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
Manually Install Python 2.7 pip without any problem !

Python2.7_install_pip Manually Install Python 2.7 pip without any problem ! Download installPip.py to your system and Run the code using this Command

Ali Jafari 1 Dec 09, 2021
Canim1 - Simple python tool to search for packages without m1 wheels in poetry lockfiles

canim1 Usage Clone the repo. Run poetry install. Then you can use the tool: ❯ po

Korijn van Golen 1 Jan 25, 2022
Labspy06 With Python

Labspy06 Profil Nama : Nafal mumtaz fuadi Nim : 312110457 Kelas : T1.21.A.2 Latihan 1 Ubahlah kode dibawah ini menjadi fungsi menggunakan lambda impor

Mas Nafal 1 Dec 12, 2021
peace-performance (Rust) binding for python. To calculate star ratings and performance points for all osu! gamemodes

peace-performance-python Fast, To calculate star ratings and performance points for all osu! gamemodes peace-performance (Rust) binding for python bas

9 Sep 19, 2022
A tool for fixing inconsistent timestamp metadata (atime, ctime, and mtime).

Mtime Fixer Mtime Fixer is a tool for fixing inconsistent timestamp metadata (atime, ctime, and mtime). Sometimes timestamp metadata of folders are in

Halit Şimşek 2 Jan 11, 2022
Deis v1, the CoreOS and Docker PaaS: Your PaaS. Your Rules.

This repository (deis/deis) is no longer developed or maintained. The Deis v1 PaaS based on CoreOS Container Linux and Fleet has been replaced by Deis

Deis 6.1k Jan 04, 2023
LPCV Winner Solution of Spring Team

LPCV Winner Solution of Spring Team

22 Jul 20, 2022
This is a library for simulate probability theory problems specialy conditional probability

This is a library for simulate probability theory problems specialy conditional probability. It is also useful to create custom single or joint distribution with specific PMF or PDF to get probabilit

Mohamadreza Kariminejad 6 Mar 30, 2022
An addin for Autodesk Fusion 360 that lets you view your design in a Looking Glass Portrait 3D display

An addin for Autodesk Fusion 360 that lets you view your design in a Looking Glass Portrait 3D display

Brian Peiris 12 Nov 02, 2022
JD-backup is an advanced Python script, that will extract all links from a jDownloader 2 file list and export them to a text file.

JD-backup is an advanced Python script, that will extract all links from a jDownloader 2 file list and export them to a text file.

Kraken.snv 3 Jun 07, 2022
Project Faros is a reference implimentation of Red Hat OpenShift 4 on small footprint, bare-metal clusters.

Project Faros Project Faros is a reference implimentation of Red Hat OpenShift 4 on small footprint, bare-metal clusters. The project includes referen

project: Faros 9 Jul 18, 2022
A topology optimization framework written in Taichi programming language, which is embedded in Python.

Taichi TopOpt (Under Active Development) Intro A topology optimization framework written in Taichi programming language, which is embedded in Python.

Li Zhehao 41 Nov 17, 2022
Really bad lisp implementation. Fun with pattern matching.

Lisp-py This is a horrible, ugly interpreter for a trivial lisp. Don't use it. It was written as an excuse to mess around with the new pattern matchin

Erik Derohanian 1 Nov 23, 2021
Viewflow is an Airflow-based framework that allows data scientists to create data models without writing Airflow code.

Viewflow Viewflow is a framework built on the top of Airflow that enables data scientists to create materialized views. It allows data scientists to f

DataCamp 114 Oct 12, 2022
XlvnsScriptTool - Tool for decompilation and compilation of scripts .SDT from the visual novel's engine xlvns

XlvnsScriptTool English Dual languaged (rus+eng) tool for decompiling and compiling (actually, this tool is more than just (dis)assenbler, but less th

Tester 3 Sep 15, 2022
Um jogo para treinar COO em python

WAR DUCK Este joguinho bem simples tem como objetivo treinar um pouquinho de POO com python. Não é nada muito complexo mas da pra se divertir Como rod

Gabriel Jospin 3 Sep 19, 2021
Similarity checking of sign languages

Similarity checking of sign languages This repository checks for similarity betw

Tonni Das Jui 1 May 13, 2022
Location of public benchmarking; primarily final results

CSL_public_benchmark This repo is intended to provide a periodically-updated, public view into genome sequencing benchmarks managed by HudsonAlpha's C

HudsonAlpha Institute for Biotechnology 15 Jun 13, 2022
Timetable scripts for python

Timetable Scripts timetable_to_json: https://beta.elektronplus.pl/timetable classes_taught_by_teacher: a.adam (aa) ['1Tc', '1Td', '3Te', '3Ti', '4Tf',

Elektron++ 2 Jan 02, 2022
Repo Home WPDrawBot - (Repo, Home, WP) A powerful programmatic 2D drawing application for MacOS X which generates graphics from Python scripts. (graphics, dev, mac)

DrawBot DrawBot is a powerful, free application for macOS that invites you to write Python scripts to generate two-dimensional graphics. The built-in

Frederik Berlaen 342 Dec 27, 2022