SMARTS Pattern Configuration¶
Provides definitions for various sets of SMARTS patterns used in to find and match specific atom types. Additionally, it includes a helper function for remapping atom types for easier lookups.
AVAILABLE_ATOM_TYPES
module-attribute
¶
AVAILABLE_ATOM_TYPES = {name: ifor (i, name) in enumerate(_Atom_Type_Names)}
Type: dict[str, int]: A dictionary mapping atom type names (strings) to unique integer identifiers.
SmartsPatternRegistry ¶
Bases: Enum
A registry of SMARTS patterns for atom typing.
Each atom type is represented by a string key and a SMARTS pattern. See the definitions below for further details, and follow the links for the corresponding SMARTS patterns.
HBOND_ACCEPTOR
class-attribute
instance-attribute
¶
HBOND_ACCEPTOR = HBOND_ACCEPTOR_SMARTS
Hydrogen bond acceptor SMARTS patterns. See definitions for details.
XBOND_ACCEPTOR
class-attribute
instance-attribute
¶
XBOND_ACCEPTOR = {None: HBOND_ACCEPTOR_SMARTS, '': '[Xx]'}
Halogen bond acceptor SMARTS patterns. See definitions for details. Note that we provide a nonsensical string to avoid duplicate entries in the Enum.
XBOND_DONOR
class-attribute
instance-attribute
¶
XBOND_DONOR = {'donor': SMARTS_STR_XBD}
Halogen bond donor SMARTS patterns. See definitions for details.
WEAK_HBOND_ACCEPTOR
class-attribute
instance-attribute
¶
WEAK_HBOND_ACCEPTOR = {None: HBOND_ACCEPTOR_SMARTS, 'c-x halogens': SMARTS_STR_XBD}
Weak hydrogen bond acceptor SMARTS patterns. In addition to the standard hydrogen bond acceptor SMARTS patterns, this also includes halogen bond acceptor SMARTS patterns.
WEAK_HBOND_DONOR
class-attribute
instance-attribute
¶
WEAK_HBOND_DONOR = {'donor': SMARTS_STR_WHBD}
Weak hydrogen bond donor SMARTS patterns. See definitions for details.
POS_IONISABLE
class-attribute
instance-attribute
¶
POS_IONISABLE = POSITIVELY_IOINISABLE_SMARTS
Positively ionisable SMARTS patterns. See definitions for details.
NEG_IONISABLE
class-attribute
instance-attribute
¶
NEG_IONISABLE = {'O acidic group': SMARTS_STR_NI_O_ACIDIC_GRP, 'anions': SMARTS_STR_NI_ANIONS}
Negatively ionisable SMARTS patterns. It includes two types of patterns: acidic oxygen and anions.
HYDROPHOBE
class-attribute
instance-attribute
¶
HYDROPHOBE = {'hydrophobe': SMARTS_STR_HYDROPHOBIC}
Hydrophobic SMARTS patterns. See definitions for details.
CARBONYL_OXYGEN
class-attribute
instance-attribute
¶
CARBONYL_OXYGEN = {'oxygen': SMARTS_STR_CARBONYL_OXYGEN}
Carbonyl oxygen SMARTS patterns. See definitions for details.
CARBONYL_CARBON
class-attribute
instance-attribute
¶
CARBONYL_CARBON = {'carbon': SMARTS_STR_CARBONYL_CARBON}
Carbonyl carbon SMARTS patterns. See definitions for details.
AROMATIC
class-attribute
instance-attribute
¶
AROMATIC = AROMATIC_SMARTS
Aromatic SMARTS patterns. See definitions for details.