def ether_groups(gra, filterlst=()):
""" Determine the location of ether groups
Returns a lsts of idxs of C-O-C groups
"""
ether_grps = tuple()
# Determing the indices of all rings in the molecule
_ring_idxs = ring_idxs(rings(gra))
coc_grps = two_bond_idxs(gra, asymb1='C', cent='O', asymb2='C')
for coc_grp in coc_grps:
c1_idx, o_idx, c2_idx = coc_grp
if not _ring_idxs:
ether_grps += ((c1_idx, o_idx, c2_idx),)
else:
for idxs in _ring_idxs:
if not set(coc_grp) <= set(idxs):
ether_grps += ((c1_idx, o_idx, c2_idx),)
ether_grps = filter_idxs(ether_grps, filterlst=filterlst)
return ether_grps
def ether_groups(gra, filterlst=()):
""" Determine the location of ether groups. The locations are
specified as tuple of idxs indicating the C-O-C atoms
of the group: (C-idx, O-idx, C-idx).
:param gra: molecular graph
:type gra: molecular graph data structure
:rtype: tuple(int)
"""
ether_grps = tuple()
# Determing the indices of all rings in the molecule
_ring_idxs = ring_idxs(rings(gra))
coc_grps = two_bond_idxs(gra, symb1='C', cent='O', symb2='C')
for coc_grp in coc_grps:
c1_idx, o_idx, c2_idx = coc_grp
if not _ring_idxs:
ether_grps += ((c1_idx, o_idx, c2_idx), )
else:
for idxs in _ring_idxs:
if not set(coc_grp) <= set(idxs):
ether_grps += ((c1_idx, o_idx, c2_idx), )
ether_grps = filter_idxs(ether_grps, filterlst=filterlst)
return ether_grps
def epoxide_groups(gra):
""" Determine the location of epoxide groups
Return C-O-C ring: only good for a 1,2-epoxide
"""
epox_grps = tuple()
# Determing the indices of all rings in the molecule
_ring_idxs = ring_idxs(rings(gra))
coc_grps = two_bond_idxs(gra, asymb1='C', cent='O', asymb2='C')
for coc_grp in coc_grps:
c1_idx, o_idx, c2_idx = coc_grp
if _ring_idxs:
for idxs in _ring_idxs:
if set(coc_grp) <= set(idxs):
epox_grps += ((c1_idx, o_idx, c2_idx),)
return epox_grps
def epoxy_groups(gra):
""" Determine the location of 1,2-epoxy groups. The locations are
specified as tuple-of-tuple of idxs indicating the C-O-C atoms
of the group: (C-idx, O-idx, C-idx).
:param gra: molecular graph
:type gra: molecular graph data structure
:rtype: tuple(int)
"""
epox_grps = tuple()
# Determing the indices of all rings in the molecule
_ring_idxs = ring_idxs(rings(gra))
coc_grps = two_bond_idxs(gra, symb1='C', cent='O', symb2='C')
for coc_grp in coc_grps:
c1_idx, o_idx, c2_idx = coc_grp
if _ring_idxs:
for idxs in _ring_idxs:
if set(coc_grp) <= set(idxs):
epox_grps += ((c1_idx, o_idx, c2_idx), )
return epox_grps
def _rotor_counts(gra, symbs):
""" Count up various types of bonds for a structure.
:param gra: molecular graph of species
:type gra: automol graph data structure
:param symbs: atomic symbols of species
:type symbs: tuple(str)
:rtype: tuple(float)
"""
# Initialize the rotor counts
n_pp, n_ps, n_pt, n_pq = 0, 0, 0, 0
n_ss, n_st, n_sq = 0, 0, 0
n_tt, n_tq = 0, 0
n_qq = 0
n_co, n_oo = 0, 0
n_ss_ring, n_rings = 0, 0
# Get the rings and the number
rings = _rings(gra)
ring_keys = set(ring_idxs(_rings(gra)))
n_rings = len(rings)
# Loop over the bonds and count the number of atoms
neighbors = atoms_neighbor_atom_keys(gra)
for bnd in bond_keys(gra):
key1, key2 = bnd
spair = (symbs[key1], symbs[key2])
if spair == ('C', 'C'):
# Figure out which neighbors are not hydrogen and count the number
atom1_neighbors = neighbors[key1]
numc1 = 0
for neighbor1 in atom1_neighbors:
if symbs[neighbor1] != 'H':
numc1 += 1
atom2_neighbors = neighbors[key2]
numc2 = 0
for neighbor2 in atom2_neighbors:
if symbs[neighbor2] != 'H':
numc2 += 1
# Determine appropriate term to increment
npair = (numc1, numc2)
if npair == (1, 1):
n_pp += 1
elif npair in ((1, 2), (2, 1)):
n_ps += 1
elif npair in ((1, 3), (3, 1)):
n_pt += 1
elif npair in ((1, 4), (4, 1)):
n_pq += 1
elif npair == (2, 2):
if {key1, key2} <= ring_keys:
n_ss_ring += 1
else:
n_ss += 1
elif npair in ((2, 3), (3, 2)):
n_st += 1
elif npair in ((2, 4), (4, 2)):
n_sq += 1
elif npair == (3, 3):
n_tt += 1
elif npair in ((3, 4), (4, 3)):
n_tq += 1
elif npair == (4, 4):
n_qq += 1
elif spair in (('C', 'O'), ('O', 'C')):
n_co += 1
elif spair == ('O', 'O'):
n_oo += 1
# Compile counts into a tuple
return (n_pp, n_ps, n_pt, n_pq, n_ss, n_st, n_sq, n_tt, n_tq, n_qq, n_co,
n_oo, n_ss_ring, n_rings)
def _rotor_counts(gra, symbs):
""" Count up various types of rotors
"""
# Initialize the rotor counts
n_pp, n_ps, n_pt, n_pq = 0, 0, 0, 0
n_ss, n_st, n_sq = 0, 0, 0
n_tt, n_tq = 0, 0
n_qq = 0
n_co, n_oo = 0, 0
n_ss_ring, n_rings = 0, 0
# Get the rings and the number
rings = automol.graph.rings(gra)
ring_keys = set(ring_idxs(automol.graph.rings(gra)))
n_rings = len(rings)
# Loop over the bonds and count the number of atoms
neighbors = automol.graph.atom_neighbor_keys(gra)
for bnd in automol.graph.bond_keys(gra):
key1, key2 = bnd
spair = (symbs[key1], symbs[key2])
if spair == ('C', 'C'):
# Figure out which neighbors are carbons and count the number
atom1_neighbors = neighbors[key1]
numc1 = 0
for neighbor1 in atom1_neighbors:
if symbs[neighbor1] == 'C':
numc1 += 1
atom2_neighbors = neighbors[key2]
numc2 = 0
for neighbor2 in atom2_neighbors:
if symbs[neighbor2] == 'C':
numc2 += 1
# Determine appropriate term to increment
npair = (numc1, numc2)
if npair == (1, 1):
n_pp += 1
elif npair in ((1, 2), (2, 1)):
n_ps += 1
elif npair in ((1, 3), (3, 1)):
n_pt += 1
elif npair in ((1, 4), (4, 1)):
n_pq += 1
elif npair == (2, 2):
if {key1, key2} <= ring_keys:
n_ss_ring += 1
else:
n_ss += 1
elif npair in ((2, 3), (3, 2)):
n_st += 1
elif npair in ((2, 4), (4, 2)):
n_sq += 1
elif npair == (3, 3):
n_tt += 1
elif npair in ((3, 4), (4, 3)):
n_tq += 1
elif npair == (4, 4):
n_qq += 1
elif spair in (('C', 'O'), ('O', 'C')):
n_co += 1
elif spair == ('O', 'O'):
n_oo += 1
# Compile counts into a tuple
return [
n_pp, n_ps, n_pt, n_pq, n_ss, n_st, n_sq, n_tt, n_tq, n_qq, n_co, n_oo,
n_ss_ring, n_rings
]
def _rotor_counts(gra, symbs):
""" Count up various types of rotors
"""
# Initialize the rotor counts
n_pp, n_ps, n_pt, n_pq = 0, 0, 0, 0
n_ss, n_st, n_sq = 0, 0, 0
n_tt, n_tq = 0, 0
n_qq = 0
n_co, n_oo = 0, 0
n_ss_ring, n_rings = 0, 0
# Get the rings and the number
rings = automol.graph.rings(gra)
ring_keys = set(ring_idxs(automol.graph.rings(gra)))
n_rings = len(rings)
# Loop over the bonds and count the number of atoms
neighbors = automol.graph.atom_neighbor_keys(gra)
for bnd in automol.graph.bond_keys(gra):
key1, key2 = bnd
symb1, symb2 = symbs[key1], symbs[key2]
if symb1 == 'C' and symb2 == 'C':
# Figure out which neighbors are carbons and count the number
atom1_neighbors = neighbors[key1]
numc1 = 0
for neighbor1 in atom1_neighbors:
if symbs[neighbor1] == 'C':
numc1 += 1
atom2_neighbors = neighbors[key2]
numc2 = 0
for neighbor2 in atom2_neighbors:
if symbs[neighbor2] == 'C':
numc2 += 1
# Determine appropriate term to increment
if numc1 == 1 and numc2 == 1:
n_pp += 1
elif (numc1 == 1 and numc2 == 2) or (numc1 == 2 and numc2 == 1):
n_ps += 1
elif (numc1 == 1 and numc2 == 3) or (numc1 == 3 and numc2 == 1):
n_pt += 1
elif (numc1 == 1 and numc2 == 4) or (numc1 == 4 and numc2 == 1):
n_pq += 1
elif numc1 == 2 and numc2 == 2:
if {key1, key2} <= ring_keys:
n_ss_ring += 1
else:
n_ss += 1
elif (numc1 == 2 and numc2 == 3) or (numc1 == 3 and numc2 == 2):
n_st += 1
elif (numc1 == 2 and numc2 == 4) or (numc1 == 4 and numc2 == 2):
n_sq += 1
elif numc1 == 3 and numc2 == 3:
n_tt += 1
elif (numc1 == 3 and numc2 == 4) or (numc1 == 4 and numc2 == 3):
n_tq += 1
elif numc1 == 4 and numc2 == 4:
n_qq += 1
elif (symb1 == 'C' and symb2 == 'O') or (symb1 == 'O'
and symb2 == 'C'):
n_co += 1
elif symb1 == 'O' and symb2 == 'O':
n_oo += 1
# Compile counts into a tuple
return [
n_pp, n_ps, n_pt, n_pq, n_ss, n_st, n_sq, n_tt, n_tq, n_qq, n_co, n_oo,
n_ss_ring, n_rings
]