
####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_rna1/6FPQ_target.pdb" \
  -m "./input/protein_rna1" \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-chain A] -a2 [-chain B]]" \
  --subselect-atoms "[-chain A]" \
  --output-with-identities \
| column -t
target           model             t_id  m_id  residue_residue_cadscore  residue_sites_cadscore  identity_of_residues  identity_of_atoms  identity_of_chains
6FPQ_target.pdb  6FPQ_model1a.pdb  6     0     0.704417                  0.73661                 100                   100                100
6FPQ_target.pdb  6FPQ_model1b.pdb  6     1     0.659809                  0.710854                100                   100                100
6FPQ_target.pdb  6FPQ_model2a.pdb  6     2     0.381626                  0.375183                100                   100                100
6FPQ_target.pdb  6FPQ_model2b.pdb  6     3     0.373695                  0.405748                100                   100                100
6FPQ_target.pdb  6FPQ_model3a.pdb  6     4     0.113882                  0.451957                100                   100                100
6FPQ_target.pdb  6FPQ_model3b.pdb  6     5     0.106027                  0.451912                100                   100                100

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_rna1/6FPQ_target.pdb" \
  -m "./input/protein_rna1" \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-protein] -a2 [-nucleic]]" \
  --subselect-atoms "[-protein]" \
  --output-with-identities \
| column -t
target           model             t_id  m_id  residue_residue_cadscore  residue_sites_cadscore  identity_of_residues  identity_of_atoms  identity_of_chains
6FPQ_target.pdb  6FPQ_model1a.pdb  6     0     0.704417                  0.73661                 100                   100                100
6FPQ_target.pdb  6FPQ_model1b.pdb  6     1     0.659809                  0.710854                100                   100                100
6FPQ_target.pdb  6FPQ_model2a.pdb  6     2     0.381626                  0.375183                100                   100                100
6FPQ_target.pdb  6FPQ_model2b.pdb  6     3     0.373695                  0.405748                100                   100                100
6FPQ_target.pdb  6FPQ_model3a.pdb  6     4     0.113882                  0.451957                100                   100                100
6FPQ_target.pdb  6FPQ_model3b.pdb  6     5     0.106027                  0.451912                100                   100                100

####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_rna1/6FPQ_target.pdb" \
  -m "./input/protein_rna1" \
  --scoring-levels atom residue \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-protein] -a2 [-nucleic]]" \
  --subselect-atoms "[-protein]" \
| column -t
target           model             t_id  m_id  residue_residue_cadscore  atom_atom_cadscore  residue_sites_cadscore  atom_sites_cadscore
6FPQ_target.pdb  6FPQ_model1a.pdb  6     0     0.704417                  0.315272            0.73661                 0.662628
6FPQ_target.pdb  6FPQ_model1b.pdb  6     1     0.659809                  0.374996            0.710854                0.724907
6FPQ_target.pdb  6FPQ_model2a.pdb  6     2     0.381626                  0.020043            0.375183                0.38015
6FPQ_target.pdb  6FPQ_model2b.pdb  6     3     0.373695                  0.017079            0.405748                0.415593
6FPQ_target.pdb  6FPQ_model3a.pdb  6     4     0.113882                  0.016045            0.451957                0.343089
6FPQ_target.pdb  6FPQ_model3b.pdb  6     5     0.106027                  0.011168            0.451912                0.374575

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_rna1/6FPQ_target.pdb" \
  -m "./input/protein_rna1" \
  --scoring-levels atom residue \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-protein] -a2 [-nucleic]]" \
  --subselect-atoms "[-protein]" \
  --conflate-atom-types \
| column -t
target           model             t_id  m_id  residue_residue_cadscore  atom_atom_cadscore  residue_sites_cadscore  atom_sites_cadscore
6FPQ_target.pdb  6FPQ_model1a.pdb  6     0     0.704417                  0.324089            0.73661                 0.656477
6FPQ_target.pdb  6FPQ_model1b.pdb  6     1     0.659809                  0.392014            0.710854                0.724368
6FPQ_target.pdb  6FPQ_model2a.pdb  6     2     0.381626                  0.020043            0.375183                0.374615
6FPQ_target.pdb  6FPQ_model2b.pdb  6     3     0.373695                  0.017079            0.405748                0.420352
6FPQ_target.pdb  6FPQ_model3a.pdb  6     4     0.113882                  0.016045            0.451957                0.344302
6FPQ_target.pdb  6FPQ_model3b.pdb  6     5     0.106027                  0.011168            0.451912                0.372483

####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_rna1/6FPQ_target.pdb" \
  -m "./input/protein_rna1/6FPQ_model1a.pdb" \
  --scoring-levels residue \
  --scoring-types contacts \
  --subselect-contacts "[-a1 [-protein] -a2 [-nucleic]]" \
  --conflate-atom-types \
  --local-output-formats pdb contactmap graphics-pymol \
  --local-output-levels residue atom \
  --output-dir ./output/protein_rna1/output_dir_01 \
| column -t
target           model             t_id  m_id  residue_residue_cadscore
6FPQ_target.pdb  6FPQ_model1a.pdb  1     0     0.704417

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_rna1/6FPQ_target.pdb" \
  -m "./input/protein_rna1/6FPQ_model1a.pdb" \
  --scoring-levels atom \
  --scoring-types contacts \
  --subselect-contacts "[-a1 [-protein] -a2 [-nucleic]]" \
  --conflate-atom-types \
  --local-output-formats contactmap \
  --local-output-levels atom residue chain \
  --output-dir ./output/protein_rna1/output_dir_02 \
| column -t
target           model             t_id  m_id  atom_atom_cadscore
6FPQ_target.pdb  6FPQ_model1a.pdb  1     0     0.324089

####################################################################

find ./input/protein_rna1/ -type f -name '*model*' \
| cadscore-lt \
  --scoring-levels residue \
  --scoring-types contacts \
  --subselect-contacts '[-a1 [-protein] -a2 [-nucleic]]' \
  --output-dir ./output/protein_rna1/output_dir_v03 \
  --extremely-compact-output \
  --clustering-thresholds 0.3 0.4 0.5 0.6 0.7 0.8 0.9

find ./input/protein_rna1/ -type f -name '*model*' \
| cadscore-lt \
  --scoring-levels residue \
  --scoring-types contacts \
  --subselect-contacts '[-a1 [-protein] -a2 [-nucleic]]' \
  --output-dir ./output/protein_rna1/output_dir_v04 \
  --clustering-thresholds 0.3 0.4 0.5 0.6 0.7 0.8 0.9 \
| column -t
target            model             t_id  m_id  residue_residue_cadscore
6FPQ_model3a.pdb  6FPQ_model3b.pdb  4     5     0.878349
6FPQ_model3b.pdb  6FPQ_model3a.pdb  5     4     0.877782
6FPQ_model1a.pdb  6FPQ_model1b.pdb  0     1     0.854266
6FPQ_model1b.pdb  6FPQ_model1a.pdb  1     0     0.849624
6FPQ_model2b.pdb  6FPQ_model2a.pdb  3     2     0.84137
6FPQ_model2a.pdb  6FPQ_model2b.pdb  2     3     0.837263
6FPQ_model1a.pdb  6FPQ_model2a.pdb  0     2     0.377615
6FPQ_model1a.pdb  6FPQ_model2b.pdb  0     3     0.373931
6FPQ_model2a.pdb  6FPQ_model1a.pdb  2     0     0.368113
6FPQ_model1b.pdb  6FPQ_model2b.pdb  1     3     0.36464
6FPQ_model1b.pdb  6FPQ_model2a.pdb  1     2     0.35661
6FPQ_model2a.pdb  6FPQ_model1b.pdb  2     1     0.344747
6FPQ_model2b.pdb  6FPQ_model1a.pdb  3     0     0.344366
6FPQ_model2b.pdb  6FPQ_model1b.pdb  3     1     0.332512
6FPQ_model3a.pdb  6FPQ_model2a.pdb  4     2     0.201901
6FPQ_model2b.pdb  6FPQ_model3a.pdb  3     4     0.188873
6FPQ_model3a.pdb  6FPQ_model2b.pdb  4     3     0.188156
6FPQ_model3b.pdb  6FPQ_model2a.pdb  5     2     0.183383
6FPQ_model2a.pdb  6FPQ_model3a.pdb  2     4     0.183358
6FPQ_model3b.pdb  6FPQ_model2b.pdb  5     3     0.173589
6FPQ_model2b.pdb  6FPQ_model3b.pdb  3     5     0.16057
6FPQ_model2a.pdb  6FPQ_model3b.pdb  2     5     0.152587
6FPQ_model1a.pdb  6FPQ_model3a.pdb  0     4     0.13624
6FPQ_model1b.pdb  6FPQ_model3b.pdb  1     5     0.129939
6FPQ_model1b.pdb  6FPQ_model3a.pdb  1     4     0.129754
6FPQ_model1a.pdb  6FPQ_model3b.pdb  0     5     0.125677
6FPQ_model3a.pdb  6FPQ_model1a.pdb  4     0     0.089375
6FPQ_model3b.pdb  6FPQ_model1b.pdb  5     1     0.087488
6FPQ_model3b.pdb  6FPQ_model1a.pdb  5     0     0.084623
6FPQ_model3a.pdb  6FPQ_model1b.pdb  4     1     0.078454

####################################################################



