SyntheticEvolution/plot_all_3d.sh at main · automl/SyntheticEvolution · GitHub

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#! /bin/bash

# plot 3D structures

echo "Plotting 3D structures..."

conda activate synEvo

# echo "Start with RNAformer vs AlphaFold 3"

# python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformer --alphafold-pred-dir evaluation/predictions/alphafold --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name AlphaFold --alg2-name RNAformer --rf-color green --af3-color blue --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --view-store-dir pymol_views --view-mode rotation

# echo "Plotting RNAformer vs SpotRNA"

# python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformer --alphafold-pred-dir evaluation/predictions/spotrna --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name SPOT-RNA --alg2-name RNAformer --rf-color green --af3-color tv_red --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --view-store-dir pymol_views --view-mode rotation

# echo "Plotting RNAformer vs RNAfold"

# python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformer --alphafold-pred-dir evaluation/predictions/rnafold --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name RNAfold --alg2-name RNAformer --rf-color green --af3-color deepteal --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --view-store-dir pymol_views --view-mode rotation

# echo "Plotting RNAformer vs DSSR-3D"

# python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformer --alphafold-pred-dir evaluation/predictions/dssr --gt-dir evaluation/predictions/gt --out-dir paper_figures --views-dir pymol_views --specific-id 1SJ4 --buffer 25 --alg1-name DSSR --alg2-name RNAformer --rf-color green --af3-color purpleblue --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent

# python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformer --alphafold-pred-dir evaluation/predictions/dssr --gt-dir evaluation/predictions/gt --out-dir paper_figures --views-dir pymol_views --specific-id 4P8Z --buffer 25 --alg1-name DSSR --alg2-name RNAformer --rf-color green --af3-color purpleblue --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent

# echo "done."


# AF3

python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformer --alphafold-pred-dir evaluation/predictions/alphafold --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name AlphaFold --alg2-name RNAformer --rf-color green --af3-color blue --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --views-dir pymol_views --specific-id 2PLY

python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformerN100 --alphafold-pred-dir evaluation/predictions/alphafold3 --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name AlphaFold --alg2-name RNAformerN100 --rf-color green --af3-color blue --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --views-dir pymol_views --specific-id 2PLY

# SPOT-RNA
python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformerN100 --alphafold-pred-dir evaluation/predictions/spotrnaN100 --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name SPOT-RNAN100 --alg2-name RNAformerN100 --rf-color green --af3-color tv_red --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --views-dir pymol_views --specific-id 1SJ4

# RNAfold
python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformerN100 --alphafold-pred-dir evaluation/predictions/rnafoldN100 --gt-dir evaluation/predictions/gt --out-dir paper_figures --buffer 25 --alg1-name RNAfoldN100 --alg2-name RNAformerN100 --rf-color green --af3-color deepteal --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --views-dir pymol_views --specific-id 1SJ4

# DSSR-3D
python plot_3d_structures.py --rnaformer-pred-dir evaluation/predictions/rnaformerN100 --alphafold-pred-dir evaluation/predictions/dssrN100 --gt-dir evaluation/predictions/gt --out-dir paper_figures --views-dir pymol_views --buffer 25 --alg1-name DSSRN100 --alg2-name RNAformerN100 --rf-color green --af3-color purpleblue --gt-color gray --gt-rna-color brightorange --pred-rna-color magenta --plot-rna-only --show-plot --transparent --views-dir pymol_views --specific-id 1SJ4