rdkit/mmpdb issues and pull requests

#69 - update get_atom_order_in_smiles to work with RDKit 2024.3 and above

Pull Request - State: closed - Opened by thras-deepcure 3 months ago - 2 comments

#68 - Push mmpdb 3.1 to PyPI

Issue - State: closed - Opened by ESRE-dev 3 months ago - 1 comment

#67 - Consider adding RDKit to the package dependencies

Issue - State: open - Opened by ESRE-dev 3 months ago - 2 comments

#66 - Fix _smilesAtomOutputOrder parsing for RDKit 2024.03.6 or newer (Issue #7749)

Pull Request - State: closed - Opened by ricrogz 3 months ago - 2 comments

#65 - mmpdb fragment fails with RDKit 2024.03.6 or newer

Issue - State: closed - Opened by ricrogz 3 months ago

#64 - Support for double-cut linkers with 0 atoms

Issue - State: open - Opened by baoilleach 4 months ago - 1 comment

#63 - Unexpected results from Generate

Issue - State: open - Opened by lydiaauch 4 months ago

#62 - 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?

Issue - State: open - Opened by Yueming-Yin 9 months ago

#61 - Update fragment_types.py to add SanitizeMol calls

Pull Request - State: open - Opened by JWallaceEvotec 9 months ago

#60 - Error of "sqlite3.OperationalError: database is locked"

Issue - State: closed - Opened by chengthefang 10 months ago - 1 comment

#59 - How to solve "sqlite3.OperationalError: database is locked" error?

Issue - State: closed - Opened by CheminfoBlue 10 months ago

#58 - Release the latest version into PyPI?

Issue - State: open - Opened by ywu 11 months ago - 3 comments

#57 - Use version-independent *[H] in fragment_molecule_on_explicit_hydrogens()

Pull Request - State: open - Opened by i-tub about 1 year ago

#56 - Possible SQL injection vulnerability

Issue - State: closed - Opened by Tenchberry over 1 year ago - 2 comments

#55 - Compatibility with Python 3.10

Pull Request - State: closed - Opened by stevenshave over 1 year ago - 2 comments

#54 - Unexpected generated molecule with double cuts MMPDB

Issue - State: open - Opened by alicecapecchi over 1 year ago - 4 comments

#53 - V3 dev

Pull Request - State: closed - Opened by adalke over 1 year ago - 1 comment

#52 - Turning on --property flag leading to a smaller number of transformed structures

Issue - State: open - Opened by chengthefang almost 2 years ago

#51 - Automatically get MMPs for a given data set

Issue - State: closed - Opened by pykao about 2 years ago - 4 comments

#50 - Obtain list of matched pairs with common core from an ID.

Issue - State: open - Opened by isohelio about 2 years ago - 4 comments

#49 - Support for CXSMILES

Issue - State: closed - Opened by Jha-Prajjwal over 2 years ago - 4 comments

#48 - AttributeError: module 'main' has no attribute 'spec'

Issue - State: open - Opened by alyferryhalo over 2 years ago

#47 - [docs] README.md: create installation guide

Issue - State: open - Opened by alyferryhalo over 2 years ago - 5 comments

#46 - Error when using "--out mmpa"

Issue - State: closed - Opened by baoilleach almost 3 years ago - 4 comments

#45 - mmpdb transform behaves unexpectedly

Issue - State: open - Opened by mu-wang almost 3 years ago - 5 comments

#44 - Which "cut-smarts" patterns (i.e. fragmentation parameters) are used by default for Transform function?

Issue - State: closed - Opened by chengthefang about 3 years ago - 1 comment

#43 - Can we specify the environmental radius when generating the mmpdb?

Issue - State: closed - Opened by chengthefang about 3 years ago - 11 comments

#42 - Use importlib.resources instead of file

Issue - State: closed - Opened by adalke over 3 years ago - 1 comment

#41 - Remove vendered use of peewee

Issue - State: closed - Opened by adalke over 3 years ago - 1 comment

#40 - organize command-line processing and move to click

Issue - State: closed - Opened by adalke over 3 years ago - 4 comments

#39 - [WIP] Fragdb proposal

Pull Request - State: closed - Opened by adalke over 3 years ago - 1 comment

#38 - Use SQLAlchemy to work with the database

Issue - State: open - Opened by adalke over 3 years ago - 1 comment

#37 - store fragments in a SQLite db instead of JSON-Lines

Issue - State: closed - Opened by adalke over 3 years ago - 2 comments

#36 - cannot fix the AttributeError: module 'main' has no attribute 'spec'

Issue - State: closed - Opened by JS0108 over 3 years ago - 2 comments

#35 - How to build mmpdb with large data set

Issue - State: closed - Opened by iwatobipen over 3 years ago - 4 comments

#34 - Update tests to support new options

Pull Request - State: closed - Opened by bp-kelley over 3 years ago - 1 comment

#33 - How to get environment smiles?

Issue - State: closed - Opened by iwatobipen over 3 years ago - 3 comments

#32 - To increase the max_rotatable_bonds?

Issue - State: open - Opened by brendaferrari over 3 years ago - 2 comments

#31 - sqlite3.OperationalError: database or disk is full when indexing

Issue - State: closed - Opened by chengthefang over 3 years ago - 8 comments

#30 - Failure with mmpdb fragment for some specific smiles

Issue - State: open - Opened by chengthefang almost 4 years ago - 7 comments

#29 - Use generator for stats_info instead of list

Pull Request - State: closed - Opened by i-tub almost 4 years ago - 2 comments

#28 - No statistics information in the output when using transform without property argument

Issue - State: closed - Opened by chengthefang almost 4 years ago - 2 comments

#27 - Memory error with mmpdb fragment for large dataset

Issue - State: closed - Opened by chengthefang almost 4 years ago - 4 comments

#26 - How to get the chemical information for each rule environment with a given rule?

Issue - State: closed - Opened by chemcomp-Jen almost 4 years ago - 5 comments

#25 - fix jupyter/ipython compatibility

Pull Request - State: closed - Opened by msteijaert almost 5 years ago - 1 comment

#24 - no_regioisomer filter could be useful

Issue - State: open - Opened by KramerChristian about 5 years ago
Labels: enhancement

#23 - Smallest transformation only appears to not reduce to H>>X transformation

Issue - State: open - Opened by KramerChristian about 5 years ago
Labels: enhancement

#22 - Smallest-transformation-only does not reduce all double cuts to single cuts

Issue - State: open - Opened by KramerChristian about 5 years ago
Labels: enhancement

#21 - mmpdb transform --min-constant-size N - AttributeError: 'Fragmentation' object has no attribute 'num_variable_heavies'

Issue - State: open - Opened by Niaev about 5 years ago - 1 comment

#20 - --smallest-transformation-only doesn't work for some transformations

Issue - State: open - Opened by mahendra-awale about 5 years ago

#19 - support supervised fragmentation

Pull Request - State: closed - Opened by adalke over 5 years ago

#18 - Add property information to CSV export

Issue - State: open - Opened by mrcblt over 5 years ago - 1 comment
Labels: enhancement

#17 - Stop cutting aliphatic C-Halogen bonds

Issue - State: open - Opened by KramerChristian over 5 years ago
Labels: enhancement

#16 - Enable Specification of exchange Fragment in mmpdb transform

Issue - State: open - Opened by KramerChristian over 5 years ago
Labels: enhancement

#15 - multiple smarts in --cut-smarts

Issue - State: open - Opened by acquaregia over 5 years ago - 10 comments
Labels: enhancement

#14 - Use lru_cache from functools

Pull Request - State: closed - Opened by gedeck over 5 years ago - 4 comments

#13 - Incorrect atom mappings for the new generated molecules via transformation

Issue - State: closed - Opened by chengthefang over 5 years ago - 9 comments

#12 - Can I get a table of all rules, as well as the number of pairs, and statistics for each rule?

Issue - State: closed - Opened by chengthefang almost 6 years ago - 5 comments

#11 - How to output a list of ID of compounds forming pairs?

Issue - State: closed - Opened by den2882 almost 6 years ago - 5 comments

#10 - How to know the number of pairs & rules from generated .mmpdb file?

Issue - State: closed - Opened by chengthefang almost 6 years ago - 2 comments

#9 - --min-heavies-per-const-frag 3 option looses some transformations

Issue - State: closed - Opened by ValeryPolyakov almost 6 years ago - 17 comments

#8 - update setup.py and copyright dates

Pull Request - State: closed - Opened by adalke almost 6 years ago - 1 comment

#7 - Test

Pull Request - State: closed - Opened by OriolLopezMassaguer about 6 years ago

#6 - Out of memory when indexing a large fragment file

Issue - State: closed - Opened by ValeryPolyakov over 6 years ago - 31 comments
Labels: enhancement

#5 - fixed typo in the *_num_heavies attribute and added a filter max-variable-size

Pull Request - State: closed - Opened by prakashrathi over 6 years ago - 4 comments
Labels: bug, enhancement

#4 - ujson is not appreciably faster than json

Issue - State: open - Opened by adalke over 6 years ago

#3 - Symmetric variable fragments are not replaced in both possible directions

Issue - State: closed - Opened by KramerChristian over 6 years ago - 1 comment
Labels: bug

#2 - changes for the 2.1 release

Pull Request - State: closed - Opened by adalke over 6 years ago - 2 comments
Labels: bug

#1 - Open question: chemical formula equivalent to mmpdb

Issue - State: closed - Opened by tantrev almost 7 years ago - 2 comments
Labels: question

GitHub / rdkit/mmpdb issues and pull requests