def get_superposable_atoms(polymer, segments, atom_types=["CA", "N", "C", "CB"]):
result = []
allowed_i = []
residues = polymer.residues()
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i, j))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms() if a.type in atom_types])
return result
def get_superposable_atoms(polymer,
segments,
atom_types=['CA', 'N', 'C', 'CB', 'O']):
result = []
allowed_i = []
residues = polymer.residues()
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i, j + 1))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms() if a.type in atom_types])
return result
def get_superposable_all_atoms(polymer, segments):
atom_types = [
'CA', 'N', 'C', 'CB', 'CD', 'CD1', 'CD2', 'CE', 'CE1', 'CE2', 'CE3',
'CG', 'CG1', 'CG2', 'CH2', 'CZ', 'CZ2', 'CZ3', 'ND1', 'ND2', 'NE',
'NE1', 'NE2', 'NH1', 'NH2', 'NZ', 'O', 'OD1', 'OD2', 'OE1', 'OE2',
'OG', 'OG1', 'OH', 'OXT', 'SD', 'SG', 'CEN'
]
result = []
allowed_i = []
residues = polymer.residues()
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i, j + 1))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms() if a.type in atom_types])
return result
def get_superposable_atoms(polymer, segments, atom_types=['CA', 'N', 'C', 'CB']):
result = []
allowed_i = []
residues = polymer.residues()
#if no segments provided, take the whole backbone
if len(segments) == 0:
print "no segments given, using backbone"
for i, residue in enumerate(residues):
result.extend([a for a in residue.atoms() if a.type in atom_types])
else:
print segments
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i,j))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms() if a.type in atom_types])
return result
def get_superposable_all_atoms(polymer, segments):
atom_types=['CA', 'N', 'C', 'CB',
'CD', 'CD1', 'CD2', 'CE', 'CE1',
'CE2', 'CE3', 'CG', 'CG1', 'CG2',
'CH2', 'CZ', 'CZ2', 'CZ3', 'ND1',
'ND2', 'NE', 'NE1', 'NE2', 'NH1',
'NH2', 'NZ', 'O', 'OD1', 'OD2',
'OE1', 'OE2', 'OG', 'OG1', 'OH',
'OXT', 'SD', 'SG', 'CEN']
result = []
allowed_i = []
residues = polymer.residues()
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i,j+1))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms()
if a.type in atom_types])
return result