Open Source Python Molecular Science Software
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Python Molecular Science Software
View 2688 business solutionsBrowse free open source Python Molecular Science Software and projects below. Use the toggles on the left to filter open source Python Molecular Science Software by OS, license, language, programming language, and project status.
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design. Please visits PyRx home page to learn more about PyRx and watch videos on how to use it. -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us - kabeermuzammil614@gmail.com MzDOCK Development - Available on WindowsOS and Linux ubuntu 22.04 and more - Software Authorship - Muzammil Kabier -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
Rent Manager SoftwareRent Manager is award-winning property management software built for residential, commercial, and short-term-stay portfolios of any size. The program’s fully customizable features include a double-entry accounting system, maintenance management/scheduling, marketing integration, mobile applications, more than 450 insightful reports, and an API that integrates with the best PropTech providers on the market.
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5 -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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RDKit
Open-Source Cheminformatics and Machine Learning
A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches. -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
SIEM | API Security | Log Management SoftwareBuilt on the Graylog Platform, Graylog Security is the industry’s best-of-breed threat detection, investigation, and response (TDIR) solution. It simplifies analysts’ day-to-day cybersecurity activities with an unmatched workflow and user experience while simultaneously providing short- and long-term budget flexibility in the form of low total cost of ownership (TCO) that CISOs covet. With Graylog Security, security analysts can:
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
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RetroScheme- Get Your Retrosynthesis
- RetroScheme is used for molecule sketching and retrosynthesis
RetroScheme was specifically designed to help Chemists in knowing potential starting material through retrosynthetic analysis. The App is basically a GUI wrapper for the library Aizynthfinder from Astrazeneca.. - The App is coupled with molecular sketching tool to sketch your compound - This was made to be easy for the user and can be used endlessly to assist in potential new drug synthesis -
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PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.
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Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.
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PocketAnalyzerPCA combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.
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ERmod
Approximate solvation free energy calculator
ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation software, such as LAMMPS, GROMACS and/or AMBER. -
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nwbas2ecce
nwbas2ecce converts nwchem basis set files to the ECCE format
The basis sets included with ECCE have -- as far as I can tell -- not been updated for many years. In addition, many of the newer basis sets that come with nwchem aren't included, such as the def2- series. nwbas2ecce is a python script that aims to automate as much as possible of the conversion process of a nwchem basis set file into the files necessary for ECCE to included it in the basis set tool. The process isn't completely automatic, but I also believe that it shouldn't be to avoid stuff-ups -- however, the amount of manual editing is kept to a minimum. Note that these script are run in the terminal. The screenshot is of the basis set tool in ECCE, not this piece of software. -
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2DFLT
Program for Normalization, Averaging and Editing of In Situ Data Sets
2DFLT it is first out of two programs which allows implementation of Phase Sensitive Detection (PSD) and/or Modulated Enhanced Diffraction (MED) techniques on the in situ data. This software allows collecting individual data files from in situ experiment into one dataset. After that this data set can be visualized, edited, normalized and averaged. Resulted data can be saved as one flat file (FLT-format) which can be used for PSD/MED calculations via 2DMED software (http://sourceforge.net/projects/twodmed/?source=directory). 2DFLT specifically was written to target in situ X-ray Powder Diffraction data from synchrotron measurements. Hence it can read CHI, XYE (TOPAS), FXYE(GSAS/ GSASII) and XY- files formats. However it can read general in situ data written into individual TXT or XY – files. -
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2DMED
Phase Sensitive Detection and Modulated Enhanced Diffraction Software
2DMED it is the second out of two programs which allows implementation of Phase Sensitive Detection (PSD) and/or Modulated Enhanced Diffraction (MED) techniques on the in situ data. This software takes normalized and averaged in situ data in flat file format (FLT) and performs PSD transformation which has been described in Urakawa, A.et al. Chem. Eng. Science 2008, 63, 4902. User can choose demodulation index k and perform several demodulation calculations. This is extremely important since demodulation calculations at k = 2 on in situ powder diffraction data represent implementation of MED method which been described in Chernyshov, D. et al. Acta Cryst. 2011, A67, 327. Demodulated data can be then viewed on 2D and/or 1D plot and analyses with different tools including In Phase Plot, Maximum Amplitude Plot and Positive Pattern Plot. Demodulated data also can be saved in ASCII format for further analysis. -
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This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein's backbone.
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A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).
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Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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CellPublisher is a free, open source program to improve the navigation of biological pathways. It converts CellDesigner diagrams into fully-featured maps that live inside a browser. The navigation is based on the Google maps API.
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Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
