├── .gitignore ├── CITATION.cff ├── LICENSE ├── README.md ├── cg2all.ipynb ├── cg2all ├── __init__.py ├── data │ ├── calpha_geometry_params.dat │ ├── martini.top │ ├── martini2.top │ ├── martini3.top │ ├── primo.top │ ├── residue_constants.pkl │ ├── residue_geometry_params.bound.dat │ └── residue_geometry_params.harmonic.dat ├── lib │ ├── __init__.py │ ├── check_rigid_groups.py │ ├── create_pdblist.py │ ├── generate_rigid_body.py │ ├── get_ic_from_structure.py │ ├── libcg.py │ ├── libconfig.py │ ├── libcryoem.py │ ├── libdata.py │ ├── libloss.py │ ├── libmetric.py │ ├── libmodel.py │ ├── libpdb.py │ ├── libpdbname.py │ ├── libter.py │ ├── numpy_basics.py │ ├── pdbfile.patch │ ├── residue_constants.py │ ├── residue_constants_base.py │ ├── snippets.py │ └── torch_basics.py ├── script │ ├── convert_all2cg.py │ ├── convert_cg2all.py │ └── cryo_em_minimizer.py └── set │ ├── targets.pdb.29k │ ├── targets.pdb.6k │ ├── targets.test.pdb │ ├── targets.train.pdb.29k │ ├── targets.train.pdb.6k │ └── targets.valid.pdb ├── cryo_em_minimizer.ipynb ├── poetry.lock ├── pyproject.toml └── tests ├── 1ab1_A.bb.pdb ├── 1ab1_A.cacm.pdb ├── 1ab1_A.calpha.pdb ├── 1ab1_A.casc.pdb ├── 1ab1_A.martini.pdb ├── 1ab1_A.martini3.pdb ├── 1ab1_A.mc.pdb ├── 1ab1_A.pdb ├── 1ab1_A.primo.pdb ├── 1ab1_A.residue.pdb ├── 1ab1_A.sc.pdb ├── 1jni.calpha.dcd ├── 1jni.calpha.pdb ├── 3isr.af2.pdb ├── 3isr_5.mrc ├── 3iyg.pdb ├── LAF1rgg.sample.pdb ├── Q9EP54.sample.pdb └── __init__.py /.gitignore: -------------------------------------------------------------------------------- 1 | cg2all/model/*.ckpt 2 | .DS_ 3 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/README.md -------------------------------------------------------------------------------- /cg2all.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all.ipynb -------------------------------------------------------------------------------- /cg2all/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/__init__.py -------------------------------------------------------------------------------- /cg2all/data/calpha_geometry_params.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/calpha_geometry_params.dat -------------------------------------------------------------------------------- /cg2all/data/martini.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/martini.top -------------------------------------------------------------------------------- /cg2all/data/martini2.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/martini2.top -------------------------------------------------------------------------------- /cg2all/data/martini3.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/martini3.top -------------------------------------------------------------------------------- /cg2all/data/primo.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/primo.top -------------------------------------------------------------------------------- /cg2all/data/residue_constants.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/residue_constants.pkl -------------------------------------------------------------------------------- /cg2all/data/residue_geometry_params.bound.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/residue_geometry_params.bound.dat -------------------------------------------------------------------------------- /cg2all/data/residue_geometry_params.harmonic.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/data/residue_geometry_params.harmonic.dat -------------------------------------------------------------------------------- /cg2all/lib/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cg2all/lib/check_rigid_groups.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/check_rigid_groups.py -------------------------------------------------------------------------------- /cg2all/lib/create_pdblist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/create_pdblist.py -------------------------------------------------------------------------------- /cg2all/lib/generate_rigid_body.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/generate_rigid_body.py -------------------------------------------------------------------------------- /cg2all/lib/get_ic_from_structure.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/get_ic_from_structure.py -------------------------------------------------------------------------------- /cg2all/lib/libcg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libcg.py -------------------------------------------------------------------------------- /cg2all/lib/libconfig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libconfig.py -------------------------------------------------------------------------------- /cg2all/lib/libcryoem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libcryoem.py -------------------------------------------------------------------------------- /cg2all/lib/libdata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libdata.py -------------------------------------------------------------------------------- /cg2all/lib/libloss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libloss.py -------------------------------------------------------------------------------- /cg2all/lib/libmetric.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libmetric.py -------------------------------------------------------------------------------- /cg2all/lib/libmodel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libmodel.py -------------------------------------------------------------------------------- /cg2all/lib/libpdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libpdb.py -------------------------------------------------------------------------------- /cg2all/lib/libpdbname.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libpdbname.py -------------------------------------------------------------------------------- /cg2all/lib/libter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/libter.py -------------------------------------------------------------------------------- /cg2all/lib/numpy_basics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/numpy_basics.py -------------------------------------------------------------------------------- /cg2all/lib/pdbfile.patch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/pdbfile.patch -------------------------------------------------------------------------------- /cg2all/lib/residue_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/residue_constants.py -------------------------------------------------------------------------------- /cg2all/lib/residue_constants_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/residue_constants_base.py -------------------------------------------------------------------------------- /cg2all/lib/snippets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/snippets.py -------------------------------------------------------------------------------- /cg2all/lib/torch_basics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/lib/torch_basics.py -------------------------------------------------------------------------------- /cg2all/script/convert_all2cg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/script/convert_all2cg.py -------------------------------------------------------------------------------- /cg2all/script/convert_cg2all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/script/convert_cg2all.py -------------------------------------------------------------------------------- /cg2all/script/cryo_em_minimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/script/cryo_em_minimizer.py -------------------------------------------------------------------------------- /cg2all/set/targets.pdb.29k: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/set/targets.pdb.29k -------------------------------------------------------------------------------- /cg2all/set/targets.pdb.6k: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/set/targets.pdb.6k -------------------------------------------------------------------------------- /cg2all/set/targets.test.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/set/targets.test.pdb -------------------------------------------------------------------------------- /cg2all/set/targets.train.pdb.29k: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/set/targets.train.pdb.29k -------------------------------------------------------------------------------- /cg2all/set/targets.train.pdb.6k: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/set/targets.train.pdb.6k -------------------------------------------------------------------------------- /cg2all/set/targets.valid.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cg2all/set/targets.valid.pdb -------------------------------------------------------------------------------- /cryo_em_minimizer.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/cryo_em_minimizer.ipynb -------------------------------------------------------------------------------- /poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/poetry.lock -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/pyproject.toml -------------------------------------------------------------------------------- /tests/1ab1_A.bb.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.bb.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.cacm.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.cacm.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.calpha.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.calpha.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.casc.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.casc.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.martini.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.martini.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.martini3.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.martini3.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.mc.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.mc.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.primo.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.primo.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.residue.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.residue.pdb -------------------------------------------------------------------------------- /tests/1ab1_A.sc.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1ab1_A.sc.pdb -------------------------------------------------------------------------------- /tests/1jni.calpha.dcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1jni.calpha.dcd -------------------------------------------------------------------------------- /tests/1jni.calpha.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/1jni.calpha.pdb -------------------------------------------------------------------------------- /tests/3isr.af2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/3isr.af2.pdb -------------------------------------------------------------------------------- /tests/3isr_5.mrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/3isr_5.mrc -------------------------------------------------------------------------------- /tests/3iyg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/3iyg.pdb -------------------------------------------------------------------------------- /tests/LAF1rgg.sample.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/LAF1rgg.sample.pdb -------------------------------------------------------------------------------- /tests/Q9EP54.sample.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/cg2all/HEAD/tests/Q9EP54.sample.pdb -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | --------------------------------------------------------------------------------