Package schrodinger :: Package application :: Package desmond :: Module feputils

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Module feputils

Classes

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OPLSSettingManager
Simple context manager to modify and restore user's mmfile search path, if appropriate.

ProteinProcessManager
A lightweight thread that spawns the protein reliability process to run in the background.

LabelSpinner
This object replaces a label's icon with a spinning progress icon when start() is called.

ProteinCheckLabelSpinner

Functions

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tuple

run_protein_reliability(protein_file)
Takes a protein ct and returns a message indicating problems, if any.

read_protein_reliability(p, std_err, reportfile, outputfile)

launch_protein_reliability(protein_file)

is_prepped(protein)
Check if a protein has been prepared in Protein PrepWizard

get_protein_label_string(ct)
Returns a string for use in GUI to indicate the protein.

format_protein_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.

setup_protein_warning(protein_label, protein_warning_label)
Utility function to set up a protein warning label.

setup_protein_health_button(protein_health_btn)
utility function to set up protein health toolbutton.

get_warning_pixmap(widget_height, widget_width=None)
Returns a standardized pixmap for a given widget size

get_proteins(ct_list)
Iterates through a list of structures and returns only the proteins

get_ligands(ct_list)
Iterates through a list of structures and returns only the ligands.

list

import_pt_entries()
Imports selected entries from the project table.

import_pv_file(filename)
Imports a list of structures from a structure file.

get_opls_dir_setting()

list

make_fep_cmd(cd_params, ao, jobname, struct_fname, opt=[])
Generates an FEP command list based on the specified parameters.

generate_scripts(cd_params, jobname, cmd, opls_dir_setting)

Variables

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maestro = schrodinger.get_maestro()

ENTRY_ID_KEY = 's_fepmapper_entryid'

NO_CACHE_STRING = 'No cache string'

__package__ = 'schrodinger.application.desmond'

Function Details

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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).

Parameters:

protein_file (schrodinger.structure.Structure) - A protein to assess

Returns: tuple

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

is_prepped(protein)

Check if a protein has been prepared in Protein PrepWizard

Parameters:

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

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

format_protein_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

setup_protein_warning(protein_label, protein_warning_label)

Utility function to set up a protein warning label. This is done to provide a consistent look for protein warnings across several panels.

Parameters:

protein_label (QtWidgets.QLabel) - The protein or receptor label
protein_warning_label (QtWidgets.QLabel) - The label that will hold the warning image

setup_protein_health_button(protein_health_btn)

utility function to set up protein health toolbutton. This button becomes visible when protein health check detects any problems. This is done to provide consistent look across several panels.

Parameters:

protein_health_btn (QtWidgets.QToolButton) - toolbutton that is used to bring up protein relaiability report panel.

get_proteins(ct_list)

Iterates through a list of structures and returns only the proteins

Parameters:

ct_list (list) - a list of structures

get_ligands(ct_list)

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

Parameters:

ct_list (list) - a list of structures

import_pt_entries()

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

Returns: list: a list of imported structures. Each structure is tagged with a property 's_fepmapper_entryid' to store the entry id.

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.

Parameters:

filename (str) - the filename

make_fep_cmd(cd_params, ao, jobname, struct_fname, opt=`[]`)

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
master_msj_fname (str) - the filename for the master msj file
struct_fname (str) - the filename for the input structure

Returns: list

a command list for launching the job

Module feputils

run_protein_reliability(protein_file)

is_prepped(protein)

get_protein_label_string(ct)

format_protein_label(ct, label, max_chars=40)

setup_protein_warning(protein_label, protein_warning_label)

setup_protein_health_button(protein_health_btn)

get_proteins(ct_list)

get_ligands(ct_list)

import_pt_entries()

import_pv_file(filename)

make_fep_cmd(cd_params, ao, jobname, struct_fname, opt=[])

make_fep_cmd(cd_params, ao, jobname, struct_fname, opt=`[]`)