schrodinger.application.matsci.deswidgets module¶

Contains widgets that are useful in MatSci desmond panels.

schrodinger.application.matsci.deswidgets.get_row_from_proj_table(struct)¶

Given an input structure, return the row from the project table

Parameters: st (schrodinger.structure.Structure) – structure to get associated row of from project table
Return type: schrodinger.project.project.ProjectRow
Returns: the row from project table

schrodinger.application.matsci.deswidgets.get_cms_path_from_proj_table(struct, traj=False)¶

Get cms path and optionally trajectory path for the passed structure in maestro from project table

Parameters

struct (schrodinger.structure.Structure) – Structure to get associated cms
traj (bool) – If True, get traj for the passed structure. Default is False.

Return type

tuple(str or None, str or None)

Returns

Path to the associated cms file and trajectory for the structure. None if there is no associated cms.

schrodinger.application.matsci.deswidgets.check_cms_trj_properties_are_found(cms_file, trj_dir, source_path)¶

Check if the CMS and trj properties were found and raise ValueError if not

Parameters

str (trj_dir) – Path to source cms and trj folder
str – Path to the associated CMS file
str – Path to the associated trajectory

Return str,str

Path to the cms file trajectory frames if both are found.

Raises

ValueError – Raises error if the cms file or trajectory is not found

schrodinger.application.matsci.deswidgets.get_cms_and_trj_path(struct, source_path=None)¶

Get trajectory and cms path for the passed structure in maestro

Parameters

schrodinger.structure.Structure (struct) – Structure to get associated cms and trajectory of
str (source_path) – Path to source cms and trj folder in case they do not exist in the working folder. Structure source path will be used in case it is not passed.

Return str,str

Path to the cms file trajectory frames if both are found.

Raises

ValueError – In case the cms file or trajectory is not found

class schrodinger.application.matsci.deswidgets.FrameSpinBox(layout, commands=None)¶

Bases: schrodinger.ui.qt.swidgets.SSpinBox

A spin box to change and set the frames for the trajectory

__init__(layout, commands=None)¶

Create a FrameSpinBox instance

Parameters

layout (QLayout) – If supplied, the FrameSpinBox created will be added to this layout
commands (list) – The list of callbacks for the valueChanged signal.

class schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog(master)¶

Bases: schrodinger.ui.qt.swidgets.SDialog

Trajectory range selector dialog with fixed labels, a spinbox for step, and no overlapping of sliders

DIALOG_SIZE = (490, 160)¶

__init__(master)¶: Create a TrajRangeSelectorDialog instance

layOut()¶: Layout the widgets in the Dialog

updateRangeLabel()¶: Function to change label when spinbox values are changed or slider is moved

slidersMoved()¶: Sets values in spinboxes and label when the sliders are moved

reset()¶: Reset the widgets

getStep()¶

Get the trajectory step

Return int: The step

getFrames()¶

Get the frame numbers based on the range and step

Return list: list of frames numbers

accept()¶: Save the step value in addition to what parent does

reject()¶: Restore step value in addition to what parent does

setTrajLimits(min_f, max_f, step_size)¶

Set the limits for trajectory range

Parameters

min_f (float) – minimum value of the trajectory frames
max_f (float) – maximum value of the trajectory frames
step_size (float) – step size of the frames

setTempRangeToSlider(traj_range)¶

Set temporary trajectory range values to the range selection widgets

Parameters: traj_range (SimpleNamespace) – set of values for the minimum and maximum number of frames and the step size.

setTempTrajRange()¶: Read values from widgets and store the temporary range value in traj_range property

changeLimitsEnd()¶: Change limits of end time spin box to reflect the left slider position

changeLimitsStart()¶: Change limits of start time spin box to reflect the right slider position

getRangeLabel()¶

This function returns text string showing trajectory range in ns.

Returns: range string
Return type: str

class schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame(layout)¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Frame that adds trajectory selection button and label. It is connected to a dialog to select the trajectory range

__init__(layout)¶

Parameters: layout (QLayout) – layout to add the button to

updateTrajectoryRangeLabel()¶: Update the trajectory range label with new range from traj dialog and correct the text

showTrajRangeSelectorDialog()¶: Show traj dialog

updateTrj(trj_path)¶

Load new trajectory range

Parameters: trj_path (str) – path to the trajectory.
Return bool: True if trajectory range was loaded, else False

getFlags()¶: Get flags for current selected trajectory range

getRange()¶

Get current range of frames selected

Return type: tuple(int)
Returns: lower limit and upper limit of the selected range of frames

setRange(start_val=None, end_val=None)¶

Set the frame range (in number and not time) for trajectory selection

Parameters

start_val (int) – lower limit for frame in trajectory selection
end_val (int) – upper limit for frame in trajectory selection

setEnabled(state)¶

Enable or disable the button and label for showing the traj dialog

Parameters: state (bool) – True to enable the button, and False to disable

reset()¶: Reset the frame

getInputs()¶

Get the minimum, maximum and step value of trajectory frames

Returns: min,max and step value of trajectory frames
Return type: dict

schrodinger.application.matsci.deswidgets.copy_cms_and_trj(cms_file, trj_path, jobname)¶

Copy cms and trj to the job directory

Parameters

cms_file (str) – The path to the input cms file
trj_path (str) – The path to the input trj dir
jobname (str) – The job name

class schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin¶

Bases: schrodinger.application.matsci.appbase.BaseAnalysisGui

Class for extension of af2 to add widgets to gui for desmond trajectory analysis.

addLoadTrajButton(layout, setup_method=None, allow_gcmc=True)¶

Load button to load structure from workspace and associated trajectory

Parameters

layout (QLayout) – layout to add the button and range selector to
setup_method (callable) – The method to call to setup the panel
allow_gcmc (bool) – Whether gcmc cms’s should be allowed

resetPanel()¶

Reset the panel variables and widgets set by this mixin

Raises: NotImplementedError – Will raise error if load button is not added

toggleStateMain(state)¶

Enable and disable trajectory traj button and label

Parameters: state (bool) – True to enable the button, and False to disable

getTrajFlags()¶

Get the command line flags for cms file, trajectory path, and trajectory range.

Return list: A list of command line flags and values

validateCMS()¶

Check if valid structure has been loaded.

Return type: bool or (bool, str)
Returns: The bool is True if file is loaded. False with message pop up if file is not loaded.

class schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider(layout=None, command=None, parent=None)¶

Bases: object

Mixin class to add the time slider and play/pause buttons and related methods.

INTERVAL = 100¶

ICON_SIZE = 24¶

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

Add time slider and play button to the layout

Parameters

layout (QLayout) – Layout to place the time slider into
command (python callable) – The callback for the valueChanged signal.
parent (QWidget) – The widget that owns this table widget
time_stamps (list) – Trajectory time range data to set the timer interval

addTimerButton(layout=None)¶

Add Timer button to the timer

Parameters: layout (QWidgets.QHBoxLayout) – Layout to add the play/pause button

initVariables()¶: Initialize variables

toggleTimer()¶: Response to the timer button

repeatingMethod()¶: Repeating method for timer. Resets the timer to start position.

setTimeSlider(time_stamps)¶

Set the time range, maximum and minimum value for the time slider.

Parameters: time_stamps (list) – Trajectory time range data to set the timer interval

floatValue()¶

Get the current float value. The float value differs from the slider value in that the slider value is an integer, while the float value is a float calculated by multiplying float_step by the integer value.

Return type: float
Returns: The current widget float value

setFloatValue(float_value)¶

Set the current float value of the slider. The value gets rounded to the nearest acceptable slider value.

Parameters: float_value (float) – The value to set

reset()¶: Reset the time slider

class schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

Class to link the inputs from the panel to the model.task.input object and: define input parameters

Parameters

cms_file (tasks.Taskfile) – The cms file on which trajectory density analysis calculations will be performed
trj (tasks.TaskFile) – The associated trajectory of the input cms file
trj_max (int) – Maximum value of the trajectory frames
trj_min (int) – Minimum value of the trajectory frames
trj_step (int or None) – Step size of the frames if the frames need to be skipped. None if nothing is skipped

cms_file: schrodinger.tasks.tasks.TaskFile¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

trj: schrodinger.tasks.tasks.TaskFile¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

trj_max: int¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

trj_min: int¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

trj_step: int¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

setAttributes(inputs)¶

Set the attributes of the instance of model.task.input

Parameters: inputs (dict) – inputs from all the stages in the panel

cms_fileChanged¶