changelog

0.2.13

- add sample_func argument to control fragment sampling and biasing the selection
- add utils.sample_csp3 function implementing fragment selection biased by the fraction of sp3-carbon atoms

0.2.12

- add support of tab-delimited files with fragments and environments (useful if names/SMILES contain commas)

0.2.11

- add support of custom functions to filter fragments chosen for attachment/replacing
- add an example how to implement and use filtering function to README
- add an auxiliary function get_replacements

0.2.10

- fix to enable compatibility with python 3.11

0.2.9

- fix a lost molecule in output of grow and mutate

0.2.8

- add link to crem.imtm.cz to README
- change default separator in fragmentation.py to tab
- fix description of arguments for grow_mol
- fix output of molecules identical to the input structure

0.2.7

- add to mutate and grow functions treatment of topologically equivalent atoms

0.2.6

- add a module to enumerate compounds based on a seed molecules using scaffold or analog modes

0.2.5

- x2 code speed up
- fix pickling mol properties in multiprocessing
- add a tutorial on machine learning and CReM

0.2.4

- add support of custom parameters which can be used for fragment selection (**kwargs in mutate_mol, grow_mol, link_mols). A user can add custom parameters (e.g. pharmacophore features count, TPSA, etc) for each fragment in additional columns of a database and use these columns for fragment pre-filtering.

0.2.3

- fixed leakage of resources due to not closed pool in generators

0.2.2

- added jupyter notebook with examples
- fix mutate_mol generator for Python 3.7 and later

0.2.1

- fix link operation to return all possible links irrespectively to the order of linked molecules

0.2

- faster selection of random replacements
- added bash script crem_create_frag_db.sh to generate fragment database in one step
- fixed the RDKit bug which prevents fragmentation with three attachment points