mmpdb
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rdkit
A package to identify matched molecular pairs and use them to predict property changes.
The transform rules in mmpdblib appears to miss some apparent cases. A test case with the following structures: ```tsv OC(c(cccc1)c1O)=O mol1 CCCCCCCC(c(cc1)cc(C(O)=O)c1O)=O mol2 CCCCCC(c(cc1)cc(C(O)=O)c1O)=O mol3 ``` with some properties: ```tsv...
This is a work-in-progress to replace the JSON-Lines fragment file with SQLite-based file. For full details see https://github.com/rdkit/mmpdb/issues/37 . - The fragment filename (if not given) defaults to "input.fragdb" -...
In 2019 [kzfm gave an example](http://blog.kzfmix.com/entry/1560658590) of using [SQLAlchemy](https://www.sqlalchemy.org/) to work with the database. In my work to [replace the JSON-Lines fragment format with a SQLite-based format](https://github.com/rdkit/mmpdb/issues/37) I quickly discovered...
I would like to do fragmentation on a dataset with 145 peptides. When I tried with mmpdb it says "too many rotatable bonds". Is there any way to increase the...
Hi all, I am using mmpdb fragment to parse a subset of SureChembl database, and then I found the mmpdb fragment will fail for some specific smiles. I wonder if...
On Windows, the options `--min-variable-size` and `--min-constant-size` of **transform** command aren't working. It is saying that, in the line 909 in `mmpdblib/analysis_algorithms.py`, a Fragmentation object has no attribute 'num_variable_heavies'. I'm...
Double- and triple-cuts can produce regioisomers, where the constant parts are just swapped. Examples are these transformations: Double cut: [*:1]CC1(CC1)[*:2] >> [*:1]C1(CC1)C[*:2] Triple cut: [*:1]c1cc([*:2])c([*:3])cc1 >> [*:1]c1cc([*:3])c([*:2])cc1 It may be...
The Smallest-transformation-only appears to not reduce single-cut transformations to H>>X transformations. For example, the transformation [*:1]c1ccccc1 >> [*:1]c1ccc(F)cc1 is still in the database, although it could be reduced to [*:1][H]...
With the current implementation of smallest-transformation only, some reducible double-cut transformations are still present in the database. For example, this transformation [*:1]C(F)[*:2] >> [*:1]C(Cl)[*:2] can be reduced to that transformation...
A "--smallest-transformation-only" option doesn't produce desirable result with some transformations. It seems that there is conflict between --smallest-transformation-only option (use during indexing) with --min-heavies-per-const-frag option (use during fragmentation) For example,...
