def _check_i_seqs(atom_group1, atom_group2, i_seqs):
atoms = []
for i_seq in i_seqs:
for atom in list(atom_group1.atoms()) + list(atom_group2.atoms()):
if atom.i_seq == i_seq:
atoms.append(atom)
break
d2 = linking_utils.get_distance2(*atoms) # XXXX needs to be sym aware
if d2 > 9: return False
return True
def _check_i_seqs(atom_group1, atom_group2, i_seqs):
atoms = []
for i_seq in i_seqs:
for atom in list(atom_group1.atoms())+list(atom_group2.atoms()):
if atom.i_seq==i_seq:
atoms.append(atom)
break
d2 = linking_utils.get_distance2(*atoms) # XXXX needs to be sym aware
if d2>9: return False
return True
def predict_protonation(ag, verbose=False):
from cctbx import geometry
from mmtbx.monomer_library.linking_utils import get_distance2
from math import sqrt
# from cctbx_geometry_restraints_ext import *
# from cctbx.array_family import flex
"""
his1 = -37.35*X1 + 15.57*X2 - 0.64*X3 + 0.76*X4 + 17.30
his2 = -2.16*X1 - 6.08*X2 + 0.56*X3 + 0.42*X4 - 94.46
X1 = ND1-CE1
X2 = CE1-NE2
X3 = -ND1-
X4 = -NE2-
his1<0 ~> ND1 protonated
his1>0
his2<0 ~> NE2 protonated
his2>0 ~> doubly protonated
"""
bonds = {
("ND1", "CE1") : None,
("NE2", "CE1") : None,
}
if verbose:
for atom in ag.atoms():
print atom.quote()
for i, tmp_atom in enumerate(bonds):
atoms = []
for j in range(2):
for atom in ag.atoms():
if atom.name.strip()==tmp_atom[j]:
atoms.append(atom)
break
if len(atoms)==2:
d2=get_distance2(*atoms)
bonds[tmp_atom]=sqrt(d2)
angles = {
("CG", "ND1", "CE1") : None,
("CE1","NE2", "CD2") : None,
}
for i, tmp_atom in enumerate(angles):
atoms = []
for j in range(3):
for atom in ag.atoms():
if atom.name.strip()==tmp_atom[j]:
atoms.append(atom.xyz)
break
if len(atoms)==3:
angle=geometry.angle((atoms)).angle_model
angles[tmp_atom]=angle
if None in bonds.values() or None in angles.values(): return None
his1 = 17.30 - 0.64*angles[("CG", "ND1", "CE1")]
his1 += 0.76*angles[("CE1","NE2", "CD2")]
his1 -= 37.35*bonds[("ND1", "CE1")]
his1 += 15.57*bonds[("NE2", "CE1")]
his2 = -94.46 + 0.56*angles[("CG", "ND1", "CE1")]
his2 += 0.42*angles[("CE1","NE2", "CD2")]
his2 -= 2.61*bonds[("ND1", "CE1")]
his2 -= 6.08*bonds[("NE2", "CE1")]
if verbose:
print 'his1',his1
print 'his2',his2
return (his1, his2)
def predict_protonation(ag, verbose=False):
from cctbx import geometry
from mmtbx.monomer_library.linking_utils import get_distance2
from math import sqrt
# from cctbx_geometry_restraints_ext import *
# from cctbx.array_family import flex
"""
his1 = -37.35*X1 + 15.57*X2 - 0.64*X3 + 0.76*X4 + 17.30
his2 = -2.16*X1 - 6.08*X2 + 0.56*X3 + 0.42*X4 - 94.46
X1 = ND1-CE1
X2 = CE1-NE2
X3 = -ND1-
X4 = -NE2-
his1<0 ~> ND1 protonated
his1>0
his2<0 ~> NE2 protonated
his2>0 ~> doubly protonated
"""
bonds = {
("ND1", "CE1"): None,
("NE2", "CE1"): None,
}
if verbose:
for atom in ag.atoms():
print atom.quote()
for i, tmp_atom in enumerate(bonds):
atoms = []
for j in range(2):
for atom in ag.atoms():
if atom.name.strip() == tmp_atom[j]:
atoms.append(atom)
break
if len(atoms) == 2:
d2 = get_distance2(*atoms)
bonds[tmp_atom] = sqrt(d2)
angles = {
("CG", "ND1", "CE1"): None,
("CE1", "NE2", "CD2"): None,
}
for i, tmp_atom in enumerate(angles):
atoms = []
for j in range(3):
for atom in ag.atoms():
if atom.name.strip() == tmp_atom[j]:
atoms.append(atom.xyz)
break
if len(atoms) == 3:
angle = geometry.angle((atoms)).angle_model
angles[tmp_atom] = angle
if None in bonds.values() or None in angles.values(): return None
his1 = 17.30 - 0.64 * angles[("CG", "ND1", "CE1")]
his1 += 0.76 * angles[("CE1", "NE2", "CD2")]
his1 -= 37.35 * bonds[("ND1", "CE1")]
his1 += 15.57 * bonds[("NE2", "CE1")]
his2 = -94.46 + 0.56 * angles[("CG", "ND1", "CE1")]
his2 += 0.42 * angles[("CE1", "NE2", "CD2")]
his2 -= 2.61 * bonds[("ND1", "CE1")]
his2 -= 6.08 * bonds[("NE2", "CE1")]
if verbose:
print 'his1', his1
print 'his2', his2
return (his1, his2)
