def create_and_add_MBR_residue(pdb, memb_chain, highest_atom_number):
rsd = MyPDB.Residue('MBR', 1, memb_chain)
X, Y, Z = [25, -25, -25, 25, 25, -25, -25,
25], [25, 25, -25, -25, 25, 25, -25,
-25], [15, 15, 15, 15, -15, -15, -15, -15]
for i, x, y, z in zip(range(1, 9), X, Y, Z):
rsd.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + i,
name='C%i' % i,
res_type_3='MBR',
chain=memb_chain,
res_seq_num=1,
x=x,
y=y,
z=z,
element='O' if z == 15 else 'N',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
chn = MyPDB.Chain(memb_chain, {1: rsd})
chn.add_residue(rsd)
pdb.add_chain(chn)
def create_and_add_MBR_residue(pdb, memb_chain, highest_atom_number):
inn = MyPDB.Residue('INN', 1, memb_chain)
atom_num = 1
i = 1
for x in range(-30, 30):
for y in range(-30, 30):
inn.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + atom_num,
name='%i' % i,
res_type_3='INN',
chain=memb_chain,
res_seq_num=1,
x=x,
y=y,
z=-15,
element='N',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
atom_num += 1
i += 1
out = MyPDB.Residue('OUT', 2, memb_chain)
i = 1
for x in range(-30, 30):
for y in range(-30, 30):
out.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + atom_num,
name='%i' % i,
res_type_3='MID',
chain=memb_chain,
res_seq_num=2,
x=x,
y=y,
z=15,
element='O',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
atom_num += 1
i += 1
mid = MyPDB.Residue('MID', 3, memb_chain)
i = 1
for x in range(-30, 30):
for y in range(-30, 30):
mid.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + atom_num,
name='%i' % i,
res_type_3='MID',
chain=memb_chain,
res_seq_num=3,
x=x,
y=y,
z=0,
element='C',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
atom_num += 1
i += 1
chn = MyPDB.Chain(memb_chain, {1: inn, 2: out, 3: mid})
chn.add_residue(inn)
chn.add_residue(out)
chn.add_residue(mid)
pdb.add_chain(chn)
