Autotests: Allow for stereo-bonds (up and down) to be a bond between AA and LGA #9062

Source task(s):

• Allow for stereo-bonds (up and down) to be a bond between AA and LGA #8254

Cases:

• Check that if a bond is formed between two APs where at least one of them has a stereo-bond (up or down, not either) between LGA and AA, the bond between the monomers should also appear as a stereo-bond
• Verify that if the stereo-bond has the LGA at the narrow end, it should be treated as a simple single bond.
• Verify that if only one AP has a stereo bond between LGA and AA, and the narrow end of the bond is at the AA, the bond between the monomers should remain be that stereo-bond with the same AA at the narrow end.
• Check that if both APs have a stereo bond between LGA and AA, and the narrow ends of the bonds are at the AAa, the bond between the monomers should be a simple single bond.
• Verify that in macromolecules mode, the bonds between monomers should still appear as simple single bonds
• Check that in molecules mode, if both monomers that participate in a bond are expanded, the bond can appear as a stereo-bond.
• Verify that the definition of the potential LGA is now: Every atom that has one and only one simple-single, up or down bond to another atom in the structure, and is not already an LGA.
• Check that users are able to set APs with a stereo-bond between LGA and AA.
• Check that users are able to select part of the structure where the last selected and the first not-selected atoms have a stereo-bond (up or down) between them, and get a default AP assigned upon entering the monomer creation wizard.
• Save structure with stereo bond between AA and LGA to KET and open
• Save structure with stereo bond between AA and LGA to MOL V3000 and open
• Save structure with stereo bond between AA and LGA to KET and open (Macro mode)
• Save structure with stereo bond between AA and LGA to MOL V3000 and open (Macro mode)
• Save structure with stereo bond between AA and LGA to SVG
• Save structure with stereo bond between AA and LGA to SVG (Macro mode)
• Save structure with stereo bond between AA and LGA to PNG