Chemistry

This menu includes a set of chemistry field related settings:

• General

  • Isotopic parent
  • Isomer identifier generation
  • Axial stereo and atropisomer differentiation
  • Positive charge
  • Balanced charge

• Salts and solvates
• Standardizer
• Structure Checker
• Stereo Analyzer

General

The General settings include the followings:

The General Chemistry Settings

Isotopic parent

If ON isotopic structures are registered as different parent compounds, otherwise these are registered as new versions of the normalized structure to the same parent compound.

Isomer identifier generation

If ON, structures with OR flags (enhanced stereochemistry) are registered as individual parent compounds during auto-registration. For each registration an ISOMER label with an integer increment is added.

Structure with OR flag

When you click on 'Find' or turn ON 'Advanced mode' and register, you can see also the similar compounds.

Stereoisomers displayed as similar compounds

 {info} Structures with OR flag can be registered as new compounds.

 {warning} In order to register unknown isomers as new compounds when using the [Remove Attached Data fixer](https://docs.chemaxon.com/display/docs/structure-checker_attached-data.md), you need to provide the Excluded "Unknown" property:

<AttachedDataChecker excluded="UNKNOWN" fixMode="fix" fixerClassName="chemaxon.fixers.RemoveAttachedDataFixer"/>

Axial stereo and atropisomer differentiation

If ON, atropisomer structures can be registered as separate parent compounds, otherwise different atropisomers will be registered under the same parent.

Atropisomer differentiation

If ON, allenes can be registered as separate parent compounds, otherwise different allenes will be registered under the same parent. More information about axial stereocenters can be found here.

Allene differentiation

Positive charge

Controls whether the check for the structures with positive charges (where structure-salt proton transfer can occur) should be enabled.

Balanced charge

Controls whether the check for unbalanced charges should be enabled.

Salts and solvates

The list of Salts and Solvates contained by the dictionary are displayed here. New salts/solvates can be added from here one by one and unused salts/solvates can be deleted. For uploading a list of salt and/or solvates use the Upload page.

The Salt and Solvate settings page

On the Settings card, you can set the appearance of the Salt/Solvate panel, the rounding of the parent multiplicity, and the salt/solvate multiplicity fractional precision.

How to add a salt or solvate :

1. Click on the Add salt button.
2. Draw or import the structure of the salt/solvate and set a name for it.

Add salt by drawing

1. Click on the Add salt button.
2. In case of success, we will be informed about the received ID of the salt or solvate.

How to delete a salt or solvate:

Since version 19.20.0 it is possible to delete unused salts/solvates.

1. Choose one or more of the unused salts/solvates to be deleted.

   • Salts/solvates that are currently in use by the system cannot be deleted. A salt/solvate is considered to be used in the following cases:
   • A registered compound contains it.
   • A deleted compound contained it.
   • A salt/solvate is considered to be unused and can be deleted:
   • It has never been used.
   • Registration of the compound with this salt/solvate failed and it is in the staging area.
   • It has been removed during amendment from all of the compounds that contained it.

2. Click to the Delete selected button.

Delete unused salts

1. Click to Proceed to confirm deletion.

Standardizer

The default general and parent Standardizer configurations

The list of available standardizer actions is available here.

Structure Checker

Since CR version 21.20.0 three categories of structure checkers (including Quality warnings) are found in the Registration system:

1. Quality Checkers are executed for each regstration and prevent registration if unfixed.
   These checkers can be configured in:
   • "do_not_fix" mode: The structure with error will not be fixed automatically, the registration is prevented.
   • "fix" mode: If available, fixer can be set to fix the structural problems.

2. Quality Warnings are executed for each registration, do not prevent registration if unfixed, just generate warnings.
   These checkers can be configured in:

   • "do_not_fix" mode: The structure with error will not be fixed, just a warning message will be visible.
   • "fix" mode: If available, fixer can be set to fix the structural problems.

3. Source-based checkers are set for a given source to be used during the registration.
   These checkers can be configured in:

• "do_not_fix" mode: The structure with error will not be fixed automatically, the registration is prevented.
• "fix" mode: If available, fixer can be set to fix the structural problems.

During autoregistration the source-based checkers, if configured, are executed.

Before version 22.11.0: source-based checkers and fixers are not applied by default in advanced mode registration, bulk upload, and submission pages, but need to be enabled manually.

Since version 22.11.0: All source-based checkers are enabled by default in advanced mode registration, bulk upload, and submission pages. Please find more information below.

Source-based checker configuration

Source-based checkers in advanced mode registration

All source-based checkers are enabled by default in advanced mode registration, bulk upload, and submission pages.

• If fixMode is set to "fix", the fixer provided in configuration is selected as default.
• If no fixerClassName is given, the "Do not fix" is selected as default
• If set fixMode is valid and different from "fix", e.g. "do_not_fix" or "ask", "Do not fix" is selected as default.

Default source-based checker setting can be modified manually during the advanced registration, bulk upload or registration from the Submission page.

You can find more details on the Structure Checker and Structure Fixer page.

The Quality Checkers, Quality Warnings and the Source-based Structure Checker settings page

Structure errors and warnings on the Registration page

 {warning} In order to register structures with enhanced stereo (_e.g._ OR flag) or structures having "STEREO" data (_e.g._ 'Major' applied by Fixer in Stereo Analyzer) as new compounds when using the [Remove Attached Data fixer](https://docs.chemaxon.com/display/docs/structure-checker_attached-data.md), you need to provide the 'Excluded' property:

<AttachedDataChecker excluded="UNKNOWN,STEREO" fixMode="fix" fixerClassName="chemaxon.fixers.RemoveAttachedDataFixer"/>

 {warning} In order to get a detailed structure checker error message, you can use the 'name' property. An example with CovalentCounterionChecker:

 <CovalentCounterionChecker FixMode="fix" FixerClassName="chemaxon.fixers.CovalentCounterionFixer" name="REGISTRAR_Detailed_Error_Message" />

Detailed Structure Checker error message on the Submission page

Detailed Structure Checker error message tooltip in the Staging area

Stereo Analyzer

The default Stereo Analyzer Configuration (it will be improved)