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 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 init_all_rotamers(
): # 'FIXED_RES_CHAIN' : {'FIXED_RES_NUM' : { CANDIDATE_RES_1 : [ transformed_residues ] }}
for chain in candidate_chains:
all_rotamers[chain] = {}
for res_fixed_num in candidate_ids:
all_rotamers[chain][res_fixed_num] = {}
for rot_name_1 in residue_names_1:
all_rotamers[chain][res_fixed_num][rot_name_1] = []
for moving in all_moving[res_name_dict[rot_name_1]]:
aligned = return_aligned(
moving, structure[idm(chain)][chain][res_fixed_num])
aligned_copy = Residue((" ", res_fixed_num, " "),
res_name_dict[rot_name_1], " ")
# Residue((" ", 279, " "), resname, " ")
for i in aligned:
aligned_copy.add(i.copy())
all_rotamers[chain][res_fixed_num][rot_name_1].append(
aligned_copy)
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 place_atom(element, position, resname, chain):
global runtime_mark_id
res_temp = Residue((" ", runtime_mark_id, " "), resname, " ")
runtime_mark_id += 1
atom_temp = Atom("X", position, 0.0, 1, " ", "X", runtime_mark_id, element)
res_temp.add(atom_temp)
chain.add(res_temp)
def place_line(element, position1, position2, resname, chain):
global runtime_mark_id
res_temp = Residue((" ", runtime_mark_id, " "), resname, " ")
runtime_mark_id += 1
atom_temp1 = Atom("X1", position1, 0.0, 1, " ", "X", runtime_mark_id,
element)
atom_temp2 = Atom("X2", position2, 0.0, 1, " ", "X", runtime_mark_id,
element)
res_temp.add(atom_temp1)
res_temp.add(atom_temp2)
chain.add(res_temp)
def place_atoms(atoms, element, resname, chain):
global runtime_mark_id
res_temp = Residue((" ", runtime_mark_id, " "), resname, " ")
runtime_mark_id += 3
n = 0
for a in atoms:
n += 1
atom_temp = Atom("X" + str(n), a.get_coord(), 0.0, 1, " ", "X",
runtime_mark_id, element)
res_temp.add(atom_temp)
chain.add(res_temp)
def makeSer(segID, N, CA, C, O, geo):
'''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)
##print(res)
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, N, CA, C, O, geo):
'''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)
##print res
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 makeLeu(segID, N, CA, C, O, geo):
'''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 makeMet(segID, N, CA, C, O, geo):
'''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 makeMet(segID, N, CA, C, O, geo):
'''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, N, CA, C, O, geo):
'''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 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)
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 build_residues(list_blueprints, list_names):
list_residues = []
resname = res_rev_name_dict[list_blueprints[0][0][2]]
rotamer_dict[resname] = []
for list_rotamer in list_blueprints:
new_res = Residue((" ", 279, " "), resname,
" ") # RESET TOTAL_RES_ID TO 1 ON SUBSEQUENT RUNS?
rotamer_dict[resname].append(list_rotamer[5][1])
for blueprint_atom in list_rotamer:
new_atom = Atom(blueprint_atom[0], blueprint_atom[6],
blueprint_atom[8], blueprint_atom[7],
blueprint_atom[1], blueprint_atom[0], 1,
blueprint_atom[10])
# INIT: NAME, COORDINATES, BFACTOR, OCCUPANCY, ALTLOC, FULL NAME, SERIAL NUMBER, ELEMENT
new_atom.set_parent(new_res)
new_res.add(new_atom)
list_residues.append(new_res)
return list_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, 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 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 makeLys(segID, N, CA, C, O, geo):
'''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 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 makeLys(segID, N, CA, C, O, geo):
'''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 makeTyr(segID, N, CA, C, O, geo):
'''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 makeIle(segID, N, CA, C, O, geo):
'''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 build_tetrahedron(list_res, co, coords): # Optimize
len_max = 0
temp_candidates = []
for res_origin in list_res:
for atom_origin_name in coord_name_dict[res_rev_name_dict[
res_origin.get_resname()]]:
atom_origin = res_origin[atom_origin_name]
co_dist = atom_origin - co
if np.abs(co_dist - coord_radius) > coord_tolerance:
continue
set_edges = [co, atom_origin]
while add_edge(120, list_res, set_edges):
pass
set_edges.remove(co)
invalid = False
for set_other in temp_candidates:
if invalid:
break
same = True
for atom in set_edges:
for atom_other in set_other[1]:
if atom.get_id() == atom_other.get_id():
if atom.get_parent().get_resname(
) == atom_other.get_parent().get_resname():
if atom.get_parent().get_id(
)[0] == atom_other.get_parent().get_id()[0]:
if atom - atom_other != 0:
same = False
break
if same:
invalid = True
if invalid:
continue
histidines = []
for a in set_edges:
a_parent = a.get_parent()
if a_parent.get_resname() == "HIS":
if a_parent not in histidines:
histidines.append(a_parent)
if len(set_edges) > len_max:
len_max = len(set_edges)
if not search_for_HIS_by_keeping_all or len(histidines) == 0:
del temp_candidates[:]
temp_candidates.append(
[co, set_edges, len_max,
len(histidines)])
elif len(set_edges) == len_max:
temp_candidates.append(
[co, set_edges, len_max,
len(histidines)]
) # SHOULD MAYBE ALSO BE UNDER CONTROL OF "HIS" SETTING? OR IMPLEMENT A FAST SEARCH? OR CLASH TOGGLE
for candidate in temp_candidates:
if len(candidate[1]) > 1:
invalid = True # Check for structures coming from the same chain
for a1 in candidate[1]:
for a2 in candidate[1]:
if a1 != a2:
if a1.get_parent().get_full_id(
)[0][2] != a2.get_parent().get_full_id()[0][2]:
invalid = False
if invalid:
print("Skipping candidate set (T):")
for a in candidate[1]:
print(a.get_parent().get_full_id())
continue
water_id = 4000
positions = []
v_co = to_vector(co.get_coord())
for a in candidate[1]:
positions.append(to_vector(a.get_coord()) - v_co)
a1 = positions[0]
a2 = positions[1]
r = rotaxis(np.pi * 2 / 3, a1)
a3 = v_co + a2.left_multiply(r)
r = rotaxis(-np.pi * 2 / 3, a1)
a4 = v_co + a2.left_multiply(r)
water_positions = [a3, a4]
for wt_p in water_positions:
empty = True
for p in positions:
if dist(wt_p, v_co + p) < 1:
empty = False
if empty:
water_residue = Residue((" ", water_id, " "), "HOH", " ")
water = Atom("CA", wt_p, 0.0, 1, " ", "CA", water_id, "SR")
water.set_parent(water_residue)
water_residue.add(water)
water_id += 1
candidate[1].append(water)
save_candidate(candidate[0], candidate[1], candidate[2],
candidate[3], "T", coords)
def build_octahedron(list_res, co, coords):
len_max = 0
temp_candidates = []
for res_origin in list_res:
for atom_origin_name in coord_name_dict[res_rev_name_dict[
res_origin.get_resname()]]:
atom_origin = res_origin[atom_origin_name]
co_dist = atom_origin - co
if np.abs(co_dist - coord_radius) > coord_tolerance:
continue
set_edges = [co, atom_origin]
while add_edge(90, list_res, set_edges):
pass
set_edges.remove(co)
invalid = False
for set_other in temp_candidates:
if invalid:
break
same = True
for atom in set_edges:
for atom_other in set_other[1]:
if atom.get_id() == atom_other.get_id():
if atom.get_parent().get_resname(
) == atom_other.get_parent().get_resname():
if atom.get_parent().get_id(
)[0] == atom_other.get_parent().get_id()[0]:
if atom - atom_other != 0:
same = False
break
if same:
invalid = True
if invalid:
continue
histidines = []
for a in set_edges:
a_parent = a.get_parent()
if a_parent.get_resname() == "HIS":
if a_parent not in histidines:
histidines.append(a_parent)
if len(set_edges) > len_max:
len_max = len(set_edges)
if not search_for_HIS_by_keeping_all or len(histidines) == 0:
del temp_candidates[:]
temp_candidates.append(
[co, set_edges, len_max,
len(histidines)])
elif len(set_edges) == len_max:
temp_candidates.append(
[co, set_edges, len_max,
len(histidines)])
for candidate in temp_candidates:
if len(candidate[1]) > 1:
invalid = True # Check for structures coming from the same chain
for a1 in candidate[1]:
for a2 in candidate[1]:
if a1 != a2:
if a1.get_parent().get_full_id(
)[0][2] != a2.get_parent().get_full_id()[0][2]:
invalid = False
if invalid:
print("Skipping candidate set (O, {}):".format(
len(candidate[1])))
for a in candidate[1]:
print(a.get_parent().get_full_id())
continue
if len(candidate[1]) > 2:
water_id = 3000
positions = []
v_co = to_vector(co.get_coord())
for a in candidate[1]:
positions.append(to_vector(a.get_coord()) - v_co)
a1 = positions[0]
a2 = 0
for i in range(1, len(positions)):
if np.abs(a1.angle(positions[i]) * 180 / np.pi - 90) < 15:
a2 = positions[i]
break
a3 = v_co - a1
a4 = v_co - a2
a5 = v_co + cross(a1, a2).normalized().right_multiply(coord_radius)
a6 = v_co - cross(a1, a2).normalized().right_multiply(coord_radius)
water_positions = [a3, a4, a5, a6]
for wt_p in water_positions:
empty = True
for p in positions:
if dist(wt_p, v_co + p) < 1:
empty = False
if empty:
water_residue = Residue((" ", water_id, " "), "HOH", " ")
water = Atom("CA", wt_p, 0.0, 1, " ", "CA", water_id, "SR")
water.set_parent(water_residue)
water_residue.add(water)
water_id += 1
candidate[1].append(water)
save_candidate(candidate[0], candidate[1], candidate[2],
candidate[3], "O", coords)
elif len(candidate[1]) == 2:
water_id = 3500
positions = []
v_co = to_vector(co.get_coord())
for a in candidate[1]:
positions.append(to_vector(a.get_coord()) - v_co)
if np.abs(positions[0].angle(positions[1]) * 180 / np.pi -
90) < 15:
a1 = positions[0]
a2 = positions[1]
a3 = v_co - a1
a4 = v_co - a2
a5 = v_co + cross(a1,
a2).normalized().right_multiply(coord_radius)
a6 = v_co - cross(a1,
a2).normalized().right_multiply(coord_radius)
water_residue = Residue((" ", water_id, " "), "HOH", " ")
water = Atom("CA", a3, 0.0, 1, " ", "CA", water_id, "SR")
water.set_parent(water_residue)
water_residue.add(water)
water_id += 1
candidate[1].append(water)
water_residue = Residue((" ", water_id, " "), "HOH", " ")
water = Atom("CA", a4, 0.0, 1, " ", "CA", water_id, "SR")
water.set_parent(water_residue)
water_residue.add(water)
water_id += 1
candidate[1].append(water)
water_residue = Residue((" ", water_id, " "), "HOH", " ")
water = Atom("CA", a5, 0.0, 1, " ", "CA", water_id, "SR")
water.set_parent(water_residue)
water_residue.add(water)
water_id += 1
candidate[1].append(water)
water_residue = Residue((" ", water_id, " "), "HOH", " ")
water = Atom("CA", a6, 0.0, 1, " ", "CA", water_id, "SR")
water.set_parent(water_residue)
water_residue.add(water)
water_id += 1
candidate[1].append(water)
save_candidate(candidate[0], candidate[1], candidate[2],
candidate[3], "O", coords)
def makeTyr(segID, N, CA, C, O, geo):
'''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 makeTrp(segID, N, CA, C, O, geo):
'''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 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 makeGln(segID, N, CA, C, O, geo):
'''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 makeHis(segID, N, CA, C, O, geo):
'''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")
##Create Residue Data Structure
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 makeHis(segID, N, CA, C, O, geo):
'''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")
##Create Residue Data Structure
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 makeIle(segID, N, CA, C, O, geo):
'''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 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 makeGln(segID, N, CA, C, O, geo):
'''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 makeTrp(segID, N, CA, C, O, geo):
'''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
coord_atom):
break
aligned_rotamer_copy = Residue(
(current_res_id,
runtime_residue_id,
current_chain), res_name_dict[
aligned_rotamer_resname],
current_res_id)
runtime_residue_id += 2
for atom in aligned_rotamer:
temp_atom = atom.copy()
temp_atom.set_parent(
aligned_rotamer_copy)
aligned_rotamer_copy.add(
temp_atom)
identical = False
for res in candidates: # Check for duplication source?
if return_rmsd(
res,
aligned_rotamer_copy
) == 0:
identical = True
if identical:
break
candidates.append(
aligned_rotamer_copy)