Andrew Dalke

Going back to acquaregia's request, can you give an example of of the SMIRKS you are interested in? I can see two steps that might be affected: 1) limit the...

The `mmpdb fragment` subcommand supports the `--max-rotatable-bonds` option to change the default. From the `--help` for that subcommand: ``` --max-rotatable-bonds N Maximum number of rotatable bonds (default: 10) ``` However,...

I believe what's happening is that transform works on the variable part, but hydrogens aren't treated as the variable `*[H]` but instead are treated as a special case. If so,...

As Jérôme and Christian point out, hydrogen transformations were explicitly not included as there would be too many. The `transform` option lets you specify a specific hydrogen to consider, by...

Just switched the implementation over to use [dataclasses](https://docs.python.org/3/library/dataclasses.html) instead of the manual class definitions using `__slots__`, `__init__` and `__repr__`. After tuning, the overall performance is the same as the hand-written...

I developed a [prototype using SQLAlchemy](https://github.com/adalke/mmpdb/tree/fragdb_sqlalchemy_proposal) to generate the new fragment database instead of using [hand-built SQL queries](https://github.com/adalke/mmpdb/tree/fragdb_proposal) My test set was 100 SMILES. With low-level SQL queries and 4...

This is not likely to happen as described. The property file can specify multiple properties, and the CSV output structure isn't able to handle that data meaningfully. It would be...

For @chengthefang , I cannot reproduce the problem using mmpdb3, available from https://github.com/adalke/mmpdb . Perhaps some of the changes I did for version 3 resolves your issue? For @PARODBE ,...

It's an SQLite3 file. This is the format specified by the [SQLite](https://sqlite.org/index.html) embedded relational database, and accessible from Python via the [sqlite3](https://docs.python.org/3/library/sqlite3.html) module. The specific schema is at https://github.com/adalke/mmpdb/blob/v3-dev/mmpdblib/fragment_schema.sql ....

I don't have a patch. I don't have the Java skills, nor the ability to decide which patch is most appropriate for the project, especially given the known long-term plans...