schrodinger.application.matsci.reportutils module

Utilities for creating MatSci reports.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.reportutils.Footer(text, height)

Bases: tuple

height

Alias for field number 1

text

Alias for field number 0

class schrodinger.application.matsci.reportutils.ReportInfo(panel, output_dir, base_name, outputs)

Bases: object

Manages information about the report request. Contains user inputs as well as panel data.

__init__(panel, output_dir, base_name, outputs)

Create an instance and store arguments

Parameters

  • panel (af2.App) – The panel for which the report is requested

  • output_dir (str) – The directory to write the report files in

  • base_name (str) – The base name for the exported files and folders

  • outputs (list) – The outputs that the user has requested for the report

pdfRequested()

Determine whether a pdf was requested for the report

Return type

bool

Returns

Whether a pdf was requested for the report

imagesRequested()

Determine whether images were requested for the report

Return type

bool

Returns

Whether images were requested for the report

dataRequested()

Determine whether raw data was requested for the report

Return type

bool

Returns

Whether raw data was requested for the report

getPDFPath()

Get the path to the report pdf file

Return type

str

Returns

path to the report pdf file

getCsvFilePath()

Get the path to the data csv file

Return type

str

Returns

path to the data csv file

getImagesDirPath()

Get the path to the images directory

Return type

str

Returns

path to the images directory

setFigures(figures)

Set the figures for the report

Parameters

figures (matplotlib.figure.Figure) – The figures for the report

okToWrite()

Ensure that target files and folders don’t already exist, or if they do, they can be overwritten

Return type

bool

Returns

Whether we are clear to write

class schrodinger.application.matsci.reportutils.PDFBuilder(report_info, left_margin=27.0, top_margin=72.0, right_margin=18.0, bottom_margin=72.0)

Bases: object

Contains features shared by all MatSci PDF builder classes.

__init__(report_info, left_margin=27.0, top_margin=72.0, right_margin=18.0, bottom_margin=72.0)

Create a PDFBuilder instance. Store and initialize variables.

Parameters

  • report_info (ReportInfo) – The report information object

  • left_margin (int) – The left margin for the pdf

  • top_margin (int) – The top margin for the pdf

  • right_margin (int) – The right margin for the pdf

  • bottom_margin (int) – The bottom margin for the pdf

build()

Build the report pdf. Calls methods that should be defined in derived classes to add flowables and footers.

addFlowables()

Add flowables to the pdf, such as headers, titles, paragraphs, tables and images. Should be defined in derived classes.

addFooters()

Add footers. Should be defined in derived classes.

writeParagraphs(paragraphs)

Add the paragraphs to the pdf as flowables.

Parameters

paragraphs (list) – A list of strings, each of which should be a paragraph

addFigure(figure, box_x, box_y)

Add the figure to the pdf as a flowable.

Parameters

  • figure (matplotlib.figure.Figure) – The figure to add to the pdf

  • box_x – The width of the box that the image should be fitted in

  • box_y – The height of the box that the image should be fitted in

getTempImageFilename()

Get a temporary image file path and add it to the list of files to be cleaned up.

Return type

str

Returns

A temporary image file path

cleanupTempFiles()

Clean up all the temporary files

getTableStyle(column_headers=True, row_headers=False, align_center=True)

Create a platypus table style based on desired headers and alignment

Parameters

  • column_headers (bool) – Whether the table columns have headers

  • row_headers (bool) – Whether the table rows have headers

  • align_center (bool) – Whether align center should be used for all cells

Return type

list of tuples

Returns

A platypus table style based on desired headers and alignment

addSpacer()

Add a space between the last and next flowables

class schrodinger.application.matsci.reportutils.CanvasWithHeaderAndFooter(*args, **kwargs)

Bases: schrodinger.application.desmond.rl_helper.NumberedCanvas

Canvas that automatically adds matsci logo to the header, and allows custom footers in addition to the page number and “Report generated” string.

FOOTERS = {}
__init__(*args, **kwargs)

Create an instance.

drawFixedContents(*args)

Draw fixed pdf contents such as headers, footers and fixed graphics

class schrodinger.application.matsci.reportutils.ReportOutputsDialog(*args, default_base_name='', report_btn=True, images_btn=True, data_btn=True, **kwargs)

Bases: schrodinger.ui.qt.swidgets.SDialog

Dialog for allowing the user to specify requested report outputs. Calls the report generation method of the panel when the user accepts.

DIR_SELECTOR_ID = 'REPORT_UTILS_DIR_SELECTOR_ID'
__init__(*args, default_base_name='', report_btn=True, images_btn=True, data_btn=True, **kwargs)

Create an instance.

Parameters

  • report_btn (bool) – Whether PDF Report checkbox should be in the dialog

  • images_btn (bool) – Whether Plots checkbox should be in the dialog

  • data_btn (bool) – Whether Data checkbox should be in the dialog

layOut()

Lay out the widgets.

accept()

Get user inputs and call the report generation method of the panel.

schrodinger.application.matsci.reportutils.save_figure(figure, file_path, panel)

Exports the figure to a file, showing an error if it fails.

Parameters

  • figure (matplotlib.figure.Figure) – The figure to export

  • file_path (str) – The path to the image file to be created

  • panel (af2.App) – The panel to show any error in

Return type

bool

Returns

Whether the image export was successful

schrodinger.application.matsci.reportutils.save_images(report_info)

Save all images in the report information object to the output directory

Parameters

report_info (ReportInfo) – The report information object containing the figures

schrodinger.application.matsci.reportutils.sub_script(text, size=10)
Parameters

  • text (str or int or float) – The text to write as a subscript

  • size (int) – The font size of the subscript

Return type

str

Returns

The text formatted to appear as a subscript in the report

schrodinger.application.matsci.reportutils.super_script(text, size=10)
Parameters

  • text (str or int or float) – The text to write as a superscript

  • size (int) – The font size of the superscript

Return type

str

Returns

The text formatted to appear as a superscript in the report

schrodinger.application.matsci.reportutils.save_matplotlib_figure(figures, pdf_name)

Save or Append the matplotlib figure to a pdf

Parameters

  • figures (list) – list of matplotlib figure to be added to the pdf

  • pdf_name (str) – filename for the pdf file