.gitignore

# Prerequisites
*.d

# Compiled Object files
*.slo
*.lo
*.o
*.obj

# Precompiled Headers
*.gch
*.pch

# Compiled Dynamic libraries
*.so
*.dylib
*.dll

# Fortran module files
*.mod
*.smod

# Compiled Static libraries
*.lai
*.la
*.a
*.lib

# Executables
*.exe
*.out
*.app

# PyCharm
.idea/
venv/
__pycache__/

# Project Specific (C++)
bin/
CMakeFiles/
cmake_lib
CMakeCache.txt
CMakeLists.txt
*.cmake

# Protein files
*.pdb
*.fasta
*.aln  # Multiple Sequence Alignment (MSA) files

# Condor error output directory
data/scripts/outerr/

# Data directories
alignments/
antibody_database/
antibody_dataset/
casp11/
casp11_h5/
dists/
fastas/
flanked_h3_fastas/
flanked_h3_pdbs/
MNIST/
pssms/
single_chain_fastas/
tertiary/
alignment_jackhmmer/
jackhmmer_out/
profiles/


# MSA programs
CCMgen/
CCMpred/

openprotein/
proteinnet/

# Etc.
*.p  # Pickle files
*.swp
*.csv
*.tsv
*.txt
*.zip
.ipynb_checkpoints/
deeph3/temp/
deeph3/models/
deeph3/data/scripts/outerr/
ROSETTA_CRASH.log
deeph3/WeightedCrossEntropyLoss.pyc
deeph3/__init__.pyc
deeph3/jefftest.py
deeph3/model_out.p
deeph3/VHH_out.p
output_dir/