schrodinger.application.desmond.feputils module

class schrodinger.application.desmond.feputils.ProteinReliabilityTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.tasks.SubprocessCmdTask

DEFAULT_TASKDIR_SETTING = 2

REPORT_FILE_NAME = 'prot_probs.txt'

OUTPUT_FILE_NAME = 'prot_rel.mae'

class Input(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

protein_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

protein_fileChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

protein_fileReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

receptor_issue_msg: str

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

model: schrodinger.protein._reliability.ModelCheck

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

modelChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

modelReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

receptor_issue_msgChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

receptor_issue_msgReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

getPotentialReceptorIssues() → str

makeCmd()

calling_contextChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

calling_contextReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

failure_infoChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

failure_infoReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

input: parameters.CompoundParam

inputChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

inputReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

max_progressChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

max_progressReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

nameChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

nameReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

output: parameters.CompoundParam

outputChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

outputReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

progressChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

progressReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

progress_stringChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

progress_stringReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

statusChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

statusReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

schrodinger.application.desmond.feputils.run_protein_reliability(protein_file)

Takes a protein ct and returns a message indicating problems, if any.

Warning

This function runs very slowly (i.e., easily around 20 seconds).

Note

This function must not directly be run from a GUI thread since it uses task.wait to wait for completion of a task.

Parameters

protein_file (str) – Path to the protein file to assess

Returns

A tuple that contains a message indicating any problems with the protein and model that can be used to bring up protein reliability panel.

Return type

tuple

schrodinger.application.desmond.feputils.is_prepped(protein)

Check if a protein has been prepared in Protein PrepWizard

Parameters

protein (protein: schrodinger.structure.Structure) – protein to check

class schrodinger.application.desmond.feputils.LabelSpinner(text=None, parent=None)

Bases: PyQt6.QtWidgets.QLabel

A label that can replace its icon with a spinning progress icon.

DEFAULT_ICON_HEIGHT = 10

ANIMATION_TIME = 250

animationTimeElapsed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(text=None, parent=None)

updateAnimationSize()

Set the size of the spinner animation to the height of the current permanent icon, or else some default value if it is not available.

updatePermanentPic()

Set the permenent icon picture to the current pixmap value and update the size of the spinner animation to match.

setPixmap(pixmap)

Set a new pixmap, and update the spinner animation frames in response.

The setTemporaryPixmap() method should be called internally when setting a temporary pixmap for the spinner animation frames and other temporary icon images.

Parameters

pixmap (QtGui.QPixmap) – the icon to be displayed by this label

setTemporaryPixmap(pixmap)

Set the displayed pixmap without overwriting the “permanent” cached pixmap value or altering the size of the animation frames. Meant to be used to display animation frames or other temporary icon images.

Parameters

pixmap (QtGui.QPixmap) – the icon to be displayed by this label

updateAnimation()

Advance the animation by one frame. This method gets called periodically while the spinner is running.

start()

Start the spinner animation.

stop()

Stop the spinner animation and restore the original icon.

class schrodinger.application.desmond.feputils.BaseSpinnerWidget(*args, **kwargs)

Bases: schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin, PyQt6.QtWidgets.QWidget

A widget that maintains a label and a button for displaying health check status information.

Variables

tooltip_calculating (str) – the tooltip text for when the health is being calculated

tooltip_calculating = ''

initSetOptions()

Suggested subclass use: set instance variables, excluding layouts and subwidgets. Also use here to (optionally) apply the legacy stylesheet spacing settings (PANEL-19101).

initSetUp()

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

initLayOut()

Create a vertical layout for the widget (widget_layout) and populate it with two vertical sub-layouts: main_layout and bottom_layout.

If the user has specified the ui data member, insert the resultant ui_widget into main_layout.

If the widget already has a layout defined, this method will produce a warning (but not a traceback). main_layout and bottom_layout will be inserted into the existing widget layout, which will not be the same as widget_layout. It is therefore recommended that this mixin is used only with widgets that do not already have a layout.

Suggested subclass use: create, initialize, and populate layouts.

initFinalize()

Suggested subclass use: perform any remaining initialization.

showSubwidgets(show_label, show_button)

Convenience method for showing or hiding the label and button.

Raise

ValueError

Parameters

• show_label (bool) – whether to show the label

• show_button (bool) – whether to show the button

start()

Display a spinning animation in the label widget.

stop()

Stop the animation and restore the original icon.

setButtonIcon(icon)

Parameters

icon (QtGui.QIcon) – the icon to display in the button

setLabelPixmap(pixmap)

Parameters

pixmap (QtGui.QPixmap) – the pixmap to display in the label

clearLabelPixmap()

Replace the label pixmap with a transparent pixmap.

setLabelToolTip(text)

setButtonToolTip(text)

class schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget(parent=None, use_cache=False)

Bases: schrodinger.application.desmond.feputils.BaseSpinnerWidget

A protein checker widget that includes a button to display the health status and a label to display a spinner. Shows a spinning animation in the label while the check is running.

Variables

receptorHealthChanged (QtCore.pyqtSignal(str)) – signal emitted containing the tooltip for the visible widget (label or button)

results_cache = {}

tooltip_calculating = 'Calculating protein health'

receptorHealthChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(parent=None, use_cache=False)

Parameters

use_cache (bool) – whether or not to cache results based upon the string representation, which introduces latency in the string generation, but saves completed results and checks if the protein changes before starting a new check thread when calling setProtein. Defaults to False.

initSetOptions()

Suggested subclass use: set instance variables, excluding layouts and subwidgets. Also use here to (optionally) apply the legacy stylesheet spacing settings (PANEL-19101).

initSetUp()

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

initSetDefaults()

Set widget to its default state. If the widget uses a model/mapper, it’s preferable to reset the widget state by resetting the model.

start()

Start the protein health check and spinner animation.

startValidate()

Returns

whether a health check needs to be run

Return type

bool

stop()

Stop the spinner animation and health check process task.

onFinishedTask()

Stop the spinner animation and display the health check results.

updateToolTips()

Update widget tooltips depending on the status of the health check.

finish()

Display the health check results. If there are any problems, the warning label is set to visible and the tooltip will report the issue. If there are no problems, the label is hidden.

setProtein(protein)

Set the protein for the spinner, stopping and restarting the spinner with the new protein if it has changed or if _use_cache is False. :param protein: the new protein :type protein: structure.Structure

showProteinHealthReport()

Bring up protein reliability panel to show results of protein check.

schrodinger.application.desmond.feputils.truncate_label(label, label_string, max_chars=40)

Sets the text on a label to label_string, truncating the text if necessary and setting the full text in a tooltip, if the text has been truncated. The original tooltip text will be returned.

Parameters

• label (QtWidgets.QLabel) – the label to modify

• label_string (str) – the text for the label

• max_chars (int) – maximum number of characters in the label text

Returns

the original tooltip text

Return type

str

schrodinger.application.desmond.feputils.get_protein_label_string(ct)

Returns a string for use in GUI to indicate the protein. Returns the title if available; otherwise returns a short description. If called with None, returns “–“.

Parameters

ct (schrodinger.structure.Structure) – the protein

schrodinger.application.desmond.feputils.format_structure_label(ct, label, max_chars=40)

Sets the protein name on a label, truncating the text if necessary and setting the untruncated text in a tooltip, if the text has been truncated.

Parameters

• ct (schrodinger.structure.Structure) – the protein

• label (QtWidgets.QLabel) – The label to modify

• max_chars (int) – The max number of characters to allow on the label

schrodinger.application.desmond.feputils.get_proteins(ct_list)

Iterates through a list of structures and returns only the proteins

Parameters

ct_list (list) – a list of structures

schrodinger.application.desmond.feputils.get_ligands(ct_list)

Iterates through a list of structures and returns only the ligands.

Parameters

ct_list (list) – a list of structures

schrodinger.application.desmond.feputils.import_pt_entries()

Imports selected entries from the project table. For convenience, workspace-included proteins are also imported.

Returns

a list of imported structures. Each structure is tagged with a property ‘s_fepmapper_entryid’ to store the entry id.

Return type

list

schrodinger.application.desmond.feputils.import_pv_file(filename)

Imports a list of structures from a structure file. Typically used on PV files, but can be used on any structure file. :param filename: the filename :type filename: str

schrodinger.application.desmond.feputils.get_opls_dir_cmd(opls_dir)

Construct and return the cmd for the given OPLS directory.

Parameters

opls_dir (str) – OPLS directory path

Returns

a command list for the OPLS directory

Return type

list[str]

schrodinger.application.desmond.feputils.get_restart_opls_dir(jobname)

Create opls dir command for use in restarting/extending scripts

Parameters

jobname (str) – Jobname

Returns

a command list for the OPLS directory

Return type

list[str]

schrodinger.application.desmond.feputils.make_fep_cmd(cd_params, ao, jobname, struct_fname, opt=[], opls_dir=None, use_ffbuilder=False, opls_version=16)

Generates an FEP command list based on the specified parameters.

Parameters

• cd_params (dict) – config dialog parameters

• ao (dict) – FEP Advanced Options (AO) parameters

• jobname (str) – the jobname

• main_msj_fname (str) – the filename for the main msj file

• struct_fname (str) – the filename for the input structure

• opls_dir (str or None) – OPLS directory path

• use_ffbuilder (bool) – whether ffbuilder arguments should be used

• opls_version (int) – the OPLS version to use for the FEP+ job

Returns

a command list for launching the job

Return type

list

schrodinger.application.desmond.feputils.write_script(fname, cmd)

Write the list of commands to a script file and make the file executable.

Parameters

• fname (str) – the filename of the script file

• cmd (list of str) – the list of commands

schrodinger.application.desmond.feputils.generate_scripts(cd_params, jobname, cmd, opls_dir_setting, use_ffbuilder=False)

Write the start, restart and extend scripts.

Parameters

• cd_params (dict) – the configuration dialog parameters

• jobname (str) – the job name

• cmd (list of str) – the command list

• opls_dir_setting (list of str) – the opls_dir_setting

• use_ffbuilder (bool) – whether ffbuilder arguments should be used

schrodinger.application.desmond.feputils.get_restraints_file_options() → list[str, str]

Returns the command line options for the receptor restraints file. Expects the restraints file to always have the same name.

schrodinger.application.desmond.feputils.generate_ffbuilder_options(ffb_host, ffb_subjobs=0)

Generates command for using FFBuilder in the FEP executable