Here is a brief description of the files in this repository:
Standard Git ignore file to specify untracked files to ignore.
Miscellaneous notes about the project.
This file, providing an overview of the repository.
Markdown document for configuring Fail2Ban on a Raspberry Pi.
Shell script to generate the README.md file.
LaTeX template for articles.
LaTeX Beamer style file for presentation headers.
LaTeX Beamer template for presentations.
FastBeamer specific LaTeX Beamer style file for presentation headers.
Bibliography file for LaTeX FastBeamer presentations.
Python script for FastBeamer, likely assisting with presentation generation.
PNG image of the LaTeX logo, used in FastBeamer presentations.
SVG image of the LaTeX logo, used in FastBeamer presentations.
Test LaTeX file for the FastBeamer setup.
Shell script to convert images to PDF format.
Shell script to compile a LaTeX report.
LaTeX file containing content related to spherical coordinates.
TikZ LaTeX code for drawing a 3D grid with colors.
TikZ LaTeX code for drawing a 3D grid without colors.
TikZ LaTeX code for drawing a 3D rotating arrow.
TikZ LaTeX code for drawing diagrams related to Reinforcement Learning.
TikZ LaTeX code for drawing amino acid structures.
TikZ LaTeX code for drawing a blob shape.
TikZ LaTeX code for drawing a cube without annotations.
TikZ LaTeX code for drawing diagrams related to metadynamics.
TikZ LaTeX code for drawing a peptidic chain.
TikZ LaTeX code for drawing perpendicular lines.
TikZ LaTeX code for drawing the phenylalanine molecule.
TikZ LaTeX code for drawing phenylalanine with channels.
TikZ LaTeX code for drawing a protein cavity.
README file for the C logit module.
C source code for a logistic regression (logit) function.
Python setup script for building the C logit module.
Python test script for the C logit module.
README file for the C sum module.
Shell script to compile the C sum module.
Python main script demonstrating the use of the C sum module.
Pure Python implementation of a sum function for comparison with C.
C source code for a sum function.
Python script for clustering algorithms.
Command-line interface for DBM database operations.
Initialization file for the Grid2 Python package.
Python implementation of Dijkstra's algorithm for 2D grids.
Initialization file for the Grid3 Python package.
Python script for operations on adjacency matrices in 3D grids, including move and shortest_path functions.
Python script for aligning 3D grids.
MRC file containing 3D grid data (e.g., electron density map).
MRC file containing translated 3D grid data.
Python script for applying Gaussian filters to 3D grid data.
Python script for calculating gradients on 3D grids.
Python script for line operations on 3D grids.
Python module for reading and writing MRC file format.
Python script to convert PDB structures to density maps on a 3D grid.
Initialization file for the HDF5 Python package.
Python script for batch processing HDF5 files.
Python module for managing HDF5 datasets, including a random key generation function.
Image showing a speed test comparison for HDF5 operations.
Test text file for HDF5 operations.
Utility functions for HDF5 operations.
Python script implementing a Self-Organizing Map (SOM) index.
Python script for generating spectrograms.
Executable for the TMalign program.
C++ source code for the TMalign program, containing functions for structural alignment like TMalign_main.
Executable for the USalign program.
C++ source code for the USalign program, including template classes for pstream and functions like MMalign, MMdock, and mTMalign for structural alignment and docking.
Initialization file for the TMalign Python package.
PDB file containing protein structure data, used as input for TMalign.
PDB file containing protein structure data, used as input for TMalign.
GZipped CIF file containing protein structure data.
PDB file containing receptor and ligand structure data.
List of model PDB files for TMalign.
List of native PDB files for TMalign.
GZipped record file used as input for TMalign.
Shell script with helper functions for TMalign.
Python wrapper or utility script for running TMalign.
Python script for calculating TM-score.
Python class Timer for measuring elapsed time, with reset method.
Initialization file for the main Python package.
Python class NNindex for Nearest Neighbor indexing using Annoy, with load method.
README file for the Annoy Python module.
Initialization file for the Annoy Python package.
Example usage script for the Annoy Nearest Neighbor index.
Python script for scaling data in conjunction with Annoy.
Python script for basis transformation operations.
Initialization file for the box Python package.
Python script defining box-related operations.
Python script for preparing structures for docking using UCSF Chimera.
Shell script to run dock preparation with Chimera.
Python script for plotting confidence ellipses.
Column definition file for test data.
Record file containing test data.
Another column definition file for test data.
Another record file containing test data.
Python script to run tests on record files.
Another Python script to run tests on record files.
Python class Debugger for debugging purposes, includes a test multiplication function.
Python script to decode email content.
Simple Python script to echo input.
Python script for managing a timetable/schedule.
Python class ETA for estimating time of arrival, with a __call__ method.
Initialization file for the Faiss Python package.
Python script demonstrating Faiss PQFastScan for approximate nearest neighbor search.
Another Python script demonstrating Faiss PQFastScan.
Python script for testing Faiss functionalities.
Python script for searching files.
Shell script with general utility functions.
Python script to download email attachments.
Python script for reading lines from a file.
Python script to get the source code of a function.
Python script to shorten Git URLs.
Initialization file for the Graphein Python package.
Python script utilizing Graphein for protein graph operations.
Git ignore file for the gym directory.
README file for the gym environment.
Initialization file for the gym Python package.
Python script for extracting features from gym environments.
Python class Loader for saving and loading models in gym environments, with save and load methods.
Python class MullerEnv defining a gym environment based on the Muller potential, including potential functions and environment interaction methods.
Python script for making predictions using the Muller gym environment.
Python script for training models in the Muller gym environment.
Python script to compute file hashes.
Python script for hierarchical sorting of pairwise matrices.
Initialization file for the Holoviews Python package.
Python script for a Holoviews application, serving a scatter plot.
A large text file, possibly for testing file I/O performance.
Python script for interpolation methods.
Shell script to set up a local Google Colab environment for Jupyter.
Python implementation of the Kabsch algorithm for optimal rotation.
Python script for Kernel Density Estimation.
Python script for hierarchical clustering linkage.
Python script to list available matplotlib colormaps.
Python script with utility functions for lists.
Python script for detecting local peaks in data.
Python script for loading PDB files for map alignment.
Initialization file for the mapalign Python package.
Shell script to compile C code for map alignment.
Python wrapper for C functions used in map alignment.
PDB file containing protein structure data for map alignment.
PDB file containing protein structure data for map alignment.
Python script for eigenvalue calculations in map alignment.
C source code for initializing matrices used in map alignment.
Python script implementing map alignment algorithms.
Log file from a map alignment run on PDB 3u97_A.
C source code for the Smith-Waterman algorithm, likely used for sequence alignment.
Python script for 3D matching algorithms.
Initialization file for the matplotlib_utils Python package.
Python script for creating interactive sliders with Matplotlib.
Python script for generating or solving mazes.
Initialization file for the Modeller Python package.
Python script to align PDB structures based on sequences.
Python class System for building protein systems in Modeller, with set_coords and minimize methods.
Command-line interface for Modeller operations.
Python script to repair protein structures using Modeller.
SMILES file containing 1000 molecules from the DUDE dataset.
Initialization file for the mols Python package.
Python script to draw molecules from SMILES strings.
Python script implementing a Relational Graph Convolutional Network (RGCN).
SMILES file containing test molecules for HMT.
SMILES file containing test molecules for graph operations.
Python script for converting molecular structures to graph representations, including a MolDataset class.
Python script to plot molecular embeddings.
Backup file of an RGCNN model checkpoint.
Another backup file of an RGCNN model checkpoint.
Shell script to split a SMILES file into smaller chunks.
Utility functions for molecular graph operations.
Python script for calculating Ligand RMSD, including get_coords function.
Another Python script for calculating Ligand RMSD.
Python script for finding the maximum common substructure between molecules.
Python script to convert MOL2 files to PDBQT format.
Python script for molecular file format conversions.
Python script for calculating molecular properties.
Python script for calculating molecular similarity based on Maximum Common Substructure.
Makefile for the molecular similarity module.
Python script for molecular similarity calculation using graph embeddings.
Shell script to run molecular similarity calculation using graph embeddings.
Python script for general molecular similarity calculations.
Shell script to run molecular similarity calculations.
GZipped record file for molecular similarity testing.
Text file for molecular similarity testing.
Text file containing similarity results from molecular similarity testing.
Python script using OpenBabel to generate canonical SMILES.
Python script for calculating RAScore.
Shell script to run RAScore calculations.
Python script containing RDKit fixes or utility functions, including get_coords function.
Shell script for running RDKit fixes.
Python script to sample SMILES strings.
Python script to convert SDF files to SMILES strings.
Python script to split molecular files.
Python script for calculating moving averages.
Python script defining the Muller potential function and muller_mat for generating a potential map.
Python script demonstrating multiprocessing with a file lock.
Python module for managing NetCDF4 datasets, including a random key generation function.
README file for the numpy command-line interface.
Shell script to generate the README for npcli.
Python script providing a command-line interface for NumPy operations.
Shell script to run the numpy command-line interface.
Initialization file for the OpenMM Python package.
Python script for running Molecular Dynamics simulations with OpenMM, including functions to add PLUMED forces and run simulations.
PLUMED input file for molecular dynamics simulations.
Python class MetaSystem extending OpenMM Topology, used for building and minimizing protein systems.
Python script for calculating pairwise RMSDs between structures.
Python script for generating and manipulating parametric curves.
Python script for Principal Component Analysis (PCA).
Command-line interface for PCA.
Python script to convert multiple PDB files to a DCD trajectory file.
Python script for generating protein surface representations from PDB files.
Python script for Process Information Monitor.
Initialization file for the point_set_registration Python package.
Python implementation of Coherent Point Drift (CPD) for point set registration.
Python implementation of non-rigid Coherent Point Drift (CPD) for point set registration.
Python script implementing a progress bar.
General Python script for project-related utilities.
Python script for projection operations.
Python script for handling protein coordinates.
README file for the Deminer protein module.
Initialization file for the Deminer protein Python package.
Shell script to check for errors in Deminer runs.
Shell script to encode PDB files using Deminer.
Shell script to monitor GPU memory usage for Deminer.
Shell script to plot loss curves from Deminer training.
Shell script to plot loss from a specific file in Deminer.
Shell script to test a dataset with Deminer.
Shell script to run Deminer training.
Shell script to update a Deminer model.
Python script implementing the Deminer model for protein analysis.
Python script for loading PDB files for protein VAE.
README file for the protein VAE module.
Initialization file for the protein VAE Python package.
Python script for a Contact Map Variational Autoencoder (CMA-VAE).
Python script to encode PDB files using the VAE.
Log file from PDB filtering process for VAE.
Python script for fold searching using the VAE.
Shell script to generate a list of PDB files for the VAE.
README file for VAE models.
List of PDB files used for VAE training/testing.
Shell script to run all tests for the protein VAE.
Python script to test the encoder component of the protein VAE.
Utility functions for protein VAE, including compute_pad.
Python script implementing the Variational Autoencoder (VAE) for proteins.
Initialization file for the main protein Python package.
Initialization file for the cmapfit Python package.
Python script for fitting contact maps.
PDB file used as data for contact map fitting.
PDB file used as data for contact map fitting.
PDB file used as data for contact map fitting.
PDB file used as data for contact map fitting.
Python script for loading protein coordinates from PDB files, with get_coords function.
Python script to count beta strands in a protein structure.
PDB file containing protein structure data.
Python script for delineating protein structures.
Python script for protein density calculations.
README file for the protein depiction module.
Initialization file for the protein depiction Python package.
Python script for depicting protein structures.
PNG image depicting protein 3j7h.
PNG image depicting protein 3jc8.
Shell script for protein docking preparation.
Singularity image file for ESMFold.
Shell script to run ESMFold.
Python script for running ESMFold inference.
FASTA file for testing ESMFold.
Python script to filter PDB files.
Python script for flexible fitting of protein structures.
Python script to extract chains from PDB files.
Shell script to extract chains from PDB files.
Python script to calculate contact maps for proteins.
Python script to retrieve the title from a PDB file.
Python script to fetch protein data from UniProt.
Python script to download PDB files.
Standard PDB file for amino acid reference.
PDB file containing protein structure data for graph analysis.
SDF file for the crystal ligand of the aa2ar target from DUDE100.
PDB file for the receptor of the aa2ar target from DUDE100.
SDF file for the crystal ligand of the ace target from DUDE100.
PDB file for the receptor of the ace target from DUDE100.
SDF file for the crystal ligand of the aces target from DUDE100.
PDB file for the receptor of the aces target from DUDE100.
SDF file for the crystal ligand of the ada17 target from DUDE100.
PDB file for the receptor of the ada17 target from DUDE100.
SDF file for the crystal ligand of the adrb1 target from DUDE100.
PDB file for the receptor of the adrb1 target from DUDE100.
SDF file for the crystal ligand of the adrb2 target from DUDE100.
PDB file for the receptor of the adrb2 target from DUDE100.
SDF file for the crystal ligand of the akt1 target from DUDE100.
PDB file for the receptor of the akt1 target from DUDE100.
SDF file for the crystal ligand of the aldr target from DUDE100.
PDB file for the receptor of the aldr target from DUDE100.
SDF file for the crystal ligand of the aofb target from DUDE100.
PDB file for the receptor of the aofb target from DUDE100.
SDF file for the crystal ligand of the bace1 target from DUDE100.
PDB file for the receptor of the bace1 target from DUDE100.
SDF file for the crystal ligand of the cah2 target from DUDE100.
PDB file for the receptor of the cah2 target from DUDE100.
SDF file for the crystal ligand of the casp3 target from DUDE100.
PDB file for the receptor of the casp3 target from DUDE100.
SDF file for the crystal ligand of the cdk2 target from DUDE100.
PDB file for the receptor of the cdk2 target from DUDE100.
SDF file for the crystal ligand of the cp2c9 target from DUDE100.
PDB file for the receptor of the cp2c9 target from DUDE100.
SDF file for the crystal ligand of the def target from DUDE100.
PDB file for the receptor of the def target from DUDE100.
SDF file for the crystal ligand of the dhi1 target from DUDE100.
PDB file for the receptor of the dhi1 target from DUDE100.
SDF file for the crystal ligand of the dpp4 target from DUDE100.
PDB file for the receptor of the dpp4 target from DUDE100.
SDF file for the crystal ligand of the drd3 target from DUDE100.
PDB file for the receptor of the drd3 target from DUDE100.
SDF file for the crystal ligand of the dyr target from DUDE100.
PDB file for the receptor of the dyr target from DUDE100.
SDF file for the crystal ligand of the egfr target from DUDE100.
PDB file for the receptor of the egfr target from DUDE100.
SDF file for the crystal ligand of the esr2 target from DUDE100.
PDB file for the receptor of the esr2 target from DUDE100.
SDF file for the crystal ligand of the fa10 target from DUDE100.
PDB file for the receptor of the fa10 target from DUDE100.
SDF file for the crystal ligand of the fkb1a target from DUDE100.
PDB file for the receptor of the fkb1a target from DUDE100.
SDF file for the crystal ligand of the fnta target from DUDE100.
PDB file for the receptor of the fnta target from DUDE100.
SDF file for the crystal ligand of the gria2 target from DUDE100.
PDB file for the receptor of the gria2 target from DUDE100.
SDF file for the crystal ligand of the hivrt target from DUDE100.
PDB file for the receptor of the hivrt target from DUDE100.
SDF file for the crystal ligand of the hs90a target from DUDE100.
PDB file for the receptor of the hs90a target from DUDE100.
SDF file for the crystal ligand of the jak2 target from DUDE100.
PDB file for the receptor of the jak2 target from DUDE100.
SDF file for the crystal ligand of the lck target from DUDE100.
PDB file for the receptor of the lck target from DUDE100.
SDF file for the crystal ligand of the mapk2 target from DUDE100.
PDB file for the receptor of the mapk2 target from DUDE100.
SDF file for the crystal ligand of the mk14 target from DUDE100.
PDB file for the receptor of the mk14 target from DUDE100.
SDF file for the crystal ligand of the mmp13 target from DUDE100.
PDB file for the receptor of the mmp13 target from DUDE100.
SDF file for the crystal ligand of the nram target from DUDE100.
PDB file for the receptor of the nram target from DUDE100.
SDF file for the crystal ligand of the parp1 target from DUDE100.
PDB file for the receptor of the parp1 target from DUDE100.
SDF file for the crystal ligand of the pde5a target from DUDE100.
PDB file for the receptor of the pde5a target from DUDE100.
SDF file for the crystal ligand of the pgh2 target from DUDE100.
PDB file for the receptor of the pgh2 target from DUDE100.
SDF file for the crystal ligand of the plk1 target from DUDE100.
PDB file for the receptor of the plk1 target from DUDE100.
SDF file for the crystal ligand of the ppara target from DUDE100.
PDB file for the receptor of the ppara target from DUDE100.
SDF file for the crystal ligand of the ppard target from DUDE100.
PDB file for the receptor of the ppard target from DUDE100.
SDF file for the crystal ligand of the pparg target from DUDE100.
PDB file for the receptor of the pparg target from DUDE100.
SDF file for the crystal ligand of the ptn1 target from DUDE100.
PDB file for the receptor of the ptn1 target from DUDE100.
SDF file for the crystal ligand of the pur2 target from DUDE100.
PDB file for the receptor of the pur2 target from DUDE100.
SDF file for the crystal ligand of the pyrd target from DUDE100.
PDB file for the receptor of the pyrd target from DUDE100.
SDF file for the crystal ligand of the reni target from DUDE100.
PDB file for the receptor of the reni target from DUDE100.
SDF file for the crystal ligand of the rxra target from DUDE100.
PDB file for the receptor of the rxra target from DUDE100.
SDF file for the crystal ligand of the sahh target from DUDE100.
PDB file for the receptor of the sahh target from DUDE100.
SDF file for the crystal ligand of the src target from DUDE100.
PDB file for the receptor of the src target from DUDE100.
SDF file for the crystal ligand of the thrb target from DUDE100.
PDB file for the receptor of the thrb target from DUDE100.
SDF file for the crystal ligand of the try1 target from DUDE100.
PDB file for the receptor of the try1 target from DUDE100.
SDF file for the crystal ligand of the tysy target from DUDE100.
PDB file for the receptor of the tysy target from DUDE100.
SDF file for the crystal ligand of the urok target from DUDE100.
PDB file for the receptor of the urok target from DUDE100.
SMILES file containing 100 test molecules from the DUDE dataset.
PDB file for a ligand, used in protein graph analysis.
PDF document, likely a research paper related to protein graph methods.
Screenshot image for documentation related to protein graphs.
Another screenshot image for documentation related to protein graphs.
Another screenshot image for documentation related to protein graphs.
Python script implementing message passing mechanisms for graph neural networks.
Python script for general protein graph manipulation and analysis.
Shell script to pull data for protein graph analysis.
Shell script to run protein graph related tasks.
Python script for embedding protein Surface Accessible Surface Area (SASA) features.
Python script for self-embedding in protein graph models.
Python script for embedding TM-score related features in protein graph models.
Python script for database interactions in protein interaction prediction.
Python script for loading PDB files for protein interaction prediction.
Python script implementing a SquashLayer, likely for a neural network.
Initialization file for the protein interaction prediction Python package.
PDB file used as data for protein interaction prediction.
Python script for protein interaction prediction.
Python script defining neural network architectures for interaction prediction.
Python script implementing a U-Net architecture, likely for protein interaction prediction.
Utility functions for protein interaction prediction, including get_coords.
Python script implementing a VAE for protein interaction prediction.
Python script for internal residue information in proteins.
Python script for Principal Component Analysis (PCA) on protein data.
Python script to convert PDB files to FASTA sequence files.
Python script for searching PDB database.
Python script for selecting specific parts of PDB files.
Directory containing DUDE100 data for pocket alignment.
SMILES file containing 16 test molecules from DUDE for pocket alignment.
Python script for calculating pocket similarity.
Python script for rotating protein structures.
Python class Internal for calculating and managing internal spherical coordinates of protein C-alpha traces, with write method.
Python script for loading BLAST results for protein SSCL.
Python script for loading PDB files for protein SSCL.
Initialization file for the protein Self-Supervised Contrastive Learning (SSCL) Python package.
Python script for SCOP benchmark analysis in SSCL.
Python script for t-SNE visualization of SCOP data in SSCL.
Python script for SCOP related analysis.
Python script defining the encoder architecture for protein SSCL.
Python script for fold searching using protein SSCL.
List of PDB files used for protein SSCL.
Shell script to process BLAST results for SSCL.
Python script for training protein SSCL models.
Utility functions for protein SSCL, including get_coords and compute_pad.
Python script for loading BLAST results for geometric protein SSCL.
Initialization file for the geometric protein SSCL Python package.
Python script defining the encoder architecture for geometric protein SSCL.
Python script for training geometric protein SSCL models.
Shell script for testing protein-related functionalities.
Python script for protein rolling operations.
Python script mimicking awk-like functionality.
Python script mimicking cat-like functionality.
Initialization file for the PyMOL Python package.
Python script for building molecular structures in PyMOL.
Python script for adding captions in PyMOL.
Python script for creating CGO arrows in PyMOL.
Python script for coloring by hydrophobicity in PyMOL.
Python script for coloring objects by data in PyMOL.
Python script to connect consecutive residues in PyMOL.
Python script for reading DCD trajectory files in PyMOL.
Python script for calculating distances in PyMOL.
Python script for visualizing docking footprints in PyMOL.
Python script to find surface residues in PyMOL.
Python script to get distances between atoms in PyMOL.
Jupyter notebook for interactive PyMOL sessions.
Shell script to launch interactive PyMOL sessions.
Python script for retrieving ligand information in PyMOL.
Python script to load trajectories from NumPy files into PyMOL.
Python script to merge molecular objects in PyMOL.
Python script to modify amino acids in PyMOL.
Python script for outlining objects in PyMOL.
Python script for PyMOL Remote Procedure Call (RPC).
Python script to renumber residues in PyMOL.
Python script for Surface Accessible Surface Area (SASA) calculations in PyMOL.
Python script to select binding pockets in PyMOL.
Python script to split molecular objects in PyMOL.
Python script for secondary structure analysis in PyMOL.
Python script to symmetrize molecular objects in PyMOL.
Python script implementing a cached dataset for PyTorch.
Python script implementing a generic dataset for PyTorch.
Python script implementing a dataset for gzipped files in PyTorch.
Python script implementing a dataset for text files in PyTorch.
Python script for loading density data for PyTorch.
Python script implementing Multidimensional Scaling (MDS) for PyTorch.
Python script for MDS on point clouds using PyTorch.
Python script implementing a MultiHeadAttention module for PyTorch.
Python script for loading PDB files for PyTorch models.
Text file containing feature data (X) for PyTorch.
GZipped text file containing feature and label data (Xy) for PyTorch.
Initialization file for the PyTorch Python package.
Python script implementing a contrastive loss function for PyTorch.
Python script for unpickling PyTorch models on CPU.
Python script for distance calculations in PyTorch.
Shell script with helper functions for PyTorch.
Python script to make input for MDS with PyTorch.
MOL2 file containing molecular data.
MOL2 file containing receptor-ligand complex data.
Python script for docking preparation in a mol2graph context.
File defining atom types for MOL2 files.
Python script to convert MOL2 files to graph representations for PyTorch.
README file for the PyTorch Geometric (PyG) module.
Python script implementing a Graph Convolutional Network (GCN) using PyTorch Geometric.
Python script for benchmarking PyTorch performance.
Python script implementing a 3D ResNet architecture for PyTorch.
Python script to convert TensorBoard logs to CSV format.
Python script to convert data into PyTorch tensors.
Python script implementing a generic training loop for PyTorch models.
Python script for generating samples from a truncated normal distribution in PyTorch.
Text file containing label data (y) for PyTorch.
Python script for random number generation.
Python script for reading Python shelve files.
Python script for handling record-formatted data, including functions like get_data, read_file, run.
Python script with utilities for record-formatted data, including get_item, add_item, load.
Python script for resampling data.
Python script for calculating RMSD of trajectories against multiple references.
Python script for 3D rotation operations.
Python script implementing a ruler tool.
Shell script to run the ruler tool.
Python script for image or data segmentation.
Initialization file for the sequences Python package.
Python script for sequence alignment operations.
FASTA file containing sequence data.
FASTA file containing sequence data.
Python script for parsing FASTA files.
FASTA file containing petase enzyme sequences.
Python script for printing sequence alignments.
Python script for profile-based sequence alignment.
Python script to build a sequence identity index.
Shell script to get FASTA sequences from PDB files.
Python script to extract sequences.
Python script for sequence alignment.
Python implementation of the Smith-Waterman algorithm for local sequence alignment.
Python script to convert HDF5 files to shelve files.
Python module for managing shelve datasets, including a random key generation function.
Image showing a speed test comparison for shelve operations.
Python script for temporary shelve file operations.
Python script for sliding window operations.
Initialization file for the Streamlit Python package.
Example Streamlit application script.
Python script for structural alignment.
Python script for calculating structural distances.
Test file in custom .pyrec format.
Python script for time series analysis, including a split function.
Initialization file for the toymodels Python package.
Python script for Monte Carlo simulations with toy models, including potential and move functions.
Python script for time-series related utilities.
Python script for uniform weighting schemes.
Python script to shorten URLs.
Python script for writing to temporary files.
Initialization file for the Xonsh Python package.
Python script for Xonsh shell events.
HTML file for displaying DHT22 sensor data on Raspberry Pi.
Shell script to run a temperature sampling daemon on Raspberry Pi.
Python script to plot temperature data from DHT22 sensor.
Python script to sample temperature and humidity from DHT22 sensor.
Shell script to periodically sample temperature from DHT22 sensor.
Executable for the LSalign program.
Shell script to run LSalign with record files.
Shell script to run LSalign with SMILES files.
Shell script with helper functions for LSalign.
Shell script to run LSalign.
GZipped record file for LSalign testing.
Shell script for archiving files.
README file for the Argos shell scripts.
Shell script to run Argos-related functionalities (for GNOME Shell extension).
Argos script to display rclone status.
Argos script to display top processes.
Argos script to display weather information, updated every 15 minutes.
Shell script using awk to extract fields from PDB files.
Shell script for arithmetic calculations using awk.
Shell script for processing CSV files using awk.
Shell script for extracting fields from text using awk.
Shell script for joining files using awk.
Shell script for pasting file columns using awk.
Shell script with helper functions for awkpaste tests.
Shell script for processing TSV files using awk.
Shell script to show progress of Back In Time backups.
Shell script for displaying a progress bar.
Shell script for generating bar charts from data.
Shell script for comparing two bar charts.
Shell script for managing dotfiles (e.g., "bash, markdown, fish").
Shell script for bidirectional synchronization.
Shell script for managing a cache directory.
Shell script to concatenate columns of files.
Shell script for timing command execution.
Shell script to convert CLUSTAL W alignment output to sequence identity.
Shell script to compress PDF files.
Test text file 'a'.
Test text file 'b'.
Another test text file 'b2'.
Test text file 'c'.
Another test text file 'c2'.
Shell script to track disk free space.
Markdown document detailing DVD rescue procedures.
Shell script to generate an empty LaTeX Beamer slide.
LaTeX file for an empty Beamer slide.
Shell script to empty the trash and delete files.
Shell script for decrypting files.
Shell script for encrypting files.
Shell script to check if two files are identical.
Shell script to find mail files.
Shell script with general utility functions.
Shell script to get homology information from UniProt.
Shell script to retrieve ligand information.
Shell script to get current location information.
Shell script for managing gitignore files.
Shell script to convert Google Calendar events to remind format.
Shell script to check if a file has changed.
Shell script to display head and tail of files.
Shell script for system hibernation.
Shell script for hierarchical viewing of files.
PDF document detailing image resolutions.
Shell script to resample PNG images in a directory.
Shell script to launch interactive PyMOL.
Shell script to convert JSON to record format.
Shell script to convert JSON to YAML.
Shell script to backup KeePass databases.
Shell script for keyboard utilities.
Shell script to disable the keyboard.
Shell script to enable the keyboard.
Shell script for listing files by their last 5 lines.
Shell script to generate a linearly spaced sequence of numbers.
Shell script to list common exit codes.
Shell script to list functions.
Shell script to list GPU information.
Shell script for listing files with size and count.
Shell script for listing files by time.
Shell script for metadata operations.
Shell script to get mouse location.
Shell script to display mouse position.
Shell script to install Nerd Fonts.
Python script for Natural Language Processing tasks.
Shell script to run NLP tasks.
Makefile for Ollama.
Modelfile for Ollama, defining a custom large language model.
README file for the Ollama setup.
Shell script for generating AI-powered Git commit messages using Ollama.
Shell script to run the CodeLlama model with Ollama.
Shell script to install Ollama.
Shell script to interact with Ollama.
Shell script to start the Ollama server.
Shell script for paginated cat output.
Shell script for batch downloading PDB files.
Shell script to search PDB by sequence.
Shell script to add page numbers to PDF files.
Shell script to perform shell command evaluation.
Shell script to process FASTA files.
Shell script to display a progress list.
Executable for hbplus, a hydrogen bond calculation tool.
Shell script to run hbplus.
Definition file for pocket alignment.
Shell script for protein pocket alignment.
Python script to select protein pockets.
Shell script to interact with PyMOL for PDB operations.
Shell script to perform BLAST searches on PDB sequences.
Shell script to convert PDB files to FASTA format.
Shell script for parallel command execution.
Shell script for calculations using Python.
Shell script to generate random text.
Shell script for processing record files using awk.
GZipped record file for recawk testing.
Shell script with helper functions for recawk tests.
Shell script to list recently accessed files.
Shell script to generate an agenda from remind files.
Shell script to generate a calendar from remind files.
Shell script to convert Google Calendar to remind format.
iCal file for 'off' events in remind.
iCal file for 'vacation zone C' events in remind.
Shell script to restart KDE Plasma shell.
Shell script for interactive file deletion.
Shell script to rsync home directory.
Executable or script for running cached commands.
Shell script to calculate the reverse complement of a DNA sequence.
Shell script to shuffle sequences.
Shell script for interactive directory navigation (e.g., "select in terminal").
Shell script to convert a website to a PDF.
Shell script for smart renaming of files.
Shell script for spell checking text.
Shell script for squashing files or directories.
Shell script for unsquashing files or directories.
Shell script to run SSHFS commands.
Shell script for viewing tabular data.
Shell script for interacting with Microsoft Teams.
Shell script for organizing files.
Shell script to generate timestamps.
Python script for numerical operations related to TM-score calculations.
Shell script to find maximum TM-score.
Shell script to run TM-score for multiple comparisons.
Shell script to calculate TM-score.
Python script for clustering based on TM-score.
Shell script to format TM-score output.
Python script to plot TM-score results.
Shell script to trim whitespace or characters from text.
Shell script to display the running time of tsp (task spooler) jobs.
Shell script to display the status of tsp (task spooler) jobs.
Shell script to unwrap text.
Shell script to update system packages or applications.
Shell script to update PDB files.
Shell script to compress executables using UPX.
Shell script to view mail content.
Shell script to get weather information.
Shell script for performing web searches.
Shell script to download files from Google Drive using wget.
Shell script to convert YAML to JSON.
Shell script to decompress and concatenate gzipped files.
Singularity definition file for the IMP (Integrative Modeling Platform) software.
Makefile for building Singularity images.
README file for the Singularity directory.
Singularity definition file for RFdiffusion protein design software.
Shell script to run RFdiffusion within Singularity.
Singularity definition file for the 'aider' tool (AI coding assistant).
Singularity definition file for a general-purpose image.
Makefile for AlphaFold3 Singularity image.
Shell script to run AlphaFold3 prediction within Singularity.
Singularity definition file for AlphaFold3.
JSON file containing input data for AlphaFold3 folding.
Singularity definition file for the 'alv' tool.
Singularity definition file for Annoy.
Makefile for AtomSurf Singularity image.
Singularity definition file for AtomSurf software.
Makefile for Boltzman generator Singularity image.
Shell script to run Boltzman generator predictions within Singularity.
Singularity definition file for Boltzman generator.
Another Singularity definition file for Boltzman generator.
FASTA file containing sequence data for Boltzman generator.
FASTA file containing sequence data for Boltzman generator.
YAML configuration file for Boltzman generator with 1t4e data.
Python script for handling modified residues in Boltzman generator.
Makefile for Bougui Singularity image.
Singularity definition file for Bougui (version 1).
Singularity definition file for Bougui (version 2).
Makefile for Chimera within Bougui Singularity image.
Singularity definition file for Chimera within Bougui.
Archived dependency file for Bougui.
Makefile template file for Neovim within Bougui.
Apptainer (Singularity) definition template for Neovim within Bougui.
Base Singularity definition file for Neovim within Bougui.
Singularity definition file for Neovim within Bougui.
Python template file for Neovim within Bougui.
Shell script template file for Neovim within Bougui.
Vim configuration file for Neovim within Bougui.
Shell script for building Singularity images.
Singularity definition file for ChimeraX.
Makefile for ColabFold Singularity image.
README file for the Conda Singularity setup.
Shell script to build an extra shell within Conda Singularity.
Singularity definition file for a Conda environment.
Singularity definition file for extra Conda environment components.
Vim configuration file for GitHub integration within Conda Singularity.
Neovim initialization file within Conda Singularity.
Singularity definition file for PyMOL within Conda.
Singularity definition file for PyTorch within Conda.
Singularity definition file for a shell environment within Conda.
Singularity definition file for a Debian base image.
PNG image of caffeine molecule for DECIMER.
Singularity definition file for DECIMER (Deep lEarning for Chemical IMage rEcognition).
Shell script to convert image to SMILES using DECIMER.
Python script to run DECIMER.
Singularity image file for DiffDock Conda environment.
Singularity definition file for DiffDock (protein-ligand docking).
Shell script to run DiffDock within Singularity.
Vim configuration file for GitHub integration within DiffDock Singularity.
Neovim initialization file within DiffDock Singularity.
Singularity definition file for ESMFold.
Python script for ESM sequence operations within ESMFold.
Python test script for ESMFold.
Vim configuration file for GitHub integration within ESMFold Singularity.
Neovim initialization file within ESMFold Singularity.
Singularity definition file for PyTorch within ESMFold.
Shell script to run ESM sequence operations.
Singularity definition file for a shell environment within ESMFold.
Makefile for Evo2 Singularity image.
Singularity definition file for Evo2 (Evolutionary protein design).
Singularity definition file for Foldseek.
Shell script to run Foldseek within Singularity.
Singularity definition file for FreeCAD.
Singularity definition file for the GEMS software.
Singularity definition file for Genscore.
Singularity definition file for Gesim.
Singularity definition file for GitHub CLI (gh).
Shell script for Git operations within Singularity.
Singularity definition file for Glances (system monitoring tool).
Shell script to run Glances within Singularity.
Makefile for Gnina Singularity image.
Singularity definition file for Gnina (molecular docking).
Singularity definition file for Gnomon.
Singularity definition file for Grex (regular expression generator).
Archived dependency file for InDeep.
PDB file containing protein structure data for InDeep.
Singularity definition file for InDeep (protein modeling).
Shell script to run Large Language Models (LLMs) within Singularity.
Singularity definition file for Meld (diff and merge tool).
Shell script to run Meld within Singularity.
Shell script to run Neovim within Singularity.
Singularity definition file for nvitop (NVIDIA GPU monitoring).
Shell script to run nvitop within Singularity.
Singularity definition file for Ollama.
Makefile for OpenMM-GROMACS Singularity images.
Singularity definition file for GROMACS, PLUMED, PyTorch, and InDeep combined.
Singularity definition file for GROMACS, PLUMED, and PyTorch combined.
Singularity definition file for GROMACS and PLUMED combined.
Singularity definition file for GROMACS.
Singularity definition file for OpenMM and PLUMED combined.
Singularity definition file for OpenMM.
Singularity definition file for PLUMED and PyTorch combined.
Singularity definition file for PLUMED.
Makefile for OpenMM Singularity images.
Makefile for OpenMM-PLUMED Apptainer images.
Apptainer definition file for OpenMM and PLUMED.
Apptainer definition file for OpenMM.
Apptainer definition file for PLUMED.
Singularity definition file for OpenMM and PLUMED.
Singularity definition file for OpenMM.
Singularity definition file for PLUMED.
Shell script to run PDBsumup within Singularity.
Shell script to run pigz (parallel gzip) within Singularity.
Singularity definition file for PLIP (Protein-Ligand Interaction Profiler).
reStructuredText README file for the ProLIF module.
Singularity definition file for ProLIF (Protein-Ligand Interaction Fingerprints).
Python test script for ProLIF.
Singularity definition file for extra PyTorch Geometric (PyG) components.
Singularity image file for a shell environment with PyTorch Geometric (PyG).
Singularity definition file for PyMOL.
Singularity definition file for PyTorch.
Singularity definition file for QMEAN (protein quality estimation).
Singularity definition file for RAScore.
Singularity definition file for RASP (RNA Secondary structure Analysis and Prediction).
Singularity definition file for RASP using Mamba.
Makefile for Rosetta Singularity image.
Singularity definition file for Rosetta (protein modeling).
General shell script to run Singularity images.
Singularity definition file for Seaborn (statistical data visualization).
Shell script for local installation commands within Singularity shell.
Singularity definition file for extra components in a shell image.
Shell script for GET/POST requests within Singularity shell.
Vim configuration file for GitHub integration within Singularity shell.
Neovim initialization file within Singularity shell.
Singularity definition file for a general shell environment.
Makefile for Shell-GPT Singularity image.
Internal shell script for Shell-GPT.
Shell script to run Shell-GPT within Singularity.
Singularity definition file for Shell-GPT.
Shell script for basic Singularity commands.
Shell script for starting a Singularity shell.
Singularity definition file for tmate (terminal sharing).
Shell script to update a specific Bougui Singularity image file.
Makefile for Vortex Singularity image.
Singularity definition file for Vortex.
SLURM script to run Vortex within Singularity.
Singularity definition file for Wormhole (secure file transfer).
Markdown tutorial on how to enable hibernation in Ubuntu.
Markdown tutorial on how to use Jupyter with PyMOL.