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152a0911f1
* documentation for release draft start * trajectory.png * update readme to rf3-lab paths, annotate TODOs * add input_pdbs, demo.json * Update README.md example pngs * tasks pngs * Update README.md - restructure pngs and application links * Update README.md mc * Update README.md add ipynb kernel export instruction * mpnn all.ipynb * open and edit tutorial.zip * Update run_inf_tutorial.sh * remove outputs * cleanup * rename * soft code hbplus executable * rename modelforge to foundry (rfd3) README * fix: enabled running rfd3, mpnn inline * cleanup * remove todos, one remaining * clear outputs --------- Co-authored-by: Raktim Mitra <raktim@digs> Co-authored-by: Raktim Mitra <raktim@localhost> Co-authored-by: Rohith Krishna <rohith@localhost> Co-authored-by: Raktim Mitra <raktim@digs.ipd.uw.edu>
43 lines
1.2 KiB
JSON
Executable File
43 lines
1.2 KiB
JSON
Executable File
{
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"dsDNA_basic": {
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"input": "./input_pdbs/1bna.pdb",
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"contig": "A1-10,/0,B15-24,/0,120-130",
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"length": "140-150",
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"ori_token": [24,20,10]
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},
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"dsDNA_complex": {
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"input": "./input_pdbs/2r5z.pdb",
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"contig": "C5-18,/0,D24-37,/0,40-50,A146-154,80-90",
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"length": "147-167",
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"unindex": "/0,/0,B251-B255",
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"select_fixed_atoms": {
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"C9-14":"ALL",
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"D28-33":"ALL",
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"C5-8,C15-18": "",
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"D24-27,D34-37": ""
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},
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"ori_token":[25,35,20],
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"select_hbond_acceptor": {"C16":"N7,O6", "D31-32":"N7", "D28-30":"OP1,OP2,O3',O5'"},
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"select_hbond_donor": {"D31-32":"N6"}
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},
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"ssDNA_basic": {
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"input": "./input_pdbs/5o4d.pdb",
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"contig": "A1-23,/0,120-130",
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"length": "143-153",
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"ori_token": [-5,-10,8]
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},
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"ssDNA_diffused_from_dsDNA_pdb":{
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"input": "./input_pdbs/1bna.pdb",
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"contig": "A1-10,/0,120-130",
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"length": "130-140",
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"select_fixed_atoms": {"A1-10":""}
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},
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"RNA_basic": {
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"input": "./input_pdbs/1q75.pdb",
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"contig": "A1-15,/0,120-130",
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"length": "135-145",
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"ori_token": [15,2,-4]
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}
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}
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