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Copy pathPDBHandler.py
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PDBHandler.py
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import numpy as np
from scipy.special import comb
import Leapy
import os, sys
import math
import copy
HOMEDIR='/home/pietroa/Python/'
_CRYST1_FORMAT_STRING = '{:6}{:9.3f}{:9.3f}{:9.3f}{:7.2f}{:7.2f}{:7.2f}\n'
_CONECT_FORMAT_STRING = '{:6}{:5d}{:5d}\n'
_ATOM_FORMAT_STRING = '{:4} {:6d} {:4} {:3} {:5} {:7.3f} {:7.3f} {:7.3f} {:5.2f} {:5.2f}\n'
class Atom(object):
def __init__(self, number, name, resname, resnumber, chainid, coord, occupancy, bfactor, element=None):
self.number = int(number)
self.name = name
self.resname = resname
self.resnumber = int(resnumber)
self.chainid = chainid
self.coord = coord
self.x = self.coord[0]
self.y = self.coord[1]
self.z = self.coord[2]
self.occupancy = occupancy
self.bfactor = bfactor
self.id = '{} of {}{}'.format(name, resname, resnumber)
def __repr__(self):
return self.name
def get_name(self):
return self.name
def get_resname(self):
return self.resname
def get_resnum(self):
return self.resnumber
def set_resname(self, resname):
self.resname = resname
def set_resnum(self, resnumber):
self.resnumber = resnumber
def set_name(self, name):
self.name = name
def get_coord(self):
return self.coord
def calc_distance(self, atom):
ax = self.get_coord()[0]
ay = self.get_coord()[1]
az = self.get_coord()[2]
bx = atom.get_coord()[0]
by = atom.get_coord()[1]
bz = atom.get_coord()[2]
distance = math.sqrt((bx - ax) ** 2 + (by - ay) ** 2 + (bz - az) ** 2)
return distance
def get_number(self):
return self.number
def get_id(self):
return self.id
def formatted(self):
return _ATOM_FORMAT_STRING.format('ATOM', self.number, self.name, self.resname, self.resnumber, self.x, self.y, self.z, self.occupancy, self.bfactor)
def change_name(self, name):
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, self.x, self.y, self.z, self.occupancy, self.bfactor)
def superimposed1(self, name, atom):
x = atom.get_coord()[0] - 0.001
y = atom.get_coord()[1] - 0.001
z = atom.get_coord()[2] - 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def superimposed2(self, name, atom):
x = atom.get_coord()[0] - 0.002
y = atom.get_coord()[1] - 0.002
z = atom.get_coord()[2] - 0.002
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def superimposed3(self, name, atom):
x = atom.get_coord()[0] + 0.001
y = atom.get_coord()[1] + 0.001
z = atom.get_coord()[2] + 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def superimposed4(self, name, atom):
x = atom.get_coord()[0] + 0.002
y = atom.get_coord()[1] + 0.002
z = atom.get_coord()[2] + 0.002
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def halfway_between(self, name, atom1, atom2):
x = (atom2.get_coord()[0] + atom1.get_coord()[0])/2
y = (atom2.get_coord()[1] + atom1.get_coord()[1])/2
z = (atom2.get_coord()[2] + atom1.get_coord()[2])/2
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def halfway_between1(self, name, atom1, atom2):
x = ((atom2.get_coord()[0] + atom1.get_coord()[0])/2) - 0.001
y = ((atom2.get_coord()[1] + atom1.get_coord()[1])/2) - 0.001
z = ((atom2.get_coord()[2] + atom1.get_coord()[2])/2) - 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def halfway_between2(self, name, atom1, atom2):
x = ((atom2.get_coord()[0] + atom1.get_coord()[0])/2) + 0.001
y = ((atom2.get_coord()[1] + atom1.get_coord()[1])/2) + 0.001
z = ((atom2.get_coord()[2] + atom1.get_coord()[2])/2) + 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def halfway_after1(self, name, atom1, atom2):
x = ((3*atom2.get_coord()[0] - atom1.get_coord()[0])/2) - 0.001
y = ((3*atom2.get_coord()[1] - atom1.get_coord()[1])/2) - 0.001
z = ((3*atom2.get_coord()[2] - atom1.get_coord()[2])/2) - 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def halfway_after2(self, name, atom1, atom2):
x = ((3*atom2.get_coord()[0] - atom1.get_coord()[0])/2) + 0.001
y = ((3*atom2.get_coord()[1] - atom1.get_coord()[1])/2) + 0.001
z = ((3*atom2.get_coord()[2] - atom1.get_coord()[2])/2) + 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def thirdone_between(self, name, atom1, atom2):
x = (atom2.get_coord()[0] + 2*atom1.get_coord()[0])/3
y = (atom2.get_coord()[1] + 2*atom1.get_coord()[1])/3
z = (atom2.get_coord()[2] + 2*atom1.get_coord()[2])/3
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def thirdtwo_between(self, name, atom1, atom2):
x = (2*atom2.get_coord()[0] + atom1.get_coord()[0])/3
y = (2*atom2.get_coord()[1] + atom1.get_coord()[1])/3
z = (2*atom2.get_coord()[2] + atom1.get_coord()[2])/3
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def thirdone_between1(self, name, atom1, atom2):
x = (atom2.get_coord()[0] + 2*atom1.get_coord()[0])/3 - 0.001
y = (atom2.get_coord()[1] + 2*atom1.get_coord()[1])/3 - 0.001
z = (atom2.get_coord()[2] + 2*atom1.get_coord()[2])/3 - 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def thirdtwo_between1(self, name, atom1, atom2):
x = (2*atom2.get_coord()[0] + atom1.get_coord()[0])/3 - 0.001
y = (2*atom2.get_coord()[1] + atom1.get_coord()[1])/3 - 0.001
z = (2*atom2.get_coord()[2] + atom1.get_coord()[2])/3 - 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def quarterone_between1(self, name, atom1, atom2):
x = (atom2.get_coord()[0] + 3*atom1.get_coord()[0])/4
y = (atom2.get_coord()[1] + 3*atom1.get_coord()[1])/4
z = (atom2.get_coord()[2] + 3*atom1.get_coord()[2])/4
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def quarterone_between2(self, name, atom1, atom2):
x = (atom2.get_coord()[0] + 3*atom1.get_coord()[0])/4 + 0.001
y = (atom2.get_coord()[1] + 3*atom1.get_coord()[1])/4 + 0.001
z = (atom2.get_coord()[2] + 3*atom1.get_coord()[2])/4 + 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def quarterone_between3(self, name, atom1, atom2):
x = (atom2.get_coord()[0] + 3*atom1.get_coord()[0])/4 - 0.001
y = (atom2.get_coord()[1] + 3*atom1.get_coord()[1])/4 - 0.001
z = (atom2.get_coord()[2] + 3*atom1.get_coord()[2])/4 - 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def quartertwo_between1(self, name, atom1, atom2):
x = (3*atom2.get_coord()[0] + atom1.get_coord()[0])/4
y = (3*atom2.get_coord()[1] + atom1.get_coord()[1])/4
z = (3*atom2.get_coord()[2] + atom1.get_coord()[2])/4
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
def quartertwo_between2(self, name, atom1, atom2):
x = (3*atom2.get_coord()[0] + atom1.get_coord()[0])/4 + 0.001
y = (3*atom2.get_coord()[1] + atom1.get_coord()[1])/4 + 0.001
z = (3*atom2.get_coord()[2] + atom1.get_coord()[2])/4 + 0.001
return _ATOM_FORMAT_STRING.format('ATOM', self.number, name, self.resname, self.resnumber, x, y, z, self.occupancy, self.bfactor)
class Residue(object):
def __init__(self, resname, resnumber):
self.resname = resname
self.resnumber = resnumber
self.id = '{}{}'.format(resname, resnumber)
self.atom_list = []
self.atom_dict = {}
def __repr__(self):
return self.id
def get_resname(self):
return self.resname
def set_resname(self, resname):
self.resname = resname
for atom in self.atom_list:
atom.set_resname(resname)
def get_resnumber(self):
return self.resnumber
def set_resnumber(self, resnumber):
self.resnumber = resnumber
for atom in self.atom_list:
atom.set_resnum(resnumber)
def get_id(self):
return self.id
def get_atomlist(self):
for t in self.atom_dict:
print t
def add_atom(self, atom):
atom_name = atom.get_name()
self.atom_list.append(atom)
self.atom_dict[atom_name] = atom
class Structure(object):
def __init__(self, name):
self.name = name
self.atom_list = []
self.atom_dict = {}
self.residue_list = []
self.residue_dict = {}
self.other_list = []
self.other_dict = {}
self.id = 'PDB read as {}'.format(name)
def __repr__(self):
return self.id
def get_residue(self, resnum):
return self.residue_list[resnum]
def get_reslist(self):
for t in self.residue_dict:
print t
def add_atom(self, atom):
atom_number = atom.get_number()
self.atom_list.append(atom)
self.atom_dict[atom_number] = atom
def add_residue(self, residue):
residue_number = residue.get_resnumber()
self.residue_list.append(residue)
self.residue_dict[residue_number] = residue
def add_ter(self, ter):
ter_position = ter.ter_position()
self.other_list.append(ter)
self.other_dict[ter_position] = ter
def add_cryst1(self, cryst1):
self.other_list.append(cryst1)
self.other_dict['Cryst1'] = cryst1
def add_conect(self, conect):
conect_name = conect.__repr__()
self.other_list.append(conect)
self.other_dict[conect_name] = conect
class Ter_record(object):
def __init__(self, position):
self.position = position
self.kind = 'TER'
self.tag = '{}\n'.format('TER')
self.id = 'Ter following atom {}'.format(position)
def __repr__(self):
return self.id
def ter(self):
return self.tag
def ter_position(self):
return self.position
class Cryst1_record(object):
def __init__(self, xbox, ybox, zbox, xangle, yangle, zangle):
self.xbox = xbox
self.ybox = ybox
self.zbox = zbox
self.boxdim = np.array((xbox, ybox, zbox), "f")
self.boxangles = np.array((xangle, yangle, zangle), "f")
self.xangle = xangle
self.yangle = yangle
self.zangle = zangle
self.kind = 'Cryst1'
self.id = 'Cryst1 Record'
def __repr__(self):
return self.id
def formatted(self):
return _CRYST1_FORMAT_STRING.format('CRYST1', self.xbox, self.ybox, self.zbox, self.xangle, self.yangle, self.zangle)
def box_side(self):
return self.xbox
def box_angle(self):
return self.xangle
def box_dimensions(self):
return self.boxdim
def box_angles(self):
return self.boxangles
class Conect_record(object):
def __init__(self, atom1, atom2):
self.atom1 = int(atom1)
self.atom2 = int(atom2)
self.kind = 'Conect'
self.id = 'Conect Record between atoms {} and {}'.format(atom1, atom2)
def __repr__(self):
return self.id
def formatted(self):
return _CONECT_FORMAT_STRING.format('CONECT', self.atom1, self.atom2)
def atoms(self):
return self.atom1, self.atom2
def readpdb(file):
structure = Structure('curr')
pdb = open(file, 'r')
data = pdb.readlines()
current_resnumber = None
for line in data:
line = line.rstrip('\n')
record_type = line [0:6].strip()
if record_type == "ATOM" or record_type == "HETATM":
number = line[6:11].strip()
name = line[12:16].strip()
resname = line[17:20].strip()
chainid = line[21].strip()
resnumber = int(line[22:27].split()[0])
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = np.array((x, y, z), "f")
try:
occupancy = float(line[54:60])
except:
occupancy = 1.00
try:
bfactor = float(line[60:66])
except:
bfactor = 0.00
curr_atom = Atom(number, name, resname, resnumber, chainid, coord, occupancy, bfactor)
try:
if curr_residue.get_resnumber() != resnumber:
if resnumber in structure.residue_dict or resnumber is 0:
curr_residue = Residue(resname, resnumber+10000)
curr_atom.set_resnum(resnumber+10000)
structure.add_residue(curr_residue)
else:
curr_residue = Residue(resname, resnumber)
structure.add_residue(curr_residue)
except NameError:
if resnumber in structure.residue_dict or resnumber is 0:
curr_residue = Residue(resname, resnumber+10000)
curr_atom.set_resnum(resnumber+10000)
structure.add_residue(curr_residue)
else:
curr_residue = Residue(resname, resnumber)
structure.add_residue(curr_residue)
structure.residue_dict[curr_residue.get_resnumber()].add_atom(curr_atom)
structure.add_atom(curr_atom)
elif record_type == "TER":
curr_ter = Ter_record(curr_atom.get_number())
structure.add_ter(curr_ter)
elif record_type == "CONECT":
atom1, atom2 = line[7:20].split()
curr_conect = Conect_record(atom1, atom2)
structure.add_conect(curr_conect)
elif record_type == "CRYST1":
xbox = float(line[8:15])
ybox = float(line[17:24])
zbox = float(line[26:33])
xangle = float(line[34:40])
yangle = float(line[41:47])
zangle = float(line[48:54])
cryst1 = Cryst1_record(xbox, ybox, zbox, xangle, yangle, zangle)
structure.add_cryst1(cryst1)
return structure
def savepdb(struct, out):
pdb = open(out, 'w')
try:
pdb.write(struct.other_dict['Cryst1'].formatted())
except KeyError:
pass
for res in struct.residue_list:
for atom in res.atom_list:
pdb.write(atom.formatted())
try:
pdb.write(struct.other_dict[atom.get_number()].ter())
except:
pass
for oth in struct.other_dict:
try:
if oth.startswith('Conect'):
pdb.write(struct.other_dict[oth].formatted())
except:
pass
pdb.write('END\n')
pdb.close()
def sulpher(struct, pdb):
sulfurs = []
sp = {}
with open('{}Param_files/Stock/Staple.param'.format(HOMEDIR), 'r') as b:
data = b.readlines()[1:]
for line in data:
sp[line.split()[0]] = []
for point in line.split()[1:]:
sp[line.split()[0]].append(str(point))
b.close()
import re
regex = re.compile('..X')
for res in struct.residue_list:
nome = res.get_resname()
if re.match(regex, nome):
for i in enumerate(sp[nome]):
if i[0] >= 1:
sulfurs.append(res.atom_dict[sp[nome][i[0]]])
for sul1 in sulfurs[:]:
s1 = {}
try:
sulfurs.remove(sul1)
sulph = sulfurs
for sul2 in sulph[:]:
key, value = sul2, sul1.calc_distance(sul2)
s1[key] = float(value)
prox = min(s1, key=s1.get)
curr_conect = Conect_record(sul1.get_number(), prox.get_number())
struct.add_conect(curr_conect)
sulfurs.remove(prox)
except:
pass
pdb = open(pdb, 'w')
try:
pdb.write(struct.other_dict['Cryst1'].formatted())
except KeyError:
pass
for res in struct.residue_list:
for atom in res.atom_list:
pdb.write(atom.formatted())
try:
pdb.write(struct.other_dict[atom.get_number()].ter())
except:
pass
for oth in struct.other_dict:
try:
if oth.startswith('Conect'):
pdb.write(struct.other_dict[oth].formatted())
except:
pass
pdb.write('END\n')
pdb.close()
def glyremover(struct, resnum):
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() in ['N1', 'H1', 'HA13', 'C1', 'O1', 'N2', 'H2']:
struct.residue_dict[resnum].atom_list.remove(atom)
pdb = open('Mutated.pdb', 'w')
try:
pdb.write(struct.other_dict['Cryst1'].formatted())
except KeyError:
pass
for res in struct.residue_list:
for atom in res.atom_list:
if atom.get_name() == 'PC':
atom.set_name('Cl-')
atom.set_resname('Cl-')
if atom.get_name() == 'PN':
atom.set_name('Na+')
atom.set_resname('Na+')
pdb.write(atom.formatted())
try:
pdb.write(struct.other_dict[atom.get_number()].ter())
except:
pass
for oth in struct.other_dict:
try:
if oth.startswith('Conect'):
pdb.write(struct.other_dict[oth].formatted())
except:
pass
pdb.write('END\n')
pdb.close()
ctrl = open('chop.in', 'w')
ctrl.write("source {}Param_files/Essentials/cmd.ff14SB+\n".format(HOMEDIR))
ctrl.write("source leaprc.lipid14\n")
ctrl.write("Mut = loadpdb Mutated.pdb\n")
ctrl.write("savepdb Mut Mut_leap.pdb\n")
ctrl.write("quit\n")
ctrl.close()
Leapy.run('chop.in')
if struct.other_dict['Cryst1']:
f = open('Mut_leap.pdb', 'r+')
temp = f.read()
f.close()
f = open('Mut_leap.pdb', 'w+')
f.write(struct.other_dict['Cryst1'].formatted())
f.write(temp)
f.close()
s = readpdb('Mut_leap.pdb')
sulpher(s, 'Mut_leap.pdb')
os.remove('chop.in')
def glyadder(struct, resid, resnum, end):
struct.residue_dict[resnum].atom_dict['N1'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['N1'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['N1'].set_name('N')
struct.residue_dict[resnum].atom_dict['H1'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['H1'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['H1'].set_name('H')
struct.residue_dict[resnum].atom_dict['CAX'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['CAX'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['CAX'].set_name('CA')
struct.residue_dict[resnum].atom_dict['HAX2'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['HAX2'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['HAX2'].set_name('HA2')
struct.residue_dict[resnum].atom_dict['HAX3'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['HAX3'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['HAX3'].set_name('HA3')
struct.residue_dict[resnum].atom_dict['C1'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['C1'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['C1'].set_name('C')
struct.residue_dict[resnum].atom_dict['O1'].set_resname('GLY')
if end == 'C':
struct.residue_dict[resnum].atom_dict['O1'].set_resnum(resnum+1)
struct.residue_dict[resnum].atom_dict['O1'].set_name('O')
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_resname() == 'VXI':
atom.set_resname(resid)
if end == 'N':
atom.set_resnum(resnum+1)
for res in struct.residue_list[:]:
if res.get_resnumber() > resnum:
res.set_resnumber(res.get_resnumber()+1)
pdb = open('Mutated.pdb', 'w')
try:
pdb.write(struct.other_dict['Cryst1'].formatted())
except KeyError:
pass
for res in struct.residue_list:
for atom in res.atom_list:
if atom.get_name() == 'PC':
atom.set_name('Cl-')
atom.set_resname('Cl-')
if atom.get_name() == 'PN':
atom.set_name('Na+')
atom.set_resname('Na+')
pdb.write(atom.formatted())
try:
pdb.write(struct.other_dict[atom.get_number()].ter())
except:
pass
for oth in struct.other_dict:
try:
if oth.startswith('Conect'):
pdb.write(struct.other_dict[oth].formatted())
except:
pass
pdb.write('END\n')
pdb.close()
ctrl = open('chop.in', 'w')
ctrl.write("source {}Param_files/Essentials/cmd.ff14SB+\n".format(HOMEDIR))
ctrl.write("source leaprc.lipid14\n")
ctrl.write("Mut = loadpdb Mutated.pdb\n")
ctrl.write("savepdb Mut Mut_leap.pdb\n")
ctrl.write("quit\n")
ctrl.close()
Leapy.run('chop.in')
if struct.other_dict['Cryst1']:
f = open('Mut_leap.pdb', 'r+')
temp = f.read()
f.close()
f = open('Mut_leap.pdb', 'w+')
f.write(struct.other_dict['Cryst1'].formatted())
f.write(temp)
f.close()
s = readpdb('Mut_leap.pdb')
sulpher(s, 'Mut_leap.pdb')
os.remove('chop.in')
def cut_to_gly(struct, resnum):
# Determine if it is terminal
Term = 'None'
try:
struct.residue_dict[resnum].atom_dict['H3']
Term = 'N'
except:
pass
try:
struct.residue_dict[resnum].atom_dict['OXT']
Term = 'C'
except:
pass
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() in ['CB']:
atom.set_name('HA3')
if atom.get_name() in ['HA']:
atom.set_name('HA2')
if Term == 'N':
if atom.get_name() not in ['N', 'H1', 'H2', 'H3', 'CA', 'HA2', 'HA3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
elif Term == 'C':
if atom.get_name() not in ['N', 'H', 'CA', 'HA2', 'HA3', 'C', 'O', 'OXT']:
struct.residue_dict[resnum].atom_list.remove(atom)
elif Term == 'None':
if atom.get_name() not in ['N', 'H', 'CA', 'HA2', 'HA3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
struct.residue_dict[resnum].set_resname('GLY')
return struct
def alldmaker(struct):
struct2 = copy.deepcopy(struct)
struct3 = Structure('curr3')
num_of_res = max(struct2.residue_dict)
for resid in reversed(struct2.residue_list):
if resid.get_resname() not in ('NHE', 'NME', 'ACE'):
if resid.get_resname() not in ('PRO'):
for atom in resid.atom_list:
if atom.get_name() in ['N']:
atom.set_name('C')
elif atom.get_name() in ['H']:
atom.set_name('O')
elif atom.get_name() in ['C']:
atom.set_name('N')
elif atom.get_name() in ['O']:
atom.set_name('H')
elif resid.get_resname() in ('PRO'):
for atom in resid.atom_list[:]:
if atom.get_name() not in ['N', 'C', 'O', 'CA', 'HA']:
resid.atom_list.remove(atom)
else:
if atom.get_name() in ['N']:
atom.set_name('C')
elif atom.get_name() in ['C']:
atom.set_name('N')
elif atom.get_name() in ['O']:
atom.set_name('H')
elif atom.get_name() in ['HA']:
atom.set_name('HA2')
elif atom.get_name() in ['CA']:
atom.set_name('CA')
resid.set_resname('GLY')
resid.set_resnumber(num_of_res + 1 - resid.get_resnumber())
struct3.add_residue(resid)
return struct3
def cut_to_gly_PRO(struct, resnum):
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() in ['CB']:
atom.set_name('HA3')
if atom.get_name() in ['HA']:
atom.set_name('HA2')
if atom.get_name() in ['CD']:
atom.set_name('H')
if atom.get_name() not in ['N', 'H', 'CA', 'HA2', 'HA3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
struct.residue_dict[resnum].set_resname('GLY')
return struct
def invert_CYX(struct, resnum):
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() in ['CB']:
atom.set_name('HA1')
if atom.get_name() in ['HA']:
atom.set_name('CB')
if atom.get_name() in ['HA1']:
atom.set_name('HA')
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'SG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
return struct
def chop(struct, resid, resnum):
# Determine if it is terminal
struct.residue_dict[resnum].set_resname(resid)
Term = 'None'
try:
struct.residue_dict[resnum].atom_dict['H3']
Term = 'N'
except:
pass
try:
struct.residue_dict[resnum].atom_dict['OXT']
Term = 'C'
except:
pass
if resid == 'ABU':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG1', 'HG2', 'HG3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid in ('ALA', 'DAA'):
if Term == 'N':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H1', 'H2', 'H3', 'CA', 'HA', 'CB', 'HB1', 'HB2', 'HB3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
struct.residue_dict[resnum].set_resname('ALA')
elif Term == 'C':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB1', 'HB2', 'HB3', 'C', 'O', 'OXT']:
struct.residue_dict[resnum].atom_list.remove(atom)
struct.residue_dict[resnum].set_resname('ALA')
elif Term == 'None':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB1', 'HB2', 'HB3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
struct.residue_dict[resnum].set_resname('ALA')
if resid in ('ALX'):
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid in 'AIB':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB11', 'HB12', 'HB13', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AnE':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'CD1', 'HD1', 'CD2', 'HD2', 'CE', 'CZ', 'OH1', 'OH2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'ANN':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'CD1', 'HD1', 'CD2', 'HD2', 'CE', 'HE', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'ARG':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'HD2', 'HD3', 'NE', 'HE', 'CZ', 'NH1', 'HH11', 'HH12', 'NH2', 'HH21', 'HH22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMC':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'SG', 'HG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMD':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'OD1', 'OD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AME':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'OE2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMF':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'CD1', 'HD1', 'CE1', 'HE1', 'CZ', 'HZ', 'CE2', 'HE2', 'CD2', 'HD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMH':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB', 'HB12', 'HB13', 'CG', 'ND1', 'CD2', 'HD2', 'CE1', 'HE1', 'NE2', 'HE2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMI':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB1', 'CG2', 'HG21', 'HG22', 'HG23', 'CG1', 'HG12', 'HG13', 'CD1', 'HD11', 'HD12', 'HD13', 'HG13', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AML':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG', 'CD1', 'HD11', 'HD12', 'HD13', 'CD2', 'HD21', 'HD22', 'HD23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMK':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG2', 'HG3', 'CD', 'HD2', 'HD3', 'CE', 'HE2', 'HE3', 'NZ', 'HZ1', 'HZ2', 'HZ3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMM':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG2', 'HG3', 'SD', 'CE', 'HE1', 'HE2', 'HE3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMN':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'OD1', 'ND2', 'HD21', 'HD22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMP':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG2', 'HG3', 'CD', 'HD2', 'HD3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMQ':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'NE2', 'HE21', 'HE22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMR':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'HG2', 'HG3', 'CD', 'HD2', 'HD3', 'NE', 'HE', 'CZ', 'NH1', 'HH11', 'HH12', 'NH2', 'HH21', 'HH22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMS':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'OG', 'HG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMT':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB1', 'CG2', 'HG21', 'HG22', 'HG23', 'OG1', 'HG1', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMV':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB1', 'CG1', 'HG11', 'HG12', 'HG13', 'CG2', 'HG21', 'HG22', 'HG23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMW':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'CD1', 'HD1', 'NE1', 'HE1', 'CE2', 'CZ2', 'HZ2', 'CH2', 'HH2', 'CZ3', 'HZ3', 'CE3', 'HE3', 'CD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMY':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'CB2', 'HB21', 'HB22', 'HB23', 'CB1', 'HB12', 'HB13', 'CG', 'CD1', 'HD1', 'CD2', 'HD2', 'CE1', 'HE1', 'CE2', 'HE2', 'CZ', 'OH', 'HH', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'AMX':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'OD1', 'ND2', 'HD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'ASN':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'OD1', 'ND2', 'HD21', 'HD22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'ASP':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'OD1', 'OD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'BAA':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1A':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB1', 'HB2', 'HB3', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2A':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB1', 'HB2', 'HB3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1C':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'SG', 'HG', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2C':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'SG', 'HG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1D':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'CG', 'OD1', 'OD2', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2D':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'CG', 'OD1', 'OD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1E':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'OE2', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2E':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'OE2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1F':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'CG', 'CD1', 'HD1', 'CD2', 'HD2', 'CE1', 'HE1', 'CE2', 'HE2', 'CZ', 'HZ', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2F':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'CG', 'CD1', 'HD1', 'CD2', 'HD2', 'CE1', 'HE1', 'CE2', 'HE2', 'CZ', 'HZ', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1I':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB', 'CG2', 'HG21', 'HG22', 'HG23', 'CG1', 'HG12', 'HG13', 'CD1', 'HD11', 'HD12', 'HD13', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2I':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB', 'CG2', 'HG21', 'HG22', 'HG23', 'CG1', 'HG12', 'HG13', 'CD1', 'HD11', 'HD12', 'HD13', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1L':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'CG', 'HG', 'CD1', 'HD11', 'HD12', 'HD13', 'CD2', 'HD21', 'HD22', 'HD23', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1M':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'SD', 'CE', 'HE1', 'HE2', 'HE3', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2M':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'SD', 'CE', 'HE1', 'HE2', 'HE3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1Q':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'NE2', 'HE21', 'HE22', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2Q':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'NE2', 'HE21', 'HE22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1T':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB', 'CG2', 'HG21', 'HG22', 'HG23', 'OG1', 'HG1', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2T':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB', 'CG2', 'HG21', 'HG22', 'HG23', 'OG1', 'HG1', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1V':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB', 'CG1', 'HG11', 'HG12', 'HG13', 'CG2', 'HG21', 'HG22', 'HG23', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2V':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB', 'CG1', 'HG11', 'HG12', 'HG13', 'CG2', 'HG21', 'HG22', 'HG23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B1S':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA1', 'CB', 'HB2', 'HB3', 'OG', 'HG', 'CA2', 'HA22', 'HA23', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'B2S':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA2', 'CB', 'HB2', 'HB3', 'OG', 'HG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'BzE':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'CD1', 'HD1', 'CD2', 'HD2', 'CE1', 'HE1', 'CE2', 'HE2', 'CZ', 'CH', 'OT1', 'OT2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'C6W':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'CD1', 'HD1', 'NE1', 'HE1', 'CE2', 'CZ2', 'HZ2', 'CH2', 'ClH2', 'CZ3', 'HZ3', 'CE3', 'HE3', 'CD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'CBA':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG', 'CD1', 'HD11', 'HD12', 'CD2', 'HD21', 'HD21', 'CE', 'HE2', 'HE3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'CYS':
if Term == 'N':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H1', 'H2', 'H3' 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'HG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
elif Term == 'C':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'HG', 'C', 'O', 'OXT']:
struct.residue_dict[resnum].atom_list.remove(atom)
elif Term == 'None':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'HG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'CYX':
if Term == 'N':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H1', 'H2', 'H3' 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
elif Term == 'C':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'C', 'O', 'OXT']:
struct.residue_dict[resnum].atom_list.remove(atom)
elif Term == 'None':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'DAB':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'ND', 'HD1', 'HD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid in ('DAX'):
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'OD1', 'OD2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'DBN':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'ND', 'NE', 'NZ', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'DPR':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'NG', 'HG1', 'HG2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'ECX':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG', 'CD', 'HD2', 'HD3', 'CE', 'HE2', 'HE3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'GAB':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA1', 'HA12', 'HA13', 'CA2', 'HA22', 'HA23', 'CA3', 'HA32', 'HA33', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'GLN':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'NE2', 'HE21', 'HE22', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'GLU':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'OE2', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)
if resid == 'GLY':
for atom in struct.residue_dict[resnum].atom_list[:]:
if atom.get_name() not in ['N', 'H', 'CA', 'HA2', 'HA3', 'C', 'O']:
struct.residue_dict[resnum].atom_list.remove(atom)