Structure Checker in MarvinSketch

Content

Introduction
Usage in MarvinSketch
- Setting Structure Checker configuration
- Start Structure Checker
List of available checkers
- Examples of available checkers and their fixers
Links

Introduction

Structure Checker is a tool for filtering drawing mistakes or special structural elements. Registering a compound in a company's database might limit the user in, for example, the introduction of non-natural isotopes, query bonds, species with charge, etc. The Structure Checker works with predefined checking elements and you can choose which ones should be considered when you run a check. Structure checker runs a check on the molecule(s) features and lists them in a separate window with the option to refresh when you make changes to your drawing.

Structure Checker's command line tool (structurechecker), Structure Checker GUI, and API for batch usage requires a Structure Checker license. This guide refers to the checkers available free in MarvinSketch as an add-on.

Usage

Setting Structure Checker configuration

Before you start using the Structure Checker in MarvinSketch, consult the list of available checkers in the Preferences dialog (Edit > Preferences > Checkers tab).

The default list contains checkers in alphabetical order.
Two types of checkers are listed and are distinguished by the additional 'error' tag and by different icons:

Error detecting checkers: Error checkers are looking for chemically wrong molecule parts (e.g. valence errors, overlapping atoms);
Feature detecting checkers: Feature checkers searches the selected molecule characteristics which in the specific structures are not considered as an error (e.g. query properties).

Click on the name of the checker to see additional options and select the needed options by clicking the tick box.

Checking order

Some molecule properties might change after fixing an issue. You can define a checking sequence by moving up or down the list elements. The order of the checkers may be important in case you run a Fix All action.
In order to change the sequence of the checker items, select the checker from the list and click on the up

or down

icon on the right side of the dialog window.

Add and remove checker items

To discard items from the checking sequence, select the checker and click on the

button.
For adding new elements to the list, click on the

button and select the relevant checker.

Save and load checker lists

Different checking lists might be needed for different compound families. To make checking simpler, you can save your checking list to your computer and open it again if you are editing the same molecule type. Click the Save button

to save your settings and click the Load button

to open a saved configuration list.

Structurechecker configuration files may contain erroneous checker(s), i.e., Invalid Checker(s).

	If the imported configuration file contains invalid checker(s), a warning message will appear that informs the user about the issue.
	Remove the invalid checker(s) from the list to accept the proper configuration.

Start Structure Checker

You can open Structure Checker at any stage of your work. As you click on the Check structure icon

in the toolbar, or in the Structure menu, or left-click the Checker button in the statusbar, or shortcut ctrl+r, a window will appear next to the MarvinSketch window. The molecule regions found by the Structure Checker are highlighted on the canvas with a light red color. If you click on any checker message, the affected area changes color to darker red. If you move the cursor over one of the affected region, the appropriate checker message is highlighted in the checker list.

Recheck the structure

After you have changed the structure (including accepting a fix), the checker will offer re-checking: click on the Check structure again in the Structure Checker window.

re-check

Another option is to turn on automatic re-checking: click the Enable automatic checking at the bottom of the text. At any point you can allow the Structure Checker to fix the issues one by one or every of them by a single click.

Automatic structure checking

Turn on Automatic Check to follow every drawing step you make by a quick check. This option is switched on in the Structure menu or right-clicking the Checker

button on the status bar which then becomes colored.

In case of an error, a red exclamation mark appears . Left-clicking on this icon opens the Structure Checker window, where all the warnings are listed.
While the molecules are scanned for checker issues, an olive question mark appears on the status bar.
If the molecule is correct, a green check mark appears in the Checker icon on the status bar.

List of available checkers and fixers

Links

List of available checkers
Structure Checker GUI
structurechecker Command-Line Tool
Structure Checker Developer Guide