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 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 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 build_cacb_representation(self, old_struct, new_st, atom_names):
"""
builds new structure composed of atom_name atoms only
for nucleic acids these are ["C4'", "P"], for proteins ["CA", "CB"]
"""
for atom in old_struct.struct.get_atoms():
new_chain = list(new_st.get_chains())[0]
if atom.name in atom_names:
resi = atom.get_parent()
if new_chain.has_id(resi.id): pass
else:
new_resi = Residue(resi.id, resi.resname, " ")
new_chain.add(new_resi)
new_resi.add(atom)
del self.fa_struct
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 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 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 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 build_3pnucleic_representation(self, old_struct, new_st):
"""
builds new structure composed of atom_name atoms only
for nucleic acids these are ["C4'", "P", "N1"/"N9"]
N1 is taken for ADE and GUA; N9 for CYT, URA, THY
"""
for resi in old_struct.struct.get_residues():
if resi.has_id("N9"):
atom_names = ["C4'", "P", "N9"]
else:
atom_names = ["C4'", "P", "N1"]
new_chain = list(new_st.get_chains())[0]
for atom in resi:
if atom.name in atom_names:
resi = atom.get_parent()
if new_chain.has_id(resi.id): pass
else:
new_resi = Residue(resi.id, resi.resname, " ")
new_chain.add(new_resi)
new_resi.add(atom)
del self.fa_struct
def select_structure(selector, structure):
new_structure = Structure(structure.id)
for model in structure:
if not selector.accept_model(model):
continue
new_model = Model(model.id, model.serial_num)
new_structure.add(new_model)
for chain in model:
if not selector.accept_chain(chain):
continue
new_chain = Chain(chain.id)
new_model.add(new_chain)
for residue in chain:
if not selector.accept_residue(residue):
continue
new_residue = Residue(residue.id, residue.resname,
residue.segid)
new_chain.add(new_residue)
for atom in residue:
if selector.accept_atom(atom):
new_residue.add(atom)
return new_structure
def createPDBFile(self):
"Create test CIF file with 12 Atoms in icosahedron vertexes"
from Bio.PDB.Structure import Structure
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom
from Bio.PDB.mmcifio import MMCIFIO
import os
CIFFILENAME = "/tmp/out.cif"
# create atom struct with ico simmety (i222r)
icosahedron = Icosahedron(circumscribed_radius=100, orientation='222r')
pentomVectorI222r = icosahedron.getVertices()
# create biopython object
structure = Structure('result') # structure_id
model = Model(1, 1) # model_id,serial_num
structure.add(model)
chain = Chain('A') # chain Id
model.add(chain)
for i, v in enumerate(pentomVectorI222r, 1):
res_id = (' ', i, ' ') # first arg ' ' -> aTOm else heteroatom
res_name = "ALA" #+ str(i) # define name of residue
res_segid = ' '
residue = Residue(res_id, res_name, res_segid)
chain.add(residue)
# ATOM name, coord, bfactor, occupancy, altloc, fullname, serial_number,
# element=None)
atom = Atom('CA', v, 0., 1., " ", " CA ", i, "C")
residue.add(atom)
io = MMCIFIO()
io.set_structure(structure)
# delete file if exists
if os.path.exists(CIFFILENAME):
os.remove(CIFFILENAME)
io.save(CIFFILENAME)
return CIFFILENAME
def create_structure(coords, pdb_type, remove_masked):
"""Create the structure.
Args:
coords: 3D coordinates of structure
pdb_type: predict or actual structure
remove_masked: whether to include masked atoms. If false,
the masked atoms have coordinates of [0,0,0].
Returns:
structure
"""
name = protein.id_
structure = Structure(name)
model = Model(0)
chain = Chain('A')
for i, residue in enumerate(protein.primary):
residue = AA_LETTERS[residue]
if int(protein.mask[i]) == 1 or remove_masked == False:
new_residue = Residue((' ', i + 1, ' '), residue, ' ')
j = 3 * i
atom_list = ['N', 'CA', 'CB']
for k, atom in enumerate(atom_list):
new_atom = Atom(name=atom,
coord=coords[j + k, :],
bfactor=0,
occupancy=1,
altloc=' ',
fullname=" {} ".format(atom),
serial_number=0)
new_residue.add(new_atom)
chain.add(new_residue)
model.add(chain)
structure.add(model)
io = PDBIO()
io.set_structure(structure)
io.save(save_dir + name + '_' + pdb_type + '.pdb')
return structure
def makeGly(segID: int, N, CA, C, O, geo: Geo) -> Residue:
"""Creates a Glycine residue"""
res = Residue((" ", segID, " "), "GLY", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
return res
def makePro(segID: int, N, CA, C, O, geo: ProGeo) -> Residue:
"""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 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 atoms_to_residues(atoms, atomsPerRes, seqid, resnames=None):
"""
Builds a list of residues from a list of atoms, where each residue
i the list has 'atomsPerRes' atoms per residue. All residues are
set to 'A', if no residue names are given.
"""
# Check the arguments
if (len(atoms) % atomsPerRes) != 0:
raise ValueError, "Mismatch between list length and atoms per residues."
if resnames==None:
resnames = [" A" for _ in xrange(len(atoms)/atomsPerRes)]
residues = []
res = None
for (i,atom) in enumerate(atoms):
# Residue number
resnumber = i // atomsPerRes
# Create a new residue
if (i % atomsPerRes) == 0:
if res!=None:
residues.append(res)
res = Residue((" ", resnumber, " "), resnames[resnumber], seqid)
res.add(atom)
# Add an atom
else:
res.add(atom)
if res!=None:
residues.append(res)
return residues
def makeAla(segID, N, CA, C, O, geo):
'''Creates an Alanine 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
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")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "ALA", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
return res
def makeAla(segID: int, N, CA, C, O, geo: AlaGeo) -> Residue:
"""Creates an Alanine 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
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")
res = Residue((" ", segID, " "), "ALA", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
return res
def makeRes(segID, N, CA, C, O, geo):
'''Creates a Glycine residue'''
##Create Residue Data Structure
res= Residue((' ', segID, ' '), aa1to3[geo.residue_name], ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
return res
def makeGly(segID, N, CA, C, O, geo):
'''Creates a Glycine residue'''
##Create Residue Data Structure
res= Residue((' ', segID, ' '), "GLY", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
##print(res)
return res
def makeGly(segID: int, N, CA, C, O, geo: Geo) -> Residue:
"""Creates a Glycine residue"""
##Create Residue Data Structure
res = Residue((" ", segID, " "), "GLY", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
##print(res)
return res
def build_martini_representation(self, old_struct, new_st):
"""
Reduces complexity of protein residue to the MARTINI coarse grained model:
CA, O, Bead(s) in specific atom location.
Reference:
Monticelli et al. The MARTINI coarse-grained force field: extension to proteins.
J. Chem. Theory Comput. (2008) vol. 4 (5) pp. 819-834
"""
conversion_table = {
"L": ["CG"],
"V": ["CB"],
"E": ["CB"],
"d": ["CG"],
"T": ["CB"],
"Q": ["CB"],
"S": ["CB"],
"A": [],
"G": [],
"K": ["CG", "CE"],
"I": ["CD1"],
"R": ["CG", "NE"],
"N": ["CG"],
"P": ["CG"],
"F": ["CG", "CE1", "CE2"],
"Y": ["CG", "CE1", "CE2"],
"H": ["CB", "ND1", "NE2"],
"M": ["CG"],
"W": ["CB", "CD1", "CD2", "CE2"],
"C": ["SG"],
"LEU": ["CG"],
"VAL": ["CB"],
"GLU": ["CB"],
"ASP": ["CG"],
"THR": ["CB"],
"GLN": ["CB"],
"SER": ["CB"],
"ALA": [],
"GLY": [],
"LYS": ["CG", "CE"],
"ILE": ["CD1"],
"ARG": ["CG", "NE"],
"ASN": ["CG"],
"PRO": ["CG"],
"PHE": ["CG", "CE1", "CE2"],
"TYR": ["CG", "CE1", "CE2"],
"HIS": ["CB", "ND1", "NE2"],
"MET": ["CG"],
"TRP": ["CB", "CD1", "CD2", "CE2"],
"CYS": ["SG"],
}
for resi in old_struct.struct.get_residues():
new_chain = list(new_st.get_chains())[0]
#print "@@@", resi.resname, resi.id
hetname = resi.id[0].split("_")
if hetname[0] == "H": continue
for atom in resi:
resname = resi.resname.strip()
if atom.name in conversion_table[resname] or atom.name == "CA":
resi = atom.get_parent()
if new_chain.has_id(resi.id): pass
else:
new_resi = Residue(resi.id, resi.resname, " ")
new_chain.add(new_resi)
new_resi.add(atom)
del self.fa_struct
def makeTrp(segID: int, N, CA, C, O, geo: TrpGeo) -> Residue:
"""Creates a Tryptophan 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_NE1_length = geo.CD1_NE1_length
CG_CD1_NE1_angle = geo.CG_CD1_NE1_angle
CB_CG_CD1_NE1_diangle = geo.CB_CG_CD1_NE1_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
CD2_CE3_length = geo.CD2_CE3_length
CG_CD2_CE3_angle = geo.CG_CD2_CE3_angle
CB_CG_CD2_CE3_diangle = geo.CB_CG_CD2_CE3_diangle
CE2_CZ2_length = geo.CE2_CZ2_length
CD2_CE2_CZ2_angle = geo.CD2_CE2_CZ2_angle
CG_CD2_CE2_CZ2_diangle = geo.CG_CD2_CE2_CZ2_diangle
CE3_CZ3_length = geo.CE3_CZ3_length
CD2_CE3_CZ3_angle = geo.CD2_CE3_CZ3_angle
CG_CD2_CE3_CZ3_diangle = geo.CG_CD2_CE3_CZ3_diangle
CZ2_CH2_length = geo.CZ2_CH2_length
CE2_CZ2_CH2_angle = geo.CE2_CZ2_CH2_angle
CD2_CE2_CZ2_CH2_diangle = geo.CD2_CE2_CZ2_CH2_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")
nitrogen_e1 = calculateCoordinates(CB, CG, CD1, CD1_NE1_length,
CG_CD1_NE1_angle, CB_CG_CD1_NE1_diangle)
NE1 = Atom("NE1", nitrogen_e1, 0.0, 1.0, " ", " NE1", 0, "N")
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_e3 = calculateCoordinates(CB, CG, CD2, CD2_CE3_length,
CG_CD2_CE3_angle, CB_CG_CD2_CE3_diangle)
CE3 = Atom("CE3", carbon_e3, 0.0, 1.0, " ", " CE3", 0, "C")
carbon_z2 = calculateCoordinates(CG, CD2, CE2, CE2_CZ2_length,
CD2_CE2_CZ2_angle, CG_CD2_CE2_CZ2_diangle)
CZ2 = Atom("CZ2", carbon_z2, 0.0, 1.0, " ", " CZ2", 0, "C")
carbon_z3 = calculateCoordinates(CG, CD2, CE3, CE3_CZ3_length,
CD2_CE3_CZ3_angle, CG_CD2_CE3_CZ3_diangle)
CZ3 = Atom("CZ3", carbon_z3, 0.0, 1.0, " ", " CZ3", 0, "C")
carbon_h2 = calculateCoordinates(CD2, CE2, CZ2, CZ2_CH2_length,
CE2_CZ2_CH2_angle,
CD2_CE2_CZ2_CH2_diangle)
CH2 = Atom("CH2", carbon_h2, 0.0, 1.0, " ", " CH2", 0, "C")
##Create Residue DS
res = Residue((" ", segID, " "), "TRP", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD1)
res.add(CD2)
res.add(NE1)
res.add(CE2)
res.add(CE3)
res.add(CZ2)
res.add(CZ3)
res.add(CH2)
return res
def makeTyr(segID: int, N, CA, C, O, geo: TyrGeo) -> Residue:
"""Creates a Tyrosine 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
CZ_OH_length = geo.CZ_OH_length
CE1_CZ_OH_angle = geo.CE1_CZ_OH_angle
CD1_CE1_CZ_OH_diangle = geo.CD1_CE1_CZ_OH_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")
oxygen_h = calculateCoordinates(CD1, CE1, CZ, CZ_OH_length,
CE1_CZ_OH_angle, CD1_CE1_CZ_OH_diangle)
OH = Atom("OH", oxygen_h, 0.0, 1.0, " ", " OH", 0, "O")
##Create Residue Data S
res = Residue((" ", segID, " "), "TYR", " ")
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)
res.add(OH)
return res
def makePhe(segID: int, N, CA, C, O, geo: PheGeo) -> Residue:
"""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")
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 makeHis(segID: int, N, CA, C, O, geo: HisGeo) -> Residue:
"""Creates a Histidine 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_ND1_length = geo.CG_ND1_length
CB_CG_ND1_angle = geo.CB_CG_ND1_angle
CA_CB_CG_ND1_diangle = geo.CA_CB_CG_ND1_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
ND1_CE1_length = geo.ND1_CE1_length
CG_ND1_CE1_angle = geo.CG_ND1_CE1_angle
CB_CG_ND1_CE1_diangle = geo.CB_CG_ND1_CE1_diangle
CD2_NE2_length = geo.CD2_NE2_length
CG_CD2_NE2_angle = geo.CG_CD2_NE2_angle
CB_CG_CD2_NE2_diangle = geo.CB_CG_CD2_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")
nitrogen_d1 = calculateCoordinates(CA, CB, CG, CG_ND1_length,
CB_CG_ND1_angle, CA_CB_CG_ND1_diangle)
ND1 = Atom("ND1", nitrogen_d1, 0.0, 1.0, " ", " ND1", 0, "N")
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, ND1, ND1_CE1_length,
CG_ND1_CE1_angle, CB_CG_ND1_CE1_diangle)
CE1 = Atom("CE1", carbon_e1, 0.0, 1.0, " ", " CE1", 0, "C")
nitrogen_e2 = calculateCoordinates(CB, CG, CD2, CD2_NE2_length,
CG_CD2_NE2_angle, CB_CG_CD2_NE2_diangle)
NE2 = Atom("NE2", nitrogen_e2, 0.0, 1.0, " ", " NE2", 0, "N")
res = Residue((" ", segID, " "), "HIS", " ")
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(ND1)
res.add(CD2)
res.add(CE1)
res.add(NE2)
return res
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")
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 makeArg(segID: int, N, CA, C, O, geo: ArgGeo) -> Residue:
"""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")
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 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")
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
else:
bfactors = zeros(len(points))
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']
}, {
'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')
