rdkit_step package#

Submodules#

rdkit_step.metadata module#

This file contains metadata to help describe the featurizers.

rdkit_step.rdkit module#

Non-graphical part of the RDKit step in a SEAMM flowchart

class rdkit_step.rdkit.Rdkit(flowchart=None, title='RDKit', extension=None, logger=<Logger rdkit_step.rdkit (WARNING)>)[source]#

Bases: Node

The non-graphical part of a RDKit step in a flowchart.

Parmaeters#

parserconfigargparse.ArgParser

The parser object.

optionstuple

It contains a two item tuple containing the populated namespace and the list of remaining argument strings.

subflowchartseamm.Flowchart

A SEAMM Flowchart object that represents a subflowchart, if needed.

parametersRdkitParameters

The control parameters for RDKit.

See also

TkRdkit, Rdkit, RdkitParameters

analyze(indent='', **kwargs)[source]#

Do any analysis of the output from this step.

Also print important results to the local step.out file using “printer”.

Parameters:

indent (str) – An extra indentation for the output

description_text(P=None)[source]#

Create the text description of what this step will do. The dictionary of control values is passed in as P so that the code can test values, etc.

Parameters:

P (dict) – An optional dictionary of the current values of the control parameters.

Returns:

A description of the current step.

Return type:

str

property git_revision#

The git version of this module.

run()[source]#

Run a RDKit

property version#

The semantic version of this module.

rdkit_step.rdkit_parameters module#

Control parameters for the RDKit step in a SEAMM flowchart

class rdkit_step.rdkit_parameters.RdkitParameters(defaults={}, data=None)[source]#

Bases: Parameters

The control parameters for RDKit.

The developer will add a dictionary of Parameters to this class. The keys are parameters for the current plugin, which themselves might be dictionaries.

You need to replace the “time” example below with one or more definitions of the control parameters for your plugin and application.

Parameters:

  • parameters – A dictionary containing the parameters for the current step. Each key of the dictionary is a dictionary that contains the the following keys: kind, default, default_units, enumeration, format_string, description and help text.

  • parameters["kind"] (custom) – Specifies the kind of a variable. While the “kind” of a variable might be a numeric value, it may still have enumerated custom values meaningful to the user. For instance, if the parameter is a convergence criterion for an optimizer, custom values like “normal”, “precise”, etc, might be adequate. In addition, any parameter can be set to a variable of expression, indicated by having “$” as the first character in the field. For example, $OPTIMIZER_CONV.

  • parameters["default"] ("integer" or "float" or "string" or "boolean" or) – “enum” The default value of the parameter, used to reset it.

  • parameters["default_units"] (str) – The default units, used for resetting the value.

  • parameters["enumeration"] (tuple) – A tuple of enumerated values.

  • parameters["format_string"] (str) – A format string for “pretty” output.

  • parameters["description"] (str) – A short string used as a prompt in the GUI.

  • parameters["help_text"] (tuple) – A longer string to display as help for the user.

See also

Rdkit, TkRdkit, Rdkit, RdkitParameters, RDKitStep

Examples

: parameters = { “time”: { “default”: 100.0, “kind”: “float”, “default_units”: “ps”, “enumeration”: tuple(), “format_string”: “.1f”, “description”: “Simulation time:”, “help_text”: (“The time to simulate in the dynamics run.”) }, }

parameters = {'features': {'default': [], 'default_units': None, 'description': 'RDKit Descriptors', 'enumeration': (), 'format_string': '', 'help_text': 'The list of RDKit descriptors', 'kind': 'list'}, 'table': {'default': 'table1', 'default_units': '', 'description': 'Table to use:', 'enumeration': None, 'format_string': '', 'help_text': 'Table to store the features', 'kind': 'string'}, 'where': {'default': 'Database', 'default_units': '', 'description': 'Where to store the features:', 'enumeration': ('Database', 'Table', 'Both'), 'format_string': '', 'help_text': 'Where to store the features', 'kind': 'string'}}#

rdkit_step.rdkit_step module#

class rdkit_step.rdkit_step.RdkitStep(flowchart=None, gui=None)[source]#

Bases: object

Helper class needed for the stevedore integration.

This must provide a description() method that returns a dict containing a description of this node, and create_node() and create_tk_node() methods for creating the graphical and non-graphical nodes.

Parameters:

  • my_description ({description, group, name}) – A human-readable description of this step. It can be several lines long, and needs to be clear to non-expert users. It contains the following keys: description, group, name.

  • my_description["description"] (tuple) – A description of the RDKit step. It must be clear to non-experts.

  • my_description["group"] (str) – Which group in the menus to put this step. If the group does not exist it will be created. Common groups are “Building”, “Calculations”, “Control” and “Data”.

  • my_description["name"] (str) – The name of this step, to be displayed in the menus.

create_node(flowchart=None, **kwargs)[source]#

Create and return the new node object.

Parameters:

  • flowchart (seamm.Node) – A non-graphical SEAMM node

  • **kwargs (keyworded arguments) – Various keyworded arguments such as title, namespace or extension representing the title displayed in the flowchart, the namespace for the plugins of a subflowchart and the extension, respectively.

Return type:

Rdkit

See also

Rdkit

create_tk_node(canvas=None, **kwargs)[source]#

Create and return the graphical Tk node object.

Parameters:

  • canvas (tk.Canvas) – The Tk Canvas widget

  • **kwargs (keyworded arguments) – Various keyworded arguments such as tk_flowchart, node, x, y, w, h representing a graphical flowchart object, a non-graphical node for a step, and dimensions of the graphical node.

Return type:

TkRdkit

See also

TkRdkit

description()[source]#

Return a description of what this extension does.

my_description = {'description': 'An interface for RDKit', 'group': 'Featurizers', 'name': 'RDKit'}#

rdkit_step.tk_rdkit module#

The graphical part of a RDKit step

class rdkit_step.tk_rdkit.TkRdkit(tk_flowchart=None, node=None, canvas=None, x=None, y=None, w=200, h=50)[source]#

Bases: TkNode

The graphical part of a RDKit step in a flowchart.

Paramaters#

tk_flowchartTkFlowchart = None

The flowchart that we belong to.

nodeNode = None

The corresponding node of the non-graphical flowchart

namespacestr

The namespace of the current step.

tk_subflowchartTkFlowchart

A graphical Flowchart representing a subflowchart

canvas: tkCanvas = None

The Tk Canvas to draw on

dialogDialog

The Pmw dialog object

xint = None

The x-coordinate of the center of the picture of the node

yint = None

The y-coordinate of the center of the picture of the node

wint = 200

The width in pixels of the picture of the node

hint = 50

The height in pixels of the picture of the node

self[widget]dict

A dictionary of tk widgets built using the information contained in RDKit_parameters.py

See also

Rdkit, TkRdkit, RdkitParameters

create_dialog(title='Specify the RDKit featurizers')[source]#

Create the dialog!

edit()[source]#

Present a dialog for editing the RDKit input

Parameters:

None –

Return type:

None

See also

TkRdkit.right_click

handle_dialog(result)[source]#

Handle the closing of the edit dialog

What to do depends on the button used to close the dialog. If the user closes it by clicking the “x” of the dialog window, None is returned, which we take as equivalent to cancel.

Parameters:

result (None or str) – The value of this variable depends on what the button the user clicked.

Return type:

None

handle_help()[source]#

Shows the help to the user when click on help button.

Parameters:

None –

Return type:

None

load_dict(tree, parent, metadata)[source]#

Custom code to load the dictionary in the test. NB. the ‘state=False’ argument prevents insert from working out the state of the parent nodes every time an item is inserted. This is done at the end with ‘tree.state()’

reset_dialog(widget=None)[source]#

Resets the dialog to the its last state

right_click(event)[source]#

Handles the right click event on the node.

Parameters:

event (Tk Event) –

Return type:

None

See also

TkRdkit.edit

Module contents#

rdkit_step A SEAMM plug-in for RDKit