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SMARTS Definitions

Contains a collection of Simplified Molecular-Input Line-Entry System (SMARTS) strings used for SMARTS pattern matching.

The SMARTS strings cater to a variety of chemical functionalities and patterns, including but not limited to hydrogen bond acceptors and donors, positively and negatively ionizable groups, hydrophobic functionalities, carbonyl groups, and aromatic systems.

Each SMARTS string represents a specific chemical pattern or functionality, with separate SMARTS strings defined for different types of hydrogen bond acceptors, such as a standard acceptor, enol, tautomeric NH, and terminal amide.

The SMARTS strings are grouped into dictionaries based on their functionality. For example, HBOND_ACCEPTOR_SMARTS includes all SMARTS strings for different types of hydrogen bond acceptors, while POSITIVELY_IOINISABLE_SMARTS contains SMARTS strings representing different types of positively ionizable groups.

The module also defines aromatic systems of varying ring sizes, ranging from 4 to 8.

Notes

SMARTS is a language used to specify substructural patterns in molecules. It extends the simpler SMILES syntax and provides a more flexible way to describe molecular patterns.

This module does not contain any functions or classes, but only data in the form of strings and dictionaries of strings.

It is expected to be used as a source of SMARTS strings for other modules and applications dealing with molecular structure processing, matching, and analysis.

AMIDE_SMARTS module-attribute 

AMIDE_SMARTS = '[NX3][CX3](=[OX1])[#6]'

HBOND_ACCEPTOR_SMARTS module-attribute 

HBOND_ACCEPTOR_SMARTS = {'acceptor': SMARTS_STR_HBA_ACCEPTOR, 'enol': SMARTS_STR_HBA_ENOL, 'tautomeric nH': SMARTS_STR_HBA_TAUTOMERIC_NH, 'NH2 terminal amide': SMARTS_STR_HBA_TERMINAL_AMIDE}

A dictionary of hydrogen bond acceptor SMARTS patterns.

Definitions

  • acceptor: Standard hydrogen bond acceptor (source)
  • enol: Enol (source)
  • tautomeric nH: Tautomeric NH (source)
  • NH2 terminal amide: NH2 terminal amide (source)

POSITIVELY_IOINISABLE_SMARTS module-attribute 

POSITIVELY_IOINISABLE_SMARTS = {'rdkit basic group': SMARTS_STR_PI_RDKIT_BASIC_GRP, 'imidazole': SMARTS_STR_PI_IMIDAZOLE, 'guanidine amidine': SMARTS_STR_PI_GUANIDINE_AMIDINE, 'rdkit posn': SMARTS_STR_PI_RDKIT_POSN, 'cations': SMARTS_STR_PI_CATIONS, 'metals': SMARTS_STR_PI_METALS}

A dictionary of positively ionizable SMARTS patterns.

Definitions

  • rdkit basic group: RDKIT basic group (source)
  • imidazole: Imidazole (source)
  • guanidine amidine: Guanidine amidine (source)
  • rdkit posn: RDKIT positive nitrogen (source)
  • cations: Cations (source)
  • metals: Metals (source)

HBOND_DONOR_SMARTS module-attribute 

HBOND_DONOR_SMARTS = {'donor': SMARTS_STR_HBD_DONOR, 'oxygen acid': SMARTS_STR_HBD_OXYGEN_ACID, 'tautomer nH': SMARTS_STR_HBD_TAUTOMERIC_NH, 'oxygen amide term': SMARTS_STR_HBD_OXYGEN_AMIDE_TERM}

A dictionary of hydrogen bond donor SMARTS patterns.

Definitions

  • donor: Standard hydrogen bond donor (source)
  • oxygen acid: Oxygen acid (source)
  • tautomer nH: Tautomer NH (source)
  • oxygen amide term: Oxygen amide terminal (source)

AROMATIC_SMARTS module-attribute 

AROMATIC_SMARTS = {'arom_4': SMARTS_STR_AROMATIC_4, 'arom_5': SMARTS_STR_AROMATIC_5, 'arom_6': SMARTS_STR_AROMATIC_6, 'arom_7': SMARTS_STR_AROMATIC_7, 'arom_8': SMARTS_STR_AROMATIC_8}

A dictionary of aromatic SMARTS patterns. The number in the key indicates the number of atoms in the aromatic ring.

Definitions

SMARTS_STR_HBA_ACCEPTOR module-attribute 

SMARTS_STR_HBA_ACCEPTOR = '[#8,#9,$([#16;H0,H1;v2,v1]),$([N;v3;!$(N-*=!@[O,N,P,S]);!$(N-!@a);!$([NH]=!@*)]),$([nH0;+0])]'

Type: str: Standard hydrogen bond acceptor. Helps define HBOND_ACCEPTOR_SMARTS.

SMARTS_STR_HBA_ENOL module-attribute 

SMARTS_STR_HBA_ENOL = '[$([nH]:@c(=O))]'

Type: str: Enol. Helps define HBOND_ACCEPTOR_SMARTS.

SMARTS_STR_HBA_TAUTOMERIC_NH module-attribute 

SMARTS_STR_HBA_TAUTOMERIC_NH = '[$([n;H1;v3;!$([nH]cccc)])]'

Type: str: Tautomeric NH. Helps define HBOND_ACCEPTOR_SMARTS.

SMARTS_STR_HBA_TERMINAL_AMIDE module-attribute 

SMARTS_STR_HBA_TERMINAL_AMIDE = '[$([N;H2;v3;$(N-C(=O))])]'

Type: str: NH2 terminal amide. Helps define HBOND_ACCEPTOR_SMARTS.

SMARTS_STR_HBD_DONOR module-attribute 

SMARTS_STR_HBD_DONOR = '[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]'

Type: str: Standard hydrogen bond donor. Helps define HBOND_DONOR_SMARTS.

SMARTS_STR_HBD_OXYGEN_ACID module-attribute 

SMARTS_STR_HBD_OXYGEN_ACID = '[$([O;H0;$(O=C([OH])-*)])]'

Type: str: Oxygen acid. Helps define HBOND_DONOR_SMARTS.

SMARTS_STR_HBD_TAUTOMERIC_NH module-attribute 

SMARTS_STR_HBD_TAUTOMERIC_NH = '[$(n:a:[nH])]'

Type: str: Tautomeric NH. Helps define HBOND_DONOR_SMARTS.

SMARTS_STR_HBD_OXYGEN_AMIDE_TERM module-attribute 

SMARTS_STR_HBD_OXYGEN_AMIDE_TERM = '[$([O;H0;$(O=C-[NH2])])]'

Type: str: Oxygen amide terminal. Helps define HBOND_DONOR_SMARTS.

SMARTS_STR_WHBD module-attribute 

SMARTS_STR_WHBD = '[#6!H0]'

Type: str: Weak hydrogen bond donor. Helps define WEAK_HBOND_DONOR.

SMARTS_STR_XBD module-attribute 

SMARTS_STR_XBD = '[Cl,Br,I;X1;$([Cl,Br,I]-[#6])]'

Type: str: Halogen bond donor. Helps define XBOND_DONOR.

SMARTS_STR_PI_RDKIT_BASIC_GRP module-attribute 

SMARTS_STR_PI_RDKIT_BASIC_GRP = '[$([N;H2&+0][C;!$(C=*)]),$([N;H1&+0]([C;!$(C=*)])[C;!$(C=*)]),$([N;H0&+0]([C;!$(C=*)])([C;!$(C=*)])[C;!$(C=*)]);!$(N[a])]'

Type: str: RDKIT basic group. Helps define POSITIVELY_IOINISABLE_SMARTS.

SMARTS_STR_PI_IMIDAZOLE module-attribute 

SMARTS_STR_PI_IMIDAZOLE = '[n;R1]1[c;R1][n;R1][c;R1][c;R1]1'

Type: str: Imidazole. Helps define POSITIVELY_IOINISABLE_SMARTS.

SMARTS_STR_PI_GUANIDINE_AMIDINE module-attribute 

SMARTS_STR_PI_GUANIDINE_AMIDINE = 'NC(=N)'

Type: str: Guanidine amidine. Helps define POSITIVELY_IOINISABLE_SMARTS.

SMARTS_STR_PI_RDKIT_POSN module-attribute 

SMARTS_STR_PI_RDKIT_POSN = '[#7;+;!$([N+]-[O-])]'

Type: str: RDKIT positive nitrogen. Helps define POSITIVELY_IOINISABLE_SMARTS.

SMARTS_STR_PI_CATIONS module-attribute 

SMARTS_STR_PI_CATIONS = '[$([*+1,*+2,*+3]);!$([N+]-[O-])]'

Type: str: Cations. Helps define POSITIVELY_IOINISABLE_SMARTS.

SMARTS_STR_PI_METALS module-attribute 

SMARTS_STR_PI_METALS = '[Li,Be,Na,Mg,Al,K,Ca,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Ga,Rb,Sr,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Cs,Ba,La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi,Po,Fr,Ra,Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf]'

Type: str: Metals. Helps define POSITIVELY_IOINISABLE_SMARTS.

SMARTS_STR_NI_ANIONS module-attribute 

SMARTS_STR_NI_ANIONS = '[*-1,*-2]'

Type: str: Anions. Helps define NEG_IONISABLE.

SMARTS_STR_NI_O_ACIDIC_GRP module-attribute 

SMARTS_STR_NI_O_ACIDIC_GRP = '[$([OH,O-]-[C,S,N,P,Cl,Br,I]=O),$(O=[C,S,N,P,Cl,Br,I]-[OH,O-])]'

Type: str: Oxygen acidic group. Helps define NEG_IONISABLE.

SMARTS_STR_HYDROPHOBIC module-attribute 

SMARTS_STR_HYDROPHOBIC = '[#6+0!$(*~[#7,#8,F]),SH0+0v2,s+0,Cl+0,Br+0,I+0]'

Type: str: Hydrophobic. Helps define HYDROPHOBE.

SMARTS_STR_CARBONYL_OXYGEN module-attribute 

SMARTS_STR_CARBONYL_OXYGEN = '[$([OH0]=[CX3,c]);!$([OH0]=[CX3,c]-[OH,O-])]'

Type: str: Carbonyl oxygen. Helps define CARBONYL_OXYGEN.

SMARTS_STR_CARBONYL_CARBON module-attribute 

SMARTS_STR_CARBONYL_CARBON = '[$([CX3,c]=[OH0]);!$([CX3,c](=[OH0])-[OH,O-])]'

Type: str: Carbonyl carbon. Helps define CARBONYL_CARBON.

SMARTS_STR_AROMATIC_4 module-attribute 

SMARTS_STR_AROMATIC_4 = '[a;r4,!R1&r3]1:[a;r4,!R1&r3]:[a;r4,!R1&r3]:[a;r4,!R1&r3]:1'

Type: str: Aromatic 4. Helps define AROMATIC_SMARTS.

SMARTS_STR_AROMATIC_5 module-attribute 

SMARTS_STR_AROMATIC_5 = '[a;r5,!R1&r4,!R1&r3]1:[a;r5,!R1&r4,!R1&r3]:[a;r5,!R1&r4,!R1&r3]:[a;r5,!R1&r4,!R1&r3]:[a;r5,!R1&r4,!R1&r3]:1'

Type: str: Aromatic 5. Helps define AROMATIC_SMARTS.

SMARTS_STR_AROMATIC_6 module-attribute 

SMARTS_STR_AROMATIC_6 = '[a;r6,!R1&r5,!R1&r4,!R1&r3]1:[a;r6,!R1&r5,!R1&r4,!R1&r3]:[a;r6,!R1&r5,!R1&r4,!R1&r3]:[a;r6,!R1&r5,!R1&r4,!R1&r3]:[a;r6,!R1&r5,!R1&r4,!R1&r3]:[a;r6,!R1&r5,!R1&r4,!R1&r3]:1'

Type: str: Aromatic 6. Helps define AROMATIC_SMARTS.

SMARTS_STR_AROMATIC_7 module-attribute 

SMARTS_STR_AROMATIC_7 = '[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]1:[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:1'

Type: str: Aromatic 7. Helps define AROMATIC_SMARTS.

SMARTS_STR_AROMATIC_8 module-attribute 

SMARTS_STR_AROMATIC_8 = '[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]1:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:[a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]:1'

Type: str: Aromatic 8. Helps define AROMATIC_SMARTS.