diff --git a/src/atom.py b/src/atom.py index b96dbb1..e869a2a 100644 --- a/src/atom.py +++ b/src/atom.py @@ -52,17 +52,23 @@ class Residue: E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f return(E) - def get_turns(self, residues, turns): + def get_turns(self, residues): """ Get all the turns from a specific residue. """ + turns = {} i = residues.index(self) + k = 0 for j in range(3,6): if(i+j): + last = j + j+=1 + print(j) + if(k>2): + sheet_end = last + + print("SHEET", sheet_start, sheet_end) + + def get_sheets2(self): + """ + Bridges between ladders. + Check if 1 bridge between one ladder and one or more other ladders. + Iterate over all residues of one ladder and check if bridge with other residues + of the other ladders. + """ + sheets = {} + for ladder in ladders: + for ladd2 in ladders: + for bridge in ladders[ladder]['bridges']: + if bridge.res_partner in res_list(ladders[ladd2]): + print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner, + "ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end']) + #print("stop ladder 2") + print("stop ladder 1") + + def get_ladders2(self, bridges, residues): ladders = {} diff --git a/src/dssp.py b/src/dssp.py index 6dd0c2a..bc4c156 100644 --- a/src/dssp.py +++ b/src/dssp.py @@ -49,12 +49,11 @@ else: #print(residues[2].atoms, residues[0].resid, residues[1].resid) print(get_TCO(residues[2],residues[3])) - turns = {} + #turns = {} ladders = {} for i,res in enumerate(residues): # res.get_turns(residues, turns) - # res.get_helix(residues, turns) - res.get_bridges(residues) + #res.get_helix(residues) + #res.get_bridges(residues) res.get_ladders(residues, ladders) - - + #res.get_sheets(residues)