Scripts specific to the foldon project that you seriously freaking need to keep track of.
addloop_renum.py adds a loop defined by 'loop.pdb' to an existing pdb file. All atom indices are hard-coded for 1rfo.pdb
alex rmsd finder copied from Alex DeGrage (ajd98)
conc.py calculates the concentration of your (currently dimer) in a 125A sphere.
count_events_200 calculates kinetic properties (k_on, off, etc) based on number of events/total time in a state
count_native_contacts counts the number of unique native contacts in a given system.go.contacts format.
dihedrals.py functional script which modifies internal.parameters based on atom indices
dihedrals_ali presumably functional script which modifies many things in 2 chains of a single pdb. written by ali sinan saglam (asinansaglam)
indi comp plots plotting script for comparison
native_contacts more or less a copy of ugh_fraction_native_contacts, written with Alex DeGrage (ajd98)
new go contacts i literally can't remember what this does
nonrandom modified randomorientations (from ajd98) which separates chains of 1rfo and separates them in native orientation
one rmsd modified rmsd_2 for a single calculation
plot fr nc srsly old plotting script for native contacts array output from ugh_fraction_native_contacts.py
plot moving average example plotting script for a moving instantaneous average
randomorientations script by ajd98 for orienting monomers according to a random matrix. sources within code because alex is the best
randomorientations restart modified version of the above which works with the restart.file format rather than .pdb
renum go contacts ASS modified from ali sinan saglam (asinansaglam) to renumber go contacts within system.go.contacts
renum oriented takes 1rfo_oriented (output of separatechains) and removes junk. poorly named
rmsd from ajd98
rmsd_2 modified from ajd98, calculates rmsd relative to permutations of the three monomers
rmsd scf modified of rmsd_2, calculates rmsd relative to reference scf structure
separatechains takes 1rfo.pdb and writes 3 pdbs, one for each monomer
tails.py wow this was a long time ago. theoretically takes rmsd of tail regions of 1rfo monomers, tracks along course of a trajectory.
tryp_calc calculates minimum distance between tryptophan residues in 3 monomers of 1rfo
tryptophan tracker & tryptophan tracker scf uses same method as tails.py to track tryptophans through course of trajectory (untested)
ugh fraction native contacts calculates and records atom pairs which are within 5.5A +- 1.2*equilibrium distance in a given structure
ugh scf nc does the same thing as above, with the atom indices changed for the single chain foldon.