TrDesign w/ Partial Hallucination support
Download Models
wget -qnc https://files.ipd.uw.edu/krypton/TrRosetta/models.zip
wget -qnc https://files.ipd.uw.edu/krypton/TrRosetta/bkgr_models.zip
unzip -qqo models.zip
unzip -qqo bkgr_models.zip
IMPORTANT: Modify DB_DIR in utils.py, set path to models
Run example
python design.py -p 1QYS.pdb -o tmp.txt
HELP
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TrRosetta for Design
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--len= -l : set length for unconstrained design
--out= -o : filename prefix for output
--num= -n : number of designs
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Backbone Design (if PDB provided)
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--pdb= -p : PDB for fixed backbone design
--chain= -c : specify chain to use
--mask= -m : set positions to rebuild ['start-end:min-max,...']
NOTE: the positions are zero-indexed, first position=0
use 'start-end' to specify region to rebuild
use 'min-max' to specify length of indel
ex: '10-15:0-5' replace pos. 10-15 with variable-loop of length 0-5
ex: '10-15:5' replace pos. 10-15 with fixed-loop of length 5
ex: '10-15' remove pdb cst. from positions 10 to 15
ex: '10' remove pdb cst. from position 10
--sam= -s : number of samples per design run [if --mask]
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Extras
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--aa_weight= : weight for aa loss
--rm_aa= : disable specific amino acids from being sampled
ex: 'C' or 'W,Y,F'
--save_img : save image of contact map
--save_npz : save data for PyRosetta
--save_pdb : use magic to quickly generate PDB structure
--scwrl : use scwrl to add sidechains [if --save_pdb]
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Experimental options
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--pssm_design : design a PSSM instead of a single sequence
--pssm_mask : use PSSM in regions constrained by PDB
--msa_design : design a MSA instead of a single sequence
--msa_first : fix the first sequence (no shuffle)
--msa_num= : number of sequences in MSA
--feat_drop= : dropout rate for features
for --msa_design, we recommend 0.8
--mask_drop : disable dropout in constrained regions
--mask_feat : copy features from pdb for constrained regions
--cce_cutoff= : filter cce to CB ≤ x
--spike= : initialize design from PDB seq
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Optimization settings
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--opt_iter= : number of iterations
--opt_adam : use ADAM optimizer
--opt_decay : use GD+Decay optimizer
--opt_sample : sample from PSSM instead of taking argmax of PSSM
--serial : enable approx. serial mode
--n_models= : number of TrRosetta models to load into memory
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