def add_c_terminal_oxygens_to_atom_group(ag,
use_capping_hydrogens=False,
append_to_end_of_model=False,
c_ca_n=None,
):
#
# do we need ANISOU
#
rc = []
atom_name=' OXT'
atom_element = 'O'
bond_length=1.231
if use_capping_hydrogens:
if ag.get_atom(atom_name.strip()): return []
atom_name=" HC "
atom_element="H"
bond_length=1.
if ag.get_atom(atom_name.strip()): return []
if c_ca_n is not None:
c, ca, n = c_ca_n
else:
c = ag.get_atom("C")
if c is None: return
ca = ag.get_atom("CA")
if ca is None: return
n = ag.get_atom("N")
if n is None: return
atom = ag.get_atom('O')
dihedral = dihedral_angle(sites=[atom.xyz,
c.xyz,
ca.xyz,
n.xyz,
],
deg=True)
ro2 = construct_xyz(c, bond_length,
ca, 120.,
n, dihedral,
period=2,
)
oxys = [' O ', atom_name]
for i in range(0,2):
name = oxys[i]
atom = ag.get_atom(name.strip())
if atom:
pass #atom.xyz = ro2[i]
else:
atom = iotbx.pdb.hierarchy.atom()
atom.name = name
atom.element = atom_element
atom.occ = c.occ
atom.b = c.b
atom.segid = ' '*4
atom.xyz = ro2[i]
if append_to_end_of_model:
chain = _add_atom_to_chain(atom, ag)
rc.append(chain)
else:
# add the atom to the hierarchy
ag.append_atom(atom)
return rc
def add_side_chain_acid_hydrogens_to_atom_group(
atom_group,
anchors=None,
configuration_index=0,
bond_length=0.95,
element='H',
):
"""Add hydrogen atoms to side-chain acid in place
Args:
atom_group (TYPE): Atom group
anchors (None, optional): Atoms that specify the acids moeity
configuration_index (int, optional): Configuration to return
"""
assert element in ['H', 'D']
c, o1, o2 = anchors
if configuration_index >= 2:
tmp = o1.name
o1.name = o2.name
o2.name = tmp
tmp = o1
o1 = o2
o2 = tmp
configuration_index = configuration_index % 2
if o2.name == ' OD2':
name = ' HD2'
atom = atom_group.get_atom('CB')
elif o2.name == ' OE2':
name = ' HE2'
atom = atom_group.get_atom('CG')
else:
assert 0
if element == 'D': name = name.replace('H', 'D')
dihedral = dihedral_angle(sites=[
atom.xyz,
c.xyz,
o1.xyz,
o2.xyz,
],
deg=True)
ro2 = construct_xyz(
o2,
bond_length,
c,
120.,
o1,
dihedral,
period=2,
)
i = configuration_index
atom = atom_group.get_atom(name.strip())
if atom:
pass #atom.xyz = ro2[i]
else:
atom = new_atom_with_inheritance(name, element, ro2[i], o2)
atom_group.append_atom(atom)
def add_main_chain_o_to_atom_group(ag, c_ca_n=None):
# cetral functuon
if c_ca_n is not None:
c, ca, n = c_ca_n
else:
c = ag.get_atom("C")
if c is None: return
ca = ag.get_atom("CA")
if ca is None: return
n = ag.get_atom("N")
if n is None: return
atom = ag.get_atom('O')
dihedral = dihedral_angle(sites=[
atom.xyz,
c.xyz,
ca.xyz,
n.xyz,
],
deg=True)
ro2 = construct_xyz(
c,
bond_length,
ca,
120.,
n,
dihedral,
period=2,
)
oxys = [' O ', atom_name]
for i in range(0, 2):
name = oxys[i]
atom = ag.get_atom(name.strip())
if atom:
pass #atom.xyz = ro2[i]
else:
atom = iotbx.pdb.hierarchy.atom()
atom.name = name
atom.element = atom_element
atom.occ = c.occ
atom.b = c.b
atom.segid = ' ' * 4
atom.xyz = ro2[i]
if append_to_end_of_model:
chain = _add_atom_to_chain(atom, ag)
rc.append(chain)
else:
# add the atom to the hierarchy
ag.append_atom(atom)
#for
assert atom
def _add_hydrogens_to_atom_group_using_bad(ag,
atom_name,
atom_element,
bond_atom,
angle_atom,
dihedral_atom,
bond_length,
angle,
dihedral,
append_to_end_of_model=False,
):
rc = []
if ag.get_atom(atom_name.strip()): return []
if type(bond_atom)==type(''):
ba = ag.get_atom(bond_atom.strip())
#print bond_atom,ba.quote()
if ba is None: return
else: ba = bond_atom
if type(angle_atom)==type(''):
aa = ag.get_atom(angle_atom.strip())
#print angle_atom,aa.quote()
if aa is None: return
else: aa = angle_atom
if type(dihedral_atom)==type(''):
da = ag.get_atom(dihedral_atom.strip())
#print dihedral_atom, da.quote()
if da is None: return
else: da = dihedral_atom
ro2 = construct_xyz(ba, bond_length,
aa, angle,
da, dihedral,
period=1,
)
atom = iotbx.pdb.hierarchy.atom()
atom.name = atom_name
atom.element = atom_element
atom.occ = ba.occ
atom.b = ba.b
# altloc???
atom.hetero = ba.hetero
atom.segid = ' '*4
atom.xyz = ro2[0]
if append_to_end_of_model:
chain = _add_atom_to_chain(atom, ag)
rc.append(chain)
else:
ag.append_atom(atom)
return rc
def add_hydrogens_to_atom_group_using_bad(
ag,
atom_name,
atom_element,
bond_atom,
angle_atom,
dihedral_atom,
bond_length,
angle,
dihedral,
append_to_end_of_model=False,
):
rc = []
if ag.get_atom(atom_name.strip()): return []
if type(bond_atom) == type(''):
ba = ag.get_atom(bond_atom.strip())
if ba is None: return []
else: ba = bond_atom
if type(angle_atom) == type(''):
aa = ag.get_atom(angle_atom.strip())
if aa is None: return []
else: aa = angle_atom
if type(dihedral_atom) == type(''):
da = ag.get_atom(dihedral_atom.strip())
if da is None: return []
else: da = dihedral_atom
ro2 = construct_xyz(
ba,
bond_length,
aa,
angle,
da,
dihedral,
period=1,
)
atom = _new_atom(atom_name, atom_element, ro2[0], ba.occ, ba.b, ba.hetero)
if append_to_end_of_model:
chain = _add_atom_to_chain(atom, ag)
rc.append(chain)
else:
ag.append_atom(atom)
return rc
def add_n_terminal_hydrogens_to_atom_group(ag,
use_capping_hydrogens=False,
append_to_end_of_model=False,
retain_original_hydrogens=True,
n_ca_c=None,
):
rc=[]
if n_ca_c is not None:
n, ca, c = n_ca_c
else:
n = ag.get_atom("N")
if n is None: return 'no N'
ca = ag.get_atom("CA")
if ca is None: return 'no CA'
c = ag.get_atom("C")
if c is None: return 'no C'
atom = ag.get_atom('H')
dihedral=120.
if atom:
dihedral = dihedral_angle(sites=[atom.xyz,
n.xyz,
ca.xyz,
c.xyz,
],
deg=True)
if retain_original_hydrogens: pass
else:
if ag.get_atom("H"): # maybe needs to be smarter or actually work
ag.remove_atom(ag.get_atom('H'))
#if use_capping_hydrogens and 0:
# for i, atom in enumerate(ag.atoms()):
# if atom.name == ' H3 ':
# ag.remove_atom(i)
# break
# add H1
rh3 = construct_xyz(n, 0.9,
ca, 109.5,
c, dihedral,
)
# this could be smarter
possible = ['H', 'H1', 'H2', 'H3', 'HT1', 'HT2']
h_count = 0
for h in possible:
if ag.get_atom(h): h_count+=1
number_of_hydrogens=3
if use_capping_hydrogens:
number_of_hydrogens-=1
#if ag.atoms()[0].parent().resname=='PRO':
# number_of_hydrogens=-1
# # should name the hydrogens correctly
if h_count>=number_of_hydrogens: return []
for i in range(0, number_of_hydrogens):
name = " H%d " % (i+1)
if retain_original_hydrogens:
if i==0 and ag.get_atom('H'): continue
if ag.get_atom(name.strip()): continue
if ag.resname=='PRO':
if i==0:
continue
atom = iotbx.pdb.hierarchy.atom()
atom.name = name
atom.element = "H"
atom.xyz = rh3[i]
atom.occ = n.occ
atom.b = n.b
atom.segid = ' '*4
if append_to_end_of_model and i+1==number_of_hydrogens:
rg = _add_atom_to_chain(atom, ag)
rc.append(rg)
else:
ag.append_atom(atom)
return rc
