:', 'enumeration': ('rdkit', 'openbabel', 'openeye'), 'format_string': 's', 'help_text': 'The flavor of SMILES to use.', 'kind': 'string'}, 'smiles string': {'default': '', 'default_units': '', 'description': 'Input:', 'enumeration': (), 'format_string': 's', 'help_text': 'The input string for the structure.', 'kind': 'string'}}

from_smiles_step.from_smiles_step module

Helper class needed for the stevedore integration. Needs to provide a description() method that returns a dict containing a description of this node, and a factory() method for creating the graphical and non-graphical nodes.

class from_smiles_step.from_smiles_step.FromSMILESStep(flowchart=None, gui=None)

Bases: object

create_node(flowchart=None, **kwargs)

Return a new node object

create_tk_node(canvas=None, **kwargs)

Return the graphical Tk node object

description()

Return a description of what this extension does

my_description = {'description': 'Creates a 3D molecular structure from a SMILES string.', 'group': 'Building', 'name': 'from SMILES'}

from_smiles_step.tk_from_smiles module

The graphical part of a fromSMILES node

class from_smiles_step.tk_from_smiles.TkFromSMILES(tk_flowchart=None, node=None, canvas=None, x=120, y=20, w=200, h=50)

Bases: TkNode

The graphical part of the From SMILES step

create_dialog()

Create a dialog for editing the SMILES string

right_click(event)

Probably need to add our dialog…

Module contents

from_smiles_step A step for generating a structure from a SMILES string.