#======================================================
# renumber pdb file based on user defined start number
#======================================================
home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb -s 35 -r 

/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/rifampicin/input/rpob_complex_model.pdb -s 29 -r 

#======================================================
# pdb_seq.py: extract seq from structure
#======================================================
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt
#/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -c A -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt

#======================================================
# pdb_mutator.py: mutate residue: FIXME, needs charm
#======================================================
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_mutator -r 39 -m XXX /home/tanu/git/Data/ethambutol/input/3byw.pdb

#======================================================
# pdb_ligand.py: list ligands within pdb
# note: works ONLY for pdb containing ligands
# this is because such pdbs contain a field 'HETATM    ' 
#======================================================
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf_b.pdb
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf.pdb

#======================================================
# pdb_ligand_tt.py: list ligands for valid pdbs AND docked complexes (my use case)
#======================================================
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/cycloserine/input/alr_complex.pdb
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb 
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/ethambutol/input/7bvf_b.pdb
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/ethambutol/input/7bvf.pdb
#======================================================
# get torsion angles
#======================================================
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_torsion /home/tanu/git/Data/rifampicin/input/rpob_complex.pdb > /home/tanu/git/Data/rifampicin/input/rpob_torsion.txt


#^^^^^^^^^^^^^^^^^^^^^^^^^^^^

# my pdb tools

#======================================================
# save specifed chains as individual pdbs
#======================================================
./pdb_chain_splitter.py -i /home/tanu/git/Data/ethambutol/input/3byw.pdb -c DF -p /home/tanu/git/Data/ethambutol/input -o 3byw

#======================================================
# save specifed chains as one pdb
#======================================================
./pdb_chain_extract.py -i /home/tanu/git/Data/ethambutol/input/3byw.pdb -c DF -p /home/tanu/git/Data/ethambutol/input -o 3byw^C