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Improved bridges exhaustive search

master
Thomas Forest 2019-09-14 23:41:58 +02:00
parent e80fdb57ab
commit e363f37ce0
4 changed files with 31 additions and 24 deletions
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5
src/atom.py
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@ -47,7 +47,4 @@ class Residue:
r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"]) r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"])
# Electrostatic interaction energy, in kcal/mole # Electrostatic interaction energy, in kcal/mole
E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
if(E<-0.5): return(E)
return(True)
else:
return(False)

2
src/dssp.py
View File

@ -14,5 +14,5 @@ else:
#print(pdb_file.residues[2].h_bond(pdb_file.residues[40])) #print(pdb_file.residues[2].h_bond(pdb_file.residues[40]))
#print(get_turns(pdb_file.residues)) #print(get_turns(pdb_file.residues))
#print(pdb_file.residues[27].h_bond(pdb_file.residues[28])) #print(pdb_file.residues[27].h_bond(pdb_file.residues[28]))
get_bridges(pdb_file.residues) print(get_bridges(pdb_file.residues))

2
src/geometry.py
View File

@ -3,4 +3,4 @@ class GeomObject:
pass pass
class Distance: class Distance:
pass

46
src/structure.py
View File

@ -19,30 +19,40 @@ def get_turns(residues):
for i,res in enumerate(residues): for i,res in enumerate(residues):
for j in range(3,6): for j in range(3,6):
if(i+j<len(residues)): if(i+j<len(residues)):
if(res.h_bond(residues[i+j])): if(res.h_bond(residues[i+j]<-0.5)):
turns.append(Turn(j)) turns.append(Turn(j))
return(turns) return(turns)
def get_bridges(residues): def get_bridges(residues):
# TODO : non-overlaping check to add
bridges = [] bridges = []
for i,res in enumerate(residues): for i in range(1,len(residues)-4):
for j, res in enumerate(residues): E_min = 0
if(i-1>=0 and i+1<len(residues) for j in range(i+2,len(residues)-1):
and j-1>=0 and j+1<len(residues)): # select triplet with the minimal energy
if((residues[i-1].h_bond(residues[j])
and residues[j].h_bond(residues[i+1]))
or(residues[j-1].h_bond(residues[i])
and residues[i].h_bond(residues[j+1]))):
bridges.append(Bridge("para"))
if(i-1>=0 and i+1<len(residues) if(residues[i-1].h_bond(residues[j])<-0.5
and j-1>=0 and j+1<len(residues)): and residues[j].h_bond(residues[i+1])<-0.5):
if((residues[i].h_bond(residues[j]) if(residues[i-1].h_bond(residues[j])+
and residues[j].h_bond(residues[i])) residues[j].h_bond(residues[i+1]))<E_min:
or(residues[i-1].h_bond(residues[j+1]) E_min = residues[i-1].h_bond(residues[j])
and residues[j-1].h_bond(residues[i+1]))): +residues[j].h_bond(residues[i+1])
bridges.append(Bridge("anti"))
if(residues[j-1].h_bond(residues[i])<-0.5
and residues[i].h_bond(residues[j+1])<-0.5):
if(residues[j-1].h_bond(residues[i])+
residues[i].h_bond(residues[j+1]))<E_min:
E_min = residues[j-1].h_bond(residues[i])
+residues[i].h_bond(residues[j+1])
#bridges.append(Bridge("para"))
if((residues[i].h_bond(residues[j])<-0.5
and residues[j].h_bond(residues[i])<-0.5)
or(residues[i-1].h_bond(residues[j+1])<-0.5
and residues[j-1].h_bond(residues[i+1])<-0.5)):
#bridges.append(Bridge("anti"))
#bridges.append(strongest_bridge)
return(bridges) return(bridges)
def get_helix(turns): def get_helix(turns):