Alexander Korolyov

Cross-reference enums causing parsing errors

2

Hi, I noticed that using this type of enum causes an error, but it seems to work with the Google protobuf library. Although it should be fixable by simply removing...

SMARTS query: Recursive SMARTS fail to find match in the reaction substructure

2

Indigo sometimes fails to find a substructure match, when using recursive SMARTS **Steps to Reproduce** 1. I was able to reproduce the error using python indigo wrapper on Win 10...

[XTB] Fails to parse double letter elements coordinates

2

Hi, I have found that when running geometry optimization of molecules with double letter elements `Cl`, `Br`, `Si` etc, the XTB parser skipps them when parsing atomcoords. Step to reproduce...

Crash of multithreaded versions of XXXInPlace() functions

8

**Describe the bug** I have experienced crashes with some of the XXXInPlace() functions in multithreaded version. When a single function failes it correctly logs the error: ``` from rdkit import...

XXXInPlace() for multiple molecules: Return list of indices indicating failures

1

**Is your feature request related to a problem? Please describe.** When running XXXInPlace() for a list of molecules it is difficult to track down the individual failures. **Describe the solution...

### Is there an existing issue for this? - [X] I have searched the existing issues and found nothing ### Bug description 'morgan' kind is causing error in FPVecTransformer, however...

DCDReporter writes incorrect timestep to DCD header causing wrong trajectory times

1

# Bug Report: DCDFile writes incorrect timestep (DELTA) to DCD header ## Summary `DCDFile` writes the integrator's timestep instead of the effective timestep (`dt * interval`) to the DCD file...