An automatic reaction network generator for reactive molecular dynamics simulation.

Overview

ReacNetGenerator

DOI:10.1039/C9CP05091D Citations Research Group

An automatic reaction network generator for reactive molecular dynamics simulation.

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys., 2020, 22 (2): 683–691, doi: 10.1039/C9CP05091D

[email protected] (Jinzhe Zeng), [email protected] (Tong Zhu)

Features

  • Processing of MD trajectory containing atomic coordinates or bond orders
  • Hidden Markov Model (HMM) based noise filtering
  • Isomers identifying accoarding to SMILES
  • Generation of reaction network for visualization using force-directed algorithm
  • Parallel computing

Guide and Tutorial

You can install ReacNetGenerator with conda:

conda install reacnetgenerator -c conda-forge
reacnetgenerator -h

See the guide to learn how to install and use ReacNetGenerattor. We also provide a series of tutorials to help you learn ReacNetGenerator.

Awards

  • The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
  • The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students

Acknowledge

  • National Natural Science Foundation of China (Grants No. 91641116)
  • National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
  • ECNU Multifunctional Platform for Innovation (No. 001)
Comments
  • Some species not showing in the network, OpenBabel errors

    Some species not showing in the network, OpenBabel errors

    Thanks for making your code available! I tried to use it to analyze a certain trajectory but I'm getting 5 errors of this type: *** Open Babel Error in ParseComplex SMILES string contains a character '[' which is invalid How can I debug this to find out what the offending SMILES was? Moreover, some species are not displayed in the html (just empty boxes). Nevertheless, OpenBabel is able to generate their depictions correctly, for example via this command: obabel -ismi s.smiles -osvg Unfortunately I cannot share my example due to its confidential nature. I will appreciate any advice!

    bug released 
    opened by mkrompiec 12
  • fix(deps): update dependency terser-webpack-plugin to v1.4.1

    fix(deps): update dependency terser-webpack-plugin to v1.4.1

    :warning: You need a paid GitHub Marketplace Plan for private repositories, so please sign up if you wish to enable this repository for continuous updates.

    This PR contains the following updates:

    | Package | Type | Update | Change | |---|---|---|---| | terser-webpack-plugin | dependencies | minor | 1.3.0 -> 1.4.1 |


    Release Notes

    webpack-contrib/terser-webpack-plugin

    v1.4.1

    Compare Source

    v1.4.0

    Compare Source

    Features

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    PR: merged size/M released 
    opened by renovate[bot] 8
  • fix: [reacnetgenerator/static/webpack] Upgrade webpack-cli: 3.3.1 → 3.3.2 (patch)

    fix: [reacnetgenerator/static/webpack] Upgrade webpack-cli: 3.3.1 → 3.3.2 (patch)

    Here is everything you need to know about this upgrade. Please take a good look at what changed and the test results before merging this pull request.

    What changed?

    ✳️ webpack-cli (3.3.1 → 3.3.2) · Repo · Changelog

    Release Notes

    3.3.2 (from changelog)

    Full Changelog

    New Features

    • opencollective prompt: add option to disable it + doc (d4643ae)
    • terser: clean old files (89e6b74)
    • terser: remove leftover files (27d5b4d)
    • terser: replace after merging master (c404655)
    • replace Uglify with Terser in generators (2b8651b)
    • use terserPlugin in loaderOptionsPlugin (14f5337)
    • use terserJsPlugin for transformations during migrate (33c6185)
    • replace uglifyJsPlugin with terserPlugin in migrate (d467f3b)
    • opencollective prompt: work on windows setting atime by code (3af73a8)
    • opencollective prompt: fix typo (c2351b1)
    • opencollective prompt: remove .lastocprint file from fs (b96ad56)
    • opencollective prompt: extract weekday to variable (790d27a)
    • opencollective prompt: set terminal cols to 80 (badc32d)
    • opencollective prompt: fix azure ci (ea0039a)
    • opencollective prompt: lint (ea906d8)
    • opencollective prompt: clear package.json modifications (f080733)
    • opencollective prompt: add prompt in postinstall script (dd9d528)

    Ast

    • change tooltip property from uglify to terser (ea9e4b8)
    • replace requires and inits for uglify with terser (3011a6c)
    • replace UglifyJsPlugin with TerserPlugin (21da35f)

    Chore

    • cli: move constants to a separate file (#798)
    • deps: fix security vulnerabilities (#857)
    • deps: upgrade lerna to fix vulnerabilities & update webpack-dev-server (#823)
    • docs: minor fixes in the docs (#874)
    • docs: removes scaffolding docs from the root (8c1db03)
    • junit: reverting the junit.xml (80fd4fa)
    • travis: removed stable (#871)
    • types: move to @types/yeoman-generator (#869)
    • addon generator to async/await (#849)
    • v.3.1.1 (d3f8e20)
    • tests: updated test regex, some helper scripts (#809)
    • types: add type information (#791)
    • replace instances of uglify with terser (f9cb8ce)
    • use actual package name in comment about removing uglify (b1cf4cc)
    • align file in the same way as other terserPlugin test fixtures (b6c6484)
    • remove gitHash from package.json (2af08be)

    Docs

    • code of conduct (#873)
    • contribute: adds table of contents and info about dependencies. (#842)
    • contributing: fixes dead link (#835)
    • opencollective prompt: improve code clarity (55992a4)
    • packages: adds downloads/month shield (6a0375a)
    • readme: fix typos, add summary of all commands (#845)
    • readme: adds contributors shield (958d064)
    • README: phrase change (3a11a16)
    • README: add link to webpack-scaffold-starter (e35a194)
    • README: update scaffolding links (74179b5)
    • serve: link to webpack-dev-server (cb68b1b)
    • serve: update docs to use webpack-dev-server (f7451d4)
    • replace tooltip link to terser plugin (4254730)
    • replace Uglify with Terser in comments (799577d)
    • replace UglifyJsPlugin with TerserPlugin in migrate docs (326f783)

    Enh

    • webpack-scaffold: improve prompt and doc (#794)

    Fix

    • add: add types (d4ce6f2)
    • add: fix runTransform (dbc3e9e)
    • add: lint code (163b309)
    • add: add handling for topScope (1162cf5)
    • bin, serve: force default package export, add serve default (#815)
    • init: refactored the init.ts success message (#810)
    • opencollective prompt: fix grammar (246db42)
    • opencollective-prompt: check write permissions (5284b7e)
    • scaffold: config file is always generated at the project root (#801)
    • utils: refactors utils (7fe3543)
    • clear up comment about default function purpose (e48507d)
    • remove unused files (ec242ab)
    • reset files (9863445)
    • replace lookups for TerserPlugin in webpack.optimise (ef23fec)

    Tests

    • update snapshots (ce9fbc8)
    • replace uglify with terser in ast-utils tests (73f493f)
    • migration: typescript (#613)

    Misc

    • chore(docs): Refactors links for badges (#859)
    • opencollective-prompt: improve grammar (e17a26d)
    • Remove tslint in favour of eslint (#834)
    • cli: refactor functions into utils and config dirs, merge yargs options (#781)
    • utils: refactors scaffold (0b28fb3)

    Does any of this look wrong? Please let us know.


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    opened by depfu[bot] 7
  • fix(deps): pin dependencies

    fix(deps): pin dependencies

    This PR contains the following updates:

    | Package | Type | Update | Change | References | |---|---|---|---|---| | popper.js | dependencies | pin | ^1.15.0 -> 1.15.0 | homepage, source | | vuepress | devDependencies | pin | ^0.14.11 -> 0.14.11 | source |

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    PR: merged size/XS squash when passing 
    opened by njzjz-bot 7
  • ValueError: Maximum BFS search size exceeded.

    ValueError: Maximum BFS search size exceeded.

    Hello, zeng My name is Changwei Liu. Thank you for your contribution to the analysis of the ReaxFF simulation. When I analyze the bonds.connect file including bond sequences produced by catalytic systems containing metal clusters, the following error occurs: ''' Traceback (most recent call last): File "/public1/home/scg3280/.conda/envs/0428_env/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/public1/home/scg3280/.conda/envs/0428_env/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar return list(map(*args)) File "reacnetgenerator/_path.py", line 217, in reacnetgenerator._path._CollectSMILESPaths._calmoleculeSMILESname File "reacnetgenerator/_path.py", line 129, in reacnetgenerator._path._CollectPaths.convertSMILES ValueError: Maximum BFS search size exceeded. This is likely due to a highly symmetric fused ring system. ''' How to solve this error? Thank you very much.

    opened by Y11190003 6
  • Error when processing the bond file of a Fe/C/H/O system

    Error when processing the bond file of a Fe/C/H/O system

    Hello,

    I am trying to run reacnetgenerator using the command "reacnetgenerator --type bond -i bonds.reaxc -a Fe C H O -n 4" on the bond file of a Fe/C/H/O system. But I get the following error:

    2021-12-07 13:10:31,604 - ReacNetGen 1.4.165 - INFO: Version: 1.4.165 Creation date: 2018-03-11 Read bond information and Detect molecules: 0timestep [00:06, ?timestep/s] 2021-12-07 13:10:37,887 - ReacNetGen 1.4.165 - ERROR: run_mp failed multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(*args)) File "reacnetgenerator/_detect.py", line 193, in reacnetgenerator._detect._DetectLAMMPSbond._readstepfunc File "reacnetgenerator/_detect.py", line 144, in reacnetgenerator._detect._Detect._connectmolecule File "reacnetgenerator/dps.pyx", line 37, in reacnetgenerator.dps.dps TypeError: 'NoneType' object is not iterable """

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last): File "reacnetgenerator/utils.py", line 440, in reacnetgenerator.utils.run_mp File "/home/ekritikos/anaconda3/lib/python3.8/site-packages/tqdm/std.py", line 1180, in iter for obj in iterable: File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 448, in return (item for chunk in result for item in chunk) File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 868, in next raise value TypeError: 'NoneType' object is not iterable multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(*args)) File "reacnetgenerator/_detect.py", line 193, in reacnetgenerator._detect._DetectLAMMPSbond._readstepfunc File "reacnetgenerator/_detect.py", line 144, in reacnetgenerator._detect._Detect._connectmolecule File "reacnetgenerator/dps.pyx", line 37, in reacnetgenerator.dps.dps TypeError: 'NoneType' object is not iterable """

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last): File "/home/ekritikos/anaconda3/bin/reacnetgenerator", line 11, in sys.exit(_commandline()) File "reacnetgenerator/commandline.py", line 59, in reacnetgenerator.commandline._commandline File "reacnetgenerator/reacnetgen.py", line 188, in reacnetgenerator.reacnetgen.ReacNetGenerator.runanddraw File "reacnetgenerator/reacnetgen.py", line 264, in reacnetgenerator.reacnetgen.ReacNetGenerator._process File "reacnetgenerator/_detect.py", line 108, in reacnetgenerator._detect._Detect.detect File "reacnetgenerator/_detect.py", line 117, in reacnetgenerator._detect._Detect._readinputfile File "reacnetgenerator/_detect.py", line 120, in reacnetgenerator._detect._Detect._readinputfile File "reacnetgenerator/utils.py", line 446, in run_mp File "reacnetgenerator/utils.py", line 440, in reacnetgenerator.utils.run_mp File "/home/ekritikos/anaconda3/lib/python3.8/site-packages/tqdm/std.py", line 1180, in iter for obj in iterable: File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 448, in return (item for chunk in result for item in chunk) File "/home/ekritikos/anaconda3/lib/python3.8/multiprocessing/pool.py", line 868, in next raise value TypeError: 'NoneType' object is not iterable

    Did you ever come across such a problem? I would appreciate some feedback. Thank you in advance.

    opened by ekritikos 6
  • chore(deps): lock file maintenance

    chore(deps): lock file maintenance

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    released 
    opened by renovate[bot] 6
  • chore(deps): bump webpack from 4.39.0 to 4.39.1 in /reacnetgenerator/static/webpack

    chore(deps): bump webpack from 4.39.0 to 4.39.1 in /reacnetgenerator/static/webpack

    Bumps webpack from 4.39.0 to 4.39.1.

    Release notes

    Sourced from webpack's releases.

    v4.39.1

    Bugfixes

    • fix problem that progress lines were too long on some terminals
    • fix a problem that ...100% is displayed instead of 100%
    Commits

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    dependencies javascript PR: unreviewed size/M 
    opened by dependabot-preview[bot] 6
  • fix(deps): update dependency webpack to v4.39.1

    fix(deps): update dependency webpack to v4.39.1

    This PR contains the following updates:

    | Package | Type | Update | Change | |---|---|---|---| | webpack | dependencies | patch | 4.39.0 -> 4.39.1 |


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    webpack/webpack

    v4.39.1

    Compare Source

    Bugfixes

    • fix problem that progress lines were too long on some terminals
    • fix a problem that ...100% is displayed instead of 100%

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    PR: merged size/S released 
    opened by renovate[bot] 6
  • fix(deps): update dependency webpack-cli to v3.3.3

    fix(deps): update dependency webpack-cli to v3.3.3

    This PR contains the following updates:

    | Package | Type | Update | Change | |---|---|---|---| | webpack-cli | dependencies | patch | 3.3.2 -> 3.3.3 |


    Release Notes

    webpack/webpack-cli

    v3.3.3

    Compare Source

    Full Changelog

    New Features

    • chore: Added type definitions for the data returned by envinfo (#​921)
    • add htmlWebpackPlugin in development (88fcfa8)
    • add mergeHandler (248b9cc)
    • generators: add generated file templates (6be9291)
    • init: generate README (c090b17)
    • init: generate tsconfig (25ab7e6)
    • init: support ts in configuration (283e089)
    • init: wip typescript support (093a36d)
    • md: formats md before committing (#​851)
    • webpack-scaffold: adds Input defaults, doc & tests (0a648f7)

    Chore

    • monorepo version update (69f7683)
    • update jest snapshots (efe8c2a)
    • monorepo version update (12a38be)
    • lockfile updates (2608179)
    • v.3.2.2 until mnorepo versioning (25c6e7b)
    • update utils version for init pkg (67b3dc7)
    • monorepo version update (ace0d4a)
    • lerna independent (16079a1)
    • sec fixes (b9711e8)
    • sec patch monorepo (9b78911)
    • v.3.3.3 (d577b0c)
    • ast-utils: undo return statements as per review (418c72c)
    • dep: commit lock (5a28a77)
    • dep: add eslint-plugin-prettier as dev dep (98ccd6f)
    • eslint: add eslint-prettier plugin (671abd5)
    • interfaces: minor modifications based on reviews (abb1a48)
    • lint: rm unused lint disables (ae4260a)
    • group imports (7fe04e9)
    • lint: fix code as per conflicting config (5bf847c)
    • reorder imports (0e0ba8a)
    • reorder imports (8a66c21)
    • reorder imports (57b47c3)
    • add some comments (95275ac)
    • lint: extend prettier config (5943f26)
    • lint: add eslint-config-prettier (4019049)
    • linting (ba0116a)
    • revise typo (a4597dd)
    • lint: format all files as per prettier plugin (f6992e6)
    • remove eslint disable comments (d72ac08)
    • use import instead of require (5ee4169)
    • update variable name (8e3f4ae)
    • update error message (8609b2b)
    • create questions.ts (7481974)
    • revise typo (be88ca9)
    • update lockfiles (a0216fe)
    • deps: update lock file (ea55cd5)
    • format: fix formatting using prettier (0b6437e)
    • infra: fix typo (98466d6)
    • infra: format all staged files on precommit (2a2e9a1)
    • infra: fix scripts to format files (876471c)
    • lint: fix lint warnings (#​926)
    • refactored the add-generator (80713fc)
    • migrate: replaces console with process stream (1df301d)
    • refactor: use all utils from the root file in generators (faabbfb)
    • utils: add valueType (43040fe)
    • utils: refactor util types (e7c5170)
    • fix azure (19e039f)
    • utils: refactors modify config helper (39be039)
    • utils: refactors ast utils (9f35073)
    • add types to import functions (8b88980)
    • refactor serve command action handler (d2c7ae4)
    • keep lowercase (c01a80b)
    • formatting (20ff530)
    • add errors for invalid params (27c6198)
    • cli: fixes linting err (9f1deb2)
    • utils: seperates interfaces from the core module (d0a4177)
    • remove trivial type (5e23da2)
    • create isImportPresent (a89645a)
    • use replaceWith (6a7e662)
    • update prop name (55d237b)
    • update parseMerge (b6a438d)
    • fix linting (c7c1a83)
    • format and revise code w.r.t style (e9d426d)
    • make config const (445ab31)
    • update parseMerge (cf85535)
    • pluginarrlength for length of the plugin (4872416)
    • made condition strict (88eec7c)
    • update types of the config (a2c49e2)
    • update variable name (1323bbf)
    • revise SECURITY.md (2a9e304)
    • revise SECURITY.md (9cdc357)
    • revise version support (90f397c)
    • add JSDoc descriptions (e023d23)
    • lint (cb5a15f)
    • lint (0782944)
    • lint (5778bdf)
    • ci: add node 12 (#​872)
    • cli: fixes code indentation (ff263f9)
    • cli: cleanup (ed4095f)
    • cli: remove findup-sync from package dir and move to utils (fe9c289)
    • cli: move constants to a separate file (#​798)
    • plugins.ts: added if-stmt for native plugins (fc9e259)
    • refactor: move questions to utils (915c4ab)
    • refactor: add generator (66bde9f)
    • utils: fix deprecated babylon (99304c4)
    • loop change (818e43e)
    • add sec & versioning policy (5e33f8a)
    • add-generator: changed the naming of the plugin in config file (7fbc3a4)
    • github: add sponsor button (88f2408)
    • refactor: update package list (e5c7f67)
    • style: fixed the indentation (e583aab)
    • added a generatePluginName method in generators utils (7d83453)
    • refactor: move schema to utils (2299848)
    • refactor: add generator (d901d49)
    • util: use relative for now (5a0952e)
    • utils: use absolute path (00a6348)

    CLI

    • fix watch options for array config (#​892)

    Docs

    • contribute: adds section seperator (cff0c55)
    • contribute: combines seperate sections for npm and yarn (aefa8eb)
    • contributing: updates the docs for the test (7656637)
    • fix link to webpack-scaffold (de0b4a0)
    • init: improve description (9856bab)
    • utils: update prettier (8b6d47b)

    Fix

    • improve checking file permission (de41351)
    • chore: Minor fix (6810182)
    • use fork cause original repo is unmaintained (383125a)
    • add: apply suggestions (ccf0dce)
    • add: add handling of merge option (eb43443)
    • add: add handling of merge option (ce51a0a)
    • ci: fixes linting error in ci (cfc0117)
    • cli: updates err message (b5e1913)
    • cli: removes the comment before err handling block (ac5a53f)
    • cli: --config-register resolves relative to root (23375bd)
    • cli: removes func return in catch instance (7d31321)
    • cli: sets stack trace limit (869024f)
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    • generators: refactor utils (17e4511)
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    • init-generator: use webpackOption types, improve test rules (a650e0e)
    • init-generator: improve types & defaults (fb23aa4)
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  • chore(js): Update vuepress: 0.14.10 → 0.14.11 (minor)

    chore(js): Update vuepress: 0.14.10 → 0.14.11 (minor)

    Here is everything you need to know about this update. Please take a good look at what changed and the test results before merging this pull request.

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    ✳️ vuepress (0.14.10 → 0.14.11) · Repo · Changelog


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  • chore(deps): lock file maintenance

    chore(deps): lock file maintenance

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  • chore(deps): update dependency query-string to v8

    chore(deps): update dependency query-string to v8

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    This PR contains the following updates:

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  • error with detecting species

    error with detecting species

    Dear developer,

    As shown in the picture, there is an unknown symbol in the red circle, which may be the overlap between O and H. And there is an unreasonable bond between Ca and O. What is the problem? 图片1

    opened by yunjian-hash 1
  • Questions on detecting correct species and reaction route in Ca

    Questions on detecting correct species and reaction route in Ca

    Dear developers,

    I am using reacnetgenerator to analyze the system containg Ca ions and SiO4 anions with water molecules. I want to find the reactions between the Ca ion and SiO4 anions. I found that the coordination number of Ca is not correct, which is no more than 4 in the results of the reacnetgenerator. in fact the coordination number of Ca is between the 4 to 7 with an average of 6.

    In addition, there is a lot of the reactions between the water molecules, which is not the concerned reactions. Is there any methods to precludes these reactions? The attached is the initial structure. Thanks so much! Ca_Si_0.67.cif.txt

    opened by yunjian-hash 3
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    Detected dependencies

    dockerfile
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    • python 3.11
    • python 3.11
    github-actions
    .github/workflows/codeql-analysis.yml
    • actions/checkout v3
    • github/codeql-action v2
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    npm
    reacnetgenerator/static/webpack/package.json
    • @njzjz/jsnetworkx 0.3.5
    • @popperjs/core 2.11.6
    • animejs 3.2.1
    • bootstrap 5.2.3
    • bootstrap-select 1.14.0-beta3
    • d3 3.5.17
    • jquery 3.6.3
    • jsrender 1.0.12
    • magnific-popup 1.1.0
    • paginationjs 2.5.0
    • popper.js 1.16.1
    • query-string 7.1.3
    • regenerator-runtime 0.13.11
    • smiles-drawer 2.0.3
    • startbootstrap-creative 7.0.6
    • css-loader 6.7.3
    • css-minimizer-webpack-plugin 4.2.2
    • cssnano 5.1.14
    • cssnano-preset-advanced 5.3.9
    • html-inline-css-webpack-plugin 1.11.1
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    • ifdef-loader 2.3.2
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    • postcss 8.4.20
    • postcss-import 15.1.0
    • postcss-loader 7.0.2
    • sass 1.57.1
    • sass-loader 13.2.0
    • script-ext-html-webpack-plugin 2.1.5
    • string-replace-webpack-plugin 0.1.3
    • style-loader 3.3.1
    • terser-webpack-plugin 5.3.6
    • url-loader 4.1.1
    • webpack 5.75.0
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Releases(v1.6.8)
  • v1.6.8(Nov 13, 2022)

    Bugfix

    • fix typos in calculate_rate by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1781

    Note: calculate_rate in previous versions gives wrong results. Please upgrade to the new version.

    Other changes

    • chore(deps): update dependency sass to v1.56.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1774
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1773
    • chore(deps): update dependency postcss to v8.4.19 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1777
    • chore(deps): update dependency sass-loader to v13.2.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1776
    • build macos universal2 wheels by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1778
    • chore(deps): update dependency webpack to v5.75.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1775
    • chore(deps): update dependency jsrender to v1.0.12 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1779
    • chore(deps): update dependency css-loader to v6.7.2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1780

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.7...v1.6.8

    Source code(tar.gz)
    Source code(zip)
  • v1.6.7(Nov 5, 2022)

    What's Changed

    • fix: move docutils deps to tox.ini by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1772

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.6...v1.6.7

    Source code(tar.gz)
    Source code(zip)
  • v1.6.6(Nov 5, 2022)

    What's Changed

    • limit the size of options in a select to 65536 by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1741
    • docs: migrate to sphinx book theme by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1742
    • docs: migrate to pydata-sphinx-theme by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1743
    • use openbabel native pbc implementation by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1744
    • deprecate base64 for compress block by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1745
    • fix: fix and minify docker images by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1746
    • docs: refactor and improve user guides by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1747
    • tests: test OB PBC bonds by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1749
    • docs: add text besides logo by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1750
    • add type check by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1751
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1752
    • docs: move ipynb files into docs by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1756
    • docs: revise docstring by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1757
    • docs: improve citations by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1758
    • docs: add an example to calculate_rate by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1759
    • removes basepython by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1760
    • chore(deps): update dependency cssnano to v5.1.14 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1761
    • chore(deps): update dependency cssnano-preset-advanced to v5.3.9 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1762
    • docs: add link to publications by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1763
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1764
    • chore(deps): update dependency sass to v1.56.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1767
    • add time to the route file by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1768
    • improve cli help by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1769
    • docs: add note about pip and python by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1770
    • docs: add analysis.ipynb by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1771

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.5...v1.6.6

    Source code(tar.gz)
    Source code(zip)
  • v1.6.5(Oct 20, 2022)

    What's Changed

    • chore(deps): update dependency postcss to v8.4.17 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1716
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1717
    • chore(deps): update dependency bootstrap to v5.2.2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1718
    • chore(deps): update dependency sass-loader to v13.1.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1719
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1720
    • chore(deps): update dependency postcss to v8.4.18 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1721
    • chore(deps): update dependency regenerator-runtime to v0.13.10 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1722
    • fix coverage for multiprocessing by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1723
    • fetch nodejs from pypi by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1724
    • migrate from setup.py to pyproject.yaml by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1726
    • pin nodejs to 16; rollback to manylinux_2014 by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1727
    • move cibuildwheel config to pyproject.toml by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1728
    • use pypi nodejs to build docs by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1729
    • remove precss by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1731
    • switch to VF2; fallback when RDKit throws error by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1730
    • update project classifiers by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1733
    • use specific package level logger; update metadata by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1732
    • fix conda recipe; revise docs by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1734
    • replace optimize-css-assets-webpack-plugin with css-minimizer-webpack-plugin by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1735
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1736
    • show formula in selects by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1737
    • switch from VF2 to SMILES but fallback to VF2 when failed by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1738
    • build wheels on more platforms by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1739
    • minify docs by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1740

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.4...v1.6.5

    Source code(tar.gz)
    Source code(zip)
  • v1.6.4(Sep 29, 2022)

    Bugfix

    • fix compatible with hmmlearn v0.2.8 by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1714, https://github.com/tongzhugroup/reacnetgenerator/pull/1715

    Other Changes

    • chore(deps): update dependency terser-webpack-plugin to v5.3.6 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1675
    • chore(deps): update dependency sass to v1.54.6 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1676
    • chore(deps): update dependency sass to v1.54.7 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1678
    • chore(deps): update dependency sass to v1.54.8 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1679
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1680
    • chore(deps): update dependency bootstrap to v5.2.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1681
    • chore(deps): update dependency sass to v1.54.9 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1682
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1691
    • bump docker image to py310 + nodejs16; do not pin digest by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1706
    • chore(deps): update dependency postcss-import to v15 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1677
    • cli: add choice to --type option by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1707
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1710
    • chore(deps): update dependency sass to v1.55.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1711
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1713

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.3...v1.6.4

    Source code(tar.gz)
    Source code(zip)
  • v1.6.3(Aug 29, 2022)

    What's Changed

    • fix undefined bootstrap issue by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1674

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.2...v1.6.3

    Source code(tar.gz)
    Source code(zip)
  • v1.6.2(Aug 29, 2022)

    What's Changed

    fix some scripts and styles in the web page

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.6.1...v1.6.2

    Source code(tar.gz)
    Source code(zip)
  • v1.6.1(Aug 10, 2022)

  • v1.6.0(Aug 10, 2022)

    What's Changed

    • chore(deps): update dependency postcss to v8.4.13 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1570
    • chore: copy fire.png to the web by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1571
    • chore(deps): update dependency sass to v1.51.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1566
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1572
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1573
    • chore(deps): update dependency webpack to v5.72.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1574
    • chore(deps): update dependency cssnano to v5.1.8 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1575
    • chore(deps): update dependency cssnano-preset-advanced to v5.3.4 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1576
    • chore(deps): update dependency postcss to v8.4.14 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1578
    • chore(deps): update dependency sass to v1.52.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1581
    • chore(deps): update dependency cssnano to v5.1.9 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1582
    • chore(deps): update dependency cssnano-preset-advanced to v5.3.5 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1583
    • chore(deps): update dependency sass to v1.52.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1584
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1585
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1586
    • chore(deps): update dependency cssnano to v5.1.10 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1588
    • chore(deps): update dependency cssnano-preset-advanced to v5.3.6 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1589
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1590
    • chore(deps): update dependency terser-webpack-plugin to v5.3.3 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1591
    • chore(deps): update dependency webpack to v5.73.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1592
    • chore(deps): update dependency cssnano to v5.1.11 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1594
    • chore(deps): update dependency cssnano-preset-advanced to v5.3.7 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1595
    • chore(deps): update dependency sass to v1.52.2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1593
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1596
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1597
    • chore(deps): update dependency sass to v1.52.3 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1599
    • chore(deps): update dependency semantic-release to v19.0.3 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1600
    • chore(deps): update actions/setup-python action to v4 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1598
    • chore(docs): update HMM information in the docs by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1601
    • chore(deps): update github/codeql-action action to v2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1565
    • chore: stop openbabel logging by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1602
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1603
    • chore(deps): update dependency webpack-cli to v4.10.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1604
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1605
    • chore(deps): update dependency mini-css-extract-plugin to v2.6.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1606
    • chore(deps): update the official rdkit package by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1607
    • chore(deps): update dependency cssnano to v5.1.12 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1608
    • chore(deps): update dependency cssnano-preset-advanced to v5.3.8 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1609
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1610
    • chore(docs): fix CDN errors by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1611
    • Migrate documentation to sphinx by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1612
    • fix online report page by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1613
    • add wheels for python 3.9 and 3.10; bump nodejs to 16 by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1614
    • chore(deps): update dependency postcss-loader to v7 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1579
    • chore(deps): update dependency sass-loader to v13 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1580
    • chore(deps): update dependency sass to v1.53.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1615
    • fix web backgroud image by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1616
    • add the methane tutorial by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1617
    • chore(deps): update dependency sass-loader to v13.0.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1618
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1619
    • chore(deps): update dependency sass-loader to v13.0.2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1620
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1621
    • removed encrypted files by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1622
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1623
    • chore(deps): update dependency postcss-loader to v7.0.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1624
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1629
    • chore(deps): update dependency bootstrap to v4.6.2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1631
    • chore(deps): update dependency sass to v1.54.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1632
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1633
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1634
    • chore(deps): update dependency webpack to v5.74.0 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1635
    • move unittest out of the package by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1637
    • fix reading atomic type from dump files by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1636
    • add test for detect by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1638
    • render SVG from smiles in the browser by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1641
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1642
    • add a tool to extract number of species by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1643
    • chore(deps): update dependency sass to v1.54.1 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1644
    • chore(deps): update dependency sass to v1.54.2 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1645
    • chore(deps): update dependency sass to v1.54.3 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1646
    • chore(deps): update dependency postcss to v8.4.16 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1647
    • chore(deps): lock file maintenance by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1648
    • add a tool to calculate rate constants by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1649
    • add cli argument to show version by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1651
    • add GUI cli to main cli by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1652
    • chore(deps): update dependency startbootstrap-creative to v7 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1185
    • chore(deps): update dependency bootstrap to v5 by @renovate in https://github.com/tongzhugroup/reacnetgenerator/pull/1145
    • write scm version to the package by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1654
    • Revert "add GUI cli to main cli" by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1656
    • add placeholder to SimpleLightbox by @njzjz in https://github.com/tongzhugroup/reacnetgenerator/pull/1655

    Full Changelog: https://github.com/tongzhugroup/reacnetgenerator/compare/v1.5.2...v1.6.0

    Source code(tar.gz)
    Source code(zip)
  • v1.5.2(Apr 30, 2022)

  • v1.5.1(Apr 30, 2022)

  • v1.5.0(Apr 23, 2022)

  • v1.4.166(Apr 14, 2022)

  • v1.4.165(Jul 20, 2021)

  • v1.4.164(Apr 2, 2021)

  • v1.4.163(Mar 29, 2021)

  • v1.4.162(Mar 25, 2021)

  • v1.4.161(Mar 25, 2021)

  • v1.4.160(Mar 10, 2021)

  • v1.4.159(Mar 2, 2021)

  • v1.4.158(Feb 26, 2021)

  • v1.4.157(Feb 23, 2021)

  • v1.4.156(Feb 10, 2021)

  • v1.4.155(Feb 8, 2021)

  • v1.4.154(Feb 8, 2021)

  • v1.4.153(Jan 19, 2021)

  • v1.4.152(Jan 11, 2021)

  • v1.4.151(Dec 5, 2020)

  • v1.4.150(Nov 5, 2020)

  • v1.4.149(Nov 3, 2020)

Owner
Tong Zhu Research Group
East China Normal University
Tong Zhu Research Group
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