Giter Club home page Giter Club logo

reacnetgenerator's Introduction

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

The latest version requires Python 3.7 or later. 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)

reacnetgenerator's People

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

reacnetgenerator's Issues

Action required: Greenkeeper could not be activated 🚨

🚨 You need to enable Continuous Integration on Greenkeeper branches of this repository. 🚨

To enable Greenkeeper, you need to make sure that a commit status is reported on all branches. This is required by Greenkeeper because it uses your CI build statuses to figure out when to notify you about breaking changes.

Since we didn’t receive a CI status on the greenkeeper/initial branch, it’s possible that you don’t have CI set up yet. We recommend using Travis CI, but Greenkeeper will work with every other CI service as well.

If you have already set up a CI for this repository, you might need to check how it’s configured. Make sure it is set to run on all new branches. If you don’t want it to run on absolutely every branch, you can whitelist branches starting with greenkeeper/.

Once you have installed and configured CI on this repository correctly, you’ll need to re-trigger Greenkeeper’s initial pull request. To do this, please click the 'fix repo' button on account.greenkeeper.io.

WS-2018-0210 Low Severity Vulnerability detected by WhiteSource

WS-2018-0210 - Low Severity Vulnerability

Vulnerable Library - lodash-3.10.1.tgz

The modern build of lodash modular utilities.

path: null

Library home page: http://registry.npmjs.org/lodash/-/lodash-3.10.1.tgz

Dependency Hierarchy:

  • jsnetworkx-0.3.4.tgz (Root Library)
    • lodash-3.10.1.tgz (Vulnerable Library)

Found in HEAD commit: de89639c71160cfb38114191c9f2de6ae339ea0c

Vulnerability Details

In the node_module "lodash" before version 4.17.11 the functions merge, mergeWith, and defaultsDeep can be tricked into adding or modifying properties of the Object prototype. These properties will be present on all objects.

Publish Date: 2018-11-25

URL: WS-2018-0210

CVSS 2 Score Details (3.5)

Base Score Metrics not available

Suggested Fix

Type: Change files

Origin: lodash/lodash@90e6199

Release Date: 2018-08-31

Fix Resolution: Replace or update the following files: lodash.js, test.js


Step up your Open Source Security Game with WhiteSource here

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.template:4.4.0

Vulnerabilities

DepShield reports that this application's usage of lodash.template:4.4.0 results in the following vulnerability(s):


Occurrences

lodash.template:4.4.0 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ vue-server-renderer:2.6.7
              └─ lodash.template:4.4.0
        └─ workbox-build:3.6.3
              └─ lodash.template:4.4.0

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.camelcase:4.3.0

Vulnerabilities

DepShield reports that this application's usage of lodash.camelcase:4.3.0 results in the following vulnerability(s):


Occurrences

lodash.camelcase:4.3.0 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ css-loader:0.28.11
              └─ lodash.camelcase:4.3.0

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.clonedeep:4.5.0

Vulnerabilities

DepShield reports that this application's usage of lodash.clonedeep:4.5.0 results in the following vulnerability(s):


Occurrences

lodash.clonedeep:4.5.0 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ stylus-loader:3.0.2
              └─ lodash.clonedeep:4.5.0

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

CVE-2018-16487 High Severity Vulnerability detected by WhiteSource

CVE-2018-16487 - High Severity Vulnerability

Vulnerable Library - lodash-3.10.1.tgz

The modern build of lodash modular utilities.

path: /tmp/git/reacnetgenerator/reacnetgenerator/static/webpack/node_modules/jsnetworkx/node_modules/lodash/package.json

Library home page: http://registry.npmjs.org/lodash/-/lodash-3.10.1.tgz

Dependency Hierarchy:

  • jsnetworkx-0.3.4.tgz (Root Library)
    • lodash-3.10.1.tgz (Vulnerable Library)

Found in HEAD commit: 2319ffc5fa9db665f58e3a465ff5faecb2594c0a

Vulnerability Details

A prototype pollution vulnerability was found in lodash <4.17.11 where the functions merge, mergeWith, and defaultsDeep can be tricked into adding or modifying properties of Object.prototype.

Publish Date: 2019-02-01

URL: CVE-2018-16487

CVSS 2 Score Details (7.5)

Base Score Metrics not available

Suggested Fix

Type: Upgrade version

Origin: https://bugzilla.redhat.com/show_bug.cgi?id=CVE-2018-16487

Release Date: 2019-02-01

Fix Resolution: 4.17.11


Step up your Open Source Security Game with WhiteSource here

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.get:4.4.2

Vulnerabilities

DepShield reports that this application's usage of lodash.get:4.4.2 results in the following vulnerability(s):


Occurrences

lodash.get:4.4.2 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ webpack-serve:1.0.4
              └─ @webpack-contrib/config-loader:1.2.1
                    └─ cosmiconfig:5.1.0
                          └─ lodash.get:4.4.2
              └─ cosmiconfig:5.1.0
                    └─ lodash.get:4.4.2

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.templatesettings:4.1.0

Vulnerabilities

DepShield reports that this application's usage of lodash.templatesettings:4.1.0 results in the following vulnerability(s):


Occurrences

lodash.templatesettings:4.1.0 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ vue-server-renderer:2.6.7
              └─ lodash.template:4.4.0
                    └─ lodash.templatesettings:4.1.0

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

Setup Airbrake for your Python application

Installation

Using pip

pip install -U airbrake

Setup

The easiest way to get set up is with a few environment variables:

(You can find your project ID and API KEY with your project's settings):

export AIRBRAKE_API_KEY=<Your project API KEY>
export AIRBRAKE_PROJECT_ID=<Your project ID>
export AIRBRAKE_ENVIRONMENT=production

and you're done!

Otherwise, you can instantiate your AirbrakeHandler by passing these values as arguments to the getLogger() helper:

import airbrake


logger = airbrake.getLogger(api_key="<Your project API KEY>", project_id=<Your project ID>)

try:
    1/0
except Exception:
    logger.exception("Bad math.")

For more information please visit our official GitHub repo.

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.throttle:4.1.1

Vulnerabilities

DepShield reports that this application's usage of lodash.throttle:4.1.1 results in the following vulnerability(s):


Occurrences

lodash.throttle:4.1.1 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ lodash.throttle:4.1.1

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.uniq:4.5.0

Vulnerabilities

DepShield reports that this application's usage of lodash.uniq:4.5.0 results in the following vulnerability(s):


Occurrences

lodash.uniq:4.5.0 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ css-loader:0.28.11
              └─ cssnano:3.10.0
                    └─ postcss-merge-rules:2.1.2
                          └─ caniuse-api:1.6.1
                                └─ lodash.uniq:4.5.0
        └─ vue-server-renderer:2.6.7
              └─ lodash.uniq:4.5.0

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

Action required: Greenkeeper could not be activated 🚨

🚨 You need to enable Continuous Integration on Greenkeeper branches of this repository. 🚨

To enable Greenkeeper, you need to make sure that a commit status is reported on all branches. This is required by Greenkeeper because it uses your CI build statuses to figure out when to notify you about breaking changes.

Since we didn’t receive a CI status on the greenkeeper/initial branch, it’s possible that you don’t have CI set up yet. We recommend using Travis CI, but Greenkeeper will work with every other CI service as well.

If you have already set up a CI for this repository, you might need to check how it’s configured. Make sure it is set to run on all new branches. If you don’t want it to run on absolutely every branch, you can whitelist branches starting with greenkeeper/.

Once you have installed and configured CI on this repository correctly, you’ll need to re-trigger Greenkeeper’s initial pull request. To do this, please click the 'fix repo' button on account.greenkeeper.io.

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash._reinterpolate:3.0.0

Vulnerabilities

DepShield reports that this application's usage of lodash._reinterpolate:3.0.0 results in the following vulnerability(s):


Occurrences

lodash._reinterpolate:3.0.0 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ vue-server-renderer:2.6.7
              └─ lodash.template:4.4.0
                    └─ lodash._reinterpolate:3.0.0
                    └─ lodash.templatesettings:4.1.0
                          └─ lodash._reinterpolate:3.0.0

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

Action required: Greenkeeper could not be activated 🚨

🚨 You need to enable Continuous Integration on Greenkeeper branches of this repository. 🚨

To enable Greenkeeper, you need to make sure that a commit status is reported on all branches. This is required by Greenkeeper because it uses your CI build statuses to figure out when to notify you about breaking changes.

Since we didn’t receive a CI status on the greenkeeper/initial branch, it’s possible that you don’t have CI set up yet. We recommend using Travis CI, but Greenkeeper will work with every other CI service as well.

If you have already set up a CI for this repository, you might need to check how it’s configured. Make sure it is set to run on all new branches. If you don’t want it to run on absolutely every branch, you can whitelist branches starting with greenkeeper/.

Once you have installed and configured CI on this repository correctly, you’ll need to re-trigger Greenkeeper’s initial pull request. To do this, please click the 'fix repo' button on account.greenkeeper.io.

CVE-2018-3721 Medium Severity Vulnerability detected by WhiteSource

CVE-2018-3721 - Medium Severity Vulnerability

Vulnerable Library - lodash-3.10.1.tgz

The modern build of lodash modular utilities.

path: null

Library home page: http://registry.npmjs.org/lodash/-/lodash-3.10.1.tgz

Dependency Hierarchy:

  • jsnetworkx-0.3.4.tgz (Root Library)
    • lodash-3.10.1.tgz (Vulnerable Library)

Found in HEAD commit: de89639c71160cfb38114191c9f2de6ae339ea0c

Vulnerability Details

lodash node module before 4.17.5 suffers from a Modification of Assumed-Immutable Data (MAID) vulnerability via defaultsDeep, merge, and mergeWith functions, which allows a malicious user to modify the prototype of "Object" via proto, causing the addition or modification of an existing property that will exist on all objects.

Publish Date: 2018-06-07

URL: CVE-2018-3721

CVSS 3 Score Details (6.5)

Base Score Metrics:

  • Exploitability Metrics:
    • Attack Vector: Network
    • Attack Complexity: Low
    • Privileges Required: Low
    • User Interaction: None
    • Scope: Unchanged
  • Impact Metrics:
    • Confidentiality Impact: None
    • Integrity Impact: High
    • Availability Impact: None

For more information on CVSS3 Scores, click here.

Suggested Fix

Type: Upgrade version

Origin: https://bugzilla.redhat.com/show_bug.cgi?id=CVE-2018-3721

Fix Resolution: Upgrade to version lodash 4.17.5 or greater


Step up your Open Source Security Game with WhiteSource here

[DepShield] (CVSS 7.4) Vulnerability due to usage of lodash.memoize:4.1.2

Vulnerabilities

DepShield reports that this application's usage of lodash.memoize:4.1.2 results in the following vulnerability(s):


Occurrences

lodash.memoize:4.1.2 is a transitive dependency introduced by the following direct dependency(s):

vuepress:0.14.9
        └─ css-loader:0.28.11
              └─ cssnano:3.10.0
                    └─ postcss-merge-rules:2.1.2
                          └─ caniuse-api:1.6.1
                                └─ lodash.memoize:4.1.2

This is an automated GitHub Issue created by Sonatype DepShield. Details on managing GitHub Apps, including DepShield, are available for personal and organization accounts. Please submit questions or feedback about DepShield to the Sonatype DepShield Community.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.