A Python wrapper around Bacting

Related tags

Miscellaneouspybacting
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'

null 54 Dec 21, 2022
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.

Chris Mungall 3 Oct 24, 2022
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

Knugi 9 Sep 28, 2022
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

Emanuele Sabato 5 Apr 11, 2022
🤖🧭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

Sergey Smirnov 9 Nov 27, 2022
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

Steve C 1 Dec 14, 2022
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

Neo4j 100 Dec 20, 2022
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

null 4 Jan 5, 2022
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

rijfas 9 Sep 8, 2022
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
GitHub Repository
More routines for operating on iterables, beyond itertools

More Itertools Python's itertools library is a gem - you can compose elegant solutions for a variety of problems with the functions it provides. In mo

2.8k Jan 02, 2023
In this project we will implement AirBnB clone using console

AirBnB Clone In this project we will implement AirBnB clone using console. Usage The shell should work like this

Nandweza Allan 1 Feb 07, 2022
Hashcrack - A non-object oriented open source, Software for Windows/Linux made in Python 3

Multi Force This project is a non-object oriented open source, Software for Wind

Radiationbolt 3 Jan 02, 2023
Taxonomy addition for complete trees

TACT: Taxonomic Addition for Complete Trees TACT is a Python app for stochastic polytomy resolution. It uses birth-death-sampling estimators across an

Jonathan Chang 3 Jun 07, 2022
Hashcrack: Hash Bruteforse tool using python

HashCrack Hash Bruteforse tool Usage hashcrack.py -n 6 -c lower -l 5 -a md5 -t 3

Lev 1 May 04, 2022
sfgp is a package that aggregates individual scripts and notebooks, primarily written for the basic analysis tasks of genetics and pharmacogenomics data.

sfgp is a package that aggregates individual scripts and notebooks, primarily written for the basic analysis tasks of genetics and pharmacogenomics data.

Vishal Sarsani 1 Mar 31, 2022
Remote execution of a simple function on the server

FunFetch Remote execution of a simple function on the server All types of Python support objects.

Decave 4 Jun 30, 2022
Meaningful and minimalist release notes for developers

Managing manual release notes is hard. Therefore, everyone tends to generate release notes from commit messages. But, you won't get a meaningful release note at the end.

codezri 31 Dec 30, 2022
The git for the Python Story Utility Package library.

PSUP, The Python Story Utility Package Module. PSUP helps making stories or games with options, diverging paths, different endings and so on. You can

Enoki 6 Nov 27, 2022
Linux Pressure Stall Information (PSI) Status App

Linux Pressure Stall Information (PSI) Status App psistat is a simple python3 program to display the PSIs and to capture/display exception events. psi

Joe D 3 Sep 18, 2022
Compiler Final Project - Lisp Interpreter

Compiler Final Project - Lisp Interpreter

2 Jan 23, 2022
libvcs - abstraction layer for vcs, powers vcspull.

libvcs - abstraction layer for vcs, powers vcspull. Setup $ pip install libvcs Open up python: $ python # or for nice autocomplete and syntax highlig

python utilities for version control 46 Dec 14, 2022
El Niño - Southern Oscillation analysis compared to minimum flow rates of rivers in northeast Brazil

ENSO (El Niño - Southern Oscillation) analysis in northeast Brazil É comprovada a influência dos fenômenos El Niño e La Niña nas secas no nordesde bra

Weyder Freire 1 Jan 13, 2022
A Python utility belt containing simple tools, a stdlib like feel, and extra batteries. Hashing, Caching, Timing, Progress, and more made easy!

Ubelt is a small library of robust, tested, documented, and simple functions that extend the Python standard library. It has a flat API that all behav

Jon Crall 638 Dec 13, 2022
python for windows extensions

This is the readme for the Python for Win32 (pywin32) extensions source code. See CHANGES.txt for recent changes. 'setup.py' is a standard distutils

27 Dec 08, 2022
Free APN For Python

Free APN For Python

XENZI GANZZ 4 Apr 22, 2022
A visidata plugin for parsing f5 ltm/gtm/audit logs

F5 Log Visidata Plugin This plugin supports the default log format for: /var/log/ltm* /var/log/gtm* /var/log/apm* /var/log/audit* It extracts common l

James Deucker 1 Jan 06, 2022
Animations made using manim-ce

ManimCE Animations Animations made using manim-ce The code turned out to be a bit complicated than expected.. It can be greatly simplified, will work

sparshg 17 Jan 06, 2023
A carrot-based color palette you didn't know you needed.

A package to produce a carrot-inspired color palette for python/matplotlib. Install: pip install carrotColors Update: pip install --upgrade carrotColo

10 Sep 28, 2021
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