MobleyLab/chemper issues and pull requests

#102 - Migrate from Travis CI to GitHub Actions

Pull Request - State: closed - Opened by mattwthompson about 2 years ago - 10 comments

#101 - Fix removed import in Python 3.10

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

#100 - not able to smirksify double bonds in different clusters for cis/trans butene

Issue - State: open - Opened by wutobias about 2 years ago - 1 comment

#99 - Ring closure bonds missing

Issue - State: open - Opened by jthorton almost 4 years ago

#98 - Fix installation doc typo

Pull Request - State: open - Opened by alexmalins almost 4 years ago

#97 - Update miniconda URL

Pull Request - State: closed - Opened by mattwthompson about 4 years ago - 1 comment

#96 - Update miniconda URL

Pull Request - State: closed - Opened by mattwthompson about 4 years ago - 2 comments

#95 - The jupyter notebooks were not updated when name changes occurred.

Issue - State: open - Opened by bannanc over 4 years ago - 2 comments
Labels: help wanted

#94 - Add new release to README

Pull Request - State: closed - Opened by bannanc over 4 years ago - 3 comments

#93 - Add mybinder support for jupyter notebook examples

Issue - State: open - Opened by bannanc almost 5 years ago
Labels: long term

#92 - add new encrypted license

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

#91 - Uncomment and fix URL tests

Issue - State: open - Opened by bannanc almost 5 years ago
Labels: long term

#90 - Make a Chemper conda package

Issue - State: closed - Opened by bannanc almost 5 years ago - 8 comments
Labels: long term

#89 - Decide how to handle possible 'static' methods

Issue - State: open - Opened by bannanc almost 5 years ago
Labels: long term

#88 - Recursive SMIRKS patterns should be considered

Issue - State: open - Opened by bannanc almost 5 years ago
Labels: long term

#87 - Remove option to remove one bond or decorator

Issue - State: open - Opened by bannanc about 5 years ago - 2 comments

#86 - Update example jupyter notebooks

Issue - State: closed - Opened by bannanc about 5 years ago - 1 comment
Labels: In PR

#85 - Update adapters to use `collections.abc`?

Issue - State: open - Opened by bannanc about 5 years ago - 2 comments
Labels: long term

#84 - Raise error if SMIRKS pattern has no indexed atoms? or update is_valid?

Issue - State: closed - Opened by bannanc about 5 years ago - 1 comment
Labels: In PR

#83 - Rename `ChemPerGraph` to `SingleGraph`

Issue - State: closed - Opened by bannanc about 5 years ago - 1 comment
Labels: In PR

#82 - API change, major doc string update, and cleaning up READMEs

Pull Request - State: closed - Opened by bannanc about 5 years ago - 20 comments
Labels: WIP

#81 - add logo

Pull Request - State: closed - Opened by bannanc about 5 years ago - 1 comment

#80 - Update badges

Issue - State: closed - Opened by bannanc about 5 years ago
Labels: In PR

#79 - Fix version conflict in ReadTheDocs

Pull Request - State: closed - Opened by bannanc about 5 years ago - 2 comments

#78 - Verify OpenEye license when checking for toolkits

Issue - State: closed - Opened by bannanc about 5 years ago
Labels: In PR

#77 - Double check all example code is being tested

Issue - State: closed - Opened by bannanc about 5 years ago
Labels: In PR

#76 - update README

Pull Request - State: closed - Opened by bannanc about 5 years ago - 1 comment

#75 - Make sure there is no (or at least hight) max substructure search

Issue - State: closed - Opened by bannanc over 5 years ago - 2 comments

#74 - Fix inconsistencies with scoring ties in networkx

Issue - State: open - Opened by bannanc over 5 years ago - 2 comments
Labels: long term

#73 - Update str for mol_toolkit atoms and bonds

Issue - State: closed - Opened by bannanc over 5 years ago
Labels: In PR

#72 - [WIP] makes protein SMIRNOFF

Pull Request - State: closed - Opened by bannanc over 5 years ago - 8 comments
Labels: WIP

#71 - Version update

Pull Request - State: closed - Opened by bannanc over 5 years ago - 1 comment

#70 - Add everything from CookieCutter

Pull Request - State: closed - Opened by bannanc over 5 years ago - 21 comments

#69 - Update README before creating release

Pull Request - State: closed - Opened by bannanc over 5 years ago - 2 comments

#68 - Test Python 3.6 on Travis

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

#67 - Use conda to install when possible

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment

#66 - Update travis python

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment

#65 - Update decoration order and environment parsing fixes

Pull Request - State: closed - Opened by bannanc over 5 years ago - 9 comments
Labels: Review

#64 - Add Windows testing support

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment

#63 - Is pathlib better than os for file management?

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: question

#62 - Fix Decorator order to be consistently bug free

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: In PR

#61 - Clean up code by improving coverage and following lgtm

Issue - State: closed - Opened by bannanc over 5 years ago
Labels: enhancement

#60 - Fix symmetry for torsions

Pull Request - State: closed - Opened by bannanc over 5 years ago - 3 comments
Labels: Review, Finished

#59 - Fix bug relating to how symmetry around valence terms is addressed

Issue - State: closed - Opened by bannanc over 5 years ago - 2 comments
Labels: Finished

#58 - Update the way layers are added per issue #56

Pull Request - State: closed - Opened by bannanc over 5 years ago - 3 comments
Labels: Review

#57 - Change recursive functions to while loops

Issue - State: open - Opened by bannanc over 5 years ago - 1 comment
Labels: question, long term

#56 - Fix bugs in `cluster_graph` on how "layers" are added

Issue - State: closed - Opened by bannanc over 5 years ago - 2 comments
Labels: bug

#55 - Add any suggestions from closed PRs

Issue - State: closed - Opened by bannanc over 5 years ago - 3 comments
Labels: In PR, minor

#54 - Extract SMIRKS reducing into its own class

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: enhancement

#53 - Should be trying variable numbers of layers?

Issue - State: open - Opened by bannanc over 5 years ago - 1 comment
Labels: question, long term

#52 - Make example and write more extensive tests for clustering

Issue - State: closed - Opened by bannanc over 5 years ago - 2 comments

#51 - Add functions for clustering fragments based on data

Pull Request - State: closed - Opened by bannanc over 5 years ago - 2 comments
Labels: WIP

#50 - Add handling for symmetry around force field parameters

Pull Request - State: closed - Opened by bannanc over 5 years ago - 2 comments
Labels: Review

#49 - Extend SMIRKSifier tests

Issue - State: closed - Opened by bannanc over 5 years ago - 2 comments

#48 - Automatically chose the number of layers

Pull Request - State: closed - Opened by bannanc over 5 years ago - 3 comments
Labels: Review

#47 - Determine the order of SMIRKS patterns

Issue - State: open - Opened by bannanc over 5 years ago - 2 comments
Labels: long term

#46 - Add Aromaticity support to chemper

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: question, minor

#45 - SMIRKSifier update to make removing decorators more efficient

Pull Request - State: closed - Opened by bannanc over 5 years ago - 3 comments
Labels: Review

#44 - Update scoring function and move to utilities

Pull Request - State: closed - Opened by bannanc over 5 years ago - 2 comments
Labels: Finished

#43 - Create a `mol_toolkit.py` file that acts as a factory

Pull Request - State: closed - Opened by bannanc over 5 years ago - 2 comments

#42 - Update intro in Docs

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

#41 - Update Clusters to use tuples and update relevant documentation and examples

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

#40 - Add more efficient decorator removal in the smirksifier

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: enhancement

#39 - Should graphs be able to `add_layer`

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: question

#38 - Automatically determine number of layers in smirksify

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: enhancement, In PR

#37 - Remove dictionary from cluster and fragment graph input

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: enhancement, Finished

#36 - Do better handling symmetry in indexed atoms in the same way we handle neighbors

Issue - State: closed - Opened by bannanc over 5 years ago - 1 comment
Labels: enhancement

#35 - Update OE License

Pull Request - State: closed - Opened by bannanc almost 6 years ago - 2 comments
Labels: Finished

#34 - Investigate SMARTS/SMIRKS syntax rules in OE/RDK

Issue - State: closed - Opened by bannanc almost 6 years ago - 2 comments
Labels: question

#33 - Replace expired OE License

Issue - State: closed - Opened by bannanc almost 6 years ago - 1 comment

#32 - Ring size decorator treated differently in OE and RDK

Issue - State: closed - Opened by bannanc almost 6 years ago - 1 comment
Labels: In PR

#31 - Can we "test" the docs

Issue - State: closed - Opened by bannanc almost 6 years ago - 2 comments
Labels: question

#30 - Add utilities for opening files, including a data directory inside chemper installed with pip, and condensed smirks output

Pull Request - State: closed - Opened by bannanc almost 6 years ago - 9 comments
Labels: Finished

#29 - Fix the docs

Issue - State: closed - Opened by bannanc almost 6 years ago - 1 comment

#28 - Matching atoms and storage in cluster_graph

Issue - State: open - Opened by bannanc almost 6 years ago - 1 comment
Labels: question, long term

#27 - Demonstrate the problem with `eq` on AtomStorage Objects

Pull Request - State: closed - Opened by bannanc almost 6 years ago - 2 comments
Labels: bug, question

#26 - Documentation and Examples Update

Pull Request - State: closed - Opened by bannanc about 6 years ago - 5 comments
Labels: WIP

#25 - Doc cleanup

Issue - State: closed - Opened by davidlmobley about 6 years ago - 3 comments
Labels: question, In PR

#24 - Add layers to cluster graphs, improve some doc strings, expand tests

Pull Request - State: closed - Opened by bannanc about 6 years ago - 3 comments
Labels: Finished

#23 - [WIP] Try using psi4numpy's utils for jupyter notebook tests

Pull Request - State: closed - Opened by bannanc about 6 years ago - 10 comments

#22 - add requirements file and Minor fixes to rst files

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#21 - Add nbval to track jupyter notebooks

Pull Request - State: closed - Opened by bannanc about 6 years ago - 7 comments

#20 - Slight reorganization of examples and remove yml files

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#19 - Update Documentation and add ReadTheDocs support

Pull Request - State: closed - Opened by bannanc about 6 years ago - 3 comments

#18 - [WIP] Add nbval to track jupyter notebooks

Pull Request - State: closed - Opened by bannanc about 6 years ago - 3 comments

#17 - add tests for jupyter notebooks

Issue - State: closed - Opened by bannanc about 6 years ago - 1 comment

#16 - fix preprint links

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#15 - Add real readme

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#14 - Make an actual README file!

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#13 - Add more complex graph tests

Issue - State: closed - Opened by bannanc about 6 years ago - 2 comments

#12 - Efficiency when searching for SMIRKS matches

Issue - State: open - Opened by bannanc about 6 years ago - 1 comment
Labels: long term

#11 - Improve cluster graph, fix recursion error, and make example notebooks

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#10 - Single molecule to graph with SMIRKS

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#9 - Adjusting mol_toolkits and travis tests for different imports

Pull Request - State: closed - Opened by bannanc about 6 years ago - 1 comment

#8 - Add implementation and tests with RDKit

Pull Request - State: closed - Opened by bannanc over 6 years ago - 2 comments

GitHub / MobleyLab/chemper issues and pull requests