schrodinger.application.matsci.cgmappinggui module

GUI elements for coarse-grained automated mapping panels.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.cgmappinggui.CommonOptionsFrame(parent, layout, driver, command=None, add_ff_cb=True, add_antifreeze_cb=True, unique_default=False)

Bases: SFrame

Frame that holds checkboxes for automated mapping options that are common to DPD and Martini.

__init__(parent, layout, driver, command=None, add_ff_cb=True, add_antifreeze_cb=True, unique_default=False)

Create the common options frame.

Parameters:
  • parent (swidgets.SFrame) – The parent frame

  • layout (QtWidgets.QBoxLayout) – The layout to place the frame in

  • driver (coarse_grain_mapping_gui_dir.coarse_grain_mapping_driver or coarse_grain_ff_builder_gui_dir.coarse_grain_ff_builder_driver) – Driver module for the GUI being used

  • add_ff_cb (bool) – Whether to add the ‘Use particle names from FF’ checkbox

  • add_antifreeze_cb (bool) – Whether to add the ‘Add antifreeze water molecules’ checkbox

  • unique_default (bool) – The default state of the unique bonds checkbox

  • command (callable) – The command to call on checkbox change

isUnique()

Returns whether checkbox checked, needed for whether to pass -unique to driver

Return type:

bool

Returns:

Whether the checkbox is checked

isAntifreeze()

Returns whether checkbox checked, needed for whether to pass -antifreeze to driver

Return type:

bool

Returns:

Whether the checkbox is checked

isStabilizeRing()

Returns whether stabilize rings is selected, needed for whether to pass -stabilize to driver. False for common options.

Return type:

bool

Returns:

False

getCmdFlags(cmd)

Add command line flags for common options. For use in CG Mapping GUI.

Parameters:

cmd (list(str)) – The list of command line flags

Return type:

list(str)

Returns:

The list of updated command line flags

updateDriverInput(driver_input)

Update the DriverInputJson with widget parameters. For use in CGFF Builder GUI.

Parameters:

driver_input (coarse_grain_ff_builder_gui.DriverInputJson) – The driver input

setState(is_auto)

Set the state of the frame’s checkboxes according to whether automated mapping is selected.

Parameters:

is_auto (bool) – Whether automated mapping is selected.

reset()

Reset the frame.

class schrodinger.application.matsci.cgmappinggui.DpdOptionsFrame(parent, layout, driver, command=None, add_ff_cb=True, add_antifreeze_cb=True, unique_default=False)

Bases: CommonOptionsFrame

Frame that holds common checkboxes plus automated DPD-specific checkboxes.

isImplicitIons()

Returns whether checkbox checked, needed for whether to pass -impl_ions to driver

Return type:

bool

Returns:

Whether the checkbox is checked

isResidueOverlap()

Returns whether checkbox checked, needed for whether to pass -res_overlap to driver

Return type:

bool

Returns:

Whether the checkbox is checked

isStabilizeRing()

Returns whether stabilize rings is checked, needed for whether to pass -stabilize to driver. False for DPD.

Return type:

bool

Returns:

False

getCmdFlags(cmd)

Add command line flags for Martini options

Parameters:

cmd (list(str)) – The list of command line flags

Return type:

list(str)

Returns:

The list of updated command line flags

updateDriverInput(driver_input)

Update the DriverInputJson with widget parameters. For use in CGFF Builder GUI.

Parameters:

driver_input (coarse_grain_ff_builder_gui.DriverInputJson) – The driver input

reset()

Reset the frame.

class schrodinger.application.matsci.cgmappinggui.MartiniOptionsFrame(parent, layout, driver, command=None, add_ff_cb=True, unique_default=False, additional_opts=False)

Bases: CommonOptionsFrame

Frame that holds checkboxes for Martini-specific automated mapping options.

__init__(parent, layout, driver, command=None, add_ff_cb=True, unique_default=False, additional_opts=False)

Create the Martini options frame

Parameters:
  • parent (AutoMappingFrame) – The auto mapping frame

  • layout (QtWidgets.QBoxLayout) – The layout to place the frame in

  • driver (coarse_grain_mapping_gui_dir.coarse_grain_mapping_driver or coarse_grain_ff_builder_gui_dir.coarse_grain_ff_builder_driver) – Driver module for the GUI being used

  • add_ff_cb (bool) – Whether to add the ‘Use particle names from FF’ checkbox

  • unique_default (bool) – The default state of the unique bonds checkbox

  • additional_opts (bool) – Whether to add additional Martini-specific options (e.g. protein restraints)

isImplicitIons()

Returns whether implicit treatment of ions is selected, needed for whether to pass -impl_ions to driver. False for Martini.

Return type:

bool

Returns:

False

isResidueOverlap()

Returns whether residue overlap is selected, needed for whether to pass -res_overlap to driver. False for Martini.

Return type:

bool

Returns:

False

isStabilizeRing()

Returns whether checkbox checked, needed for whether to pass -stabilize to driver

Return type:

bool

Returns:

Whether the checkbox is checked

isProteinRestraints()

Returns whether checkbox checked, needed for whether to pass -prot_restraints to driver

Return type:

bool

Returns:

Whether the checkbox is checked

getCmdFlags(cmd)

Add command line flags for Martini options

Parameters:

cmd (str) – The list of command line flags

Return type:

str

Returns:

The list of updated command line flags

updateDriverInput(driver_input)

Update the DriverInputJson with widget parameters. For use in CGFF Builder GUI.

Parameters:

driver_input (coarse_grain_ff_builder_gui.DriverInputJson) – The driver input

reset()

Reset the frame.

class schrodinger.application.matsci.cgmappinggui.CGTypeRadioButtonGroup(parent=None, layout=None, command=None)

Bases: SLabeledRadioButtonGroup

Radio button group for coarse-graining type.

__init__(parent=None, layout=None, command=None)

Initialize the radio button group. See parent class for details.

class schrodinger.application.matsci.cgmappinggui.MappingScaleSpinBox(layout=None, command=None)

Bases: SLabeledSpinBox

Spinbox for the target mapping scale. See parent class for details.

TOOLTIP = 'The target number of heavy atoms per coarse-grained particle to use when mapping atomistic structure to coarse-grained.'
__init__(layout=None, command=None)

Initialize the mapping scale spinbox.

class schrodinger.application.matsci.cgmappinggui.CGForceFieldMixin

Bases: object

Mixin to allow force field import widgets and related functionality to be shared with the CG Mapping GUI.

addFFWidgetsToLayout(layout, spacing=None)

Add CG force field import widgets to the given layout.

Parameters:

layout (swidgets.SVBoxLayout or swidgets.SHBoxLayout) – The layout to add widgets to

loadFFCombo()

Find all available force fields and load them into the combobox

loadFF()

Load the selected force field

importFF()

Import a force field from local location and add it to force field selection combos

useFFChanged()

React to change in force field usage selection

class schrodinger.application.matsci.cgmappinggui.MappingViewerMixin

Bases: object

getGroups()

Get atom indices associated with each coarse-grained particle

Return type:

dict

Returns:

Dictionary with key as the tuple of particle name and the particle number and value as the list of atom indices associated

colorChanged()

React to color changing in the color widget

updateCGColors()

Update the color of the particles in the coarse-grained structure based on the color widget values

viewTypeChanged(*args)

React to view type change in the radio button group. Note it is similar to updateStructure but with different arguments

updateStructure(update_color=False)

Update the structure based on the color widget values

Parameters:

update_color (bool) – Whether to update the color of the coarse-grained particles

showCGStructure()

Show the coarse-grained structure in the workspace

drawSphere(s_color, atom_index)

Draw a sphere for the coarse-grained particle using the all atom particle

Parameters:
  • s_color (Color) – The color for the sphere

  • atom_index (int) – The index of the atom in the all atom structure

Return type:

MaestroSphere

Returns:

The sphere graphic object representing the coarse-grained particle

drawEllipsoids(e_color, atom_indices)

Draw ellipsoids for the coarse-grained particles using the constituent all atom particles

Parameters:
  • e_color (Color) – The color for the ellipsoid

  • atom_indices (list) – The list of atom indices associated with the coarse-grained particle

addParticlesAsGraphics()

Add spheres/ellipsoid graphics to the workspace representing the coarse-grained particles over the atomistic structure

showMappedStructure()

Show the all atom structure with ellipsoids representing the coarse- grained particles

removeGraphics()

Remove the graphics from the workspace

class schrodinger.application.matsci.cgmappinggui.WorkspaceSignal(maestro, *args, **kwargs)

Bases: QObject

Relays the workspace changed signal into a signal that can easily be suppressed. For resetting mapping viewer tab/dialog when the workspace is changed outside of the dialog/tab functionality (otherwise the functionality can break).

signal

A pyqtSignal emitted by instances of the class.

__init__(maestro, *args, **kwargs)

Initialize the WorkspaceSignal

Parameters:

maestro (schrodinger.maestro.maestro) – The maestro module

emitSignal(what_changed)

Relay the workspace changed signal into the reset tab signal, if what_changed is WORKSPACE_CHANGED_EVERYTHING

Parameters:

what_changed (str) – The type of workspace change

connect(func)

Connect the signal to the given function

Parameters:

func (callable) – The function to connect to the signal