def get_prochirality(self):
"""
Determines whether its necessary to differentiate between
two sides of the molecule. For example Protons in R-O-CH2-N-R.
If the atom is prochiral, the side (re/si) is determined.
"""
if self.element in halogens:
self.prochiral = False
return
if self.invariom_name[1] is '@':
self.prochiral = False
if self.invariom_name[2] is '3':
print('Warning! Approximating ADP in 3 membered ring for atom {}.'.format(self.name))
return
if not get_framework_neighbors(atom=self, useH=True):
self.prochiral = False
return
neighbor0 = get_framework_neighbors(self, useH=True)
if len(neighbor0) > 1:
self.prochiral = False
return
neighbor0 = neighbor0[0]
neighbors = [atom.element for atom in get_framework_neighbors(neighbor0,
useH=True) if not atom == self]
if any(self.element == i for i in neighbors):
neighbors.remove(self.element)
if not any(self.element == i for i in neighbors):
if len(neighbors) > 1:
if not neighbors[0] == neighbors[1]:
self.prochiral = True
pos1 = self.cart
pos2 = neighbor0.cart
pos3 = cg.get_closest_atom_of_element(self.element, neighbor0, exclude=self).cart
plane_vector = cg.get_normal_vector_of_plane(pos1, pos2, pos3)
ref_element = max([proton_number[i] for i in neighbors])
ref_atom = cg.get_closest_atom_of_element(elementofnumber[ref_element], neighbor0,
exclude=self)
ref_vector = neighbor0.cart - ref_atom.cart
ref_vector /= norm(ref_vector)
if dot(ref_vector, plane_vector) > 0:
self.side = 're'
else:
self.side = 'si'
return
self.prochiral = False
def identify_molecules(self):
"""
Takes an instance of the MOLECULE class as argument and returns a
dictionary that keys an identifying integer to every atom name
specifying which of the atoms in the molecule form an 'independent'
molecule in the chemical sense.
If all atoms are part of the same molecule, all atoms get the
integer '0'.
"""
blacklist = set()
#===========================================================================
# molecules=[]
#===========================================================================
self.ID = 0
for atom1 in self.atoms:
framework = []
for atom2 in get_framework_neighbors(atom1):
if not atom1.get_name() in blacklist and not atom2.get_name() in blacklist:
framework += framework_crawler(atom1, atom2)
framework += framework_crawler(atom2, atom1)
framework = list(set(framework))
[blacklist.add(atom.get_name()) for atom in framework]
#===============================================================
# molecules.append(framework)
#===============================================================
if framework:
chem_mol = framework
for atom in framework:
atom.set_molecule_id(self.ID)
for h in get_framework_neighbors(atom, useH=True):
if h.get_element() == 'H':
h.set_molecule_id(self.ID)
chem_mol.append(h)
self.ID += 1
self.chem_mol.append(chem_mol)
for atom in self.atoms:
if atom.molecule_id == None:
atom.set_molecule_id(self.ID)
self.ID += 1
return self.ID
def iter_riding_hydrogen_atoms(atom):
return atoms_of_element(get_framework_neighbors(atom=atom, useH=True))
def iter_bound_atoms(self):
return get_framework_neighbors(self)
def averageADP(self):
cartAdp = array([0]*6)
for atom in get_framework_neighbors(self):
cartAdp += atom.adp['cart_int']
self.adp['cart_int'] = cartAdp
