datamol-io/datamol issues and pull requests

#231 - Fixing does not appear to work for inferring valence & formal charge states from molecules from some PDB files

Issue - State: open - Opened by Croydon-Brixton 5 months ago - 4 comments

#230 - Adding JSON I/O for molecules

Issue - State: open - Opened by isty2e 6 months ago - 1 comment

#229 - Conformer generation error with specific RDKit version

Issue - State: open - Opened by SergeiNikolenko 7 months ago - 1 comment

#228 - Codecov action not working

Issue - State: open - Opened by zhu0619 8 months ago
Labels: medium-priority

#227 - actions/checkout upgraded to v4

Pull Request - State: closed - Opened by zhu0619 8 months ago - 1 comment

#226 - refactor to rdFingerprintGenerator

Pull Request - State: closed - Opened by zhu0619 8 months ago - 4 comments
Labels: enhancement

#225 - Fix deprecation warning for `dm.to_fp`

Issue - State: closed - Opened by cwognum 9 months ago

#224 - Test

Issue - State: closed - Opened by Valence-JonnyHsu 11 months ago

#223 - Allow additional args for colors in lasso

Pull Request - State: closed - Opened by maclandrol about 1 year ago - 1 comment

#222 - pass max_mols to Draw.MolsToGridImage

Pull Request - State: closed - Opened by kkovary about 1 year ago - 3 comments
Labels: feature

#221 - `max_mols` is limited to 50 in `dm.to_image`

Issue - State: closed - Opened by kkovary about 1 year ago

#220 - unique_id doesn't require MD5 hashing?

Issue - State: closed - Opened by DomInvivo about 1 year ago - 8 comments

#219 - Add rdkit as a pypi dep

Pull Request - State: closed - Opened by hadim about 1 year ago - 1 comment
Labels: feature

#218 - [WIP] Experiment with pixi for CI

Pull Request - State: closed - Opened by hadim about 1 year ago - 2 comments

#217 - Added function to get the number of stereoisomers

Pull Request - State: closed - Opened by zhu0619 about 1 year ago - 3 comments
Labels: feature, fix

#216 - Compat with latest RDKit 2023.09

Pull Request - State: closed - Opened by hadim over 1 year ago - 1 comment
Labels: feature

#215 - Test new RDKit version `2023_09_1`

Issue - State: closed - Opened by hadim over 1 year ago
Labels: enhancement, good first issue

#214 - Improve the ChEMBL drugs dataset

Pull Request - State: closed - Opened by stwhitfield over 1 year ago - 2 comments
Labels: fix

#213 - Improve chembl drugs dataset

Issue - State: closed - Opened by hadim over 1 year ago - 2 comments
Labels: enhancement, good first issue

#212 - Fix ResourceWarning due to unclosed file

Pull Request - State: closed - Opened by kkovary over 1 year ago - 6 comments
Labels: fix

#211 - Resolve ResourceWarning due to unclosed file in `datamol/mol.py`

Issue - State: closed - Opened by kkovary over 1 year ago
Labels: bug

#210 - Make sure paths are string in `datamol.fs.glob`

Pull Request - State: closed - Opened by hadim over 1 year ago
Labels: fix

#209 - fix zero division error in conformers

Pull Request - State: closed - Opened by shuyana over 1 year ago - 5 comments
Labels: fix

#208 - Add two more datasets + ruff linting

Pull Request - State: closed - Opened by hadim over 1 year ago - 1 comment
Labels: feature

#207 - fix small typos

Pull Request - State: closed - Opened by mercuryseries over 1 year ago - 1 comment
Labels: fix

#206 - Better control of the circular layout in `circle_grid`

Pull Request - State: closed - Opened by hadim over 1 year ago - 1 comment
Labels: feature, fix

#205 - Non-random arrangement in circle grid

Issue - State: closed - Opened by PatWalters over 1 year ago - 4 comments
Labels: enhancement

#204 - stray print statement in datamol/viz/_lasso_highlight.py

Issue - State: closed - Opened by PatWalters over 1 year ago - 1 comment
Labels: bug

#203 - Rewrite dm.viz.circle_grid with RDKit's canvas and support grid image for lasso highlight

Pull Request - State: closed - Opened by maclandrol over 1 year ago - 2 comments
Labels: feature, fix

#202 - Removing salts, solvents and/or stereochemistry from a molecule

Issue - State: closed - Opened by zhu0619 over 1 year ago
Labels: feature

#201 - Add two new functions to remove salts and solvents from a molecule

Pull Request - State: closed - Opened by zhu0619 over 1 year ago - 10 comments
Labels: feature

#200 - Datamol CLI

Issue - State: open - Opened by hadim over 1 year ago
Labels: enhancement, question

#199 - Allow molecules grid image in `dm.viz.lasso_highlight_image()`

Issue - State: closed - Opened by hadim over 1 year ago
Labels: enhancement

#198 - Fix bugs and support atom indices as inputs in the lasso viz function

Pull Request - State: closed - Opened by hadim over 1 year ago - 1 comment
Labels: fix

#197 - New more robust datamol release process

Pull Request - State: closed - Opened by hadim over 1 year ago - 1 comment
Labels: feature

#196 - Question on dm.viz.circle_grid

Issue - State: closed - Opened by PatWalters over 1 year ago - 5 comments
Labels: bug

#195 - A couple of problems with dm.viz.lasso_highlight_image

Issue - State: closed - Opened by PatWalters over 1 year ago - 4 comments
Labels: bug, enhancement

#194 - Better doc release process + get rid of rever

Issue - State: closed - Opened by hadim over 1 year ago
Labels: low-priority

#193 - Minor change to background color of the tabs

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

#191 - Typo in the sample code on homepage

Issue - State: closed - Opened by rkakamilan over 1 year ago - 3 comments
Labels: bug

#190 - Failed to access to GCP bucket

Issue - State: closed - Opened by rkakamilan over 1 year ago - 5 comments

#189 - Add newest RDKit version and remove oldest and tested with pytest

Pull Request - State: closed - Opened by dessygil over 1 year ago - 11 comments

#188 - fuzzy_scaffold can now return a pandas dataframe that is more readable.

Pull Request - State: closed - Opened by Pakman450 over 1 year ago - 10 comments

#186 - Test and check compatibility with RDKit 2023.03.1

Issue - State: closed - Opened by hadim almost 2 years ago - 1 comment
Labels: enhancement, medium-priority

#185 - I just want to say thanks

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

#184 - Change the docs style with navigation tabs

Pull Request - State: closed - Opened by DomInvivo almost 2 years ago - 3 comments

#183 - Documentation link on google is wrong

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

#182 - Load/save dataframe #163

Pull Request - State: closed - Opened by dessygil almost 2 years ago - 6 comments

#181 - Lazy loading

Pull Request - State: closed - Opened by hadim almost 2 years ago - 11 comments

#180 - Move release process in CI only

Issue - State: closed - Opened by hadim almost 2 years ago - 1 comment
Labels: enhancement, medium-priority

#179 - Consistent image output

Pull Request - State: closed - Opened by hadim almost 2 years ago - 3 comments

#178 - New feature. Users can now use some RDKit FilterCatalog features.

Pull Request - State: closed - Opened by Pakman450 almost 2 years ago - 5 comments

#177 - Integrate lasso highlight viz functions

Pull Request - State: closed - Opened by dessygil almost 2 years ago - 8 comments

#176 - fix color bug

Pull Request - State: closed - Opened by maclandrol almost 2 years ago - 1 comment

#175 - Use docs.datamol.io subdomain instead of doc.datamol.io

Pull Request - State: closed - Opened by mercuryseries almost 2 years ago

#174 - Use docs.datamol.io instead of doc.datamol.io

Pull Request - State: closed - Opened by mercuryseries almost 2 years ago

#173 - request to add a mol2 file reader

Pull Request - State: closed - Opened by Pakman450 almost 2 years ago - 6 comments

#172 - Updated logging for _sanifix4.py

Pull Request - State: closed - Opened by cwognum almost 2 years ago - 3 comments

#171 - New doc branding

Pull Request - State: closed - Opened by hadim almost 2 years ago

#170 - Rename datamol-org to datamol-io everywhere

Pull Request - State: closed - Opened by hadim almost 2 years ago - 1 comment

#169 - Replace datamol-org by datamol-io due to org renaming

Issue - State: closed - Opened by hadim almost 2 years ago

#168 - faster way to generated mol_ids

Issue - State: closed - Opened by joao-alex-cunha almost 2 years ago - 4 comments

#167 - [PROPOSAL] Refactor `rever` files

Issue - State: closed - Opened by SauravMaheshkar almost 2 years ago - 1 comment

#166 - gh: refactor community files

Pull Request - State: closed - Opened by SauravMaheshkar almost 2 years ago - 2 comments

#165 - reformat

Pull Request - State: closed - Opened by MichelML almost 2 years ago - 3 comments

#164 - Add missing fcfp func in fingerprint functions dict

Pull Request - State: closed - Opened by MichelML almost 2 years ago - 8 comments
Labels: bug

#163 - Add flexible file reader and saver

Issue - State: closed - Opened by zhu0619 about 2 years ago - 3 comments
Labels: enhancement

#162 - feat(ci/codeql): drop autobuild

Pull Request - State: closed - Opened by SauravMaheshkar about 2 years ago - 1 comment

#161 - feat(ci): add `pip` cache to code-check workflow

Pull Request - State: closed - Opened by SauravMaheshkar about 2 years ago - 1 comment

#160 - Move the fs module to its dedicated section in the docs

Issue - State: closed - Opened by MichelML about 2 years ago - 1 comment
Labels: documentation

#159 - pdn readers and writers

Pull Request - State: closed - Opened by hadim about 2 years ago - 1 comment

#158 - Typing: `dm.to_df` output type should not be optional

Issue - State: closed - Opened by hadim about 2 years ago
Labels: bug, low-priority

#157 - Add `io` functions to read/write PDB file and block

Issue - State: closed - Opened by hadim about 2 years ago

#156 - Add utility functions to manipulate atom positions and properties

Pull Request - State: closed - Opened by hadim about 2 years ago - 1 comment

#155 - Rdkit compat

Pull Request - State: closed - Opened by hadim about 2 years ago - 1 comment

#154 - Sdf options

Pull Request - State: closed - Opened by DomInvivo about 2 years ago - 1 comment

#153 - Add new descriptor `n_stereo_centers_unspecified`

Issue - State: closed - Opened by hadim about 2 years ago
Labels: enhancement

#152 - Integrate lassohighlight

Issue - State: closed - Opened by hadim about 2 years ago - 6 comments
Labels: enhancement

#151 - Dev

Pull Request - State: closed - Opened by hadim about 2 years ago - 1 comment

#150 - `dm.read_smi()` copies a file to an already existing location

Issue - State: closed - Opened by cwognum about 2 years ago - 6 comments
Labels: bug

#149 - Faster `to_df` for mols to dataframe conversion

Pull Request - State: closed - Opened by maclandrol about 2 years ago - 2 comments

#148 - `dm.fs.glob` does not properly handle the `**` pattern properly

Issue - State: closed - Opened by cwognum about 2 years ago - 1 comment

#147 - Update Aligning.ipynb

Pull Request - State: closed - Opened by Valence-JonnyHsu over 2 years ago - 3 comments

#146 - AttributeError: module `'rdkit.Chem.Draw'` has no attribute `'_okToKekulizeMol'`

Issue - State: closed - Opened by sgalpha01 over 2 years ago - 2 comments
Labels: bug

#145 - compat with newest rdkit

Pull Request - State: closed - Opened by hadim over 2 years ago - 2 comments

#144 - Test compatibility with RDKit 2022_09_1

Issue - State: closed - Opened by hadim over 2 years ago - 1 comment
Labels: enhancement, high-priority

#143 - Reations

Pull Request - State: closed - Opened by zhu0619 over 2 years ago - 3 comments

#142 - Reaction

Pull Request - State: closed - Opened by zhu0619 over 2 years ago

#141 - add options in select_product [skip ci]

Pull Request - State: closed - Opened by zhu0619 over 2 years ago

#140 - use os.patlike to recognize string based path objects in the fs module

Pull Request - State: closed - Opened by hadim over 2 years ago - 1 comment

#139 - fs module should work with pytest `Path` objects

Issue - State: closed - Opened by hadim over 2 years ago
Labels: bug, low-priority

#138 - Update Fragment.ipynb

Pull Request - State: closed - Opened by Valence-JonnyHsu over 2 years ago - 1 comment

#137 - new doc api layout + atom indices in smiles + various

Pull Request - State: closed - Opened by hadim over 2 years ago

#136 - Change default for is_file() and fix typo in docs

Pull Request - State: closed - Opened by cwognum over 2 years ago - 1 comment

#135 - `dm.fs.is_file()` defaults to True

Issue - State: closed - Opened by cwognum over 2 years ago - 3 comments
Labels: enhancement, good first issue

#134 - Minor typo in the documentation of `dm.conformers.generate()`

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

#133 - Update Conformers.ipynb

Pull Request - State: closed - Opened by Valence-JonnyHsu over 2 years ago - 2 comments

#132 - Update Aligning.ipynb

Pull Request - State: closed - Opened by Valence-JonnyHsu over 2 years ago - 1 comment

#131 - Add single file modules as independent sections in the docs

Issue - State: closed - Opened by MichelML over 2 years ago - 1 comment
Labels: documentation, enhancement, low-priority

#130 - Add dm.read_records in io module

Issue - State: closed - Opened by MichelML over 2 years ago - 8 comments
Labels: enhancement, low-priority

GitHub / datamol-io/datamol issues and pull requests