# Step1. Pull the latest version of tutorial repo: 
cd /app/rfd_mpnn_af2_env && git pull origin main

# Step2. Copy the required target(sars2 spike protein) pdb files into the work dir: 
cd /root/ && cp -r /app/rfd_mpnn_af2_env/input/ .

# Step3. Scaffold generation option 1: RFdiffusion: unconditional binder design
python /app/RFdiffusion/scripts/run_inference.py inference.input_pdb=/app/rfd_mpnn_af2_env/input/Spike_glycoprotein.pdb 'contigmap.contigs=[B1-193/0 90-90]' 'ppi.hotspot_res=[B120,B122,B123,B160,B172]' inference.ckpt_override_path=/app/RFdiffusion/models/Complex_base_ckpt.pt denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0 inference.output_prefix=samples/uncondition

# Step3. Scaffold generation option 2: RFdiffusion: motif scaffolding binder design with ACE2 motif
python /app/RFdiffusion/scripts/run_inference.py inference.input_pdb=/app/rfd_mpnn_af2_env/input/Spike_glycoprotein_complex.pdb 'contigmap.contigs=[B1-193/0 A19-42/60-60]' inference.ckpt_override_path=/app/RFdiffusion/models/Base_ckpt.pt denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0 inference.output_prefix=samples/ace2

# Step3. Scaffold generation option 3: RFdiffusion: topology guided binder design 
python /app/RFdiffusion/scripts/run_inference.py scaffoldguided.scaffoldguided=True scaffoldguided.scaffold_dir=/app/RFdiffusion/examples/ppi_scaffolds/ scaffoldguided.target_pdb=True scaffoldguided.target_path=/app/rfd_mpnn_af2_env/input/Spike_glycoprotein.pdb scaffoldguided.target_ss=/app/rfd_mpnn_af2_env/input/Spike_glycoprotein_ss.pt scaffoldguided.target_adj=/app/rfd_mpnn_af2_env/input/Spike_glycoprotein_adj.pt 'ppi.hotspot_res=[B120,B122,B123,B160,B172]' inference.ckpt_override_path=/app/RFdiffusion/models/Complex_Fold_base_ckpt.pt denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0 inference.output_prefix=samples/scaffold_guided

# Step4. ProteinMPNN Sequence Design 
python /app/dl_binder_design/mpnn_fr/dl_interface_design.py -pdbdir ./samples/ -outpdbdir ./mpnn/ -relax_cycles 0 -seqs_per_struct 4

# Step5. Alphafold2 complex structure prediction
python /app/dl_binder_design/af2_initial_guess/predict.py -pdbdir ./mpnn/ -outpdbdir ./predictions/