├── .gitignore ├── LICENSE ├── README.md ├── configs └── empiar10028.json ├── environment.yml ├── html ├── css │ └── offcanvas.css ├── img │ ├── cryodrgn2_logo.png │ ├── logo_cryoai.gif │ └── paper_thumbnail.png └── index.html ├── imgs ├── 10028.gif ├── 10180.gif └── pipeline.png ├── notebooks └── template.ipynb ├── scripts └── run_empiar10028.sh └── src ├── __init__.py ├── analysis.py ├── commands ├── downsample.py ├── generate_volume.py ├── parse_ctf_star.py ├── parse_pose_star.py └── train.py ├── ctf.py ├── dataset.py ├── fft.py ├── lattice.py ├── lie_tools.py ├── losses.py ├── mask.py ├── metrics.py ├── models.py ├── mrc.py ├── starfile.py ├── summary.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/README.md -------------------------------------------------------------------------------- /configs/empiar10028.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/configs/empiar10028.json -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/environment.yml -------------------------------------------------------------------------------- /html/css/offcanvas.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/html/css/offcanvas.css -------------------------------------------------------------------------------- /html/img/cryodrgn2_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/html/img/cryodrgn2_logo.png -------------------------------------------------------------------------------- /html/img/logo_cryoai.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/html/img/logo_cryoai.gif -------------------------------------------------------------------------------- /html/img/paper_thumbnail.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/html/img/paper_thumbnail.png -------------------------------------------------------------------------------- /html/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/html/index.html -------------------------------------------------------------------------------- /imgs/10028.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/imgs/10028.gif -------------------------------------------------------------------------------- /imgs/10180.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/imgs/10180.gif -------------------------------------------------------------------------------- /imgs/pipeline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/imgs/pipeline.png -------------------------------------------------------------------------------- /notebooks/template.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/notebooks/template.ipynb -------------------------------------------------------------------------------- /scripts/run_empiar10028.sh: -------------------------------------------------------------------------------- 1 | python ../src/commands/train.py empiar10028 -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/analysis.py -------------------------------------------------------------------------------- /src/commands/downsample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/commands/downsample.py -------------------------------------------------------------------------------- /src/commands/generate_volume.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/commands/generate_volume.py -------------------------------------------------------------------------------- /src/commands/parse_ctf_star.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/commands/parse_ctf_star.py -------------------------------------------------------------------------------- /src/commands/parse_pose_star.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/commands/parse_pose_star.py -------------------------------------------------------------------------------- /src/commands/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/commands/train.py -------------------------------------------------------------------------------- /src/ctf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/ctf.py -------------------------------------------------------------------------------- /src/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/dataset.py -------------------------------------------------------------------------------- /src/fft.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/fft.py -------------------------------------------------------------------------------- /src/lattice.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/lattice.py -------------------------------------------------------------------------------- /src/lie_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/lie_tools.py -------------------------------------------------------------------------------- /src/losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/losses.py -------------------------------------------------------------------------------- /src/mask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/mask.py -------------------------------------------------------------------------------- /src/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/metrics.py -------------------------------------------------------------------------------- /src/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/models.py -------------------------------------------------------------------------------- /src/mrc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/mrc.py -------------------------------------------------------------------------------- /src/starfile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/starfile.py -------------------------------------------------------------------------------- /src/summary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/summary.py -------------------------------------------------------------------------------- /src/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml-struct-bio/cryofire/HEAD/src/utils.py --------------------------------------------------------------------------------