rdkit mmpdb issues - Githubissues

rdkit / mmpdb

A package to identify matched molecular pairs and use them to predict property changes.

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How to use SQL to get the table of all rules in the mmpdb file, as well as the number of pairs, and statistics for each rule?

#62 Yueming-Yin opened 1 month ago
0
Update fragment_types.py to add SanitizeMol calls

#61 JWallaceEvotec opened 2 months ago
0
Error of "sqlite3.OperationalError: database is locked"

#60 chengthefang closed 2 months ago
1
How to solve "sqlite3.OperationalError: database is locked" error?

#59 CheminfoBlue closed 2 months ago
0
Release the latest version into PyPI?

#58 ywu opened 3 months ago
2
Use version-independent *[H] in fragment_molecule_on_explicit_hydrogens()

#57 i-tub closed 3 months ago
0
Possible SQL injection vulnerability

#56 Tenchberry closed 8 months ago
2
Compatibility with Python 3.10

#55 stevenshave closed 1 year ago
2
Unexpected generated molecule with double cuts MMPDB

#54 alicecapecchi opened 1 year ago
4
V3 dev

#53 adalke closed 6 months ago
1
Turning on --property flag leading to a smaller number of transformed structures

#52 chengthefang opened 1 year ago
0
Automatically get MMPs for a given data set

#51 pykao closed 1 year ago
4
Obtain list of matched pairs with common core from an ID.

#50 isohelio opened 1 year ago
4
Support for CXSMILES

#49 Jha-Prajjwal closed 1 year ago
4
AttributeError: module '__main__' has no attribute '__spec__'

#48 alyferryhalo opened 1 year ago
0
[docs] README.md: create installation guide

#47 alyferryhalo opened 1 year ago
5
Error when using "--out mmpa"

#46 baoilleach closed 2 years ago
4
mmpdb transform behaves unexpectedly

#45 mu-wang opened 2 years ago
5
Which "cut-smarts" patterns (i.e. fragmentation parameters) are used by default for Transform function?

#44 chengthefang closed 2 years ago
1
Can we specify the environmental radius when generating the mmpdb?

#43 chengthefang closed 2 years ago
11
Use importlib.resources instead of __file__

#42 adalke closed 2 years ago
1
Remove vendered use of peewee

#41 adalke closed 2 years ago
1
organize command-line processing and move to click

#40 adalke closed 2 years ago
4
[WIP] Fragdb proposal

#39 adalke closed 6 months ago
1
Use SQLAlchemy to work with the database

#38 adalke opened 2 years ago
1
store fragments in a SQLite db instead of JSON-Lines

#37 adalke closed 2 years ago
2
cannot fix the AttributeError: module '__main__' has no attribute '__spec__'

#36 JS0108 closed 2 years ago
2
How to build mmpdb with large data set

#35 iwatobipen closed 2 years ago
4
Update tests to support new options

#34 bp-kelley closed 2 years ago
1
How to get environment smiles?

#33 iwatobipen closed 2 years ago
3
To increase the max_rotatable_bonds?

#32 brendaferrari opened 2 years ago
2
sqlite3.OperationalError: database or disk is full when indexing

#31 chengthefang closed 3 years ago
8
Failure with mmpdb fragment for some specific smiles

#30 chengthefang opened 3 years ago
7
Use generator for stats_info instead of list

#29 i-tub closed 3 years ago
2
No statistics information in the output when using transform without property argument

#28 chengthefang closed 3 years ago
2
Memory error with mmpdb fragment for large dataset

#27 chengthefang closed 3 years ago
4
How to get the chemical information for each rule environment with a given rule?

#26 chemcomp-Jen closed 3 years ago
5
fix jupyter/ipython compatibility

#25 msteijaert closed 4 years ago
1
no_regioisomer filter could be useful

#24 KramerChristian opened 4 years ago
0
Smallest transformation only appears to not reduce to H>>X transformation

#23 KramerChristian opened 4 years ago
0
Smallest-transformation-only does not reduce all double cuts to single cuts

#22 KramerChristian opened 4 years ago
0
mmpdb transform --min-constant-size N - AttributeError: 'Fragmentation' object has no attribute 'num_variable_heavies'

#21 Niaev opened 4 years ago
1
--smallest-transformation-only doesn't work for some transformations

#20 mahendra-awale opened 4 years ago
0
support supervised fragmentation

#19 adalke closed 4 years ago
0
Add property information to CSV export

#18 mrcblt opened 4 years ago
1
Stop cutting aliphatic C-Halogen bonds

#17 KramerChristian opened 4 years ago
0
Enable Specification of exchange Fragment in mmpdb transform

#16 KramerChristian opened 4 years ago
0
multiple smarts in --cut-smarts

#15 acquaregia opened 4 years ago
5
Use lru_cache from functools

#14 gedeck closed 4 years ago
4
Incorrect atom mappings for the new generated molecules via transformation

#13 chengthefang closed 5 years ago
9