def salt_bridge(molecule=None):
model = molecule.model()
metrics = MetricsModel(molecule)
positives = []
negatives = []
index = 0
complete_sides = []
bridge_pairs = {} #set up lists to add outputs to
x = 0
for chain in metrics.chains:
for residue in chain:
if residue.is_sidechain_complete == True:
complete_sides.append(True)
else:
complete_sides.append(False)
#many files are missing side chains for some residues
#these cause errors if not excepeted!
for polymer in model:
for monomer in polymer:
if complete_sides[index]: #checks if current mresiude is complete
if monomer.type().trim() in ("ARG", "LYS", "HIS"):
positives.append(monomer)
elif monomer.type().trim() in ("ASP", "GLU"):
negatives.append(monomer)
index +=1 #increments index for next residue
for positive in positives:
if positive.type().trim() == "ARG":
plus_coord = positive.find(clipper.String("CZ")).coord_orth
elif positive.type().trim() == "LYS":
plus_coord = positive.find(clipper.String("NZ")).coord_orth
elif positive.type().trim() == "HIS":
plus_coord = positive.find(clipper.String("ND1")).coord_orth
for negative in negatives:
if negative.type().trim() == "ASP":
neg_coord = negative.find(clipper.String("CG")).coord_orth
elif negative.type().trim() == "GLU":
neg_coord = negative.find(clipper.String("CD")).coord_orth
if clipper.Coord_orth.length(plus_coord, neg_coord) < 4.5:
x += 1
bridge_pairs[x] = (positive.id().trim(), negative.id().trim())
return bridge_pairs
def ss_bridge(molecule=None):
model = molecule.model()
cysteines = []
bridge_pairs = {} #set up lists to add outputs to
i = 0
for polymer in model:
for monomer in polymer:
if monomer.type().trim() == "CYS":
cysteines.append(monomer) #assemble a list of all CYS residues
for cys in cysteines:
cys_1_S = cys.find(clipper.String("SG")).coord_orth #set location of first cys
for next in cysteines:
#test first cys against all subsequent, looking for closeness (hence a bridge)
cys_2_S = next.find(clipper.String("SG")).coord_orth
if clipper.Coord_orth.length(cys_1_S, cys_2_S) < 2.6 and clipper.Coord_orth.length(cys_1_S, cys_2_S) != 0:
i += 1#gives a numbered key for use as our bridge annotation
bridge_pairs[i] = (cys.id().trim(), next.id().trim())
cysteines.remove(cys) #prevents repetition
return bridge_pairs
def salt_bridge(molecule=None):
model = molecule.model()
metrics = MetricsModel(molecule)
index = 0
complete_sides = []
list_of_dicts = [] #set up lists to add outputs to
x = 0
for chain in metrics.chains:
for residue in chain:
if residue.is_sidechain_complete == True:
complete_sides.append(True)
else:
complete_sides.append(False)
#many files are missing side chains for some residues
#these cause errors if not excepeted!
for polymer in model:
positives = []
negatives = []
bridge_pairs = {}
for monomer in polymer:
if complete_sides[index]: #checks if current mresiude is complete
if monomer.type().trim() in ("ARG", "LYS"):
positives.append(monomer)
elif monomer.type().trim() in ("ASP", "GLU"):
negatives.append(monomer)
index += 1 #increments index for next residue
for positive in positives:
if positive.type().trim() == "ARG":
plus_coord = positive.find(clipper.String("CZ")).coord_orth
elif positive.type().trim() == "LYS":
plus_coord = positive.find(clipper.String("NZ")).coord_orth
closest_range = 999
for negative in negatives:
if negative.type().trim() == "ASP":
neg_coord = negative.find(clipper.String("CG")).coord_orth
elif negative.type().trim() == "GLU":
neg_coord = negative.find(clipper.String("CD")).coord_orth
if clipper.Coord_orth.length(
plus_coord, neg_coord
) < closest_range and clipper.Coord_orth.length(
plus_coord, neg_coord) < 4.6:
closest_range = clipper.Coord_orth.length(
plus_coord, neg_coord)
paired_aa = negative
if closest_range != 999:
x += 1
bridge_pairs[x] = (positive.id().trim(),
positive.type().trim(), closest_range,
paired_aa.id().trim(),
paired_aa.type().trim())
for negative in negatives:
rep_counter = 0
distances = [0]
for key, value in bridge_pairs.items():
if negative.id().trim() in value:
rep_counter += 1
distances.append(value[2])
if rep_counter == 2:
for key, value in bridge_pairs.items():
if max(distances) in value:
del bridge_pairs[key]
if rep_counter > 2:
for key, value in bridge_pairs.items():
if negative.id().trim() in value:
del bridge_pairs[key]
list_of_dicts.append(bridge_pairs)
return list_of_dicts