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 alcohol_groups(gra, filterlst=()):
""" Determine the location alcohol groups
Returns a lsts of idxs of C-O-H groups
"""
alc_grps = two_bond_idxs(gra, asymb1='C', cent='O', asymb2='H')
alc_grps = filter_idxs(alc_grps, filterlst=filterlst)
return alc_grps
def alcohol_groups(gra, filterlst=()):
""" Determine the location of alcohol groups. The locations are
specified as tuple-of-tuple of idxs indicating the C-O-H atoms
of the group: (C-idx, O-idx, H-idx).
:param gra: molecular graph
:type gra: molecular graph data structure
:rtype: tuple(int)
"""
alc_grps = two_bond_idxs(gra, symb1='C', cent='O', symb2='H')
alc_grps = filter_idxs(alc_grps, filterlst=filterlst)
return alc_grps
def ketone_groups(gra, filterlst=()):
""" Determine the location of ketone groups
Returns C-O bond idxs
"""
ket_grps = tuple()
co_bonds = bonds_of_type(gra, asymb1='C', asymb2='O', mbond=2)
for co_bond in co_bonds:
c_idx, o_idx = co_bond
c_neighs = neighbors_of_type(gra, c_idx, asymb='H')
if not c_neighs:
ket_grps += ((c_idx, o_idx),)
ket_grps = filter_idxs(ket_grps, filterlst=filterlst)
return ket_grps
def aldehyde_groups(gra, filterlst=()):
""" Determine the location of aldehyde groups
Returns C-O bond idxs
"""
ald_grps = tuple()
co_bonds = bonds_of_type(gra, asymb1='C', asymb2='O', mbond=2)
for co_bond in co_bonds:
c_idx, o_idx = co_bond
c_neighs = neighbors_of_type(gra, c_idx, asymb='H')
if c_neighs:
ald_grps += ((c_idx, o_idx),)
ald_grps = filter_idxs(ald_grps, filterlst=filterlst)
return ald_grps
def ketone_groups(gra, filterlst=()):
""" Determine the location of ketone groups. The locations are
specified as tuple-of-tuple of idxs indicating the C-O atoms
of the group: (C-idx, O-idx).
:param gra: molecular graph
:type gra: molecular graph data structure
:rtype: tuple(int)
"""
ket_grps = tuple()
co_bonds = bonds_of_type(gra, symb1='C', symb2='O', mbond=2)
for co_bond in co_bonds:
c_idx, o_idx = co_bond
c_neighs = neighbors_of_type(gra, c_idx, symb='H')
if not c_neighs:
ket_grps += ((c_idx, o_idx), )
ket_grps = filter_idxs(ket_grps, filterlst=filterlst)
return ket_grps