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jrdkit.py
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"""
RDKit related files are included.
"""
from jchem import *
from chemspipy import ChemSpider
cs_global = ChemSpider('9fc1f087-d349-49ef-bdfb-f725fd6b81b5')
def find( sm, sg, disp = False, graph = False):
m = Chem.MolFromSmiles( sm)
results = m.GetSubstructMatches( Chem.MolFromSmarts( sg))
if graph:
show_mol( sm)
if disp:
print('Results:', results)
print('Canonical SMILES:', Chem.MolToSmiles( m))
return results
def prt_sg( m, sg = '[C]', info = ''):
matched_sg_l = m.GetSubstructMatches( Chem.MolFromSmarts( sg))
print(sg, ':', len(matched_sg_l), '-->', matched_sg_l, info)
return len(matched_sg_l)
def find_subgroups( sm = 'CNN', info = ''):
"""
return subgroups for various functional groups
"""
# sm = 'CNN' # Acetamide --> 1.58
show_mol( sm)
print('SMILES: {},'.format(sm), info)
m = Chem.MolFromSmiles( sm)
prt_sg( m, '[a]')
prt_sg( m, '[A]')
prt_sg( m, '[#6]')
prt_sg( m, '[R1]')
prt_sg( m, '[R2]')
prt_sg( m, '[r5]')
prt_sg( m, '[v4]')
prt_sg( m, '[v3]')
prt_sg( m, '[X2]')
prt_sg( m, '[H]')
prt_sg( m, '[H1]')
prt_sg( m, '*')
prt_sg( m, 'CC')
prt_sg( m, '[#6]~[#6]') # any bond
prt_sg( m, '[#6]@[#6]') # ring bond
#prt_sg( m, 'F/?[#6]=C/[Cl]')
prt_sg( m, 'F/[#6]=C/Cl')
prt_sg( m, '[!c]')
prt_sg( m, '[N,#8]')
prt_sg( m, '[#7,C&+0,+1]')
print('============================================')
sgn_d = dict()
prt_sg( m, '[C]', info = 'no subgroup')
print('')
prt_sg( m, '[CH3]', info = 'no subgroup')
sgn_d[1] = prt_sg( m, '[*CH3]', info = '#01, sol += -1.7081')
print('')
prt_sg( m, '[CH2]', info = 'no subgroup')
sgn_d[2] = prt_sg( m, '[*CH2*]', info = '#02, sol += -0.4991')
sgn_d[5] = prt_sg( m, '*=[CH2]', info = '#02, sol += -0.4991')
print('')
prt_sg( m, '[CH1]', info = 'no subgroup')
sgn_d[3] = prt_sg( m, '*[CH1]*(*)', info = '#02, sol += -0.4991')
sgn_d[6] = prt_sg( m, '*=[CH1]*', info = '#02, sol += -0.4991')
print('')
prt_sg( m, '[CH0]', info = 'no subgroup')
prt_sg( m, '*[CH0]', info = 'no subgroup')
prt_sg( m, '[*CH0]', info = 'no subgroup')
prt_sg( m, '[*CH0*](*)', info = 'no subgroup')
prt_sg( m, '*=[CH0*](*)', info = 'no subgroup')
sgn_d[4] = prt_sg( m, '*[CH0]*(*)(*)', info = '#02, sol += -0.4991')
sgn_d[7] = prt_sg( m, '*=[CH0]*(*)', info = '#02, sol += -0.4991')
sgn_d[8] = prt_sg( m, '*=[CH0]=*', info = '#02, sol += -0.4991')
sgn_d[9] = prt_sg( m, '*[CH0]#[CH1]', info = '#02, sol += -0.4991')
print('')
sgn_d[8] = prt_sg( m, '[NH2]', info = '#49, sol += 0')
sgn_d[8] = prt_sg( m, '[NH]', info = '#50, sol += 0')
sgn_d[8] = prt_sg( m, '[OH]') #26 (primary) 0.2711
def get_atoms( s_org='Oc1ccccc1', sub_s = 'ccO', detail = False, number = False):
print("Original SMILES :", s_org)
s = Chem.MolToSmiles( Chem.MolFromSmiles( s_org))
print("Canonical SMILES:", s)
print("Chemspider")
for result in cs_global.search( s):
print(result, result.common_name, result.csid)
show_mol(s)
m = Chem.MolFromSmiles(s)
for ii, atom in enumerate(m.GetAtoms()):
if number: print( ii, ':', sep = '', end = ' ')
print(atom.GetAtomicNum(), atom.GetSymbol(), atom.GetSmarts(), end=' ')
for nb in atom.GetNeighbors():
nb_idx = nb.GetIdx()
print( m.GetBondBetweenAtoms(ii,nb_idx).GetBondType(), nb_idx, end=', ')
print()
print("===========================")
if detail:
print('------------')
print("Atom status")
print('------------')
for atom in m.GetAtoms():
ii = atom.GetIdx()
print("Atom", ii, ":", atom.GetAtomicNum(), atom.GetSymbol(),
atom.GetSmarts(), atom.GetAtomicNum())
print("Neighbor atom indices and link bond types:", end = ' ')
for nb in atom.GetNeighbors():
nb_idx = nb.GetIdx()
print( m.GetBondBetweenAtoms(ii,nb_idx).GetBondType(), nb_idx, end=', ')
print()
print("atom.IsInRing:", atom.IsInRing())
print("atom.IsInRingSize(3):", atom.IsInRingSize(3))
print("atom.IsInRingSize(4):", atom.IsInRingSize(4))
print("atom.IsInRingSize(5):", atom.IsInRingSize(5))
print("atom.IsInRingSize(6):", atom.IsInRingSize(6))
for bond in atom.GetBonds():
print(bond.GetBondType())
print()
print('------------')
print("Bond status")
print('------------')
for bond in m.GetBonds():
print(bond.GetBondType())
print()
print('------------')
print("Ring status")
print('------------')
print('Chem.GetSSSR:', Chem.GetSSSR( m))
print()
print('------------')
print("Substring matching - Smart")
print('------------')
print('Substring SMILES:', sub_s)
patt = Chem.MolFromSmarts( sub_s)
print("Sets of matching indices:", m.GetSubstructMatches( patt))
def get_atoms_mol(m, sm = Chem.MolFromSmarts('ccO'), detail = False, number = False):
s_org = Chem.MolToSmiles( m)
sub_s = Chem.MolToSmarts( sm)
return get_atoms( s_org, sub_s = sub_s, detail=detail, number=number)
def get_AQ_sd():
"""
Return SMILES strings of AQ family members.
"""
AQ_sd = {
"AQ": 'O=C1c2ccccc2C(=O)c2ccccc12',
"AQS": 'OS(=O)(=O)c1ccc2C(=O)c3ccccc3C(=O)c2c1',
"AQDS": 'OS(=O)(=O)c1ccc2C(=O)c3ccc(cc3C(=O)c2c1)S(O)(=O)=O'}
return AQ_sd
def get_AQ_md():
"""
return mols of AQ family members
"""
AQ_md = {}
AQ_sd = get_AQ_sd()
for k in AQ_sd:
AQ_md[ k] = Chem.MolFromSmiles( AQ_sd[k])
return AQ_md
def generate_CSMILES( s_l, disp = False):
cs_l = []
for i, s in enumerate(s_l):
if disp: print( i, s)
cs = Chem.MolToSmiles(Chem.MolFromSmiles( s))
cs_l.append( cs)
return cs_l