def calculate_BSA(self):
"Uses NACCESS module in order to calculate the Buried Surface Area"
# Extract list of chains in the interface only
chains = list(self.get_chains())
# Create temporary structures to feed NACCESS
structure_A=Structure("chainA")
structure_B=Structure("chainB")
mA = Model(0)
mB = Model(0)
mA.add(self.model[chains[0]])
mB.add(self.model[chains[1]])
structure_A.add(mA)
structure_B.add(mB)
# Calculate SASAs
NACCESS_atomic(self.model)
NACCESS_atomic(structure_A[0])
NACCESS_atomic(structure_B[0])
sas_tot= _get_atomic_SASA(self.model)
#print 'Accessible surface area, complex:', sas_tot
sas_A= _get_atomic_SASA(structure_A)
#print 'Accessible surface aream CHAIN A :', sas_A
sas_B= _get_atomic_SASA(structure_B)
#print 'Accessible surface aream CHAIN B :',sas_B
# Calculate BSA
bsa = sas_A+sas_B-sas_tot
return [bsa, sas_A, sas_B, sas_tot]
def _rsa_calculation(self, model, chain_list, rsa_threshold):
"Uses NACCESS module in order to calculate the Buried Surface Area"
pairs=[]
# Create temporary structures to feed NACCESS
structure_A=Structure("chainA")
structure_B=Structure("chainB")
mA = Model(0)
mB = Model(0)
mA.add(model[chain_list[0]])
mB.add(model[chain_list[1]])
structure_A.add(mA)
structure_B.add(mB)
# Calculate SASAs
nacc_at=NACCESS(model)
model_values=[]
res_list = [r for r in model.get_residues() if r.id[0] == ' ']
structure_A_reslist =[r for r in structure_A[0].get_residues() if r.id[0] == ' ']
structure_B_reslist =[r for r in structure_B[0].get_residues() if r.id[0] == ' ']
for res in res_list:
model_values.append(float(res.xtra['EXP_NACCESS']['all_atoms_rel']))
sas_tot= self._get_residue_SASA(model)
#print 'Accessible surface area, complex:', sas_tot
nacc_at=NACCESS(structure_A[0])
nacc_at=NACCESS(structure_B[0])
submodel_values=[]
for res in structure_A_reslist:
if res.id[0]==' ':
submodel_values.append(float(res.xtra['EXP_NACCESS']['all_atoms_rel']))
for res in structure_B_reslist:
if res.id[0]==' ':
submodel_values.append(float(res.xtra['EXP_NACCESS']['all_atoms_rel']))
count=0
for res in res_list:
if res in structure_A_reslist and ((submodel_values[count] - model_values[count]) > rsa_threshold):
pairs.append(res)
elif res in structure_B_reslist and ((submodel_values[count] - model_values[count]) > rsa_threshold):
pairs.append(res)
count=count+1
sas_A= self._get_residue_SASA(structure_A)
#print 'Accessible surface aream CHAIN A :', sas_A
sas_B= self._get_residue_SASA(structure_B)
#print 'Accessible surface aream CHAIN B :',sas_B
# Calculate BSA
bsa = sas_A+sas_B-sas_tot
self.interface.accessibility=[bsa, sas_A, sas_B, sas_tot]
return pairs
def __create_superimposed_pdb(self):
def fill_in_chain(chain, protein_id, rotation_matrix = None):
for index,residue in enumerate(self.proteins[protein_id].get_residues()):
residue.id = (residue.id[0], index, residue.id[2])
chain.add(residue)
merged_model = Model(0)
chain_a = Chain('A')
chain_b = Chain('B')
fill_in_chain(chain_a, 0)
fill_in_chain(chain_b, 1)
merged_model.add(chain_a)
merged_model.add(chain_b)
return merged_model
class StructureBuilder(object):
"""
Deals with contructing the Structure object. The StructureBuilder class is used
by the PDBParser classes to translate a file to a Structure object.
"""
def __init__(self):
self.line_counter=0
self.header={}
def _is_completely_disordered(self, residue):
"Return 1 if all atoms in the residue have a non blank altloc."
atom_list=residue.get_unpacked_list()
for atom in atom_list:
altloc=atom.get_altloc()
if altloc==" ":
return 0
return 1
# Public methods called by the Parser classes
def set_header(self, header):
self.header=header
def set_line_counter(self, line_counter):
"""
The line counter keeps track of the line in the PDB file that
is being parsed.
Arguments:
o line_counter - int
"""
self.line_counter=line_counter
def init_structure(self, structure_id):
"""Initiate a new Structure object with given id.
Arguments:
o id - string
"""
self.structure=Structure(structure_id)
def init_model(self, model_id, serial_num = None):
"""Initiate a new Model object with given id.
Arguments:
o id - int
o serial_num - int
"""
self.model=Model(model_id,serial_num)
self.structure.add(self.model)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain=self.model[chain_id]
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
% (chain_id, self.line_counter),
PDBConstructionWarning)
else:
self.chain=Chain(chain_id)
self.model.add(self.chain)
def init_seg(self, segid):
"""Flag a change in segid.
Arguments:
o segid - string
"""
self.segid=segid
def init_residue(self, resname, field, resseq, icode):
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if field!=" ":
if field=="H":
# The hetero field consists of H_ + the residue name (e.g. H_FUC)
field="H_"+resname
res_id=(field, resseq, icode)
if field==" ":
if self.chain.has_id(res_id):
# There already is a residue with the id (field, resseq, icode).
# This only makes sense in the case of a point mutation.
warnings.warn("WARNING: Residue ('%s', %i, '%s') "
"redefined at line %i."
% (field, resseq, icode, self.line_counter),
PDBConstructionWarning)
duplicate_residue=self.chain[res_id]
if duplicate_residue.is_disordered()==2:
# The residue in the chain is a DisorderedResidue object.
# So just add the last Residue object.
if duplicate_residue.disordered_has_id(resname):
# The residue was already made
self.residue=duplicate_residue
duplicate_residue.disordered_select(resname)
else:
# Make a new residue and add it to the already
# present DisorderedResidue
new_residue=Residue(res_id, resname, self.segid)
duplicate_residue.disordered_add(new_residue)
self.residue=duplicate_residue
return
else:
# Make a new DisorderedResidue object and put all
# the Residue objects with the id (field, resseq, icode) in it.
# These residues each should have non-blank altlocs for all their atoms.
# If not, the PDB file probably contains an error.
if not self._is_completely_disordered(duplicate_residue):
# if this exception is ignored, a residue will be missing
self.residue=None
raise PDBConstructionException(
"Blank altlocs in duplicate residue %s ('%s', %i, '%s')"
% (resname, field, resseq, icode))
self.chain.detach_child(res_id)
new_residue=Residue(res_id, resname, self.segid)
disordered_residue=DisorderedResidue(res_id)
self.chain.add(disordered_residue)
disordered_residue.disordered_add(duplicate_residue)
disordered_residue.disordered_add(new_residue)
self.residue=disordered_residue
return
residue=Residue(res_id, resname, self.segid)
self.chain.add(residue)
self.residue=residue
def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname,
serial_number=None, element=None):
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
o element - string, upper case, e.g. "HG" for mercury
"""
residue=self.residue
# if residue is None, an exception was generated during
# the construction of the residue
if residue is None:
return
# First check if this atom is already present in the residue.
# If it is, it might be due to the fact that the two atoms have atom
# names that differ only in spaces (e.g. "CA.." and ".CA.",
# where the dots are spaces). If that is so, use all spaces
# in the atom name of the current atom.
if residue.has_id(name):
duplicate_atom=residue[name]
# atom name with spaces of duplicate atom
duplicate_fullname=duplicate_atom.get_fullname()
if duplicate_fullname!=fullname:
# name of current atom now includes spaces
name=fullname
warnings.warn("Atom names %r and %r differ "
"only in spaces at line %i."
% (duplicate_fullname, fullname,
self.line_counter),
PDBConstructionWarning)
atom=self.atom=Atom(name, coord, b_factor, occupancy, altloc,
fullname, serial_number, element)
if altloc!=" ":
# The atom is disordered
if residue.has_id(name):
# Residue already contains this atom
duplicate_atom=residue[name]
if duplicate_atom.is_disordered()==2:
duplicate_atom.disordered_add(atom)
else:
# This is an error in the PDB file:
# a disordered atom is found with a blank altloc
# Detach the duplicate atom, and put it in a
# DisorderedAtom object together with the current
# atom.
residue.detach_child(name)
disordered_atom=DisorderedAtom(name)
residue.add(disordered_atom)
disordered_atom.disordered_add(atom)
disordered_atom.disordered_add(duplicate_atom)
residue.flag_disordered()
warnings.warn("WARNING: disordered atom found "
"with blank altloc before line %i.\n"
% self.line_counter,
PDBConstructionWarning)
else:
# The residue does not contain this disordered atom
# so we create a new one.
disordered_atom=DisorderedAtom(name)
residue.add(disordered_atom)
# Add the real atom to the disordered atom, and the
# disordered atom to the residue
disordered_atom.disordered_add(atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add(atom)
def set_anisou(self, anisou_array):
"Set anisotropic B factor of current Atom."
self.atom.set_anisou(anisou_array)
def set_siguij(self, siguij_array):
"Set standard deviation of anisotropic B factor of current Atom."
self.atom.set_siguij(siguij_array)
def set_sigatm(self, sigatm_array):
"Set standard deviation of atom position of current Atom."
self.atom.set_sigatm(sigatm_array)
def get_structure(self):
"Return the structure."
# first sort everything
# self.structure.sort()
# Add the header dict
self.structure.header=self.header
return self.structure
def set_symmetry(self, spacegroup, cell):
pass
model = Model(1)
chain = Chain("A")
structure = Structure("ref")
num_count = 0
for i in range(0,shape(points)[0]):
num_count = num_count +1
res_id = (' ',num_count,' ')
residue = Residue(res_id,'ALA',' ')
cur_coord = tuple(points[i])
bfactor = bfactors[i]
atom = Atom('CA',cur_coord,bfactor,0,' ','CA',num_count,'C')
residue.add(atom)
chain.add(residue)
model.add(chain)
structure.add(model)
# --------------------------------------------------------------------
io=PDBIO()
io.set_structure(structure)
if ( args['dst'] is None):
fn = sys.stdout
io.save(fn)
if ( args['link'] ):
for i in range(1,shape(points)[0]):
fn.write( "CONECT%5d%5d\n" % (i, i+1))
else:
fn = args['dst']
io.save(fn)
fout = open(fn,"a")
if (args['link'] ):
refid = "ref"
structure = Structure(refid)
model_ref = Model(1)
chain_ref = Chain("A")
points_ref = ReadXYZ(ref_ptsfilename,scale)
num_count = 0
for i in range(0,shape(points_ref[IndexList])[0]):
num_count = num_count +1
res_id = (' ',num_count,' ')
residue = Residue(res_id,'ALA',' ')
cur_coord = tuple(points_ref[IndexList[i]])
atom = Atom('CA',cur_coord,0,0,' ',num_count,num_count,'C')
residue.add(atom)
chain_ref.add(residue)
model_ref.add(chain_ref)
structure.add(model_ref)
#--------------------------------------------------------------------
altid = "alt"
structure_alt = Structure(refid)
model_alt = Model(2)
chain_alt = Chain("A")
points_alt = ReadXYZ(alt_ptsfilename,scale)
num_count = 0
for i in range(0,shape(points_alt[IndexList])[0]):
num_count = num_count +1
res_id = (' ',num_count,' ')
residue = Residue(res_id,'ALA',' ')
cur_coord = tuple(points_alt[IndexList[i]])
class StructureBuilder(object):
"""
Deals with contructing the Structure object. The StructureBuilder class is used
by the PDBParser classes to translate a file to a Structure object.
"""
def __init__(self):
self.line_counter = 0
self.header = {}
def _is_completely_disordered(self, residue):
"Return 1 if all atoms in the residue have a non blank altloc."
atom_list = residue.get_unpacked_list()
for atom in atom_list:
altloc = atom.get_altloc()
if altloc == " ":
return 0
return 1
# Public methods called by the Parser classes
def set_header(self, header):
self.header = header
def set_line_counter(self, line_counter):
"""
The line counter keeps track of the line in the PDB file that
is being parsed.
Arguments:
o line_counter - int
"""
self.line_counter = line_counter
def init_structure(self, structure_id):
"""Initiate a new Structure object with given id.
Arguments:
o id - string
"""
self.structure = Structure(structure_id)
def init_model(self, model_id, serial_num=None):
"""Initiate a new Model object with given id.
Arguments:
o id - int
o serial_num - int
"""
self.model = Model(model_id, serial_num)
self.structure.add(self.model)
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.model.has_id(chain_id):
self.chain = self.model[chain_id]
warnings.warn(
"WARNING: Chain %s is discontinuous at line %i." %
(chain_id, self.line_counter), PDBConstructionWarning)
else:
self.chain = Chain(chain_id)
self.model.add(self.chain)
def init_seg(self, segid):
"""Flag a change in segid.
Arguments:
o segid - string
"""
self.segid = segid
def init_residue(self, resname, field, resseq, icode):
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if field != " ":
if field == "H":
# The hetero field consists of H_ + the residue name (e.g. H_FUC)
field = "H_" + resname
res_id = (field, resseq, icode)
if field == " ":
if self.chain.has_id(res_id):
# There already is a residue with the id (field, resseq, icode).
# This only makes sense in the case of a point mutation.
warnings.warn(
"WARNING: Residue ('%s', %i, '%s') "
"redefined at line %i." %
(field, resseq, icode, self.line_counter),
PDBConstructionWarning)
duplicate_residue = self.chain[res_id]
if duplicate_residue.is_disordered() == 2:
# The residue in the chain is a DisorderedResidue object.
# So just add the last Residue object.
if duplicate_residue.disordered_has_id(resname):
# The residue was already made
self.residue = duplicate_residue
duplicate_residue.disordered_select(resname)
else:
# Make a new residue and add it to the already
# present DisorderedResidue
new_residue = Residue(res_id, resname, self.segid)
duplicate_residue.disordered_add(new_residue)
self.residue = duplicate_residue
return
else:
# Make a new DisorderedResidue object and put all
# the Residue objects with the id (field, resseq, icode) in it.
# These residues each should have non-blank altlocs for all their atoms.
# If not, the PDB file probably contains an error.
if not self._is_completely_disordered(duplicate_residue):
# if this exception is ignored, a residue will be missing
self.residue = None
raise PDBConstructionException(
"Blank altlocs in duplicate residue %s ('%s', %i, '%s')"
% (resname, field, resseq, icode))
self.chain.detach_child(res_id)
new_residue = Residue(res_id, resname, self.segid)
disordered_residue = DisorderedResidue(res_id)
self.chain.add(disordered_residue)
disordered_residue.disordered_add(duplicate_residue)
disordered_residue.disordered_add(new_residue)
self.residue = disordered_residue
return
residue = Residue(res_id, resname, self.segid)
self.chain.add(residue)
self.residue = residue
def init_atom(self,
name,
coord,
b_factor,
occupancy,
altloc,
fullname,
serial_number=None,
element=None):
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
o element - string, upper case, e.g. "HG" for mercury
"""
residue = self.residue
# if residue is None, an exception was generated during
# the construction of the residue
if residue is None:
return
# First check if this atom is already present in the residue.
# If it is, it might be due to the fact that the two atoms have atom
# names that differ only in spaces (e.g. "CA.." and ".CA.",
# where the dots are spaces). If that is so, use all spaces
# in the atom name of the current atom.
if residue.has_id(name):
duplicate_atom = residue[name]
# atom name with spaces of duplicate atom
duplicate_fullname = duplicate_atom.get_fullname()
if duplicate_fullname != fullname:
# name of current atom now includes spaces
name = fullname
warnings.warn(
"Atom names %r and %r differ "
"only in spaces at line %i." %
(duplicate_fullname, fullname, self.line_counter),
PDBConstructionWarning)
atom = self.atom = Atom(name, coord, b_factor, occupancy, altloc,
fullname, serial_number, element)
if altloc != " ":
# The atom is disordered
if residue.has_id(name):
# Residue already contains this atom
duplicate_atom = residue[name]
if duplicate_atom.is_disordered() == 2:
duplicate_atom.disordered_add(atom)
else:
# This is an error in the PDB file:
# a disordered atom is found with a blank altloc
# Detach the duplicate atom, and put it in a
# DisorderedAtom object together with the current
# atom.
residue.detach_child(name)
disordered_atom = DisorderedAtom(name)
residue.add(disordered_atom)
disordered_atom.disordered_add(atom)
disordered_atom.disordered_add(duplicate_atom)
residue.flag_disordered()
warnings.warn(
"WARNING: disordered atom found "
"with blank altloc before line %i.\n" %
self.line_counter, PDBConstructionWarning)
else:
# The residue does not contain this disordered atom
# so we create a new one.
disordered_atom = DisorderedAtom(name)
residue.add(disordered_atom)
# Add the real atom to the disordered atom, and the
# disordered atom to the residue
disordered_atom.disordered_add(atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add(atom)
def set_anisou(self, anisou_array):
"Set anisotropic B factor of current Atom."
self.atom.set_anisou(anisou_array)
def set_siguij(self, siguij_array):
"Set standard deviation of anisotropic B factor of current Atom."
self.atom.set_siguij(siguij_array)
def set_sigatm(self, sigatm_array):
"Set standard deviation of atom position of current Atom."
self.atom.set_sigatm(sigatm_array)
def get_structure(self):
"Return the structure."
# first sort everything
# self.structure.sort()
# Add the header dict
self.structure.header = self.header
return self.structure
def set_symmetry(self, spacegroup, cell):
pass
# num_count = num_count + 1
# res_id = (' ',num_count,' ')
# residue = Residue(res_id,'ALA',' ')
# cur_coord = start_point_1
# atom = Atom('CA',cur_coord,0,1,' ',num_count,num_count,'C')
# residue.add(atom)
# chain.add(residue)
#
# num_count = num_count + 1
# res_id = (' ',num_count,' ')
# residue = Residue(res_id,'ALA',' ')
# cur_coord = start_point_2
# atom = Atom('CA',cur_coord,0,1,' ',num_count,num_count,'C')
# residue.add(atom)
# chain.add(residue)
model.add(chain[j])
structure.add(model)
# --------------------------------------------------------------------
# for model in structure:
# print
# for chain in model:
# for residue in chain:
# for atom in residue:
# print atom.get_full_id()
# print atom.coord
io=PDBIO()
io.set_structure(structure)
}, {
'name': 'C5',
'coord': PDB.Atom.array([66.402, 44.364, 11.291], 'f'),
'bfactor': 44.20,
'occupancy': 1.0,
'altloc': ' ',
'fullname': 'C5',
'serial_number': 7
}, {
'name': 'C6',
'coord': PDB.Atom.array([65.095, 44.589, 11.192], 'f'),
'bfactor': 44.33,
'occupancy': 1.0,
'altloc': ' ',
'fullname': 'C6',
'serial_number': 8
}]
my_structure.add(my_model)
my_model.add(my_chain)
my_chain.add(my_residue)
for atom in atoms:
my_atom = Atom(atom['name'], atom['coord'], atom['bfactor'],
atom['occupancy'], atom['altloc'], atom['fullname'],
atom['serial_number'])
my_residue.add(my_atom)
out = PDBIO()
out.set_structure(my_structure)
out.save('my_new_structure.pdb')
def normalize_structure(input_path: str,
pdb_id: str,
model_id: int,
chain_id: str,
primary: str,
mask: str,
save=True,
verbose=True):
assert primary
assert mask
with warnings.catch_warnings(record=True):
warnings.simplefilter("ignore", PDBConstructionWarning)
parser = PDBParser()
structure = parser.get_structure(pdb_id, input_path)
if not model_id in structure.child_dict:
try_model_id = model_id - 1
model = None
while try_model_id >= 0:
if try_model_id in structure.child_dict:
model = structure.child_dict[try_model_id]
if verbose:
print('Supposing model {} is {}...'.format(
model_id - 1, model_id))
try_model_id -= 1
if not model:
raise ValueError(
'model "{}" not found in "{}", options are {}'.format(
model_id, pdb_id, list(structure.child_dict.keys())))
else:
model = structure.child_dict[model_id]
if not chain_id in model.child_dict:
raise ValueError(
'chain "{}" not found in "{}" model "{}", options are {}'.
format(chain_id, pdb_id, model_id,
list(model.child_dict.keys())))
chain = model.child_dict[chain_id]
new_chain = normalize_chain(chain)
raw = []
for residue in chain:
try:
raw.append(resname_to_abbrev(residue.resname))
except UnknownResnameError:
# if verbose:
# print('Skipping residue "{}"'.format(residue.resname))
pass
raw = ''.join(raw)
# verify that the sequence is what we expect
normalized = []
for residue in new_chain:
try:
normalized.append(resname_to_abbrev(residue.resname))
except UnknownResnameError:
# if verbose:
# print('Skipping residue "{}"'.format(residue.resname))
pass
normalized = ''.join(normalized)
# extract the known primary sequence using the mask
masked_primary = []
for r, m in zip(primary, mask):
if m == '-':
continue
assert m == '+'
masked_primary.append(r)
masked_primary = ''.join(masked_primary)
# ensure the sequence lengths match
if len(normalized) != len(masked_primary):
raise ChainLengthError(len(normalized), len(masked_primary))
# ensure residue identities match
for i, (got, expected) in enumerate(zip(normalized, masked_primary)):
if got != expected:
raise ValueError(
'mismatch residue at position {} (got {}, expected {})'.
format(i, got, expected))
new_model = Model(model.id)
new_model.add(new_chain)
new_structure = Structure(structure.id)
new_structure.add(new_model)
if save:
out_path = input_path + '.norm'
io = PDBIO()
io.set_structure(new_structure)
io.save(out_path)
return out_path
else:
return new_structure
model_ref = Model(1)
chain_ref = Chain("A")
points_ref = ReadXYZ(ref_ptsfilename,scale)
num_count = 0
for i in range(0,shape(points_ref[IndexList])[0]):
num_count = num_count +1
# res_id = (' ',IndexList[i],' ')
res_id = (' ',num_count,' ')
residue = Residue(res_id,'ALA',' ')
cur_coord = tuple(points_ref[IndexList[i]])
# atom = Atom('CA',cur_coord,0,0,' ',num_count,num_count,'C')
atom = Atom('CA',cur_coord,0,0,' ',num_count,num_count,'C')
residue.add(atom)
chain_ref.add(residue)
model_ref.add(chain_ref)
structure.add(model_ref)
#--------------------------------------------------------------------
print ("scale=%s" % scale)
#--------------------------------------------------------------------
io=PDBIO()
io.set_structure(structure)
fn = outputfilename
io.save(fn)
fout = open(fn,"a")
for i in range(1,shape(points_ref[IndexList])[0]):
fout.write( "CONECT%5d%5d\n" % (i, i+1))
print "output file: " + outputfilename
def initialize_res(residue):
'''Creates a new structure containing a single amino acid. The type and
geometry of the amino acid are determined by the argument, which has to be
either a geometry object or a single-letter amino acid code.
The amino acid will be placed into chain A of model 0.'''
if isinstance( residue, Geo ):
geo = residue
else:
geo=geometry(residue)
segID=1
AA= geo.residue_name
CA_N_length=geo.CA_N_length
CA_C_length=geo.CA_C_length
N_CA_C_angle=geo.N_CA_C_angle
CA_coord= numpy.array([0.,0.,0.])
C_coord= numpy.array([CA_C_length,0,0])
N_coord = numpy.array([CA_N_length*math.cos(N_CA_C_angle*(math.pi/180.0)),CA_N_length*math.sin(N_CA_C_angle*(math.pi/180.0)),0])
N= Atom("N", N_coord, 0.0 , 1.0, " "," N", 0, "N")
CA=Atom("CA", CA_coord, 0.0 , 1.0, " "," CA", 0,"C")
C= Atom("C", C_coord, 0.0, 1.0, " ", " C",0,"C")
##Create Carbonyl atom (to be moved later)
C_O_length=geo.C_O_length
CA_C_O_angle=geo.CA_C_O_angle
N_CA_C_O_diangle=geo.N_CA_C_O_diangle
carbonyl=calculateCoordinates(N, CA, C, C_O_length, CA_C_O_angle, N_CA_C_O_diangle)
O= Atom("O",carbonyl , 0.0 , 1.0, " "," O", 0, "O")
if(AA=='G'):
res=makeGly(segID, N, CA, C, O, geo)
elif(AA=='A'):
res=makeAla(segID, N, CA, C, O, geo)
elif(AA=='S'):
res=makeSer(segID, N, CA, C, O, geo)
elif(AA=='C'):
res=makeCys(segID, N, CA, C, O, geo)
elif(AA=='V'):
res=makeVal(segID, N, CA, C, O, geo)
elif(AA=='I'):
res=makeIle(segID, N, CA, C, O, geo)
elif(AA=='L'):
res=makeLeu(segID, N, CA, C, O, geo)
elif(AA=='T'):
res=makeThr(segID, N, CA, C, O, geo)
elif(AA=='R'):
res=makeArg(segID, N, CA, C, O, geo)
elif(AA=='K'):
res=makeLys(segID, N, CA, C, O, geo)
elif(AA=='D'):
res=makeAsp(segID, N, CA, C, O, geo)
elif(AA=='E'):
res=makeGlu(segID, N, CA, C, O, geo)
elif(AA=='N'):
res=makeAsn(segID, N, CA, C, O, geo)
elif(AA=='Q'):
res=makeGln(segID, N, CA, C, O, geo)
elif(AA=='M'):
res=makeMet(segID, N, CA, C, O, geo)
elif(AA=='H'):
res=makeHis(segID, N, CA, C, O, geo)
elif(AA=='P'):
res=makePro(segID, N, CA, C, O, geo)
elif(AA=='F'):
res=makePhe(segID, N, CA, C, O, geo)
elif(AA=='Y'):
res=makeTyr(segID, N, CA, C, O, geo)
elif(AA=='W'):
res=makeTrp(segID, N, CA, C, O, geo)
else:
res=makeGly(segID, N, CA, C, O, geo)
cha= Chain('A')
cha.add(res)
mod= Model(0)
mod.add(cha)
struc= Structure('X')
struc.add(mod)
return struc
