0_prep_folders.sh
1_prepare.py
2_download_cifs.sh
3_get_xyz.py
4_try_to_join.py
5_gen_xyz_list.sh
6_find_knots.py
7_find_nontrivial.py
0_prep_folders.sh -- generates folders required for other prgrams;
1_prepare.py -- loads bgsu database csv file and creates lists/pdbs_chains.txt and lists/eq_classes.txt files;
2_download_cifs.sh -- downloads cif files (into cif folder) based on lists/pdbs_chains.txt file;
3_get_xyz.py -- creates xyz files (into xyz/ and ext_xyz/ folders) from cif files (using lists/pdbs_chains.txt) and max_dists.txt file, to create a file whole backbone is used (C5',C4',C3',O3',P,O5' atoms);
4_try_to_join.py -- checks if chains from same equivalence class (lists/eq_classes.txt) are so close that actually could create one chain and if yes then joins them and create new xyz file;
5_gen_xyz_list.sh -- creates sorted (by file size) list of xyz files (lists/xyz_files.txt);
6_find_knots.py -- identifies knots using topoly.alexander() in files listed in lists/xyz_files.txt and outputs results into alexander.txt;
7_find_nontrivial.py -- checks alexander.txt for chains with >50% probability of having a knot and outputs them with their maximal gap.
bgsu_3269_4A.csv
Main input is bgsu_3269_4A.csv file downloaded from BGSU RNA database. This file is 3.269 version of database with representants with 4.0 Angstrom resolution or better. Files from other versions also can be used, just pass the file as a first argument to the 1st pipeline program: python3 1_prepare.py <filename> .
alexander.txt
max_dists.txt
lists/pdbs_chains.txt
lists/eq_classes.txt
lists/xyz_files.txt
cif/*.cif
xyz/*.xyz
ext_xyz/*.xyz
alexander.txt -- file with knot probabilites for each RNA class representant; probabilities often do not sum to 100% because knots with probabilities <10% (this can be changed in 6th pipeline file by changing hide_rare parameter of topoly.alexander() function);
max_dists.txt -- file with maximal distances of gaps in RNA class representants;
lists/pdbs_chains.txt -- file with pdb and chain codes of RNA class representants;
lists/eq_classes.txt -- file with RNA class names and their representants;
lists/xyz_files.txt -- file with xyz file names sorted by their size;
cif/*.cif -- downloaded cif files of RNA class representants;
xyz/*.xyz -- created xyz files of RNA class representants, coordinates are based on C5',C4',C3',O3',P,O5' atoms;
ext_xyz/*.xyz -- same as xyz/*.xyz but with some extra information: label (atom_id-chain_id-resid_id-atom_type) and distance between a atom and previous atom.