No regular build due to fallback

Hi,


I'm getting this error when trying to get the 3d conformation of a particular molecule fragment:


No regular build due to fallback.


Clean failed.


CC1=CC=C(I)C(=O)N1





What I'm doing is:


- Importing a molecule defined by a SMILES string; I'm using the PDB 2BE2 ligand as an example, for other ligands everything works;


- Finding all the rotatable bonds according to the Topology Analyser Plugin;


- Removing those bonds and converting the molecule to fragments;


- For each fragment, find the 3D conformation via the Conformer Plugin


The error occurs when running ConformerPlugin.run(); I get that error and no conformation is generated. Although for other fragments of the same ligand it's ok.





The input ligand is:


CC1=C(CSCc2occc2)C(=C(I)C(=O)N1)Oc3cc(C)cc(C)c3


The fragment which gives an error is:


CC1=CC=C(I)C(=O)N1


Loading the fragment from the SMILES string and generating the conformation this way works well. Also generating the 2d conformation instead of 3d works.





I have attached a short program to show the problem.


Thank you!


Simone

Hi,





Thank you for the detailed description. The 3D calculation failed because a false CIS/TRANS stereo flag appeared in the fragment. This bug will be fixed in the next release, for the meantime you can work around this problem by manually deleting the C/T flags from the bonds:





for( int j = 0; j < newMol.getBondCount(); j++ ) {


MolBond bond = newMol.getBond( j );


bond.setFlags( 0, MolBond.CTUMASK );


}








Regards,


Gabor