diff --git a/src/dssp.py b/src/dssp.py index 8c80f19..71eaa40 100644 --- a/src/dssp.py +++ b/src/dssp.py @@ -3,6 +3,10 @@ import atom import sys from structure import * +def print_dssp(): + + empt_line=" " * 145 + if(len(sys.argv)<2): print("Not enough arguments! Run with --help to learn more about proper" "call structure and parameters.") @@ -15,10 +19,29 @@ else: #print(get_turns(pdb_file.residues)) #print(pdb_file.residues[27].h_bond(pdb_file.residues[28])) #print(get_bridges(pdb_file.residues)) + + turns = get_turns(pdb_file.residues) get_helix(pdb_file.residues, turns) - get_bends(pdb_file.residues) - get_chirality(pdb_file.residues) + # get_bends(pdb_file.residues) + # get_chirality(pdb_file.residues) + # bridges = get_bridges(pdb_file.residues) + # ladders = get_ladders(bridges) + # get_sheets(ladders) + + # print("NBRIDGES",len(bridges)) + bridges = get_bridges(pdb_file.residues) - ladders = get_ladders(bridges) - get_sheets(ladders) + + get_bonds(pdb_file.residues) + + print(pdb_file.residues[1].h_bond(pdb_file.residues[2])) + + residues = pdb_file.residues + e_min = 0 + for res in residues: + ene = residues[1].h_bond(res) + if ene <= e_min: + e_min = ene + best_res = res + print(residues[1].resid, best_res.resid,e_min) diff --git a/src/structure.py b/src/structure.py index 0d47bda..d2d89d2 100644 --- a/src/structure.py +++ b/src/structure.py @@ -34,7 +34,7 @@ def get_turns(residues): if(i+j0): return(bridges) else: return(False) +# def get_bonds(residues): +# for i,res1 in enumerate(residues): +# E_min = 0 +# strongest_bridge = [] +# for j in range(-5,6): +# if(i+j < len(residues)): +# res2 = residues[i+j] +# if(res1.h_bond(res2)<-0.5) and (res1.h_bond(res2)0): +# diff = strongest_bridge[0].resid - strongest_bridge[1].resid +# if( abs (diff) > 1 and abs(diff)<=5): +# print(diff) + +def get_bonds(residues): + bonds = {} + k = 0 + for i,res in enumerate(residues): + E_min = 0 + for j in range(-5,-2): + if(i+j