Amend

The [Amend] button is active for the execution of a modification in the chemical structure which can also include the modification/adding/removal of a CST, isotope, charge or salt/solvate information. With the aid of the [Amend] button structure type changes, like modifying a single type compound to a multi-component compound or adding/eliminating components to/from multi-component compounds can also be finalized.

Show History

History is designed to keep track and summarize modifications of a tree element from its initial registration.

Click here for more information about Show History

After selecting a tree element in the structure browser and clicking on the [Show History] button a new window opens divided into three parts:

• Details

• Source tree

• Target tree

Delete

With the aid of [Delete] button a lot or a version with the lot(s) underneath it or the parent compound along with the entire tree can be deleted. The deleted tree elements can be restored by using the Undelete command on the same page.
To delete a tree element choose the ID of your choice and click Delete. A "Deleting a structure" window appears confirming the ID value and ID type. Clicking Delete the operation is executed or you the window can be closed by pressing Cancel.
If you attempt to delete a PCN which is also a component of a multi-component compound a warning window appears "This component is used in the following multistructures [...]. It can not be deleted until those structures are not deleted".

Undelete

Deleted tree elements can be restored using the Undelete option. Similarly to Delete, the hierarchy is considered in this operation as well: e.g. if a PCN is undeleted the entire tree is restored within the same action.
To undelete a tree element click [Undelete], and an Undelete structure windows appears, with a drop-down menu to select the type of ID and a field to enter the ID to be restored. Clicking [Undelete] a window with the message "'Type' 'number' has been successfully undeleted" confirms the operation.
If an invalid ID was entered into the dialog box "The specified identifier was not found in the database." warning is received.
There are certain cases when the structure of a tree is changed, e.g. after a parent level amendment. The structure of a tree can even change after version or lot level amendment cases followed by twig optimizations. In these cases it will not be possible to restore (Undelete) a version or a lot which has been deleted prior the structural change of the tree. The following message will be received: "The version structure [ ] cannot be undeleted. This operation would create an inconsistent tree".

Rename LnbRef

The [Rename LnbRef] button is available only if a lot is selected in the Structure Browser. To change the LnbRef click on the [Rename LnbRef] button, type the new LnbRef into the appearing dialog box and click [Rename]. A Summary window confirms the changes made.
If an invalid LnbRef was entered in the dialog box a warning message "LnbRef [ ] is not valid according to the regular expression" is received.
If the input was an LnbRef already present in the database the The "LnbRef [ ] is already present in the database" message is received.

Move Lot

The [Move Lot] button is available only if a lot is selected in the Structure Browser. To move a lot to another version, type the CN into the search box and click on the Magnifying glass icon. After clicking on the [Move Lot] button, a Summary window confirms the changes made.

Change Restriction Level

In the Compound Registration the restriction level by default is set to 0, the record is considered unrestricted. A different restriction level can be manually set in the Submission page or can be inherited automatically during autoregistration or accepting a restricted match in the Submission page. An additional option is changing the restriction level of multiple records at the same time is Bulk Restriction in the Administration page.
The restriction level of a registered compound can be modified on the Amendment page. This type of amendment affects the entire tree irrespectively where the change was initialized. To change the restriction level from the Amendment page click on the [Change restriction level] button then set the restriction level and click on "Change restriction level". If a single compound to be restricted is not a component of a multi-component compound, the Updating Structure window appears with "You are about to update a structure, are you sure?" message. Clicking [Update Structure] the Summary window reports the performed modification.

Restriction Cascade from the Amendment Page

If a single compound is amended to become restricted all multi-component compounds that it is part of also become automatically restricted. In this case a Restriction warning window appears with "The restriction level of the following singles and multi-component structures will be affected by the current operation..." and the PCNs with old and new restriction level values are reported. Clicking Continue the Updating a structure window appears with the message "You are about to amend the restriction level of a structure which is used as a component of some multi-component structures (PCN). After the amendment, please also check the restriction levels of those structures." Clicking Update Structure the Summary window reports all the modifications including the single compound and all the multi-component compounds affected.

If a component of a multi-component compound is amended to match a restricted single (that already exists in the database), after choosing Accept or Replace the multicomponent compound will inherit the single compound's restriction level. In this case again a Restriction warning appears with the following message: "The restriction level of the following singles and multi-component structures will be affected by the current operation..." and beside the accepted single compound's PCN the PCN of the amended multi-component compound with the old and new restriction level value is reported. Clicking Continue the Summary window will show the amendment for the multi-component compound.
The restriction removal of a multi-component compound or a single compound involves no further consequences. I.e if the restriction of a multi-component compound is removed or changed, the restriction of the components will not be affected. If a restriction of a single compound which is a component of a multi-component compound is removed, the restriction of the multi-component compound will not be affected.

Update Layout

This feature can be applied when the user prefers to display the whole tree (parent, versions and lots) with the same arrangement of the structure. The [Update Layout] button is available only for single compounds on parent level. It is not active for multi-component compounds, though the displayed fused images of the multi-component compounds will be renewed if the component structures are updated. However the stored structures of the multi-component compounds will still remain the same.
When a preparation has been registered for first time the arrangement of its chemical structure will be inherited by its version and parent. The fused images of the following versions having only different salt/solvate information but the very same chemical structure are also based on this first representation. However, versions containing new isotope(s) and/or charge(s) are registered with their actual arrangement of their structure, which might lead to a tree having structures with different arrangements. Applying the Update Layout after a structure was modified results in an updated tree from the structure point of view, since all versions and lots will inherit the same new arrangement of the structure.
To change the chemical structure it is enough to click on the structure area on parent level and the Structure Editor will be loaded. After clicking the Update Layout a Summary window appears displaying the new arrangement of the structure.
This modification is considered as an "Update Structure Molfile" operation in the Summary / History / Audit.
The Update Layout cannot be used for versions/lots containing isotopes or charges on an explicit H. In these cases all the other versions/lots (except the ones having isotopes or charges on an explicit H) are updated according to the parent's structure.

Change Mol Weight

To set a user-supplied molecular weight click on the [Change Molweight] button (available on parent and version levels) and the Change Mol Weight window will open. The appearing Updating window confirms the modification(s) and the user-supplied molecular weight will be displayed on the information pane.
Compound Registration enables restoring of the calculated molecular masses. For that just click on the [Change Molweight] button available on version level and the Changing Molweight window will open, then clear the values and click Update both version and parent or Update version only. As a result the calculated molecular weight will be set.
The user-supplied molecular molweight of a version is inherited by the corresponding lots, but the user-supplied molecular molweight of the parent compound is applied only at parent level. Later on the accepted matches will inherit automatically the user-supplied molweight.
If any modification of a record with user-supplied molecular weight is initialized a Confirm amending the structure warning window with "This structure has a user-supplied molecular weight." is received. Clicking Continue amending the structurethe appropriate field will be active.
Please note that

• this type of amendment can be performed exclusively at version level

• the molecular formula is not affected by setting user-supplied molecular weight.

Parent Level Amendment

In the case when the amendment was initiated from a parent structure (parent level amendment, PLA), if there are no parent matches to the modified structure, the PCN will be kept for the modified structure. At parent level those structure changes can be performed which do not involve isotopes, charges or salts/solvates (since these are not stored on a parent level).

Version Level Amendment

In case of a version level amendment (VLA), if the version is the only version of the parent and there are no parent matches after the structure modifications, the amendment is considered as a PLA and the PCN will be kept for the modified structure (this process is also called as twig optimization).
If the version is not the only version of a parent and the version will still match with the original parent (e.g. changing only the salt/solvate info, charges or isotopes), the version will receive a new CN and all the lots will be moved under it. If the version is not the only version of a parent, and there are no parent matches after the structure modifications, the version with its lot(s) will be moved under a new PCN. Please note that amendment at version level are allowed only if the version to be changed contains at least one lot.

Lot Level Amendment

In case of a lot level amendment (LLA), if the lot is the only lot of the only version of a parent and there are no parent matches after the structure modifications, the amendment is considered a PLA and the PCN will be kept for the modified structure (twig optimization).
If the lot is not the only lot of a parent and the lot will still match with the original parent (e.g. changing only the salt/solvate info, charges or isotopes), the lot will be moved under a newly created CN or if a version with the same structure exists, under the matching CN. If the lot is not the only lot of a parent, and there are no parent matches after the structure modifications, the lot with its version will be moved under a new PCN (where new CN in case of new versions and new LN will be generated).

Version and Lot Level Amendment Involving Charges or Isotopes

If the amended version has charges or isotopes (in accept cases) or if the replaced tree has versions with charges or isotopes (in replace cases), the changes are made automatically, i.e. charges and isotopes are copied to the new structure (in case of accept) or charges and isotopes are copied to the existing structures (in case of replace).
VLA and LLA cannot be performed automatically when charges or isotopes/charges are present on an explicit hydrogen. In these cases manual version fix is needed. For more details about manual version fix please consult the Version Correction Page chapter on the Submission Page.
Some tautomer match cases involving isotopes or charges cannot be handled automatically. Manual version fix is needed when a structure is amended to a symmetric isotopic keto form and the (non-symmetric) enol form is accepted, e.g. when amending on version or lot level a structure to (2-13C)cyclopentan-1-one and cyclopent-1-en-1-ol from the DB is accepted. In this case the isotope can be put in two possible positions (2 or 5) and the user can decide it in a version correction page. A very similar case is when a structure is amended to a symmetric keto form having a charge (e.g.: 5-hydroxy-4-oxopiperidin-3-olate 1xNa+) and the enol form (1,2,3,6-tetrahydropyridine-3,4,5-triol ) is accepted ( table 2 ).

Table 2. Structures involved in manual version fix (accept case with charge)

Manual version fix is needed when a structure is amended to an enol form and the symmetric but isotopic/charged keto form is replaced. E.g. (2-13C)cyclopentan-1-one is already present in the DB and a structure is amended to cyclopent-1-en-1-ol, then the tautomer match is replaced ( table 3 ).

Table 3. Structures involved in manual version fix (replace case with isotope)

Parent Level Amendment Involving Versions with Charges or Isotopes

Parent level amendment cannot be performed automatically when the tree contains version(s) with salt and/or isotopes and the original structure is a symmetric molecule (e.g. benzene is amended to toluene at parent level, but there was a (13C)benzene version present in the tree). In these cases manual version fix is needed. For more details please consult the Version Correction Page from the Submission Page chapter. Version correction page will appear and manual fix will be needed also in cases when e.g. amending on parent level a carboxylic acid to its to carboxylate ester when a carboxylate version exists. In this case the user will find out through the version correction page that the change made on parent level will cause a valence error on the version. In this case he can cancel the amendment or carry on and make the change also on the version causing valence error. But later this can be corrected in a following version level amendment step (when e.g. the carboxylate ester having a negatively charged Oxygen and 1xNa+ as charge can be modified to a neutral carboxylate ester having a neutral/no salt). This is a real case, since currently there is no opportunity to change the salt/solvate information (or neither the CST) on the version correction page.