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Marsilea-viz
marsilea

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

51K 311 13
scikit-fingerprints
scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

20K 363 29
HiroYokoyama
moleditpy

MoleditPy -- A cross-platform, simple, and intuitive molecular editor built in Python. Please note that these codes are written with the assistance of LLM.

15K 4 0
Croydon-Brixton
pymol-remote

Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)

15K 37 3
HiroYokoyama
moleditpy-linux

MoleditPy -- A cross-platform, simple, and intuitive molecular editor built in Python. Please note that these codes are written with the assistance of LLM.

11K 4 0
DrrDom
pmapper

3D pharmacophore signatures and fingerprints

11K 113 24
ysig
grakel

A scikit-learn compatible library for graph kernels

10K 641 103
DrrDom
crem

CReM: chemically reasonable mutations framework

3K 268 44
script-notation
linearscript

SCRIPT V3.1: A deterministic, RDKit-independent molecular notation with 100% round-trip stereo parity, materials science extensions, biopolymer support, and formal LALR grammar.

2K 0 0
PaccMann
pytoda

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

1K 29 7
ysig
grakel-dev

A scikit-learn compatible library for graph kernels

1K 641 103
jajupmochi
graphkit-learn

A Python library for graph kernels, graph edit distances, and graph pre-images

1K 128 18
emapco
chem-mrl

Chem-MRL: SMILES-based Matryoshka Representation Learning Embedding Model

892 4 0
zotko
xyz2graph

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

810 86 22
kzra
pykrev

FT-MS data analysis with Python

743 16 6
afloresep
chelombus

Clustering and visualization of billions of molecules (or other high-dimensional data). 1 billion, 100K clusters, less than 3 hours, one GPU.

573 5 2
bio2bel
bio2bel-chebi

A Bio2BEL package for converting Chemical Entities of Biological Interest (ChEBI) to BEL

503 1 0
kamilpytlak
moleculapy

👨‍🔬 A command-line application that utilizes the RDKit library to compute molecular descriptors and fingerprints, aiding in the analysis and characterization of chemical structures

481 1 1
ci-lab-cz
cremdock

CReM-dock: generation of chemically reasonable molecules guided by molecular docking

474 29 6
akuroiwa
chem-ant

Select materials to output molecules similar to the target molecule with MCTS Solver and Genetic Programming.

439 6 1
Acetylsalicylsaeure
pymopac

a python wrapper to interact with the semiempirical quantum chemistry program MOPAC

411 1 1
Mishima-syk
psikit

A thin wrapper library for Psi4 and RDKit

398 106 22
N720720
lindemann

lindemann is a python package to calculate the Lindemann index of a lammps trajectory

368 24 5
the-metabolic-disassembler
metadisassembler

The Metabolic Disassembler

340 3 1
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