Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / aspuru-guzik-group/selfies issues and pull requests

#127 - Invalid molecules with positive charged C, P, S

Issue - State: closed - Opened by MarioKrenn6240 about 2 months ago - 1 comment
Labels: bug

#126 - Generating visual comparison between SMILES and SELFIES

Issue - State: closed - Opened by ndhieunguyen about 2 months ago - 1 comment
Labels: question

#125 - Handling of radicals in kekulization (fix #120)

Pull Request - State: closed - Opened by robpollice about 2 months ago

#124 - Two dataset links in README not working

Issue - State: closed - Opened by robpollice about 2 months ago - 2 comments
Labels: documentation

#123 - random selfies to valid smiles

Issue - State: open - Opened by DawnJYe 2 months ago - 7 comments
Labels: question

#122 - xyz2selfies

Issue - State: open - Opened by AFelixLiu 3 months ago - 3 comments
Labels: question

#121 - Model SELFIES VAE

Issue - State: closed - Opened by KatynaSada 5 months ago - 3 comments
Labels: question

#120 - Kekulization Failure

Issue - State: closed - Opened by Olabisi-Aishat-Bello 6 months ago - 3 comments
Labels: bug, question

#119 - Add testing for python 3.11

Pull Request - State: closed - Opened by ctk3b 6 months ago

#118 - SELFIES decoding for some tokens

Issue - State: closed - Opened by Olabisi-Aishat-Bello 6 months ago - 2 comments
Labels: question

#117 - Errors in Translating SMILES to SELFIES

Issue - State: closed - Opened by btyu 7 months ago - 2 comments
Labels: question

#116 - Replace recursion with stack (fix #115)

Pull Request - State: closed - Opened by haydn-jones 7 months ago - 2 comments

#115 - Decoding failure for SELFIES string

Issue - State: closed - Opened by haydn-jones 7 months ago - 1 comment
Labels: bug

#114 - Error in SELFIES conversion when a sulfur is connected to an aromatic carbon

Issue - State: closed - Opened by KunhuanLiu 8 months ago - 3 comments
Labels: question

#113 - Fail to transform SMILES to SELFIES

Issue - State: closed - Opened by tszslovewanpu 12 months ago - 2 comments
Labels: question

#112 - [BUG] Wrong output SELFIES and Attribution map

Issue - State: closed - Opened by acharkq about 1 year ago - 2 comments

#111 - Period not added with alphabet function

Issue - State: closed - Opened by KatynaSada about 1 year ago - 2 comments
Labels: question

#110 - fix #104 Add check for dot symbol and warn user

Pull Request - State: open - Opened by vandrw over 1 year ago - 2 comments

#109 - About conversion from A 2 B back2 A

Issue - State: closed - Opened by tszslovewanpu over 1 year ago - 2 comments
Labels: question

#108 - Random SELFIES

Issue - State: closed - Opened by lhallee over 1 year ago - 3 comments

#107 - Update test_selfies.py

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

#106 - Support for polymer SMILES added

Pull Request - State: open - Opened by onecoinbuybus over 1 year ago - 1 comment

#105 - Selfies for most common substructure search

Issue - State: closed - Opened by peiyaoli over 1 year ago - 1 comment
Labels: question

#104 - Preserving the dot symbol (".") in the alphabet

Issue - State: closed - Opened by vandrw over 1 year ago - 1 comment
Labels: question

#103 - Represent Ring-Couplings

Issue - State: closed - Opened by wolnikla over 1 year ago - 5 comments
Labels: question

#102 - Selfies encoder adds spurious nitrogen to molecule

Issue - State: closed - Opened by TheGoldstone over 1 year ago - 4 comments
Labels: question

#101 - vae/gan using selfies

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

#100 - Supplementary Information not available

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

#99 - "input violates the currently-set semantic constraints" for RDKit-valid SMILES

Issue - State: closed - Opened by isty2e almost 2 years ago - 4 comments
Labels: question

#98 - Questions about SELFIES Syntax

Issue - State: closed - Opened by hanm19 almost 2 years ago - 1 comment
Labels: question

#97 - Canonical SELFIES

Issue - State: closed - Opened by tobigithub about 2 years ago - 3 comments

#96 - SELFIES to SMILES decoding not reversible

Issue - State: closed - Opened by anoushka2000 about 2 years ago - 4 comments

#95 - Nano particle selfies

Issue - State: closed - Opened by jessielyons about 2 years ago - 4 comments
Labels: question

#94 - Question about getting attribution for rings?

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

#93 - Fix incorrect version in __init__.py

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

#92 - Encoding disconnected compounds

Issue - State: closed - Opened by RoryGarlandGlam over 2 years ago - 5 comments
Labels: question

#91 - Appearance of P and S in SELFIES representation for molecules that do not contain P or S.

Issue - State: closed - Opened by R-applet over 2 years ago - 2 comments
Labels: question

#90 - Can I convert the SELFIES to 3D molecular geometry?

Issue - State: closed - Opened by Eipgen over 2 years ago - 1 comment
Labels: question

#89 - Fixed index counting bug in attribution

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

#88 - [=Branch1] vs [Branch1] ?

Issue - State: closed - Opened by EtienneReboul over 2 years ago - 1 comment
Labels: question

#87 - Randomization feature

Issue - State: open - Opened by whitead almost 3 years ago
Labels: enhancement

#86 - Standardized python versions

Pull Request - State: closed - Opened by whitead almost 3 years ago - 1 comment

#85 - Clarify Python Version

Issue - State: closed - Opened by whitead almost 3 years ago - 2 comments

#84 - Improvements to attribution

Pull Request - State: closed - Opened by whitead almost 3 years ago - 1 comment

#83 - Update for index table documentation needed ??

Issue - State: closed - Opened by EtienneReboul almost 3 years ago - 2 comments

#82 - Generate molecule string from atom properties

Issue - State: closed - Opened by dgm2 almost 3 years ago - 2 comments
Labels: question

#81 - Update README.md

Pull Request - State: closed - Opened by ncfrey almost 3 years ago

#80 - Comprehensive Vocabulary

Issue - State: closed - Opened by keshavd almost 3 years ago - 4 comments
Labels: question

#79 - Attribution Map Encoder Ordering

Issue - State: closed - Opened by whitead almost 3 years ago - 1 comment
Labels: enhancement

#78 - Attribution map improvements (#75)

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

#77 - Add strict decoder option

Pull Request - State: closed - Opened by masrul about 3 years ago - 2 comments

#76 - Limitations of SELFIES to represent stereochemistry

Issue - State: closed - Opened by sphuber about 3 years ago - 3 comments
Labels: question

#75 - Mapping attribution of tokens between encoder and decoder

Pull Request - State: closed - Opened by whitead about 3 years ago - 8 comments

#74 - Constants.py

Issue - State: closed - Opened by twoXes about 3 years ago - 1 comment
Labels: question

#73 - SELFIE encoding fails with PF6- or hypervalent Phosphorus

Issue - State: closed - Opened by bananenpampe about 3 years ago - 3 comments
Labels: question

#72 - SELFIES for defects

Issue - State: open - Opened by SergeiVKalinin about 3 years ago
Labels: enhancement, question

#71 - Index symbol customization

Pull Request - State: closed - Opened by csnbritt over 3 years ago - 5 comments

#70 - To get SELFIES characters of specific substructure

Issue - State: closed - Opened by SejeongPark8354 over 3 years ago - 5 comments
Labels: question

#69 - Index symbol customization questions/enhancement suggestions

Issue - State: open - Opened by csnbritt over 3 years ago - 2 comments
Labels: enhancement, question

#68 - SELFIES tokens list

Issue - State: closed - Opened by Kohulan over 3 years ago - 7 comments
Labels: question

#67 - Questions for the grammar

Issue - State: closed - Opened by hwidong-na over 3 years ago - 1 comment
Labels: question

#66 - Supporting old SELFIES symbols in decoder

Pull Request - State: closed - Opened by alstonlo over 3 years ago

#65 - Generative model are producing invalid molecules with SELFIES?

Issue - State: closed - Opened by HelloJocelynLu over 3 years ago - 4 comments
Labels: bug

#64 - v2.0.0

Pull Request - State: closed - Opened by alstonlo over 3 years ago

#63 - Functions for Quotient Graph and SELFIES

Issue - State: closed - Opened by SamCox822 over 3 years ago - 5 comments
Labels: enhancement

#62 - Error handling and general sense on SELFIES generation

Issue - State: closed - Opened by chupvl over 3 years ago - 4 comments
Labels: bug

#61 - Please ignore - accidentally created PR

Pull Request - State: closed - Opened by alstonlo over 3 years ago

#60 - Hangs on some invalid SMILES inputs with hanging open parenthesis

Issue - State: closed - Opened by supersciencegrl over 3 years ago - 2 comments
Labels: bug

#59 - fixes parsing of SELFIES with incorrect bracket-ing

Pull Request - State: closed - Opened by clavigne over 3 years ago

#58 - Selfies alphabet token changes

Issue - State: closed - Opened by whitead over 3 years ago - 3 comments
Labels: enhancement

#57 - refactored _parse_selfies

Pull Request - State: closed - Opened by masrul over 3 years ago - 8 comments

#56 - Added cache for get_semantic_robust_alphabet

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

#55 - Potential bug in kekulization

Issue - State: closed - Opened by adamoyoung over 3 years ago - 4 comments
Labels: bug

#54 - Update README.md

Pull Request - State: closed - Opened by akshat998 over 3 years ago - 1 comment

#53 - Mistakes on encoder/decoder nitro group

Issue - State: closed - Opened by gtteixeira over 3 years ago - 1 comment
Labels: question

#52 - SELFIES encoding bug

Issue - State: closed - Opened by Kohulan over 3 years ago - 2 comments
Labels: question

#51 - Irritation with 'selfies_to_encoding' and 'encoding_to_selfies' dictionary

Issue - State: closed - Opened by niklashoelter over 3 years ago - 2 comments
Labels: help wanted, question

#50 - Bump urllib3 from 1.25.10 to 1.26.5 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#48 - Feature request: Retrieve mapping betwewen SMILES and SELFIES tokens

Issue - State: closed - Opened by jannisborn almost 4 years ago - 16 comments
Labels: enhancement

#47 - Not using <sos> tokens?

Issue - State: closed - Opened by JanoschMenke almost 4 years ago - 4 comments
Labels: question

#46 - Bump pygments from 2.6.1 to 2.7.4 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#45 - 1.0.4

Pull Request - State: closed - Opened by alstonlo almost 4 years ago - 1 comment

#44 - Issue with decoding an encoded string.

Issue - State: closed - Opened by Kohulan almost 4 years ago - 5 comments
Labels: bug

#43 - Translating SMILES to SELFIES

Issue - State: closed - Opened by oriondollar almost 4 years ago - 2 comments
Labels: question

#42 - Question regarding the output of selfies

Issue - State: closed - Opened by shiwentao00 almost 4 years ago - 7 comments
Labels: question

#41 - Wildcard Error message of encoder (and decoder)

Issue - State: closed - Opened by DocMinus almost 4 years ago - 3 comments
Labels: documentation, question

#40 - SELFIES that can't be parsed by RDKit

Issue - State: closed - Opened by skinnider about 4 years ago - 3 comments
Labels: question

#39 - Bump bleach from 3.1.5 to 3.3.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#38 - is selfies supporting stereochemistry, polyvalency, aromaticity, isotopic substitution... now?

Issue - State: closed - Opened by 5AGE-zhang about 4 years ago - 2 comments
Labels: question

#37 - Aromatic Si and Al support

Pull Request - State: closed - Opened by HelloJocelynLu about 4 years ago

#36 - question about output molecules

Issue - State: closed - Opened by fylinhub about 4 years ago - 4 comments
Labels: question

#35 - there was an absolute path

Pull Request - State: closed - Opened by UnixJunkie about 4 years ago

#34 - the conda package seems to be pyyaml, not yaml

Pull Request - State: closed - Opened by UnixJunkie about 4 years ago

#33 - Changes towards v1.0.2

Pull Request - State: closed - Opened by alstonlo over 4 years ago

#32 - if `decoder` is called on a string that doesn't end with ], instead of failing it hangs forever

Issue - State: closed - Opened by aebrer over 4 years ago - 1 comment
Labels: bug

#31 - upgraded selfies?

Issue - State: closed - Opened by woodg07 over 4 years ago - 1 comment
Labels: question

#29 - one-hot encoding functions

Pull Request - State: closed - Opened by ncfrey over 4 years ago - 2 comments

#28 - Regarding of None from smiles

Issue - State: closed - Opened by hmkim over 4 years ago - 9 comments
Labels: bug, enhancement