Package schrodinger :: Package application :: Package jaguar :: Package gui :: Module utils

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Module utils

Utility functions and classes for the Jaguar GUIs

Classes

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JaguarSettingError
An exception indicating that there was an error with the user-specified Jaguar settings

JaguarSettingWarning
A warning indicating that a user-specified Jaguar settings could not be loaded into the GUI

EnhancedComboBox
A combo box for use in the Jaguar GUI with several Pythonic enhancements

PropertiesTableWidget
A QTableWidget for the Properties table on the Properties tab

WorkspaceInclusionCheckBox
A checkbox that is skinned to look like the Project Table workspace inclusion checkbox.

ProjTableLikeView
A table view that mimics the selecting and editing behaviors of the Project Table

SpinTreatment
An enumeration of the possible spin treatment settings.

Functions

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count_num_strucs(input_selector)
Count the number of structures currently specified in the input selector widget.

find_key_for_value(mydict, value)
This function finds key corresponding to a given value in a dictionary.

float

validate_le_float_input(widget, msg=None)
This function checks whether a given line edit widget has a valid input.

catch_jag_errors(func, *args, **kwargs)
A decorator that will display any JaguarSettingErrors in an error dialog.

bool

warn_about_mmjag_unknowns(jag_input, parent=None)
If the JaguarInput object contains any unknown keywords, warn the user about the unknowns and ask them if they want to continue.

apply_jaguar_atom_naming(struc)
Apply jaguar unique atom naming to all atoms in the specified structure

int

calculate_num_protons(struc)
Calculate the number of protons in the specified structure

tuple

get_atom_info(ws_atom_num)
Get information about the specified workspace atom

tuple

atom_name_sort_key(atom_name)
Convert a Jaguar atom name into a key for use in sorting by number

str

generate_job_name(struc_name, task_name, theory, basis)
Generate an appropriate job name for a job with the specified settings.

list

host_and_cpu_args(cd_params, use_parallel_arg=True, explicit_one=False, one_subjob=False)
Build the command line arguments for passing the hostname and the number of CPUs.

Variables

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maestro = schrodinger.get_maestro()

THEORY_DFT = "DFT"

THEORY_HF = "HF"

THEORY_LMP2 = "LMP2"

MOLECULAR_CHARGE_PROP = "i_m_Molecular_charge"

SPIN_MULT_PROP = "i_m_Spin_multiplicity"

ERROR_BACKGROUND_BRUSH = QtGui.QBrush(Qt.red)

JAGUAR_IN_MAE_FILETYPES = "Jaguar Structure Input", "*.in *.ma...

atom_name_regex = re.compile("^([^\W\d]+)(\d+)$")
A regular expression that matches Jaguar atom names.

Function Details

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count_num_strucs(input_selector)

Count the number of structures currently specified in the input selector widget. Since Jaguar can't accept more than three structures, this function will return 4 for all values >= 4.

Parameters:

input_selector (schrodinger.ui.qt.appframework.JobInputFrame) - The input selector widget

find_key_for_value(mydict, value)

This function finds key corresponding to a given value in a dictionary. We assume here that values in a given dictionary are unique.

Parameters:

mydict (dict) - dictionary
value - value in dictionary. It can be any hashable type.

Returns:

key, which can be any type.

validate_le_float_input(widget, msg=None)

This function checks whether a given line edit widget has a valid input. If it does it will return a float value. Otherwise an exception will be raised. This function should only be used for line edits used to enter float numbers.

Parameters:

widget (QLineEdit) - line edit widget
msg (str) - text of exception error message

Returns: float

valid float number

catch_jag_errors(func, *args, **kwargs)

A decorator that will display any JaguarSettingErrors in an error dialog.

Returns:

If the decorated function raised a JaguarSettingError, False will be returned. Otherwise, the return value of the decorated function will be returned.

Decorators:

@decorator.decorator

warn_about_mmjag_unknowns(jag_input, parent=None)

If the JaguarInput object contains any unknown keywords, warn the user about the unknowns and ask them if they want to continue.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The JaguarInput object to check for unknown keywords
parent (PyQt4.QtGui.QWidget) - The Qt parent widget for the warning dialog

Returns: bool

True if we should continue (either there were no unknown keywords, or there were but the user wants to continue). False if we should cancel.

apply_jaguar_atom_naming(struc)

Apply jaguar unique atom naming to all atoms in the specified structure

Parameters:

struc (schrodinger.structure.Structure) - The structure to apply atom naming to

calculate_num_protons(struc)

Calculate the number of protons in the specified structure

Parameters:

struc (schrodinger.structure.Structure) - The structure to calculate protons in

Returns: int

The number of protons

get_atom_info(ws_atom_num)

Get information about the specified workspace atom

Parameters:

ws_atom_num (int) - The workspace atom number

Returns: tuple

A tuple of

The atom name (after Jaguar atom naming has been applied)
The atom number relative to the entry (rather than relative to the workspace structure)
The entry id
The entry title

atom_name_sort_key(atom_name)

Convert a Jaguar atom name into a key for use in sorting by number

Parameters:

atom_name (str) - The atom name

Returns: tuple

A tuple of (atom number, element)

generate_job_name(struc_name, task_name, theory, basis)

Generate an appropriate job name for a job with the specified settings. Any settings that are specified as None will be omitted from the job name. If a directory or file with the specified name exists in the current directory, an integer will be appended to the job name.

Parameters:

struc_name (str or NoneType) - The structure title
task_name (str or NoneType) - The task name (i.e. a shortened version of the panel name
theory (str or NoneType) - The theory method. Should be "HF", "LMP2", or the DFT functional.
basis (str or NoneType) - The basis name

Returns: str

The job name

Note: If generating multiple job names, the input for each job must be saved before the next job name is generated. Otherwise, this function will not be able to append the appropriate integer.

host_and_cpu_args(cd_params, use_parallel_arg=True, explicit_one=False, one_subjob=False)

Build the command line arguments for passing the hostname and the number of CPUs.

Parameters:

cd_params (dict) - A dictionary of the configuration dialog parameters. Must contain values for "host", "mpicpus", and "threads".
use_parallel_arg (bool) - If MPI options are not specified, should we pass the number of processors using a -PARALLEL command line argument? If False, the number of processsors will be passed using -HOST <hostname>:<number of cpus> instead.
explicit_one (bool) - Should we explicitly include the number of cpus on the command line when only single cpu has been requested? If False, only the hostname will be included on the command line. If True, "-PARALLEL 1" or "-HOST <hostname>:1" will be included. Note that this argument has no effect when more than one CPU is specified.
one_subjob (bool) - Should we explicitly specify a single subjob when passing the MPI arguments? If True, "-HOST <hostname>:1" will be included on the command line. Note that this argument has no effect when not in MPI mode or when mpisubjobs is not specified.

Returns: list

A list of command line arguments

Variables Details

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JAGUAR_IN_MAE_FILETYPES

Value:

"Jaguar Structure Input", "*.in *.mae *.maegz *.mae.gz", ("Jaguar Inpu
t", "*.in"), ("Maestro", "*.mae *.maegz *.mae.gz")

atom_name_regex

A regular expression that matches Jaguar atom names. Group 1 of the match is the element and group 2 is the number.

Value:

re.compile("^([^\W\d]+)(\d+)$")