Masskit AI is a Python package that uses the Masskit Python module and PyTorch to do machine learning on mass spectra, small molecules and peptides. Masskit AI includes:
- AI models for predicting the HCD spectra of peptides.
- AI models for computing the retention index of small molecules.
- Masskit is installed using the package managers
condaandmamba. If you do not have either installed we recommend installing mambaforge. Detailed installation instructions for macOS and Linux can be found here.
- Download the latest Masskit Windows zip file from the Releases page.
- Extract the contents of the file to a directory on your computer by navigating explorer to the
Downloads folder, right clicking on the zip file, and selecting
Extract all.... - Run
Miniforge PromptorAnaconda Promptfrom the Start menu depending on whether you installedmambaforgeor acondadistribution. - In the prompt window, use
cd masskit*to change to the directory starting withmasskitin the directory you extracted the downloads to. - Run
call init_masskit.bat /cputo create themasskit_ai_cpupackage environment.- Alternatively, if you know you have an Nvidia GPU of sufficient power
run
call init_masskit.bat /mlto create themasskit_aipackage environment.
- Alternatively, if you know you have an Nvidia GPU of sufficient power
run
- Run
pip install --find-links=. masskit masskit_ai.
Whenever using the programs in Masskit, please make sure you initialize the appropriate package environment:
- If you installed
mambaforgerunMiniforge Promptfrom the Start menu otherwise runAnaconda Promptfrom the Start menu. - If you installed the CPU only version package environment run
conda activate masskit_ai_cpu. - If you installed the GPU version package environment run
conda activate masskit_ai
- first install Masskit using these instructions.
- Change to a directory that will hold the masskit_ai directory.
- Run
git clone https://github.com/usnistgov/masskit_ai.git. - Run
cd masskit_ai. - Run
pip install ..
Whenever using the programs in Masskit, please make sure you have initialized the appropriate package environment:
- If you installed the CPU only version package environment run
conda activate masskit_ai_cpu. - If you installed the GPU only version package environment run
conda activate masskit_ai.
