learningmatter-mit
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- ▌ Drug DB Pdb · learningmatter-mit bundleSearch, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.
- ▌ Chem DB Qmof · learningmatter-mit bundleQuery the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.
- ▌ Mat Dft Vasp · learningmatter-mit bundlePrepare VASP input files, run DFT calculations (locally or remotely via atomate2), and parse VASP output results.
- ▌ Mat Disorder · learningmatter-mit bundleGenerate ordered structures from disordered starting points with partial occupancies.
- ▌ Chem React Ot · learningmatter-mit bundleGenerate transition state structures for chemical reactions using React-OT.
- ▌ Mat Xrd Calculator · learningmatter-mit bundleCalculate the X-ray Diffraction (XRD) spectrum of a material using pymatgen.
- ▌ Mat Xrd Refinement · learningmatter-mit bundlePerform Rietveld refinement from experimental XRD patterns using DARA (BGMN).
- ▌ Ml Generative Adit · learningmatter-mit bundleGenerate novel crystal structures and molecules using ADiT (All-atom Diffusion Transformer), a unified latent diffusion model.
- ▌ Chem Sorption Relax · learningmatter-mit bundlePrepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.
- ▌ Chem Sorption Widom · learningmatter-mit bundleCalculates Henry coefficient and heat of adsorption for a gas in a porous framework using Widom insertion with any supported MLIP.
- ▌ Drug Redocking Rmsd · learningmatter-mit bundleCompute symmetry-corrected heavy-atom RMSD between docked poses and a reference crystal ligand to validate docking protocols.
- ▌ Drug Retrosynthesis · learningmatter-mit bundlePredict synthetic accessibility and retrosynthetic pathways for novel molecules using the IBM RXN API.
- ▌ Mat Lammps Md · learningmatter-mit bundleBuild and run LAMMPS molecular dynamics with isolated MLIP-specific binaries (MACE, MatGL/CHGNet, FairChem) to avoid Python and Torch stack conflicts.
- ▌ Mat Stability · learningmatter-mit bundleCalculate the thermodynamic stability and energy above the convex hull (E_hull) of a material at 0K.
- ▌ Ml Mlip Speed · learningmatter-mit bundleBenchmark of inference speed of Machine Learning Interatomic Potentials (MLIPs).
- ▌ Chem Vibration · learningmatter-mit bundleCalculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
- ▌ Drug DB Chembl · learningmatter-mit bundleQuery ChEMBL web services for targets, molecules, and curated bioactivity measurements (IC50, Ki, EC50, etc.).
- ▌ Mat Elasticity · learningmatter-mit bundleCalculate the full elastic tensor and mechanical properties (bulk modulus, shear modulus, Young's modulus, Poisson's ratio) using MLIPs.
- ▌ Ml Mlip Automl · learningmatter-mitAutomate hyperparameter tuning for MLIPs (MACE, MatGL, FairChem) using an LLM-driven search framework.
- ▌ Chem DB Spectra · learningmatter-mit bundleSearch and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
- ▌ Drug DB Pubchem · learningmatter-mit bundleQuery PubChem via PUG-REST to retrieve CIDs, computed properties, synonyms, and 2D/3D SDF structures.
- ▌ Mat DB Optimade · learningmatter-mit bundleQuery the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
- ▌ Mat Raman Spectra · learningmatter-mit bundleCalculate Raman-active phonon mode frequencies and simulate Raman spectra from MLIP phonon calculations; optionally compute full Raman intensities with DFT Born charges via atomate2.
- ▌ Mat Xrd Digitizer · learningmatter-mit bundleDigitize an image of an XRD plot into a numeric .xy data file by extracting visual peaks.
- ▌ Ml Matgl Finetune · learningmatter-mit bundleFine-tune MatGL machine learning interatomic potentials on custom datasets.
- ▌ Ml Mlip Benchmark · learningmatter-mit bundleBenchmark MLIP accuracy against a labeled dataset — compute MAE/RMSE for energy/atom and forces, and generate parity plots.
- ▌ Ml Mlip Nvalchemi · learningmatter-mit bundleGPU-accelerated batched inference for MACE, MatGL (TensorNet/M3GNet/CHGNet), and FairChem MLIPs using NValchemi, enabling parallel static, relax, and MD workflows across multiple structures simultaneously.
- ▌ Chem Sorption Gcmc · learningmatter-mit bundleCalculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
- ▌ Mat Grain Boundary · learningmatter-mit bundleCalculate grain boundary energies for tilt/twist grain boundaries (Σ-CSL boundaries) using MLIPs; output γ_GB vs. misorientation angle curves and identify low-energy special boundaries.
- ▌ Mat Surface Energy · learningmatter-mit bundleCalculate surface energy of various (hkl) planes and generate the equilibrium crystal shape (Wulff shape).