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Search results for python cheminformatics
cheminformatics
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python
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104 search results found
Rdkit
⭐
2,323
The official sources for the RDKit library
Awesome Python Chemistry
⭐
971
A curated list of Python packages related to chemistry
Deep_gcns_torch
⭐
940
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
Dgl Lifesci
⭐
558
Python package for graph neural networks in chemistry and biology
Thermo
⭐
517
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
Aizynthfinder
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504
A tool for retrosynthetic planning
Datamol
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423
Molecular Processing Made Easy.
Asciimol
⭐
341
Curses based ASCII molecule viewer for terminals.
Pubchempy
⭐
315
Python wrapper for the PubChem PUG REST API.
Reinvent
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310
Chembl_webresource_client
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303
Official Python client for accessing ChEMBL API
Prolif
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286
Interaction Fingerprints for protein-ligand complexes and more
Indigo
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263
Universal cheminformatics toolkit, utilities and database search tools
Oddt
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241
Open Drug Discovery Toolkit
Stk
⭐
214
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
Molplotly
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200
add-on to plotly which show molecule images on mouseover!
Mols2grid
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195
Interactive molecule viewer for 2D structures
Smiles Transformer
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154
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
Reinvent4
⭐
150
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
Py4chemoinformatics
⭐
147
Python for chemoinformatics
Drugex
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142
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
Fragmenstein
⭐
139
Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
Global Chem
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137
A Knowledge Graph of Common Chemical Names to their Molecular Definition
Ampl
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128
The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
Ase_ani
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126
ANI-1 neural net potential with python interface (ASE)
Pysmiles
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117
A lightweight python-only library for reading and writing SMILES strings
Rdkit Pypi
⭐
112
⚛️ RDKit Python Wheels on PyPI. 💻 pip install rdkit
Kgcn
⭐
105
A graph-based deep learning framework for life science
Mol2vec
⭐
103
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
E3fp
⭐
98
3D molecular fingerprints
Lstm_chem
⭐
91
Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.
Fpsim2
⭐
89
Simple package for fast molecular similarity searches
Chemspipy
⭐
85
Python wrapper for the ChemSpider API
Aqme
⭐
73
Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io
Clamp
⭐
71
Code for the paper Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language
Ani1_dataset
⭐
71
A data set of 20 million calculated off-equilibrium conformations for organic molecules
Opencadd
⭐
70
A Python library for structural cheminformatics
Awesome Deep Learning 4 Life Sciences
⭐
65
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
Chemcoord
⭐
58
A python module for manipulating cartesian and internal coordinates.
Molvs
⭐
55
Molecule Validation and Standardization
Chembl Downloader
⭐
55
Write reproducible code for getting and processing ChEMBL
Cirpy
⭐
54
Python wrapper for the NCI Chemical Identifier Resolver (CIR)
Py4chemoinformatics
⭐
53
Python for chemoinformatics
Pdn
⭐
51
The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)
Psikit
⭐
37
psi4+RDKit
Molml
⭐
36
A library to interface molecules and machine learning.
Retrosynthesis_planner
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36
Retrosynthesis planner
Geo Gcn
⭐
35
The official implementation of the SGCN architecture.
Molgraph
⭐
34
Graph neural networks for molecular machine learning. Implemented and compatible with TensorFlow and Keras.
Arpeggio
⭐
33
Calculation of interatomic interactions in molecular structures
Chembience
⭐
33
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
Scikit Chem
⭐
32
A high level cheminformatics package for the Scientific Python stack, built on RDKit.
Scopy
⭐
32
An integrated negative design python library for desirable HTS/VS database design
Protwis
⭐
31
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
Patentchem
⭐
27
Downloads USPTO patents and finds molecules related to keyword queries
Q2 Qemistree
⭐
24
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Dst
⭐
22
(differentiable) gradient-based optimization on a chemical graph for de novo molecule design/optimization (ICLR 2022)
Icsg3d
⭐
20
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning (JCIM 2020)
Padme
⭐
20
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
Tucan
⭐
20
A molecular identifier and descriptor for all domains of chemistry.
Homebrew Cheminformatics
⭐
19
Cheminformatics formulae for the Homebrew package manager
Molecular Vae
⭐
19
Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"
Genui
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19
The backend services of the GenUI framework. The backend provides the REST API used for molecular generation, QSAR modelling and chemical space visualization.
Cheminformatics Microservice
⭐
19
This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.
Route Distances
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18
Tools and routines to calculate distances between synthesis routes and to cluster them.
Pidginv2
⭐
18
PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)
Robert
⭐
17
Automated machine learning protocols that start from CSV databases of descriptors or SMILES and produce publication-quality results in Chemistry studies with only one command line.
Adme Pred Py
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16
Python implementation of common ADME properties.
Mongodb Chemistry
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16
Ideas for chemical similarity searches in MongoDB.
Openpom
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15
Replication of the Principal Odor Map paper by Brian K. Lee et al. (2023).
Pidginv3
⭐
15
Protein target prediction using random forests and reliability-density neighbourhood analysis
Dionysus
⭐
15
For analysis of calibration, performance, and generalizability of probabilistic models on small molecular datasets. Paper on RSC Digital Discovery: https://pubs.rsc.org/en/content/articlehtml/2023/d
Aqml
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14
Amons-based quantum machine learning for quantum chemistry
Pipelines
⭐
13
Containerised components for cheminformatics and computational chemistry
Organic Chemistry Reaction Prediction Using Nmt
⭐
13
organic chemistry reaction prediction using NMT with Attention
Chemper
⭐
12
Repository for Chemical Perception Sampling Tools
Molpher Lib
⭐
12
C++/Python Library for Systematic Chemical Space Exploration
Atomlite
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11
A SQLite chemical database.
Hotpot
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11
A python package designed to communicate among various chemical and materials calculational tools
Moldoc
⭐
11
Make better chemistry documentation.
Sensaas
⭐
11
Shape-based alignment of molecules
Chembl_multitask_model
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10
Target prediction multitask neural network, with examples running it in Python, C++, Julia and JS
Rdkit Utils
⭐
10
Utilities for working with the RDKit
E3fp Paper
⭐
9
3D molecular fingerprints (E3FP) paper repo
Moldrug
⭐
9
MolDrug (from Molecule to Drug) is a python package for drug-oriented optimization on the chemical space
Himap
⭐
9
High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
Graphdot
⭐
8
Primary repo at https://gitlab.com/yhtang/graphdot
Spoc
⭐
8
An integrated Python package for molecular descriptor generation, data processing, model training, and hyper-parameter optimization.
Merpy
⭐
8
MER python interface
Qed
⭐
8
The QED (Quantitative Estimation of Drug-likeness) molecular descriptor to use in combination with RDKit
Ocsr Project
⭐
7
Optical Chemical Structure Recognition Tool (based on OSRA)
Pyisopach
⭐
7
A "fairly fast" ISOtope PAttern Calculator for Python
Reac Space Exp
⭐
7
A python implementation of open-source packages to explore the chemical reaction space associated with elementary prebiotic chemistry.
Ifg
⭐
7
A python package which extracts functional group data from SMILES codes
Kekulescope
⭐
6
Code for KekuleScope
Molecular Sdg
⭐
6
Structure Diagram Generation (SDG) for organic molecules following cheminformatics literature
Documentation
⭐
6
Sphinx-based documentation for the Open Babel project
Riff
⭐
6
Reaction-informed Fusion of Fragments (RiFF
Siamese Rnn Self Attention
⭐
6
Contains code for Siamese Recurrent Neural Network with Self-Attention for Bioactivity Prediction
Pydockrmsd
⭐
6
Root-mean-square deviation of atomic positions
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