Package schrodinger :: Package application :: Package matsci :: Module builderwidgets

Module builderwidgets

Common widgets and code for builders such as the TM Complex Builder and the Oligamer builder

Classes

TemplateCombo
A Combo Box for managing template lists

TemplateManager
A dialog that manages the user templates - currently only allows deletion

SketcherBox
Set of widgets that controls a 2D sketcher and has additional widgets that allow the user to load/save/delete templates for the sketcher and import structures from the workspace into the sketcher.

ItemRow
A row of control widgets for a ligand

StructureLabel
A label that gives information about the ligand for a given row and shows the set structure in a tooltip.

RGroupStructureToolTip
A structure tooltip that displays Rx labels for the Rx atoms

SketchDialog
A Dialog window that opens a SketcherBox instance

TMLigandRowMixin
A mixin class that takes care of minimizing bidentate transition metal complex ligand structures so that they remain planar through the R1-...-R2 bond path.

ItemRowWithTemplates
An ItemRow that holds the data for one unit and includes a combo for choosing Template structures

ComplexTemplateSketcher
A 2D sketcher that is decorated with a number of widgets for creating and saving templates.

Functions

[hide private]

str

get_builtin_directory(path, item_type)
Given a path to a script and an item type, generate the path to built-in templates for that script and item_type

convert_old_marker_props_to_new(struct)
Some template strutures may still use old-style properties to mark Rx atoms.

(dict, int)

get_marker_atom_indexes_from_structure(struct)
Get the indexes of atoms marked as Rx atoms

clear_marker_properties(struct)
Clear any marker properties that exist on the structure

set_marker_properties(struct, rx_atoms, clear=True)
Set the structure properties that store the atoms

Variables

[hide private]

__doc__ = ...

maestro = schrodinger.get_maestro()

ATOM_MARKER_PROP_BASE = 's_matsci_rx_marker_atom_'

HIGHEST_RX_MARKER_XVAL = 'i_matsci_highest_rx_xval'

OLD_FIRST_MARKER_PROP = 'i_matsci_complex_builder_site_atom1'

OLD_SECOND_MARKER_PROP = 'i_matsci_complex_builder_site_atom2'

ALL_OLD_MARKER_PROPS = ['i_matsci_complex_builder_site_atom1',...

TEMPLATE_EXTENSION = '.maegz'

TEMPLATE_GLOB = '*.maegz'

RECENT_TEMPLATE_FILE = 'recent.txt'

VALID_CHARACTERS = set([' ', '\'', '(', ')', ',', '-', '.', '0...

CUSTOM_TEMPLATE = 'Custom'

NO_TEMPLATE = 'This is not a template'

TEMP_ELEMENT = 'Br'

PREF_GROUP = 'general_builder_widgets'

RESELECT_CURRENT_TEMPLATE = 'reselect current template'

RESET_TO_DEFAULT_CUSTOM_DIR = 'reset to default custom dir'

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

get_builtin_directory(path, item_type)

Given a path to a script and an item type, generate the path to built-in templates for that script and item_type

If the script is located at /A/B/bob.py, the path returned will be /A/B/bob_dir/item_type_templates

Parameters:

path (str) - The path to the script (generated via __file__ property)
item_type (str) - The type item these templates are. Will form the base name of the template directory

Returns: str

The path to the built-in directory for templates of item_type for the script at path

convert_old_marker_props_to_new(struct)

Some template strutures may still use old-style properties to mark Rx atoms. This function converts those properties to new-style properties and removes the old ones.

Parameters:

struct (schrodinger.structure.Structure) - The structure with properties to read and modify

get_marker_atom_indexes_from_structure(struct)

Get the indexes of atoms marked as Rx atoms

Parameters:

struct (schrodinger.structure.Structure) - The structure with the Rx atoms

Returns: (dict, int)

dict keys are the int value of x in Rx, values are lists of atom indexes set to that Rx value (atom indexes are 1-based). The int return value is the highest value of x in the keys of the dictionary.

clear_marker_properties(struct)

Clear any marker properties that exist on the structure

Parameters:

struct (schrodinger.structure.Structure) - The structure with the marker properties to clear

set_marker_properties(struct, rx_atoms, clear=True)

Set the structure properties that store the atoms

Parameters:

struct (schrodinger.structure.Structure) - The structure with the Rx atoms
rx_atoms (dict) - keys are the int value of x in Rx, values are lists of atom indexes set to that Rx value (atom indexes are 1-based)
clear (bool) - Clear any existing marker properties before setting new ones

Variables Details

[hide private]

doc

Value:

"""
Common widgets and code for builders such as the TM Complex Builder an
d the
Oligamer builder

Copyright Schrodinger, LLC. All rights reserved.
"""

ALL_OLD_MARKER_PROPS

Value:

['i_matsci_complex_builder_site_atom1',
 'i_matsci_complex_builder_site_atom2']

VALID_CHARACTERS

Value:

set([' ',
     '\'',
     '(',
     ')',
     ',',
     '-',
     '.',
     '0',
...