A Python wrapper around Bacting

Overview

pybacting

Tests PyPI PyPI - License PyPI - Python Version Code style: black DOI

Python wrapper around bacting.

Usage

Based on the example from the bacting page, you can do:

from pybacting import cdk

print(cdk.fromSMILES("COC"))

Or you can use some of the more pythonic functions that wrap the functions exposed through the pybacting.cdk object:

import pybacting

print(pybacting.from_smiles("COC"))

Installation

Before installing, you'll need to make sure Maven (mvn) is available on your path. If you're on mac, use brew install maven.

$ pip install pybacting

Install the latest code from GitHub:

$ pip install git+https://github.com/cthoyt/pybacting

Download and install from source in development mode:

$ git clone https://github.com/cthoyt/pybacting
$ cd pybacting
$ pip install --editable .
You might also like...
36 key ergo split keyboard, designed around the Seeeduino Xiao platform
36 key ergo split keyboard, designed around the Seeeduino Xiao platform

Slice36 Minimalist Split Keyboard 36 key ergo split keyboard, designed around the Seeeduino Xiao platform. Inspired by the Corne, Ferris, Ben Vallack'

Python wrapper to different clients to determine how a particular term is used.

Python wrapper to different clients to determine how a particular term is used.

A Python wrapper for Matrix Synapse admin API

Synapse-admin-api-python A Python wrapper for Matrix Synapse admin API. Versioning This library now supports up to Synapse 1.45.0, any Admin API intro

Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions
Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions

xbi Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions. Description This Python script can be easi

🤖🧭Creates google-like navigation menu using python-telegram-bot wrapper

python telegram bot menu pagination Makes a google style pagination line for a list of items. In other words it builds a menu for navigation if you ha

An async API wrapper for Dress To Impress written in Python.

dti.py An async API wrapper for Dress To Impress written in Python. Some notes: For the time being, there are no front-facing docs for this beyond doc

A Python wrapper API for operating and working with the Neo4j Graph Data Science (GDS) library

gdsclient NOTE: This is a work in progress and many GDS features are known to be missing or not working properly. This repo hosts the sources for gdsc

An html wrapper for python

MessySoup What is it? MessySoup is a python wrapper for html elements. While still a ways away, the main goal is to be able to build a wesbite straigh

A simple wrapper for joy library
A simple wrapper for joy library

Joy CodeGround A simple wrapper for joy library to render joy sketches in browser using vs code, (or in other words, for those who are allergic to Jup

Comments
  • README instructions correct?

    README instructions correct?

    Following the README which writes:

    Download and install from source in development mode:
    
    ```shell
    $ git clone https://github.com/cthoyt/pybacting
    $ cd pybacting
    $ pip install --editable .
    

    ... I get this error:

    pybacting$ pip install --editable .
    ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /home/egonw/var/Projects/hub/pybacting
    (A "pyproject.toml" file was found, but editable mode currently requires a setup.py based build.)
    
    opened by egonw 4
  • ScyJava does not pick up the correct dependencies

    ScyJava does not pick up the correct dependencies

    Eclipse had a dependency issue which they recently fixed, removing archives from Maven Central. Bacting 0.0.40 was updated, giving the fixed dependency tree:

    [INFO] |  \- io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16:compile
    [INFO] |     +- org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0:compile
    [INFO] |     |  +- org.eclipse.platform:org.eclipse.osgi:jar:3.18.0:compile (version selected from constraint [3.17.0,4.0.0))
    [INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.common:jar:3.16.100:compile (version selected from constraint [3.16.0,))
    [INFO] |     |  +- org.eclipse.platform:org.eclipse.core.jobs:jar:3.13.0:compile (version selected from constraint [3.13.0,4.0.0))
    [INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.registry:jar:3.11.100:compile (version selected from constraint [3.11.0,4.0.0))
    [INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1:compile (version selected from constraint [3.10.0,4.0.0))
    [INFO] |     |  |  \- org.osgi:org.osgi.service.prefs:jar:1.1.2:compile (version selected from constraint [1.1.0,1.2.0))
    

    Here, org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1 is the fixed library (see https://github.com/eclipse-equinox/equinox.bundles/issues/54), but when installing pybacting it still depends on 3.10.0:

    [Error: ] Failed to execute goal on project managers-inchi-BOOTSTRAPPER: Could not resolve dependencies for project 
    io.github.egonw.bacting-BOOTSTRAPPER:managers-inchi-BOOTSTRAPPER:jar:0: Failed to collect dependencies at 
    io.github.egonw.bacting:managers-inchi:jar:0.0.40 -> io.github.egonw.bacting:bacting-core:jar:0.0.40 -> 
    io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16 -> org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0 -> 
    org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 -> org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0):
    No versions available for org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0) within specified range -> [Help 1]
    

    Note how it does pick up org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0 but then is happy with the broken org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 where version 3.10.1 should be used instead.

    This leaves pybacting uninstallable for now. It is yet unclear how to fix this.

    opened by egonw 1
  • Update deps

    Update deps

    Closes #4 if new JGO is installed. Some of the artifacts were POM only and were excluded (see https://github.com/scijava/scyjava/issues/30#issuecomment-892061823). For the rest, I added the managers.

    opened by cthoyt 1
  • Enable importing all bacting build artifacts

    Enable importing all bacting build artifacts

    Blocked by https://github.com/scijava/scyjava/issues/30 and transitively https://github.com/scijava/jgo/issues/31#issuecomment-548056700

    To fix this, we'll have to wait for a new release of jgo which includes the finished PR https://github.com/scijava/jgo/pull/62. Then, the issue with scyjava will magically go away. This issue can be closed with an update to pybacting's setup.cfg file to include a minimum version of jgo

    opened by cthoyt 1
Releases(v0.2.9)
Owner
Charles Tapley Hoyt
Bio/cheminformatician, open scientist, maintainer of @pybel and @pykeen, part of @indralab (he/him)
Charles Tapley Hoyt
take home quiz

guess the correlation data inspection a pretty normal distribution train/val/test split splitting amount .dataset: 150000 instances ├─8

HR Wu 1 Nov 04, 2021
Lock a program and kills it indefinitely if it is started.

Kill By Lock Lock a program and kills it indefinitely if it is started. How start it? It' simple, you just have to double-click on the python file (.p

1 Jan 12, 2022
A python trivium implemention

A python trivium implemention

tnt2402 1 Nov 12, 2021
FindUncommonShares.py is a Python equivalent of PowerView's Invoke-ShareFinder.ps1 allowing to quickly find uncommon shares in vast Windows Domains.

FindUncommonShares The script FindUncommonShares.py is a Python equivalent of PowerView's Invoke-ShareFinder.ps1 allowing to quickly find uncommon sha

Podalirius 184 Jan 03, 2023
1000+ ready code templates to kickstart your next AI experiment

AI Seed Projects Start with ready code for your next AI experiment. Choose from 1000+ code templates, across a wide variety of use cases. All examples

BlobCity, Inc 98 Jan 03, 2023
Create beautiful diagrams just by typing mathematical notation in plain text.

Penrose Penrose is an early-stage system that is still in development. Our system is not ready for contributions or public use yet, but hopefully will

Penrose 5.6k Jan 08, 2023
Find all solutions to SUBSET-SUM, including negative, positive, and repeating numbers

subsetsum The subsetsum Python module can enumerate all combinations within a list of integers which sums to a specific value. It works for both negat

Trevor Phillips 9 May 27, 2022
JLC2KICAD_lib is a python script that generate a component library for KiCad from the JLCPCB/easyEDA library.

JLC2KiCad_lib is a python script that generate a component library (schematic, footprint and 3D model) for KiCad from the JLCPCB/easyEDA library. This script requires Python 3.6 or higher.

Nicolas Toussaint 73 Dec 26, 2022
Tesla App Update Differences Extractor

Tesla App Update Differences Extractor Python program that finds the differences between two versions of the Tesla App. When Tesla updates the app a l

Adrian 5 Apr 11, 2022
A simple script that can watch a list of directories for change and does some action

plot_watcher A simple script that can watch a list of directories and does some action when a specific kind of change happens In its current implement

Charaf Errachidi 12 Sep 10, 2021
My solutions for Advent of Code 2021 🌟🎄

🌟 Advent of Code 2021 🎄 My solutions for Advent of Code 2021. About · What is Advent of Code? · Contents · Usage · Table of puzzles (TODO: add final

Amanda P. Pinha 2 Dec 05, 2022
Modern robots.txt Parser for Python

Robots Exclusion Protocol Parser for Python Robots.txt parsing in Python. Goals Fetching -- helper utilities for fetching and parsing robots.txts, inc

Moz 176 Dec 16, 2022
Minitel 5 somewhat reverse-engineered

Minitel 5 The Minitel was a french dumb terminal with an embedded modem which had its Golden Age before the rise of Internet. Typically cubic, with an

cLx 10 Dec 28, 2022
Hera is a Python framework for constructing and submitting Argo Workflows.

Hera is an Argo Workflows Python SDK. Hera aims to make workflow construction and submission easy and accessible to everyone! Hera abstracts away workflow setup details while still maintaining a cons

argoproj-labs 241 Jan 02, 2023
Auto check in via GitHub Actions

因为本人毕业离校,本项目交由在校的@hfut-xyc同学接手,请访问hfut-xyc/hfut_auto_check-in获得最新的脚本 本项目遵从GPLv2协定,Copyright (C) 2021, Fw[a]rd 免责声明 根据GPL协定,我、本项目的作者,不会对您使用这个脚本带来的任何后果

Fw[a]rd 3 Jun 27, 2021
Subscribe, listen and (in the future) download your favorite podcasts, quickly and easily.

Minimal Podcasts Player https://github.com/son-link/minimal-podcasts-player Subscribe, listen and (in the future) download your favorite podcasts, qui

Alfonso Saavedra 14 Nov 11, 2022
An attempt at furthering Factorio Calculator to work in more general contexts.

factorio-optimizer Lets do Factorio Calculator but make it optimize. Why not use Factorio Calculator? Becuase factorio calculator is not general. The

Jonathan Woollett-Light 1 Jun 03, 2022
A compiler for ARM, X86, MSP430, xtensa and more implemented in pure Python

Introduction The PPCI (Pure Python Compiler Infrastructure) project is a compiler written entirely in the Python programming language. It contains fro

Windel Bouwman 277 Dec 26, 2022
freeCodeCamp Scientific Computing with Python Project for Certification.

Time_Calculator_freeCodeCamp freeCodeCamp Scientific Computing with Python Project for Certification. Write a function named add_time that takes in tw

Rajdeep Mondal 1 Dec 23, 2021
This repository containing cross-section cut and fill calculations using Python programming language.

cross-section This repository is containing cut and fill calculations for cross-section using Python programming language. This codes is made to calcu

3 Jun 15, 2022