def makeThr(segID: int, N, CA, C, O, geo: ThrGeo) -> Residue:
"""Creates a Threonine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_OG1_length = geo.CB_OG1_length
CA_CB_OG1_angle = geo.CA_CB_OG1_angle
N_CA_CB_OG1_diangle = geo.N_CA_CB_OG1_diangle
CB_CG2_length = geo.CB_CG2_length
CA_CB_CG2_angle = geo.CA_CB_CG2_angle
N_CA_CB_CG2_diangle = geo.N_CA_CB_CG2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
oxygen_g1 = calculateCoordinates(N, CA, CB, CB_OG1_length, CA_CB_OG1_angle,
N_CA_CB_OG1_diangle)
OG1 = Atom("OG1", oxygen_g1, 0.0, 1.0, " ", " OG1", 0, "O")
carbon_g2 = calculateCoordinates(N, CA, CB, CB_CG2_length, CA_CB_CG2_angle,
N_CA_CB_CG2_diangle)
CG2 = Atom("CG2", carbon_g2, 0.0, 1.0, " ", " CG2", 0, "C")
res = Residue((" ", segID, " "), "THR", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(OG1)
res.add(CG2)
return res
def makePro(segID, N, CA, C, O, geo):
'''Creates a Proline residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle=geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_CG_length=geo.CB_CG_length
CA_CB_CG_angle=geo.CA_CB_CG_angle
N_CA_CB_CG_diangle=geo.N_CA_CB_CG_diangle
CG_CD_length=geo.CG_CD_length
CB_CG_CD_angle=geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle=geo.CA_CB_CG_CD_diangle
carbon_b= calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle, N_C_CA_CB_diangle)
CB= Atom("CB", carbon_b, 0.0 , 1.0, " "," CB", 0,"C")
carbon_g= calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle, N_CA_CB_CG_diangle)
CG= Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d= calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle, CA_CB_CG_CD_diangle)
CD= Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
##Create Residue Data Structure
res= Residue((' ', segID, ' '), "PRO", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
return res
def makeCys(segID: int, N, CA, C, O, geo: CysGeo) -> Residue:
"""Creates a Cysteine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_SG_length = geo.CB_SG_length
CA_CB_SG_angle = geo.CA_CB_SG_angle
N_CA_CB_SG_diangle = geo.N_CA_CB_SG_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
sulfur_g = calculateCoordinates(N, CA, CB, CB_SG_length, CA_CB_SG_angle,
N_CA_CB_SG_diangle)
SG = Atom("SG", sulfur_g, 0.0, 1.0, " ", " SG", 0, "S")
res = Residue((" ", segID, " "), "CYS", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(SG)
return res
def __init__(
self,
idcode,
model,
name,
x,
y,
z,
bfactor,
occupancy,
altloc,
fullname,
serial_number,
idamino,
resseq,
icode,
chainid,
segid,
resName=None,
):
coord = coord = numpy.array((x, y, z), "f")
Atom.__init__(self, str(name), coord, bfactor, occupancy, str(altloc), str(fullname), int(serial_number))
self._model = model
self._idcode = idcode
self._idamino = idamino
self._resseq = resseq
self._icode = str(icode)
self._chainid = str(chainid)
self._segid = segid
# Used when we have the resname.
self._resname = resName
def makeSer(segID: int, N, CA, C, O, geo: SerGeo) -> Residue:
"""Creates a Serine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_OG_length = geo.CB_OG_length
CA_CB_OG_angle = geo.CA_CB_OG_angle
N_CA_CB_OG_diangle = geo.N_CA_CB_OG_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
oxygen_g = calculateCoordinates(N, CA, CB, CB_OG_length, CA_CB_OG_angle,
N_CA_CB_OG_diangle)
OG = Atom("OG", oxygen_g, 0.0, 1.0, " ", " OG", 0, "O")
##Create Reside Data Structure
res = Residue((" ", segID, " "), "SER", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(OG)
return res
def makeThr(segID, N, CA, C, O, geo):
'''Creates a Threonine residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle=geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_OG1_length=geo.CB_OG1_length
CA_CB_OG1_angle=geo.CA_CB_OG1_angle
N_CA_CB_OG1_diangle=geo.N_CA_CB_OG1_diangle
CB_CG2_length=geo.CB_CG2_length
CA_CB_CG2_angle=geo.CA_CB_CG2_angle
N_CA_CB_CG2_diangle= geo.N_CA_CB_CG2_diangle
carbon_b= calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle, N_C_CA_CB_diangle)
CB= Atom("CB", carbon_b, 0.0 , 1.0, " "," CB", 0,"C")
oxygen_g1= calculateCoordinates(N, CA, CB, CB_OG1_length, CA_CB_OG1_angle, N_CA_CB_OG1_diangle)
OG1= Atom("OG1", oxygen_g1, 0.0, 1.0, " ", " OG1", 0, "O")
carbon_g2= calculateCoordinates(N, CA, CB, CB_CG2_length, CA_CB_CG2_angle, N_CA_CB_CG2_diangle)
CG2= Atom("CG2", carbon_g2, 0.0, 1.0, " ", " CG2", 0, "C")
##Create Residue Data Structure
res= Residue((' ', segID, ' '), "THR", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(OG1)
res.add(CG2)
return res
def makeCys(segID, N, CA, C, O, geo):
'''Creates a Cysteine residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle=geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_SG_length= geo.CB_SG_length
CA_CB_SG_angle= geo.CA_CB_SG_angle
N_CA_CB_SG_diangle= geo.N_CA_CB_SG_diangle
carbon_b= calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle, N_C_CA_CB_diangle)
CB= Atom("CB", carbon_b, 0.0 , 1.0, " "," CB", 0,"C")
sulfur_g= calculateCoordinates(N, CA, CB, CB_SG_length, CA_CB_SG_angle, N_CA_CB_SG_diangle)
SG= Atom("SG", sulfur_g, 0.0, 1.0, " ", " SG", 0, "S")
##Create Residue Data Structure
res= Residue((' ', segID, ' '), "CYS", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(SG)
return res
def makeVal(segID: int, N, CA, C, O, geo: ValGeo) -> Residue:
"""Creates a Valine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG1_length = geo.CB_CG1_length
CA_CB_CG1_angle = geo.CA_CB_CG1_angle
N_CA_CB_CG1_diangle = geo.N_CA_CB_CG1_diangle
CB_CG2_length = geo.CB_CG2_length
CA_CB_CG2_angle = geo.CA_CB_CG2_angle
N_CA_CB_CG2_diangle = geo.N_CA_CB_CG2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g1 = calculateCoordinates(N, CA, CB, CB_CG1_length, CA_CB_CG1_angle,
N_CA_CB_CG1_diangle)
CG1 = Atom("CG1", carbon_g1, 0.0, 1.0, " ", " CG1", 0, "C")
carbon_g2 = calculateCoordinates(N, CA, CB, CB_CG2_length, CA_CB_CG2_angle,
N_CA_CB_CG2_diangle)
CG2 = Atom("CG2", carbon_g2, 0.0, 1.0, " ", " CG2", 0, "C")
##Create Residue Data Structure
res = Residue((" ", segID, " "), "VAL", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG1)
res.add(CG2)
return res
def retrieve_ca_model(structure):
"""
chains are represented only by main chain atoms (Calfas or C4')
"""
reduced_struct = Structure('clustering_model')
my_model = Model(0)
reduced_struct.add(my_model)
main_chain_atoms = []
for ch in structure[0]:
my_chain = Chain(ch.id)
reduced_struct[0].add(my_chain)
for resi in ch:
for atom in resi:
#print "----", resi.id, resi.get_segid(), ch.id
if atom.get_name() == "CA" or atom.get_name(
) == "C4'" or atom.get_name() == "C4*":
my_residue = Residue((' ', resi.id[1], ' '),
resi.get_resname(), ' ')
atom = Atom('CA', atom.coord, 0, ' ', ' ', 'CA',
atom.get_serial_number())
my_chain.add(my_residue)
my_residue.add(atom)
main_chain_atoms.append(atom)
return reduced_struct
def initialize_res(residue: Union[Geo, str]) -> Structure:
"""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
elif isinstance(residue, str):
geo = geometry(residue)
else:
raise ValueError("Invalid residue argument:", 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 = np.array([0.0, 0.0, 0.0])
C_coord = np.array([CA_C_length, 0, 0])
N_coord = np.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")
# Check if the peptide is capped or not
if geo.residue_name == "ACE":
CA = Atom("CH3", CA_coord, 0.0, 1.0, " ", " CH3", 0, "C")
else:
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")
res = make_res_of_type(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
def addHydrogens(residue, last_c=None, last_no=None):
''' Add hydrogens to a given residue, renumbering atoms appropriately. Will also convert disordered atoms into their respective first representatives.'''
rname = residue.resname
new_atoms = []
if last_no is None:
last_no = 0
if rname in fix_dispatch:
fr = fix_dispatch[rname]
for atom in list(residue):
name = atom.id
atom.serial_number = last_no
new_atoms.append( (name, atom) )
last_no+=1
# Special case is the hydrogen on peptide backbone - dispatch manually depending on last_c
# Proline skips this step
if name=='N' and rname!='PRO' and last_c is not None and 'CA' in residue.child_dict and 'N' in residue.child_dict:
nname = ' H '
b_factor = 0.0
occupancy = 1.0
altloc = ' '
fullname = name
coords = fix0(residue['N'], last_c, residue['CA'])[0]
new_atom = Atom(nname.strip(), coords, b_factor, occupancy, altloc, nname, last_no)
last_no+=1
new_atoms.append( (new_atom.id, new_atom) )
residue.add(new_atom)
else:
if name in fr:
f = fr[name]
# Sometimes a third atom is needed
f_delta3 = getattr(f, 'delta3', None)
# Check all atoms needed for adding are in place
if f.delta1 in residue.child_dict and f.delta2 in residue.child_dict and (f_delta3 is None or f_delta3 in residue.child_dict):
fixed = f.fix(atom, residue[f.delta1], residue[f.delta2], (residue[f_delta3] if f_delta3 else None))
# Create names according to standard - prefix is only added if more than one hydrogen is introduced
if len(fixed)>1:
names = ['%dH%s' % (i+1, atom.fullname[2:]) for i in range(0,len(fixed)) ]
else:
names = [' H%s' % atom.fullname[2:] ]
for nname, coords in zip(names, fixed):
b_factor = 0.0
occupancy = 1.0
altloc = ' '
fullname = name
new_atom = Atom(nname.strip(), coords, b_factor, occupancy, altloc, nname, last_no)
last_no+=1
new_atoms.append( (new_atom.id, new_atom) )
residue.add(new_atom)
# Restructure child lists to preserve new atom order
residue.child_list = [v[1] for v in new_atoms]
residue.child_dict = dict(new_atoms)
if new_atoms:
return new_atoms, last_no
else:
return None, last_no
def __init__(self, name, coord, bfactor, occupancy, altloc, fullname, \
serial_number, element=None, mol_weight = None, vdw=None, density=None,\
state = None, index = None, atom_type = None):
self.vdw = None #VanderWaals radius for given atom
self.molweight = None #molecular weight of given atom
self.state = "free" #free/fixed
self.index = 0 #index assigned during pseudoatoms modeling
self.atom_type = "regular" #regular/pseudo
Atom.__init__(self, name, coord, bfactor, occupancy, \
altloc, fullname, serial_number, element)
def makeGln(segID: int, N, CA, C, O, geo: GlnGeo) -> Residue:
"""Creates a Glutamine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD_length = geo.CG_CD_length
CB_CG_CD_angle = geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle = geo.CA_CB_CG_CD_diangle
CD_OE1_length = geo.CD_OE1_length
CG_CD_OE1_angle = geo.CG_CD_OE1_angle
CB_CG_CD_OE1_diangle = geo.CB_CG_CD_OE1_diangle
CD_NE2_length = geo.CD_NE2_length
CG_CD_NE2_angle = geo.CG_CD_NE2_angle
CB_CG_CD_NE2_diangle = geo.CB_CG_CD_NE2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d = calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle,
CA_CB_CG_CD_diangle)
CD = Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
oxygen_e1 = calculateCoordinates(CB, CG, CD, CD_OE1_length,
CG_CD_OE1_angle, CB_CG_CD_OE1_diangle)
OE1 = Atom("OE1", oxygen_e1, 0.0, 1.0, " ", " OE1", 0, "O")
nitrogen_e2 = calculateCoordinates(CB, CG, CD, CD_NE2_length,
CG_CD_NE2_angle, CB_CG_CD_NE2_diangle)
NE2 = Atom("NE2", nitrogen_e2, 0.0, 1.0, " ", " NE2", 0, "N")
##Create Residue DS
res = Residue((" ", segID, " "), "GLN", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
res.add(OE1)
res.add(NE2)
return res
def makeLys(segID: int, N, CA, C, O, geo: LysGeo) -> Residue:
"""Creates a Lysine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD_length = geo.CG_CD_length
CB_CG_CD_angle = geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle = geo.CA_CB_CG_CD_diangle
CD_CE_length = geo.CD_CE_length
CG_CD_CE_angle = geo.CG_CD_CE_angle
CB_CG_CD_CE_diangle = geo.CB_CG_CD_CE_diangle
CE_NZ_length = geo.CE_NZ_length
CD_CE_NZ_angle = geo.CD_CE_NZ_angle
CG_CD_CE_NZ_diangle = geo.CG_CD_CE_NZ_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d = calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle,
CA_CB_CG_CD_diangle)
CD = Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
carbon_e = calculateCoordinates(CB, CG, CD, CD_CE_length, CG_CD_CE_angle,
CB_CG_CD_CE_diangle)
CE = Atom("CE", carbon_e, 0.0, 1.0, " ", " CE", 0, "C")
nitrogen_z = calculateCoordinates(CG, CD, CE, CE_NZ_length, CD_CE_NZ_angle,
CG_CD_CE_NZ_diangle)
NZ = Atom("NZ", nitrogen_z, 0.0, 1.0, " ", " NZ", 0, "N")
##Create Residue Data Structure
res = Residue((" ", segID, " "), "LYS", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
res.add(CE)
res.add(NZ)
return res
def add_residue_from_geo(structure, geo):
'''Adds a residue to chain A model 0 of the given structure, and
returns the new structure. The residue to be added is determined by
the geometry object given as second argument.
This function is a helper function and should not normally be called
directly. Call add_residue() instead.'''
resRef= getReferenceResidue(structure)
AA=geo.residue_name
segID= resRef.get_id()[1]
segID+=1
##geometry to bring together residue
peptide_bond=geo.peptide_bond
CA_C_N_angle=geo.CA_C_N_angle
C_N_CA_angle=geo.C_N_CA_angle
##Backbone Coordinages
N_CA_C_angle=geo.N_CA_C_angle
CA_N_length=geo.CA_N_length
CA_C_length=geo.CA_C_length
phi= geo.phi
psi_im1=geo.psi_im1
omega=geo.omega
N_coord=calculateCoordinates(resRef['N'], resRef['CA'], resRef['C'], peptide_bond, CA_C_N_angle, psi_im1)
N= Atom("N", N_coord, 0.0 , 1.0, " "," N", 0, "N")
CA_coord=calculateCoordinates(resRef['CA'], resRef['C'], N, CA_N_length, C_N_CA_angle, omega)
CA=Atom("CA", CA_coord, 0.0 , 1.0, " "," CA", 0,"C")
C_coord=calculateCoordinates(resRef['C'], N, CA, CA_C_length, N_CA_C_angle, phi)
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")
res=makeRes(segID, N, CA, C, O, geo)
resRef['O'].set_coord(calculateCoordinates(res['N'], resRef['CA'], resRef['C'], C_O_length, CA_C_O_angle, 180.0))
ghost= Atom("N", calculateCoordinates(res['N'], res['CA'], res['C'], peptide_bond, CA_C_N_angle, psi_im1), 0.0 , 0.0, " ","N", 0, "N")
res['O'].set_coord(calculateCoordinates( res['N'], res['CA'], res['C'], C_O_length, CA_C_O_angle, 180.0))
structure[0]['A'].add(res)
return structure
def insert_missing_residues(residues, parse_info):
"""
Create a fake residue to fill in
missing residues. The xyz coordinates will
be infinity (so it will always output no contact).
:param residues: list of only residues
:type residues: list
:param parse_info: dictionary mapping extracted info to its info
:type parse_info: dict
:returns: list of residues with inserts
:rtype: list
"""
new_residues = residues
missing_resid_position = parse_info["Missing Residues"]
for position in missing_resid_position:
new_residue = Residue((' ', position, ' '), "GLY", ' ')
new_atom = Atom(
name="CA",
coord=np.array([np.inf, np.inf, np.inf]),
bfactor=0,
occupancy=0,
altloc=' ',
fullname=" CA ",
serial_number=0
)
new_residue.add(new_atom)
new_residues.append(new_residue)
new_residues.sort()
return new_residues
def create_sphere_representation(self):
"""
each chain is here represented by centre of mass only
"""
new_struct = Structure('sphrere')
my_model = Model(0)
new_struct.add(my_model)
chain_mass_centres, index = [], 1
my_chain = Chain(self.fa_struct.chain)
new_struct[0].add(my_chain)
coord, self.molmass, self.radius = self.calculate_centre_of_complex(
self.fa_struct.struct)
my_residue = Residue((' ', index, ' '), "ALA", ' ')
coords = array(coord, 'f')
atom = Atom('CA', coords, 0, 0, ' ', ' CA', 1)
my_chain.add(my_residue)
my_residue.add(atom)
self.cg_struct = new_struct
name = "dddd" + self.fa_struct.chain
self.save_pdb(new_struct, name)
def retrieve_sphere_model(structure): #, score):
"""
each chain is here represented by centre of mass only
"""
sphere_struct = Structure('clustering_model')
my_model = Model(0)
sphere_struct.add(my_model)
#bedzie zmieniona numeracja
chain_mass_centres, index = [], 0
for chain in structure.get_chains():
my_chain = Chain(chain.id)
sphere_struct[0].add(my_chain)
coord = calculate_centre_of_complex(chain)
chain_mass_centres.append(coord)
my_residue = Residue((' ', index, ' '), chain.id, ' ')
coords = array(coord, 'f')
atom = Atom('CA', coords, 0, 0, ' ', 'CA', 1)
my_chain.add(my_residue)
my_residue.add(atom)
index += 1
del structure
return sphere_struct
def makeGlu(segID, N, CA, C, O, geo):
'''Creates a Glutamic Acid residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_CG_length=geo.CB_CG_length
CA_CB_CG_angle=geo.CA_CB_CG_angle
N_CA_CB_CG_diangle=geo.N_CA_CB_CG_diangle
CG_CD_length=geo.CG_CD_length
CB_CG_CD_angle=geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle=geo.CA_CB_CG_CD_diangle
CD_OE1_length=geo.CD_OE1_length
CG_CD_OE1_angle=geo.CG_CD_OE1_angle
CB_CG_CD_OE1_diangle=geo.CB_CG_CD_OE1_diangle
CD_OE2_length=geo.CD_OE2_length
CG_CD_OE2_angle=geo.CG_CD_OE2_angle
CB_CG_CD_OE2_diangle=geo.CB_CG_CD_OE2_diangle
carbon_b= calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle, N_C_CA_CB_diangle)
CB= Atom("CB", carbon_b, 0.0 , 1.0, " "," CB", 0,"C")
carbon_g= calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle, N_CA_CB_CG_diangle)
CG= Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d= calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle, CA_CB_CG_CD_diangle)
CD= Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
oxygen_e1= calculateCoordinates(CB, CG, CD, CD_OE1_length, CG_CD_OE1_angle, CB_CG_CD_OE1_diangle)
OE1= Atom("OE1", oxygen_e1, 0.0, 1.0, " ", " OE1", 0, "O")
oxygen_e2= calculateCoordinates(CB, CG, CD, CD_OE2_length, CG_CD_OE2_angle, CB_CG_CD_OE2_diangle)
OE2= Atom("OE2", oxygen_e2, 0.0, 1.0, " ", " OE2", 0, "O")
##Create Residue Data Structure
res= Residue((' ', segID, ' '), "GLU", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
res.add(OE1)
res.add(OE2)
return res
def makeArg(segID, N, CA, C, O, geo):
'''Creates an Arginie residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle=geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_CG_length=geo.CB_CG_length
CA_CB_CG_angle= geo.CA_CB_CG_angle
N_CA_CB_CG_diangle=geo.N_CA_CB_CG_diangle
CG_CD_length=geo.CG_CD_length
CB_CG_CD_angle=geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle=geo.CA_CB_CG_CD_diangle
CD_NE_length=geo.CD_NE_length
CG_CD_NE_angle=geo.CG_CD_NE_angle
CB_CG_CD_NE_diangle=geo.CB_CG_CD_NE_diangle
NE_CZ_length=geo.NE_CZ_length
CD_NE_CZ_angle=geo.CD_NE_CZ_angle
CG_CD_NE_CZ_diangle=geo.CG_CD_NE_CZ_diangle
CZ_NH1_length=geo.CZ_NH1_length
NE_CZ_NH1_angle=geo.NE_CZ_NH1_angle
CD_NE_CZ_NH1_diangle=geo.CD_NE_CZ_NH1_diangle
CZ_NH2_length=geo.CZ_NH2_length
NE_CZ_NH2_angle=geo.NE_CZ_NH2_angle
CD_NE_CZ_NH2_diangle=geo.CD_NE_CZ_NH2_diangle
carbon_b= calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle, N_C_CA_CB_diangle)
CB= Atom("CB", carbon_b, 0.0 , 1.0, " "," CB", 0,"C")
carbon_g= calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle, N_CA_CB_CG_diangle)
CG= Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d= calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle, CA_CB_CG_CD_diangle)
CD= Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
nitrogen_e= calculateCoordinates(CB, CG, CD, CD_NE_length, CG_CD_NE_angle, CB_CG_CD_NE_diangle)
NE= Atom("NE", nitrogen_e, 0.0, 1.0, " ", " NE", 0, "N")
carbon_z= calculateCoordinates(CG, CD, NE, NE_CZ_length, CD_NE_CZ_angle, CG_CD_NE_CZ_diangle)
CZ= Atom("CZ", carbon_z, 0.0, 1.0, " ", " CZ", 0, "C")
nitrogen_h1= calculateCoordinates(CD, NE, CZ, CZ_NH1_length, NE_CZ_NH1_angle, CD_NE_CZ_NH1_diangle)
NH1= Atom("NH1", nitrogen_h1, 0.0, 1.0, " ", " NH1", 0, "N")
nitrogen_h2= calculateCoordinates(CD, NE, CZ, CZ_NH2_length, NE_CZ_NH2_angle, CD_NE_CZ_NH2_diangle)
NH2= Atom("NH2", nitrogen_h2, 0.0, 1.0, " ", " NH2", 0, "N")
##Create Residue Data Structure
res= Residue((' ', segID, ' '), "ARG", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
res.add(NE)
res.add(CZ)
res.add(NH1)
res.add(NH2)
return res
def makePhe(segID, N, CA, C, O, geo):
'''Creates a Phenylalanine residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle=geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_CG_length=geo.CB_CG_length
CA_CB_CG_angle=geo.CA_CB_CG_angle
N_CA_CB_CG_diangle=geo.N_CA_CB_CG_diangle
CG_CD1_length=geo.CG_CD1_length
CB_CG_CD1_angle=geo.CB_CG_CD1_angle
CA_CB_CG_CD1_diangle=geo.CA_CB_CG_CD1_diangle
CG_CD2_length=geo.CG_CD2_length
CB_CG_CD2_angle=geo.CB_CG_CD2_angle
CA_CB_CG_CD2_diangle= geo.CA_CB_CG_CD2_diangle
CD1_CE1_length=geo.CD1_CE1_length
CG_CD1_CE1_angle=geo.CG_CD1_CE1_angle
CB_CG_CD1_CE1_diangle=geo.CB_CG_CD1_CE1_diangle
CD2_CE2_length=geo.CD2_CE2_length
CG_CD2_CE2_angle=geo.CG_CD2_CE2_angle
CB_CG_CD2_CE2_diangle=geo.CB_CG_CD2_CE2_diangle
CE1_CZ_length=geo.CE1_CZ_length
CD1_CE1_CZ_angle=geo.CD1_CE1_CZ_angle
CG_CD1_CE1_CZ_diangle=geo.CG_CD1_CE1_CZ_diangle
carbon_b= calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle, N_C_CA_CB_diangle)
CB= Atom("CB", carbon_b, 0.0 , 1.0, " "," CB", 0,"C")
carbon_g= calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle, N_CA_CB_CG_diangle)
CG= Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d1= calculateCoordinates(CA, CB, CG, CG_CD1_length, CB_CG_CD1_angle, CA_CB_CG_CD1_diangle)
CD1= Atom("CD1", carbon_d1, 0.0, 1.0, " ", " CD1", 0, "C")
carbon_d2= calculateCoordinates(CA, CB, CG, CG_CD2_length, CB_CG_CD2_angle, CA_CB_CG_CD2_diangle)
CD2= Atom("CD2", carbon_d2, 0.0, 1.0, " ", " CD2", 0, "C")
carbon_e1= calculateCoordinates(CB, CG, CD1, CD1_CE1_length, CG_CD1_CE1_angle, CB_CG_CD1_CE1_diangle)
CE1= Atom("CE1", carbon_e1, 0.0, 1.0, " ", " CE1", 0, "C")
carbon_e2= calculateCoordinates(CB, CG, CD2, CD2_CE2_length, CG_CD2_CE2_angle, CB_CG_CD2_CE2_diangle)
CE2= Atom("CE2", carbon_e2, 0.0, 1.0, " ", " CE2", 0, "C")
carbon_z= calculateCoordinates(CG, CD1, CE1, CE1_CZ_length, CD1_CE1_CZ_angle, CG_CD1_CE1_CZ_diangle)
CZ= Atom("CZ", carbon_z, 0.0, 1.0, " ", " CZ", 0, "C")
##Create Residue Data Structures
res= Residue((' ', segID, ' '), "PHE", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD1)
res.add(CE1)
res.add(CD2)
res.add(CE2)
res.add(CZ)
return res
def get_atoms(self):
return [
Atom(
Vector3d(
list(at.get_vector())[0],
list(at.get_vector())[1],
list(at.get_vector())[2]), at.id, at.mass)
for at in self.cg_atoms
]
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= Geo(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= np.array([0.,0.,0.])
C_coord= np.array([CA_C_length,0,0])
N_coord = np.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")
res=makeRes(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
def add_dummy_structure(self):
"""Adds a dummy atom of zero coordinates to mark a gap in visualisation
software"""
dummy_atom = Atom('DUM', np.zeros(3), 0, 1, ' ', 'DUM', -999)
dummy_residue = Residue((' ', -1 * self.chiral_id, ' '), 'DUM', '?')
dummy_residue.add(dummy_atom)
dummy_chain = Chain('?')
dummy_chain.add(dummy_residue)
self.dummy_structure = dummy_residue
return True
def makeLeu(segID: int, N, CA, C, O, geo: LeuGeo) -> Residue:
"""Creates a Leucine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD1_length = geo.CG_CD1_length
CB_CG_CD1_angle = geo.CB_CG_CD1_angle
CA_CB_CG_CD1_diangle = geo.CA_CB_CG_CD1_diangle
CG_CD2_length = geo.CG_CD2_length
CB_CG_CD2_angle = geo.CB_CG_CD2_angle
CA_CB_CG_CD2_diangle = geo.CA_CB_CG_CD2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g1 = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g1, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d1 = calculateCoordinates(CA, CB, CG, CG_CD1_length,
CB_CG_CD1_angle, CA_CB_CG_CD1_diangle)
CD1 = Atom("CD1", carbon_d1, 0.0, 1.0, " ", " CD1", 0, "C")
carbon_d2 = calculateCoordinates(CA, CB, CG, CG_CD2_length,
CB_CG_CD2_angle, CA_CB_CG_CD2_diangle)
CD2 = Atom("CD2", carbon_d2, 0.0, 1.0, " ", " CD2", 0, "C")
##Create Residue Data Structure
res = Residue((" ", segID, " "), "LEU", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD1)
res.add(CD2)
return res
def makeIle(segID: int, N, CA, C, O, geo: IleGeo) -> Residue:
"""Creates an Isoleucine residue"""
##R-group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG1_length = geo.CB_CG1_length
CA_CB_CG1_angle = geo.CA_CB_CG1_angle
N_CA_CB_CG1_diangle = geo.N_CA_CB_CG1_diangle
CB_CG2_length = geo.CB_CG2_length
CA_CB_CG2_angle = geo.CA_CB_CG2_angle
N_CA_CB_CG2_diangle = geo.N_CA_CB_CG2_diangle
CG1_CD1_length = geo.CG1_CD1_length
CB_CG1_CD1_angle = geo.CB_CG1_CD1_angle
CA_CB_CG1_CD1_diangle = geo.CA_CB_CG1_CD1_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g1 = calculateCoordinates(N, CA, CB, CB_CG1_length, CA_CB_CG1_angle,
N_CA_CB_CG1_diangle)
CG1 = Atom("CG1", carbon_g1, 0.0, 1.0, " ", " CG1", 0, "C")
carbon_g2 = calculateCoordinates(N, CA, CB, CB_CG2_length, CA_CB_CG2_angle,
N_CA_CB_CG2_diangle)
CG2 = Atom("CG2", carbon_g2, 0.0, 1.0, " ", " CG2", 0, "C")
carbon_d1 = calculateCoordinates(CA, CB, CG1, CG1_CD1_length,
CB_CG1_CD1_angle, CA_CB_CG1_CD1_diangle)
CD1 = Atom("CD1", carbon_d1, 0.0, 1.0, " ", " CD1", 0, "C")
##Create Residue Data Structure
res = Residue((" ", segID, " "), "ILE", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG1)
res.add(CG2)
res.add(CD1)
return res
def makeAsn(segID, N, CA, C, O, geo):
"""Creates an Asparagine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_OD1_length = geo.CG_OD1_length
CB_CG_OD1_angle = geo.CB_CG_OD1_angle
CA_CB_CG_OD1_diangle = geo.CA_CB_CG_OD1_diangle
CG_ND2_length = geo.CG_ND2_length
CB_CG_ND2_angle = geo.CB_CG_ND2_angle
CA_CB_CG_ND2_diangle = geo.CA_CB_CG_ND2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
oxygen_d1 = calculateCoordinates(CA, CB, CG, CG_OD1_length,
CB_CG_OD1_angle, CA_CB_CG_OD1_diangle)
OD1 = Atom("OD1", oxygen_d1, 0.0, 1.0, " ", " OD1", 0, "O")
nitrogen_d2 = calculateCoordinates(CA, CB, CG, CG_ND2_length,
CB_CG_ND2_angle, CA_CB_CG_ND2_diangle)
ND2 = Atom("ND2", nitrogen_d2, 0.0, 1.0, " ", " ND2", 0, "N")
res = Residue((" ", segID, " "), "ASN", " ")
##Create Residue Data Structure
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(OD1)
res.add(ND2)
return res
def makeMet(segID: int, N, CA, C, O, geo: MetGeo) -> Residue:
"""Creates a Methionine residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_SD_length = geo.CG_SD_length
CB_CG_SD_angle = geo.CB_CG_SD_angle
CA_CB_CG_SD_diangle = geo.CA_CB_CG_SD_diangle
SD_CE_length = geo.SD_CE_length
CG_SD_CE_angle = geo.CG_SD_CE_angle
CB_CG_SD_CE_diangle = geo.CB_CG_SD_CE_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
sulfur_d = calculateCoordinates(CA, CB, CG, CG_SD_length, CB_CG_SD_angle,
CA_CB_CG_SD_diangle)
SD = Atom("SD", sulfur_d, 0.0, 1.0, " ", " SD", 0, "S")
carbon_e = calculateCoordinates(CB, CG, SD, SD_CE_length, CG_SD_CE_angle,
CB_CG_SD_CE_diangle)
CE = Atom("CE", carbon_e, 0.0, 1.0, " ", " CE", 0, "C")
##Create Residue Data Structure
res = Residue((" ", segID, " "), "MET", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(SD)
res.add(CE)
return res
def __init__(self, pdbfile):
self.chains = []
self.cg_atoms = [] # C4' | P | N1 / N9 ==> changed in mass_center
self.atoms_triads = [] # according to cg_triads dictionary
self.pdb_residues = []
self.coords = []
self.changed_coords = False
p = PDBParser()
if len(pdbfile.split('/')) > 1:
self.name = pdbfile.split('/')[-1]
self.name = self.name.split('.')[0]
print(pdbfile)
chains = []
self.structure = p.get_structure(self.name, pdbfile)
for chain in self.structure[0]: # model_1
ch = RNAChain(chain.id)
chains.append(ch)
for residue in chain.get_residues():
res = Residue(residue.get_resname())
cg_atoms_list = []
atoms_pdb = []
for atom in residue:
coords = list(atom.get_vector())
res.add_atom(
Atom(Vector3d(coords[0], coords[1], coords[2]),
atom.id, atom.mass))
if residue.get_resname() in [' A', ' G'
] and atom.id in cg_atoms_pur:
cg_atoms_list.append(atom)
if residue.get_resname() in [' C', ' U'
] and atom.id in cg_atoms_pir:
cg_atoms_list.append(atom)
if residue.get_resname() in cg_tiads.keys(
) and atom.id in cg_tiads[residue.get_resname()]:
atoms_pdb.append(atom)
if res.atoms != [] and len(cg_atoms_list) == 3 and len(
atoms_pdb) == 5:
ch.add_residue(res)
for at in atoms_pdb:
self.atoms_triads.append(at)
self.pdb_residues.append(residue)
for at in cg_atoms_list:
self.cg_atoms.append(at)
for chain in chains:
if len(chain.residues) >= 1:
self.chains.append(chain)
self.atoms = [] #MAIN CHAIN
for atom in self.get_atoms():
if atom.kind in ["C4'", "P"]:
self.atoms.append(atom)
self.cg_atoms_all = self.get_atoms()
def makeAsp(segID: int, N, CA, C, O, geo: AspGeo) -> Residue:
"""Creates an Aspartic Acid residue"""
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_OD1_length = geo.CG_OD1_length
CB_CG_OD1_angle = geo.CB_CG_OD1_angle
CA_CB_CG_OD1_diangle = geo.CA_CB_CG_OD1_diangle
CG_OD2_length = geo.CG_OD2_length
CB_CG_OD2_angle = geo.CB_CG_OD2_angle
CA_CB_CG_OD2_diangle = geo.CA_CB_CG_OD2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
oxygen_d1 = calculateCoordinates(CA, CB, CG, CG_OD1_length,
CB_CG_OD1_angle, CA_CB_CG_OD1_diangle)
OD1 = Atom("OD1", oxygen_d1, 0.0, 1.0, " ", " OD1", 0, "O")
oxygen_d2 = calculateCoordinates(CA, CB, CG, CG_OD2_length,
CB_CG_OD2_angle, CA_CB_CG_OD2_diangle)
OD2 = Atom("OD2", oxygen_d2, 0.0, 1.0, " ", " OD2", 0, "O")
res = Residue((" ", segID, " "), "ASP", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(OD1)
res.add(OD2)
return res
def makebiopython(atomcoords, atomnos):
"""Create a list of BioPython Atoms.
This creates a list of BioPython Atoms suitable for use by
Bio.PDB.Superimposer, for example.
"""
pt = PeriodicTable()
bioatoms = []
for coords, atomno in zip(atomcoords, atomnos):
symbol = pt.element[atomno]
bioatoms.append(
Atom(symbol, coords, 0, 0, 0, symbol, 0, symbol.upper()))
return bioatoms
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):
"""Tracks line in the PDB file that is being parsed.
Arguments:
- line_counter - int
"""
self.line_counter = line_counter
def init_structure(self, structure_id):
"""Initiate a new Structure object with given id.
Arguments:
- 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:
- id - int
- 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:
- 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:
- segid - string
"""
self.segid = segid
def init_residue(self, resname, field, resseq, icode):
"""Initiate a new Residue object.
Arguments:
- resname - string, e.g. "ASN"
- field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
- resseq - int, sequence identifier
- 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:
if resname == duplicate_residue.resname:
warnings.warn("WARNING: Residue ('%s', %i, '%s','%s')"
" already defined with the same name at line %i."
% (field, resseq, icode, resname, self.line_counter),
PDBConstructionWarning)
self.residue = duplicate_residue
return
# 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
self.residue = Residue(res_id, resname, self.segid)
self.chain.add(self.residue)
def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname,
serial_number=None, element=None):
"""Initiate a new Atom object.
Arguments:
- name - string, atom name, e.g. CA, spaces should be stripped
- coord - Numeric array (Float0, size 3), atomic coordinates
- b_factor - float, B factor
- occupancy - float
- altloc - string, alternative location specifier
- fullname - string, atom name including spaces, e.g. " CA "
- 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)
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(self.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(self.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(self.atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add(self.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
def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname,
serial_number=None, element=None):
"""Initiate a new Atom object.
Arguments:
- name - string, atom name, e.g. CA, spaces should be stripped
- coord - Numeric array (Float0, size 3), atomic coordinates
- b_factor - float, B factor
- occupancy - float
- altloc - string, alternative location specifier
- fullname - string, atom name including spaces, e.g. " CA "
- 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)
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(self.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(self.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(self.atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add(self.atom)
