adjustments to viz and training loop

Author: dmoi

.gitignore

@@ -1,23 +1,132 @@
-structs/**
-struct_align/**
-afdbclusters/**
-saved_models/**
-models/**
-tmp/**
-**.h5
-**.hdf5
-**.pth
-**.pkl
-**.pt
-examples/**
-**.log
-saved_models/**
-src/__pycache__/**
-BU_all_renum/**
-.ipynb_checkpoints/**
-BU_all_renum/**
-**.fxout
-**.zip
-**.tar.gz
-**.tar
-**.txt
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# PyTorch specific
+*.pth
+*.pt
+*.pkl
+*.pickle
+runs/
+logs/
+checkpoints/
+models/
+wandb/
+lightning_logs/
+
+# Data files
+*.csv
+*.tsv
+*.json
+*.jsonl
+*.parquet
+*.npy
+*.npz
+
+# Bioinformatics files
+*.pdb
+*.fasta
+*.fa
+*.fastq
+*.fq
+*.sam
+*.bam
+*.vcf
+*.gff
+*.gtf
+*Tree
+*.index
+*.dbtype
+*.lookup
+
+
+# HDF5 files
+*.h5
+*.hdf5
+*.hdf
+
+# Large files
+*.zip
+*.tar.gz
+*.rar
+*.7z