def find_C3C4(C2, O1, mol_C):
# Find the possible neighboring C(s) of C2 (C3/C4)
C3_possibles = filter(lambda m: m['index'] != C2['index'],
mt.find_possibles(mol_C))
d_C2O1 = mt.distance(C2['rvec'], O1['rvec'])
C3_af = filter(
lambda m: mt.bond_length_filter(m['rvec'], C2[
'rvec'], CC_BOND_LENGTH, TOLERANCE_LEVEL) and mt.distance(
m['rvec'], O1['rvec']) > d_C2O1, C3_possibles
) # Change the selection of O1 to see how the code below works # Extra filter: Make sure C3 is not close to O1 (which is adjacent to C2)
C3_af_index = set()
for c3 in C3_af:
C3_af_index.add(c3['index'])
if len(C3_af_index) == 1:
C2_adj = 1 # C2 is adjacent to one C. Choose that C to be C3.
C3C4_af = C3_af
elif len(C3_af_index) == 2:
C2_adj = 2 # C2 is adjacent to two C-s. Let those C-s be C3 and C4 respectively.
C3_af_grps = []
for i in C3_af_index:
C3_af_grps.append(filter(lambda m: m['index'] == i, C3_af))
C3C4_af = list(
map(list, itertools.product(C3_af_grps[0], C3_af_grps[1])))
else:
C2_adj = 0
C3C4_af = []
return C2_adj, C3C4_af
def find_C2(O1, mol_C):
# Find the neighboring C of O1 (C2)
C2_possibles = mt.find_possibles(mol_C)
C2_af = filter(
lambda m: mt.bond_length_filter(m['rvec'], O1['rvec'], CO_BOND_LENGTH,
TOLERANCE_LEVEL), C2_possibles
) # Change the tolerance range here to see how this filter works
return C2_af
def rcs_filter(a_r, base_group, tol_range=0.1):
possible_a = mt.find_possibles([a_r]) # Find all possible rvec for a_r
possible_af1 = filter(
lambda m: mt.bond_length_atom_finder(base_group, m, tol_range),
possible_a)
return possible_af1
def find_O5_C2adj1(
C2, C3, mol_Or
): # If C2 is adjacent to one C (C3), then C3 must be connected to an O (O5).
O5_possibles = mt.find_possibles(mol_Or)
O5_af = filter(
lambda m: mt.bond_length_filter(m['rvec'], C3[
'rvec'], CO_BOND_LENGTH, TOLERANCE_LEVEL) and mt.distance(
m['rvec'], C2['rvec']) > (CO_BOND_LENGTH + TOLERANCE_LEVEL),
O5_possibles)
return O5_af
def find_C4_C2adj1(C2, C3, O5, mol_C):
# Find the possible C4
C4_possibles = filter(
lambda m: m['index'] not in (C2['index'], C3['index']),
mt.find_possibles(mol_C))
d_C3O5 = mt.distance(C3['rvec'], O5['rvec'])
C4_af = filter(
lambda m: mt.bond_length_filter(m['rvec'], C3[
'rvec'], CC_BOND_LENGTH, TOLERANCE_LEVEL) and mt.distance(
m['rvec'], O5['rvec']) > d_C3O5, C4_possibles
) # Extra filter: Make sure C4 is not close to O5 (which is adjacent to C3)
return C4_af
def find_O5_C2adj2(
C3, C4, mol_Or
): # If C2 is adjacent to two C-s (C3, C4), then O5 must be adjacent to one of C3 and C4.
O5_possibles = mt.find_possibles(mol_Or)
O5_afC3 = filter(
lambda m: mt.bond_length_filter(m['rvec'], C3[
'rvec'], CO_BOND_LENGTH, TOLERANCE_LEVEL) and mt.distance(
m['rvec'], C4['rvec']) > (CO_BOND_LENGTH + TOLERANCE_LEVEL),
O5_possibles
) # Extra filter: If O5 is connected to C3, make sure it is not too close to C4 (vice versa)
O5_afC4 = filter(
lambda m: mt.bond_length_filter(m['rvec'], C4[
'rvec'], CO_BOND_LENGTH, TOLERANCE_LEVEL) and mt.distance(
m['rvec'], C3['rvec']) > (CO_BOND_LENGTH + TOLERANCE_LEVEL),
O5_possibles)
O5_af = O5_afC3 + O5_afC4
return O5_af