The FAQ (Frequently asked questions) page contains listed questions and answers, commonly asked about the system when using the Compound Registration web application.
If you know the compound Id (PCN, CN, LN or LnbRef) you can look for your compound just using the quick search on the Compound Registration navigation bar.
For a more advanced search, you can use the Search page. Here you can locate entries already stored in the registry database using a set of filtering options. A specific search could be used with the combination of the available search criteria. The search service also supports the use of chemical structures as queries. However, there are limitations here, e.g.: only 50 compounds are returned as hits at first (then at each scroll 50 more hits will become available from the bottom of the page); the substructure search might be very slow because of the large result set. Note also that Markush structures are stored in a separate table and the regular structure and the Markush tables are not interoperable.
For large data sets including millions of compounds or a smaller set but with lots of additional data, we recommend setting up a dedicated downstream system for searching, that can be supported by one of our JChem search engines. This will enable you to perform your searches with higher performance, while also separating the search process from your registration process, which could otherwise be a bottleneck due to the shared resources.
All Ids (from parent, version, and lot level) are kept if the structure change is performed on the parent level unless the structure already exists in the DB under a different Id. In other cases, when the structural change is made on the version or lot level, new IDs will be allocated.
Structures with R-groups or with specified repeating units are considered Markush structures. In order to register such compounds a separate (Markush) license is needed. The missing Markush license is listed in the log file, while during registration an "Unknown error-chemaxon.formats.MolFormatException: Could not calculate cd_markush field" is received.
If you have a valid Markush license in place, by default, the Markush structures are not registered automatically, they are forced to be reviewed (in the Staging area) unless Advanced Registration or Registering from the Staging area is used. In order to change the default behavior, you can remove the 'RejectMarkushValidator' workflow step, and with this, the registration of Markush structures will be automatic.
More info about registering Markush structures can be found in the Compound Registration User's Guide.
Please check the server log file for missing license errors, because some generated fields might require additional calculator licenses.
You can also check the field configuration, and whether the additional data field is configured to store at the level you expect it to. For example, a field stored only at the lot level will not be visible if you open the compound version record.
On the other hand, make sure that the field is correctly configured, having "chemicalterms" for Data Generators and the proper Generator Parameters (more info at Chemical Terms Function list).
No separate JChem Cartridge license is needed. The database storing of the Registry contains normal JChem tables and these can be directly joined to other JChem Cartridge tables if required (e.g. in a downstream system).
When registering "Polymer" structure type compounds Validation error with "Polymer contains non-monomer component" can be received if the configurable "leaving groups" are not created as rules in the system. In order to register a "Polymer" compound, first, create the "leaving group pairs" within the administration settings of the Compound Registration system, then set the components (e.g. Component 1 and Component 2) in the structure editor. When navigating to "All (2)" in the structure editor you should see the created polymer in which the leaving groups are stripped and brackets are in place. More details can be found here. If the generated polymer structure is acceptable, you can initiate the registration.
On the Salts & Solvates Administration Settings page, you can set the fractional precision for salt and solvate multiplicities. The default is 0 for salts and 1 for solvates. Therefore if you provide multiplicities with higher fractional precision, these will be simply rounded to the appropriate number. In order to store salt/solvate multiplicities with the desired fractional precision, please adjust the setting.
Salts and solvates are only extracted from the registered compound structures and stored properly as version components when they are already registered in the Salts & Solvates table and the Analyze Salt Solvate Fragments Registration option is turned on (configuration settings). Make sure that your salt/solvate is stored in the database Salts & Solvates table before registering compounds with such components and that the Analyze Salt Solvate Fragments setting is on.
The Compound Registration system is set by default in a way to check the overall charge of the submitted compound structure and its salts/solvates to be neutral. If this criterion is not met the registration will fail. You might want to neutralize your submitted compound's structure with the appropriate salts/solvates and obey the rule. Or you can turn off the 'Check for balanced charge' setting on the Administration/Chemistry/General page (a system administrator role is needed).
Marvin applet and ChemDraw are supported until Compound Registration version: 21.20.0. For ChemDraw, you would also need a valid installation on your computer (more details can be found here). For a 22.6.0 or higher version of Compound Registration, only Marvin JS can be used as a structure editor. Users who previously selected Marvin applet or ChemDraw as sketchers on their profile page will be automatically migrated to MarvinJS.
Yes. Using the Quick search you can type the given parent or version Id, then on the Browse page More actions menu you can choose the "Register lot" function.
Yes. Submissions can be modified (e.g. LnbRef, CST, structure) and then saved. These will be marked as "Saved submissions" in the Staging and their original structure can be restored later or they can be registered.
Yes. If you turn on the Administration / General Settings / 'Keep unmapped fields as "Uncategorized Data" during bulk uploads' option, the Library identifier of a given upload will be added to each uploaded compound as an additional data field. You can create a new field in the Form Editor with the Field Identifier "LIBRARY" and enable it for all those levels (parent, version, and lot), for which you would like to search on the Search page. More info on the Library Id can be found on the Definition of Terms page.
The previous migration scripts have been changed in Compound Registration versions 19.21.3 and 20.8.0. Migrations to these or future versions fail from previous versions, but re-running the migration will fix the problem. More info can be found in the Compound Registration Upgrade guide.
The error indicates that your JChem table version is different from what the current Compound Registration version expects.
From Compound Registration version 22.11.0 you can use the health check endpoint (http://yourhost:8080/RegistryCxn/rest/info/health) in order to verify the table version matching. If 'down' is reported it means that the expected JChem table version is not found.
Schema migration (more info can be found in the Compound Registration Upgrade guide) should be performed properly, then try again registering compounds.
The Search page can be used for locating compounds according to their structure type (Single Structure, Mixture, Alternate, Formulation, Alternate, Polymer, and No Structure). Currently, numbers corresponding to the structure type (not the structure type itself) can be set as search criteria. Please check our documentation for more details.
The “An error occurred while bootstrapping the application” error means that the application cannot be loaded. You always need to clear the browser cache. If you are using Internet Explorer, Edge, Google Chrome, or Mozilla Firefox you can quickly clear cache with a keyboard shortcut. While in your browser, press Ctrl + Shift + Delete simultaneously on the keyboard to open the appropriate window. Make sure that "Cookies" and "Cached images and files" and items "From the beginning of time" is selected when clearing the browsing data, then restart your browser and try to reload again the Compound Registration web application.
There are 2 options:
a.) You can use our REST API. For more details please use the Compound Registration Synergy demo environment.
b.) Using the Upload page SD Files can be uploaded. It is possible to keep the original PCN and CN provided with the record if there is no match to a previously registered compound. Different mappings can be set between the SDF fields and the system (e.g. salts and multiplicities, additional data fields, users, etc.). Note that using the Upload page only single structures can be registered.
Yes, the project-based access can be enabled (configurable). In this case, registration and access (to be viewed or to be modified) of compounds will be available only if the logged in user has the specified permission within the given project. For a logged in user, the available projects will be displayed in the field drop-down list. No registration will be possible using newly given Project name(s) as additional data. Otherwise, when Project based access is disabled, Project fields can be freely used as additional data, no filtering is made.
Note that regardless of the project settings, all the submissions that lack the Project info will be visible. More info is available on the Compound Registration documentation.
Since the V3000 molfile format does not support alias atoms this info is lost during registration.
On the Search page currently only the search for registered compounds is available, the search for the salts and/or solvates from the DB is not possible. However, using version fingerprint (salt Ids with their multiplicities) as a search criteria it is possible to search for specific salts/solvates. More info on how to use the version fingerprint is available on the Search page.
Yes. By having the Advanced mode registration on, the possible matches of a compound will be visible to the user in a so-called Suggestion list. The Advanced mode will be always on if two settings are fulfilled:
When integrating the Compound Registration system with e.g. an inventory management tool we suggest using API level integration (example) or a Downstream database (please contact Chemaxon Professional Services).
Direct database level connections should be avoided since during the development of the Compound Registration system we can always change the database schema and by this, we cannot guarantee that your integration will work. On the other hand, if you change in a way the data on the database, the application itself might be unusable.
In general, you can use the Analyze Salt/Solvate procedure which is capable of extracting automatically the salt/solvate fragments from a compound's chemical structure and replacing them with references to the corresponding records in the Salts and Solvates dictionary.
During the registration of a compound, the added CST will be attached to the first atom of the structure. When using a CST, salts/solvates might not be successfully extracted if the first atom of the compound's structure belongs to the salt. In such cases, the usage of the multi-component checker can prevent the registration of wrong parent structures. From CR version 22.19 salts will be extracted correctly from all compounds with CST.
The Project value is a lot (preparation) level info that can be propagated to the parent level too (see the Field settings). Therefore to change or add the Project info you should use the lot level.
More info is available about the Project field and Project-based access.
Salts/solvates added in an abbreviated form (not using the Expand functionality of the Marvin JS structure editor) will be still shown in an expanded form in the Salts & Solvates list. However, if you register a compound with a salt/solvate component that was added this way to the system it will result in a contracted salt/solvate overlapping with the compound structure. In order to overcome this since version 22.19 the re-addition of the salt/solvate to the system in an expanded form (Salts & Solvates list) will update automatically the previously registered compound structure images.
On the count of compounds there is no limitation directly, however the bulk upload is limited in size of the uploaded file to ~ 100 Mbytes/file. Since version 21.15.0 the default maximum size has been changed to ~ 200 Mbytes/file. An arbitrary value is configurable via the RegMaxUploadSize property (byte units).
Empty Original structures may occur for registered compounds. In such a case please contact Chemaxon's support team.
Invalid structures (if the system is configured properly, more info here) can be uploaded successfully. The compounds will be stored as "No structures" while the original structure as text will be stored as additional data. Later the "No structures" can be amended on the parent compound level and the correct structure can be provided (the Ids will be kept).