Search Results - python property documentation

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics by Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.

“…Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics…”
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PyL3dMD: Python LAMMPS 3D molecular descriptors package by Panwar, Pawan, Yang, Quanpeng, Martini, Ashlie

“…–property-relationship models using machine learning. Here, we describe a suite of open-source Python-based post-processing routines, called PyL3dMD, for calculating 3D descriptors…”
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Pickaxe: a Python library for the prediction of novel metabolic reactions by Shebek, Kevin M., Strutz, Jonathan, Broadbelt, Linda J., Tyo, Keith E. J.

“… for a user’s application due to lack of exhaustive reaction rules, restriction to pre-computed networks, and difficulty in using the software due to lack of documentation…”
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Properties and Styles of Software Technology Tutorials by Arya, Deeksha M., Guo, Jin L. C., Robillard, Martin P.

“… We studied the design of tutorials in the software documentation landscape for five popular programming languages: Java, C#…”
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pyPept: a python library to generate atomistic 2D and 3D representations of peptides by Ochoa, Rodrigo, Brown, J. B., Fox, Thomas

“…We present pyPept, a set of executables and underlying python-language classes to easily create, manipulate, and analyze peptide molecules using the FASTA, HELM, or recently-developed BILN notations…”
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PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies by Cao, Dong-Sheng, Liang, Yi-Zeng, Yan, Jun, Tan, Gui-Shan, Xu, Qing-Song, Liu, Shao

“… Herein, we developed a comprehensive python package to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for drug discovery. PyDPI…”
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AtomDB: A Python Library and Database for Atomic and Promolecular Properties by Sánchez Díaz, Gabriela, Richer, Michelle, Martínez González, Marco, van Zyl, Maximilian, Pujal, Leila, Tehrani, Alireza, Bianchi, Julianna, Chuiko, Valerii, Erhard, Jannis, Meng, Fanwang, Ayers, Paul W, Heidar-Zadeh, Farnaz

“…AtomDB is a free and open-source Python library for accessing and manipulating neutral and charged atomic species and their promolecular properties…”
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A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank by Smelter, Andrey, Astra, Morgan, Moseley, Hunter N. B.

“…) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecule…”
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Logomaker: beautiful sequence logos in Python by Tareen, Ammar, Kinney, Justin B

“…Abstract Summary Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize…”
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Grid: A Python library for molecular integration, interpolation, differentiation, and more by Tehrani, Alireza, Yang, Xiaotian Derrick, Martínez-González, Marco, Pujal, Leila, Hernández-Esparza, Raymundo, Chan, Matthew, Vöhringer-Martinez, Esteban, Verstraelen, Toon, Ayers, Paul W, Heidar-Zadeh, Farnaz

“…Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g…”
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Stingray: A Modern Python Library for Spectral Timing by Huppenkothen, Daniela, Bachetti, Matteo, Stevens, Abigail L., Migliari, Simone, Balm, Paul, Hammad, Omar, Khan, Usman Mahmood, Mishra, Himanshu, Rashid, Haroon, Sharma, Swapnil, Ribeiro, Evandro Martinez, Blanco, Ricardo Valles

“…This paper describes the design and implementation of stingray, a library in Python built to perform time series analysis and related tasks on astronomical light curves…”
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scikit‐maad: An open‐source and modular toolbox for quantitative soundscape analysis in Python by Ulloa, Juan Sebastián, Haupert, Sylvain, Latorre, Juan Felipe, Aubin, Thierry, Sueur, Jérôme

“… that slows down its application in research and conservation. We present scikit‐maad, an open‐source Python package dedicated to the analysis of environmental audio recordings…”
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Metis: a python-based user interface to collect expert feedback for generative chemistry models by Menke, Janosch, Nahal, Yasmine, Bjerrum, Esben Jannik, Kabeshov, Mikhail, Kaski, Samuel, Engkvist, Ola

“… Metis is a Python-based open-source graphical user interface (GUI), designed to solve this and enable the collection of chemists…”
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GBasis: A Python library for evaluating functions, functionals, and integrals expressed with Gaussian basis functions by Kim, Taewon David, Pujal, Leila, Richer, Michelle, van Zyl, Maximilian, Martínez-González, Marco, Tehrani, Alireza, Chuiko, Valerii, Sánchez-Díaz, Gabriela, Sanchez, Wesley, Adams, William, Huang, Xiaomin, Kelly, Braden D, Vöhringer-Martinez, Esteban, Verstraelen, Toon, Heidar-Zadeh, Farnaz, Ayers, Paul W

“…GBasis is a free and open-source Python library for molecular property computations based on Gaussian basis functions in quantum chemistry…”
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Mordred: a molecular descriptor calculator by Moriwaki, Hirotomo, Tian, Yu-Shi, Kawashita, Norihito, Takagi, Tatsuya

“… It is freely available via GitHub. Mordred can be easily installed and used in the command line interface, as a web application, or as a high-flexibility Python package on all major platforms…”
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Digitalization of Legacy Datasets and Machine Learning Regression Yields Insights for Reservoir Property Prediction and Submarine-Fan Evolution: A Subsurface Example From the Lewis Shale, Wyoming by Martin, Thomas, Tadla, Jared, Jobe, Zane

“…Machine-learning algorithms have long aided in geologic property prediction from well-log data, but are primarily used to classify lithology, facies, formation, and rock types…”
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HydroPy (v1.0): a new global hydrology model written in Python by Stacke, Tobias, Hagemann, Stefan

“…). Being rewritten in Python, the new model requires much less effort in maintenance, and due to its flexible infrastructure, new processes can be easily implemented…”
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PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations by Reis, Pedro B P S, Vila-Viçosa, Diogo, Rocchia, Walter, Machuqueiro, Miguel

“…The protonation of titratable residues has a significant impact on the structure and function of biomolecules, influencing many physicochemical and ADME properties…”
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PyCDT: A Python toolkit for modeling point defects in semiconductors and insulators by Broberg, Danny, Medasani, Bharat, Zimmermann, Nils E.R., Yu, Guodong, Canning, Andrew, Haranczyk, Maciej, Asta, Mark, Hautier, Geoffroy

“…), have found widespread use in the calculation of point-defect properties. Here we have developed the Python Charged Defect Toolkit (PyCDT…”
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TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning by Pérez-García, Fernando, Sparks, Rachel, Ourselin, Sébastien

“…•Open-source Python library for preprocessing, augmentation and sampling of medical images for deep learning…”
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