def get_missing_h_in_residue(self, residue, mon_lib_srv):
missing = []
ca_xyz, xyz = None, None
mlq = rotamer_eval.mon_lib_query(residue.resname.strip().upper(),
mon_lib_srv)
if mlq is not None:
#hd_aliases = mlq.hydrogen_deuterium_aliases()
atom_name_list = []
for atom in residue.atoms():
if atom.name == " CA ":
ca_xyz = atom.xyz
if (not atom.element_is_hydrogen()):
xyz = atom.xyz
atom_name = atom.name.strip().upper()
atom_name_list.append(atom_name)
if is_deuterium(atom):
atom_name_list.append(atom_name.replace('D', 'H', 1))
#if atom_name in hd_aliases:
# atom_name_list.append(hd_aliases[atom_name])
if not ca_xyz:
ca_xyz = xyz
reference_H = []
atom_dict = mlq.atom_dict()
for at in atom_dict:
reference_H.append(at)
reference_non_H = []
for non in mlq.non_hydrogen_atoms():
reference_non_H.append(non.atom_id.strip().upper())
reference_list = [
x for x in reference_H if x not in reference_non_H
]
alternative_names = [('HA1', 'HA2', 'HA3'), ('HB1', 'HB2', 'HB3'),
('HG1', 'HG2', 'HG3'), ('HD1', 'HD2', 'HD3'),
('HE1', 'HE2', 'HE3'),
('HG11', 'HG12', 'HG13')]
for alts in alternative_names:
if (alts[0] in reference_list and alts[1] in reference_list):
if (atom_dict[alts[0]].type_energy == 'HCH2'
and atom_dict[alts[1]].type_energy == 'HCH2'):
reference_list.append(alts[2])
reference_list.remove(alts[0])
if alts[2].replace('H', 'D', 1) in atom_name_list:
atom_name_list.append(alts[2])
for atom_name in reference_list:
if atom_name not in atom_name_list:
if (atom_name == 'H' and
('H1' in atom_name_list and 'H2' in atom_name_list
and 'H3' in atom_name_list)):
continue
atom_temp = atom_name.replace("*", "'")
if atom_name.upper() == "O1P":
atom_temp = "OP1"
elif atom_name.upper() == "O2P":
atom_temp = "OP2"
if atom_temp not in atom_name_list:
missing.append(atom_name)
return xyz, missing
def exercise () :
from mmtbx.ions import server as s
import iotbx.pdb.hierarchy
import iotbx.pdb
from cctbx.eltbx import chemical_elements
# Assert that valence parameters exist for all common ions with their
# coordinating atoms
for elem in ["NA", "MG", "K", "CA", "MN", "FE", "NI", "CO", "CU", "ZN", "CD"]:
params = s.get_metal_parameters(elem)
assert (len(params.allowed_coordinating_atoms) > 0)
assert (params.charge is not None)
for elem2 in params.allowed_coordinating_atoms :
atom1 = iotbx.pdb.hierarchy.atom()
atom1.name = elem
atom1.element = elem
atom1.charge = "+" + str(params.charge)
atom2 = iotbx.pdb.hierarchy.atom()
atom2.name = elem2
atom2.element = elem2
atom2.charge = "{:+}".format(s.get_charge(elem2))
assert (s.get_valence_params(atom1, atom2) != (None, None))
# Make sure we don't crash on any ion residue names
for elem in chemical_elements.proper_upper_list():
s.get_element(elem)
s.get_charge(elem)
# Make sure we don't crash on any common residue names either
from mmtbx import monomer_library
from mmtbx.rotamer.rotamer_eval import mon_lib_query
mon_lib_srv = monomer_library.server.server()
common_residues = [getattr(iotbx.pdb, i) for i in dir(iotbx.pdb)
if i.startswith("common_residue_names") and
isinstance(getattr(iotbx.pdb, i), list)]
common_atoms = {
"H": -1,
"C": 4,
"N": -3,
"O": -2,
"S": -2,
}
for common in common_residues:
for resn in common:
mlq = mon_lib_query(resn, mon_lib_srv)
if mlq is None:
continue
for atom in mlq.atom_dict().values():
elem, charge = s._get_charge_params(resname = resn,
element = atom.type_symbol)
from libtbx import group_args
class GAtom(group_args):
def fetch_labels(self):
return group_args(resname = self.resname)
def id_str(self):
return "gatom=\"{} {}\"".format(self.resname, self.element)
def charge_as_int(self):
return int(self.charge)
gatom = GAtom(
element = atom.type_symbol,
resname = resn,
charge = "0",
)
get_charge_val, get_elem_val = s.get_charge(gatom), s.get_element(gatom)
if elem in common_atoms:
assert charge == common_atoms[elem]
assert get_charge_val == charge
assert get_elem_val == elem
# And we support all waters
for resn in iotbx.pdb.common_residue_names_water:
assert s.get_element(resn) == "O"
assert s.get_charge(resn) == -2
print "OK"
def exercise():
from mmtbx.ions import server as s
import iotbx.pdb.hierarchy
import iotbx.pdb
from cctbx.eltbx import chemical_elements
# Assert that valence parameters exist for all common ions with their
# coordinating atoms
for elem in [
"NA", "MG", "K", "CA", "MN", "FE", "NI", "CO", "CU", "ZN", "CD"
]:
params = s.get_metal_parameters(elem)
assert (len(params.allowed_coordinating_atoms) > 0)
assert (params.charge is not None)
for elem2 in params.allowed_coordinating_atoms:
atom1 = iotbx.pdb.hierarchy.atom()
atom1.name = elem
atom1.element = elem
atom1.charge = "+" + str(params.charge)
atom2 = iotbx.pdb.hierarchy.atom()
atom2.name = elem2
atom2.element = elem2
atom2.charge = "{:+}".format(s.get_charge(elem2))
assert (s.get_valence_params(atom1, atom2) != (None, None))
# Make sure we don't crash on any ion residue names
for elem in chemical_elements.proper_upper_list():
s.get_element(elem)
s.get_charge(elem)
# Make sure we don't crash on any common residue names either
from mmtbx import monomer_library
from mmtbx.rotamer.rotamer_eval import mon_lib_query
mon_lib_srv = monomer_library.server.server()
common_residues = [
getattr(iotbx.pdb, i) for i in dir(iotbx.pdb)
if i.startswith("common_residue_names")
and isinstance(getattr(iotbx.pdb, i), list)
]
common_atoms = {
"H": -1,
"C": 4,
"N": -3,
"O": -2,
"S": -2,
}
for common in common_residues:
for resn in common:
mlq = mon_lib_query(resn, mon_lib_srv)
if mlq is None:
continue
for atom in mlq.atom_dict().values():
elem, charge = s._get_charge_params(resname=resn,
element=atom.type_symbol)
from libtbx import group_args
class GAtom(group_args):
def fetch_labels(self):
return group_args(resname=self.resname)
def id_str(self):
return "gatom=\"{} {}\"".format(
self.resname, self.element)
def charge_as_int(self):
return int(self.charge)
gatom = GAtom(
element=atom.type_symbol,
resname=resn,
charge="0",
)
get_charge_val, get_elem_val = s.get_charge(
gatom), s.get_element(gatom)
if elem in common_atoms:
assert charge == common_atoms[elem]
assert get_charge_val == charge
assert get_elem_val == elem
# And we support all waters
for resn in iotbx.pdb.common_residue_names_water:
assert s.get_element(resn) == "O"
assert s.get_charge(resn) == -2
print "OK"
def get_missing_h_in_residue(self, residue, mon_lib_srv):
missing = []
ca_xyz, xyz, xyzh = None, None, None
mlq = rotamer_eval.mon_lib_query(residue.resname.strip().upper(), mon_lib_srv)
if mlq is not None:
#hd_aliases = mlq.hydrogen_deuterium_aliases()
atom_name_list = []
for atom in residue.atoms():
atom_name = atom.name.strip().upper()
if atom_name == "CA":
ca_xyz = atom.xyz
if (not atom.element_is_hydrogen()):
xyz = atom.xyz
else:
atom_name_list.append(atom_name)
xyzh = atom.xyz
if is_deuterium(atom):
atom_name_list.append(atom_name.replace('D','H',1))
#if atom_name in hd_aliases:
# atom_name_list.append(hd_aliases[atom_name])
if not ca_xyz:
ca_xyz = xyz
if not ca_xyz:
ca_xyz = xyzh
# Step 1: Get list of expected H and non-H atoms
reference = []
atom_dict = mlq.atom_dict()
for at in atom_dict:
reference.append(at)
# Step 2: Get list of expected non-H atoms
reference_non_H = []
for non in mlq.non_hydrogen_atoms():
reference_non_H.append(non.atom_id.strip().upper())
# Step 3: Get list of expected H atoms only
reference_hydrogens = [x for x in reference if x not in reference_non_H]
# Step 4: There can be naming differences: HB1+HB2 or HB2+HB3
alternative_names = [
('HA1', 'HA2', 'HA3'),
('HB1', 'HB2', 'HB3'),
('HG1', 'HG2', 'HG3'),
('HD1', 'HD2', 'HD3'),
('HE1', 'HE2', 'HE3'),
('HG11', 'HG12', 'HG13')
]
for alts in alternative_names:
if (alts[0] in reference_hydrogens and alts[1] in reference_hydrogens):
if (atom_dict[alts[0]].type_energy == 'HCH2' and
atom_dict[alts[1]].type_energy == 'HCH2'):
reference_hydrogens.append(alts[2])
reference_hydrogens.remove(alts[0])
# if alts[2].replace('H','D',1) in atom_name_list:
# atom_name_list.append(alts[2])
for atom_name in reference_hydrogens:
if atom_name not in atom_name_list:
if (atom_name == 'H' and
('H1' in atom_name_list and 'H2' in atom_name_list and 'H3' in atom_name_list)):
continue
if (atom_name.endswith('*')):
atom_temp = atom_name.replace("*", "'")
elif (atom_name.endswith('*1')):
atom_temp = atom_name.replace("*1", "'")
elif (atom_name.endswith('*2')):
atom_temp = atom_name.replace("*2", "''")
else:
atom_temp = atom_name
# if atom_name.upper() == "O1P":
# atom_temp = "OP1"
# elif atom_name.upper() == "O2P":
# atom_temp = "OP2"
if atom_temp not in atom_name_list:
if atom_temp.endswith("'"):
missing.append(atom_temp)
else:
missing.append(atom_name)
return ca_xyz, missing