Cedric Baerlocher
Reputation: 61
finding bicyclic compound and identifying them, as well as larger aromatic systems
currently I am working on a code that is able to identify some chemical groups, rings and selectively if the rings are aromatic or not. However there seems to be a problem once I want to analyze annulated ring systems like sterone and larger aromatic systems like naphtalene or indole. I know that the problem for the annulated rings comes from the part, that uses the length and multiplies it to not identify each carbon as one 'x_membered_ring'. And when using indole it finds an aromatic_6_memebred rings and a 9_membered one. How could I solve this issue so that the molecule can correctly identify all ring sytsem, while finding all unique ones and don't prints doubles? I have added some examples like Linagliptin (aromaticity, annulated rings) as well as Irinotecan , Adamantane , Cubane and Alpha-Hopan . Does someone have any propositions or advice on how to fix this issue and being able to find all rings and even give information about the annulated rings?
Thanks a lot for the help and support!
#finding chemical functional groups
from rdkit import Chem
def find_smiles_patterns(smiles):
mol = Chem.MolFromSmiles(smiles)
if mol is None:
return "Invalid SMILES string. Unable to parse molecule."
# Define a list to store the chemical groups found in the SMILES
chemical_groups = []
# SMARTS patterns to recognize chemical groups
smarts_patterns = {
'[C]=[C]': 'Alkene',
'[CX2]#[CX2]': 'Alkyne',
'[CX3]=[CX2]=[CX3]': 'Allene',
'[ClX1][CX4]': 'Alkylchloride',
'[FX1][CX4]': 'Alkylfluoride',
'[BrX1][CX4]': 'Alkylbromide',
'[IX1][CX4]': 'Alkyliodide',
'[OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]': 'Primary_alcohol',
'[OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]': 'Secondary_alcohol',
'[OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]': 'Tertiary_alcohol',
'[OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]': 'Dialkylether',
'[SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]': 'Dialkylthioether',
'[OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]': 'Alkylarylether',
'[c][OX2][c]': 'Diarylether',
'[SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]': 'Alkylarylthioether',
'[c][SX2][c]': 'Diarylthioether',
'[O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]': 'Oxonium',
'[NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]': 'Primary_aliph_amine',
'[NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]': 'Secondary_aliph_amine',
'[NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]': 'Tertiary_aliph_amine',
'[NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]': 'Quaternary_aliph_ammonium',
'[NX3H2+0,NX4H3+]c': 'Primary_arom_amine',
'[NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]': 'Secondary_arom_amine',
'[NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]': 'Tertiary_arom_amine',
'[NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]': 'Quaternary_arom_ammonium',
'[NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]': 'Secondary_mixed_amine',
'[NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]': 'Tertiary_mixed_amine',
'[NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]': 'Quaternary_mixed_ammonium',
'[N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]': 'Ammonium',
'[SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]': 'Alkylthiol',
'[SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]': 'Dialkylthioether',
'[SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]': 'Alkylarylthioether',
'[SX2D2][SX2D2]': 'Disulfide',
'[OX2H][OX2]': 'Hydroperoxide',
'[OX2D2][OX2D2]': 'Peroxo',
'[LiX1][#6,#14]': 'Organolithium_compounds',
'[MgX2][#6,#14]': 'Organomagnesium_compounds',
'[!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]': 'Organometallic_compounds',
'[$([CX3H][#6]),$([CX3H2])]=[OX1]': 'Aldehyde',
'[#6]([#6])(=O)[#6]': 'Ketone',
'C=C=O': 'Ketene',
'[$([CX3H][#6]),$([CX3H2])]=[SX1]': 'Thioaldehyde',
'[#6][CX3](=[SX1])[#6]': 'Thioketone',
'C=C=S': 'Thioketene',
'[NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]': 'Imine',
'[NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]': 'Immonium',
'[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]': 'Oxime',
'[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]' : 'Oximether',
'[OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]': 'Acetal',
'[OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]': 'Hemiacetal',
'[NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]': 'Aminal',
'[NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]': 'Hemiaminal',
'[SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]': 'Thioacetal',
'[SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]': 'Thiohemiacetal',
'[NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]': 'Halogen_acetal_like',
'[NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]': 'Acetal_like',
'[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]': 'Halogenmethylen_ester_and_similar',
'[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]': 'NOS_methylen_ester_and_similar',
'[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]': 'Hetero_methylen_ester_and_similar',
'[NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]': 'Cyanhydrine',
'[ClX1][CX3]=[CX3]': 'Chloroalkene',
'[FX1][CX3]=[CX3]': 'Fluoroalkene',
'[BrX1][CX3]=[CX3]': 'Bromoalkene',
'[IX1][CX3]=[CX3]': 'Iodoalkene',
'[OX2H][CX3;$([H1]),$(C[#6])]=[CX3]': 'Enol',
'[OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]': 'Endiol',
'[OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]': 'Enolether',
'[OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]': 'Enolester',
'[NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]': 'Enamine',
'[SX2H][CX3;$([H1]),$(C[#6])]=[CX3]': 'Thioenol',
'[SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]': 'Thioenolether',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]': 'Acylchloride',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]': 'Acylfluoride',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]': 'Acylbromide',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]': 'Acyliodide',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]': 'Acylhalide',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]': 'Carboxylic_acid',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]': 'Carboxylic_ester',
'[#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]': 'Lactone',
'[CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])': 'Carboxylic_anhydride',
'[CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]': 'Carbothioic_acid',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]': 'Carbothioic_S_ester',
'[#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]': 'Carbothioic_S_lactone',
'[CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]': 'Carbothioic_O_ester',
'[#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]': 'Carbothioic_O_lactone',
'[CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]': 'Carbothioic_halide',
'[CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]': 'Carbodithioic_acid',
'[CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]': 'Carbodithioic_ester',
'[#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]': 'Carbodithiolactone',
'[CX3](=[OX1])[NX3H1][CX3](=[OX1])[OX2H1]': 'Amide',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]': 'Primary_amide',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]': 'Secondary_amide',
'[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]': 'Tertiary_amide',
'c1cccnc1': 'Pyridine_Derivatives',
'c1cnccn1': 'Pyrazine_derivatives',
'[#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Lactam',
'[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])': 'Alkyl_imide',
'[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])': 'N_hetero_imide',
'[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])': 'Imide_acidic',
'[$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Thioamide',
'[#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Thiolactam',
'[#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]': 'Oximester',
'[NX3;!$(NC=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2;!$(NC=[O,S])]': 'Amidine',
'[CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]': 'Hydroxamic_acid',
'[CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]': 'Hydroxamic_acid_ester',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]': 'Imidoacid',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]': 'Imidoacid_cyclic',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]': 'Imidoester',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]': 'Imidolactone',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]': 'Imidothioacid',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]': 'Imidoacid_cyclic',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]': 'Imidoester',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]': 'Imidolactone',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]': 'Imidothioacid',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]': 'Imidothioacid_cyclic',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]': 'Imidothioester',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]': 'Imidothiolactone',
'[$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]': 'Amidrazone',
'[$([#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]),$([#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][$([CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])])])]': 'Amidine',
'[#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]': 'Imidolactam',
'[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]': 'Imidoylhalide',
'[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]': 'Imidoylhalide_cyclic',
'[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]': 'Alpha_aminoacid',
'[OX2H][C][CX3](=[OX1])[OX2H,OX1-]': 'Alpha_hydroxyacid',
'[NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]': 'Peptide_middle',
'[NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]': 'Peptide_C_term',
'[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]': 'Peptide_N_term',
'[#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]': 'Carboxylic_orthoester',
'[CX3]=[CX2]=[OX1]': 'Ketene',
'[#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]': 'Ketenacetal',
'[NX1]#[CX2]': 'Nitrile',
'[CX1-]#[NX2+]': 'Isonitrile',
'[#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]': 'Carbonic_acid_dieester',
'[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]': 'Carbonic_acid_esterhalide',
'[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]': 'Carbonic_acid_monoester',
'[#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]': 'Thiocarbonic_acid_dieester',
'[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]': 'Thiocarbonic_acid_esterhalide',
'[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]': 'Thiocarbonic_acid_monoester',
'[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]': 'Urea',
'[#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]': 'Thiourea',
'[#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]': 'Isourea',
'[#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]': 'Isothiourea',
'[N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]': 'Guanidine_Derivative',
'[NX3]C(=[OX1])[O;X2H,X1-]': 'Carbaminic_acid',
'[#7X3][#6](=[OX1])[#8X2][#6]': 'Urethan',
'[#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]': 'Biuret',
'[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]': 'Semicarbazide',
'[#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]': 'Carbazide',
'[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]': 'Semicarbazone',
'[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]': 'Carbazone',
'[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]': 'Thiosemicarbazide',
'[#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]': 'Thiocarbazide',
'[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]': 'Thiosemicarbazone',
'[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]': 'Thiocarbazone',
'[NX2]=[CX2]=[OX1]': 'Isocyanate',
'[OX2][CX2]#[NX1]': 'Cyanate',
'[NX2]=[CX2]=[SX1]': 'Isothiocyanate',
'[SX2][CX2]#[NX1]': 'Thiocyanate',
'[NX2]=[CX2]=[NX2]': 'Carbodiimide',
'[CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]': 'Orthocarbonic_derivatives',
'[OX2H][c]': 'Phenol',
'[OX2H][c][c][OX2H]': '1,2-Diphenol',
'[Cl][c]': 'Arylchloride',
'[F][c]': 'Arylfluoride',
'[Br][c]': 'Arylbromide',
'[I][c]': 'Aryliodide',
'[SX2H][c]': 'Arylthiol',
'[c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]': 'Iminoarene',
'[c]=[OX1]': 'Oxoarene',
'[c]=[SX1]': 'Thioarene',
'[nX3H1+0]': 'Hetero_N_basic_H',
'[nX3H0+0]': 'Hetero_N_basic_no_H',
'[nX2,nX3+]': 'Hetero_N_nonbasic',
'[o]': 'Hetero_O',
'[sX2]': 'Hetero_S',
'[a;!c]': 'Heteroaromatic',
'[!#6;!R0]': 'Heterocylcic',
'[NX2](=[OX1])[O;$([X2]),$([X1-])]': 'Nitrite',
'[SX2][NX2]=[OX1]': 'Thionitrite',
'[$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]': 'Nitrate',
'[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]': 'Nitro',
'[NX2](=[OX1])[!#7;!#8]': 'Nitroso',
'[NX1]~[NX2]~[NX2,NX1]': 'Azide',
'[CX3](=[OX1])[NX2]~[NX2]~[NX1]': 'Acylazide',
'[$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]': 'Diazo',
'[#6][NX2+]#[NX1]': 'Diazonium',
'[#7;!$(N*=O)][NX2]=[OX1]': 'Nitrosamine',
'[NX2](=[OX1])N-*=O': 'Nitrosamide',
'[$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]': 'N-Oxide',
'[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]': 'Hydrazine',
'[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]': 'Hydrazone',
'[NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]': 'Hydroxylamine',
'[SX2][NX2]=[OX1]': 'Thionitrite',
'[SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]': 'Sulfuric_acid',
'[SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]': 'Sulfuric_monoester',
'[SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]': 'Sulfuric_diester',
'[SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]': 'Sulfuric_monoamide',
'[SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Sulfuric_diamide',
'[SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]': 'Sulfuric_esteramide',
'[SX4D4](=[!#6])(=[!#6])([!#6])[!#6]': 'Sulfuric_derivative',
'[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]': 'Sulfonic_acid',
'[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Sulfonamide',
'[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]': 'Sulfonic_ester',
'[SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]': 'Sulfonic_halide',
'[SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]': 'Sulfonic_derivative',
'[SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]': 'Sulfinic_acid',
'[SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Sulfinic_amide',
'[SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]': 'Sulfinic_ester',
'[SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]': 'Sulfinic_halide',
'[SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]': 'Sulfinic_derivative',
'[SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]': 'Sulfenic_acid',
'[SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]': 'Sulfenic_amide',
'[SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]': 'Sulfenic_ester',
'[SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]': 'Sulfenic_halide',
'[SX2;$([H1]),$([H0][#6])][!#6]': 'Sulfenic_derivative',
'[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]': 'Phosphoric_acid',
'[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]' : 'Phosphoric_monoester',
'[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' : 'Phosphoric_diester',
'[PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' : 'Phosphoric_triester',
'[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphoric_monoamide',
'[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphoric_diamide',
'[PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphoric_triamide',
'[PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphoric_monoestermonoamide',
'[PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphoric_diestermonoamide',
'[PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphoric_monoesterdiamide',
'[PX4D4](=[!#6])([!#6])([!#6])[!#6]' : 'Phosphoric_acid_derivative',
'[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]': 'Phosphinic_acid',
'[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]' : 'Phosphinic_ester',
'[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphinic_amide',
'[PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]' : 'Phosphinic_acid_derivative',
'[PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]' : 'Phosphonous_acid',
'[PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]' : 'Phosphonous_monoester',
'[PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' : 'Phosphonous_diester',
'[PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphonous_monoamide',
'[PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphonous_diamide',
'[PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphonous_esteramide',
'[PX3;$([D2]),$([D3][#6])]([!#6])[!#6]' : 'Phosphonous_derivatives',
'[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]' : 'Phosphinous_acid',
'[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]' : 'Phosphinous_ester',
'[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' : 'Phosphinous_amide',
'[PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]' : 'Phosphinous_derivatives',
'[SiX4]([#6])([#6])([#6])[#6]': 'Quart_silane',
'[SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]': 'Non-quart_silane',
'[SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]': 'Silylmonohalide',
'[SiX4]([!#6])([#6])([#6])[#6]': 'Het_trialkylsilane',
'[SiX4]([!#6])([!#6])([#6])[#6]': 'Dihet_dialkylsilane',
'[SiX4]([!#6])([!#6])([!#6])[#6]': 'Trihet_alkylsilane',
'[SiX4]([!#6])([!#6])([!#6])[!#6]': 'Silicic_acid_derivative',
'[BX3]([#6])([#6])[#6]': 'Trialkylborane',
'[BX3]([!#6])([!#6])[!#6]': 'Boric_acid_derivatives',
'[BX3]([!#6])([!#6])[!#6]': 'Boronic_acid_derivative',
'[BH1,BH2,BH3,BH4]': 'Borohydride',
'[BX4]': 'Quaternary_boron',
'[!#6;!R0]': 'Heterocyclic',
'[OX2r3]1[#6r3][#6r3]1': 'Epoxide',
'[NX3H1r3]1[#6r3][#6r3]1': 'NH_aziridine',
'[D4R;$(*(@*)(@*)(@*)@*)]': 'Spiro',
'[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]' : 'Annulated_rings',
'[R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]' : 'Bridged_rings',
'[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]': 'Sugar_pattern_1',
'[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]': 'Sugar_pattern_2',
'[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]': 'Sugar_pattern_combi',
'[OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]': 'Sugar_pattern_2_reducing',
'[OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]': 'Sugar_pattern_2_alpha',
'[OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]': 'Sugar_pattern_2_beta',
'*#*[*]=,#,:[*]': 'Conjugated_tripple_bond',
'[$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]': 'Mixed_anhydrides',
'[FX1,ClX1,BrX1,IX1][!#6]': 'Halogen_on_hetero',
'[F,Cl,Br,I;!$([X1]);!$([X0-])]': 'Halogen_multi_subst',
'[F][c1ccccc1]': 'Fluoride_benzyl',
'[Cl][c1ccccc1]': 'Chloride_benzyl',
'[Br][c1ccccc1]': 'Bromide_benzyl',
'[I][c1ccccc1]': 'Iodine_benzyl',
'C1C2CC3CC1CC(C2)C3': 'Adamantane_Derivative',
'C1CCC2C(C1)CCC3C2CCC4C3CCC4': 'Sterone_Derivative',
}
# Dictionary to store matches for each chemical group
matches_dict = {name: [] for name in smarts_patterns.values()}
# Iterate over each SMARTS pattern and find matches in the molecule
for pattern, name in smarts_patterns.items():
matches = mol.GetSubstructMatches(Chem.MolFromSmarts(pattern))
if matches:
matches_dict[name].extend(matches)
# Keep track of unique matches for each chemical group
unique_matches = set()
for matches in matches_dict.values():
for match in matches:
unique_matches.add(tuple(match))
# Convert unique matches back to a list of chemical groups
for name, matches in matches_dict.items():
for match in matches:
if tuple(match) in unique_matches:
chemical_groups.append(name)
unique_matches.remove(tuple(match))
# Return the list of identified chemical groups
return chemical_groups
#finding non aromatic rings, doesn't work for annulated rings
from rdkit import Chem
def find_unique_non_aromatic_rings(smiles):
mol = Chem.MolFromSmiles(smiles)
if mol is None:
return "Invalid SMILES string. Unable to parse molecule."
# Define SMARTS patterns to recognize rings of specific sizes
ring_smarts = {
'3_membered_ring': '[r3]',
'4_membered_ring': '[r4]',
'5_membered_ring': '[r5]',
'6_membered_ring': '[r6]',
'7_membered_ring': '[r7]',
'8_membered_ring': '[r8]',
'9_membered_ring': '[r9]',
'10_membered_ring': '[r10]',
}
# Define a list to store the chemical groups found in the SMILES
chemical_groups = []
# Find matches of each ring pattern in the molecule
for name, pattern in ring_smarts.items():
ring_size = int(name.split('_')[0]) # Extract the ring size from the name
ring_matches = mol.GetSubstructMatches(Chem.MolFromSmarts(pattern))
non_aromatic_rings = [match for match in ring_matches if not any(mol.GetAtomWithIdx(idx).GetIsAromatic() for idx in match)] #exclude all aromatic rings
unique_rings_count = len(non_aromatic_rings) // ring_size # Correctly count unique rings
if unique_rings_count > 0:
chemical_groups.extend([name] * unique_rings_count)
# Return the list of identified chemical groups
return chemical_groups
#finding aromatic rings
from rdkit import Chem
def find_aromatic_ring(smiles):
mol = Chem.MolFromSmiles(smiles)
if mol is None:
return "Invalid SMILES string. Unable to parse molecule."
# Define SMARTS patterns to recognize aromatic rings of specific sizes
aromatic_ring_smarts = {
'3_membered_aromatic_ring': '[a]1[a][a]1',
'4_membered_aromatic_ring': '[a]1[a][a][a]1',
'5_membered_aromatic_ring': '[a]1[a][a][a][a]1',
'6_membered_aromatic_ring': '[a]1[a][a][a][a][a]1',
'7_membered_aromatic_ring': '[a]1[a][a][a][a][a][a]1',
'8_membered_aromatic_ring': '[a]1[a][a][a][a][a][a][a]1',
'9_membered_aromatic_ring': '[a]1[a][a][a][a][a][a][a][a]1',
'10_membered_aromatic_ring': '[a]1[a][a][a][a][a][a][a][a][a]1',
'naphthalene': '[a]1[a][a][a]2[a][a][a][a][a]2[a]1',
#other larger systems...
}
# Define a list to store the chemical groups found in the SMILES
chemical_groups = []
# Find matches of each aromatic ring pattern in the molecule
for name, pattern in aromatic_ring_smarts.items():
pattern_mol = Chem.MolFromSmarts(pattern)
if pattern_mol:
matches = mol.GetSubstructMatches(pattern_mol)
for match in matches:
ring_size = len(match)
if all(mol.GetAtomWithIdx(idx).GetIsAromatic() for idx in match):
chemical_groups.append(f'{ring_size}_membered_aromatic_ring')
return chemical_groups
#Example Usage 2
Sterone = "C1CCC2C(C1)CCC3C2CCC4C3CCC4"
Indole ="C1=CC=C2C(=C1)C=CN2"
Napthalene ="C1=CC=C2C=CC=CC2=C1"
Linagliptin = "CC#CC[N]1C3=C(N=C1N2CCCC(C2)N)N(C(=O)N(C3=O)CC5=NC4=CC=CC=C4C(=N5)C)C"
Irinotecan = "CCC1=C2CN3C(=CC4=C(C3=O)COC(=O)[C@@]4(CC)O)C2=NC5=C1C=C(C=C5)OC(=O)N6CCC(CC6)N7CCCCC7"
Adamantane = "C1C2CC3CC1CC(C2)C3"
Cubane = "C12C3C4C1C5C2C3C45"
Alpha_Hopan = "CC(C)[C@H]1CC[C@]2([C@@H]1CC[C@@]3([C@@H]2CC[C@H]4[C@]3(CC[C@@H]5[C@@]4(CCCC5(C)C)C)C)C)C"
molecules = [ Sterone, Indole, Napthalene, Linagliptin, Irinotecan, Adamantane, Cubane, Alpha_Hopan ]
for i in molecules:
smiles_string = i
print(smiles_string)
chemical_groups_found = find_smiles_patterns(smiles_string)
unique_ring_matches = find_unique_non_aromatic_rings(smiles_string)
aromatic_ring_matches = find_aromatic_ring(smiles_string)
print("Chemical groups found:", chemical_groups_found)
print("Non-aromatic rings found:", unique_ring_matches)
print("Aromatic rings found:", aromatic_ring_matches)
Upvotes: 4
Views: 121
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