Comments (2)
MehmetAzizYirik
commented on June 26, 2024
@steinbeck The number of generated isomers is correct and the same as MOLGEN. In MOLGEN, we need to test with -noaromaticity flag.
The issue regarding the oxygen is because of the atom labelling, I need to check. So not because of valences but because of the atom labelling when we write to SDF file. This will be solved when we replace our SDF writers with the CDK's SDFWriter. I will look at it today when I set the coordinates for the atoms with CDK Structure Diagram Generator.
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MehmetAzizYirik
commented on June 26, 2024
@steinbeck I solved the atom labelling issue and tested the formula with the V.1.7. It works, no oxygens with wrong valences.
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Related Issues (20)
- Add test for uneven degree sum to recognise early that no structure will be generated HOT 1
- [enhancement] MAYGEN output as SMILES HOT 5
- [enhancement] Output only total # structures without generating sdf HOT 1
- generating output sdf HOT 3
- number of threads -> 79 HOT 5
- The number of threads is not as expected.
- SDF generation issue HOT 4
- Paralellization, -m, does not work properly in V1.7. HOT 4
- Readme instructions list wrong option HOT 1
- Add an option to filter invalid valences HOT 6
- Option to constraint generation to contain specific substructures HOT 1
- feature suggestion: move version information, add help option HOT 5
- feature suggest: extend export of .sdf
- feature suggestion: extend consideration of stereo chemistry HOT 1
- Console output for -smi is not working
- There is no generated file for only -o key.
- Add structure filters HOT 1
- Cdk 2.8 was released HOT 2
- Add links in readme ? HOT 2
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