def check_for_peptide_links(
atom1,
atom2,
):
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
atom_group1 = atom1.parent()
atom_group2 = atom2.parent()
if classes1.common_amino_acid or classes2.common_amino_acid:
if classes1.common_amino_acid:
other = atom_group2
else:
other = atom_group1
if linking_utils.get_class(other.resname) not in ["other"]:
return None
# sulfur bridge
key = "SS"
if atom1.name.strip() == "SG" and atom2.name.strip(
) == "SG": # too strict?
return key, False
# test for backbond atoms
count = 0
for atom in other.atoms():
if atom.name.strip() in ["C", "N", "O"]: count += 1
if count != 3: return None
key = "TRANS"
if atom2.name.strip() == "C" and atom1.name.strip() == "N":
return key, False
elif atom1.name.strip() == "C" and atom2.name.strip() == "N":
return key, True
return False
def check_for_peptide_links(atom1,
atom2,
):
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
atom_group1 = atom1.parent()
atom_group2 = atom2.parent()
if classes1.common_amino_acid or classes2.common_amino_acid:
if classes1.common_amino_acid:
other = atom_group2
else:
other = atom_group1
if linking_utils.get_class(other.resname) not in ["other"]:
return None
# sulfur bridge
key = "SS"
if atom1.name.strip()=="SG" and atom2.name.strip()=="SG": # too strict?
return key, False
# test for backbond atoms
count = 0
for atom in other.atoms():
if atom.name.strip() in ["C", "N", "O"]: count+=1
if count!=3: return None
key = "TRANS"
if atom2.name.strip()=="C" and atom1.name.strip()=="N":
return key, False
elif atom1.name.strip()=="C" and atom2.name.strip()=="N":
return key, True
return False