rmgpy.molecule.AtomType

class rmgpy.molecule.AtomType

A class for internal representation of atom types. Using unique objects rather than strings allows us to use fast pointer comparisons instead of slow string comparisons, as well as store extra metadata. In particular, we store metadata describing the atom type’s hierarchy with regard to other atom types, and the atom types that can result when various actions involving this atom type are taken. The attributes are:

Attribute	Type	Description
label	str	A unique label for the atom type
generic	list	The atom types that are more generic than this one
specific	list	The atom types that are more specific than this one
increment_bond	list	The atom type(s) that result when an adjacent bond’s order is incremented
decrement_bond	list	The atom type(s) that result when an adjacent bond’s order is decremented
form_bond	list	The atom type(s) that result when a new single bond is formed to this atom type
break_bond	list	The atom type(s) that result when an existing single bond to this atom type is broken
increment_radical	list	The atom type(s) that result when the number of radical electrons is incremented
decrement_radical	list	The atom type(s) that result when the number of radical electrons is decremented
increment_lone_pair	list	The atom type(s) that result when the number of lone electron pairs is incremented
decrement_lone_pair	list	The atom type(s) that result when the number of lone electron pairs is decremented
The following features are what are required in a given atomtype. Any int in the list is acceptable. An empty list is a wildcard
single	list	The total number of single bonds on the atom
all_double	list	The total number of double bonds on the atom
r_double	list	The number of double bonds to any non-oxygen, nonsulfur
o_double	list	The number of double bonds to oxygen
s_double	list	The number of double bonds to sulfur
triple	list	The total number of triple bonds on the atom
quadruple	list	The total number of quadruple bonds on the atom
benzene	list	The total number of benzene bonds on the atom
lone_pairs	list	The number of lone pairs on the atom
charge	list	The partial charge of the atom

equivalent(other)

Returns True if two atom types atomType1 and atomType2 are equivalent or False otherwise. This function respects wildcards, e.g. R!H is equivalent to C.

get_features()

Returns a list of the features that are checked to determine atomtype

is_specific_case_of(other)

Returns True if atom type atomType1 is a specific case of atom type atomType2 or False otherwise.

rmgpy.molecule.get_atomtype(atom, bonds)

Determine the appropriate atom type for an Atom object atom with local bond structure bonds, a dict containing atom-bond pairs.

The atom type of an atom describes the atom itself and (often) something about the local bond structure around that atom. This is a useful semantic tool for accelerating graph isomorphism queries, and a useful shorthand when specifying molecular substructure patterns via an RMG-style adjacency list.

We define the following basic atom types:

Atom type	Description
General atom types
R	any atom with any local bond structure
R!H	any non-hydrogen atom with any local bond structure
R!H!Val7	any non-hydrogen and non-halogen atom (a non-terminal atom)
Hydrogen atom types
H	hydrogen atom with up to one single bond
Carbon atom types
C	carbon atom with any local bond structure
Ca	carbon atom with two lone pairs and no bonds
Cs	carbon atom with up to four single bonds
Csc	charged carbon atom with up to three single bonds
Cd	carbon atom with one double bond (not to O or S) and up to two single bonds
Cdc	charged carbon atom with one double bond and up to one single bond
CO	carbon atom with one double bond to oxygen and up to two single bonds
CS	carbon atom with one double bond to sulfur and up to two single bonds
Cdd	carbon atom with two double bonds
Ct	carbon atom with one triple bond and up to one single bond
Cb	carbon atom with up to two benzene bonds and up to one single bond
Cbf	carbon atom with three benzene bonds
C2s	carbon atom with one lone pair (valance 2) and up to two single bonds
C2sc	charged carbon atom with one lone pair (valance 2) and up to three single bonds
C2d	carbon atom with one lone pair (valance 2) and one double bond
C2dc	charged carbon atom with one lone pair (valance 2), one double bond and up to one single bond
C2tc	charged carbon atom with one lone pair (valance 2), one triple bond
Nitrogen atom types
N	nitrogen atom with any local bond structure
N0sc	charged nitrogen atom with three lone pairs (valance 0) with up to one single bond
N1s	nitrogen atom with two lone pairs (valance 1) and up to one single bond
N1sc	charged nitrogen atom with two lone pairs (valance 1) up to two single bonds
N1dc	charged nitrogen atom with two lone pairs (valance 1), one double bond
N3s	nitrogen atom with one lone pair (valance 3) with up to three single bonds
N3d	nitrogen atom with one lone pair (valance 3), one double bond and up to one single bond
N3t	nitrogen atom with one lone pair (valance 3) and one triple bond
N3b	nitrogen atom with one lone pair (valance 3) and two benzene bonds
N5sc	charged nitrogen atom with no lone pairs (valance 5) with up to four single bonds
N5dc	charged nitrogen atom with no lone pairs (valance 5), one double bond and up to two single bonds
N5ddc	charged nitrogen atom with with no lone pairs (valance 5) and two double bonds
N5dddc	charged nitrogen atom with with no lone pairs (valance 5) and three double bonds
N5tc	charged nitrogen atom with with no lone pairs (valance 5), one triple bond and up to one single bond
N5b	nitrogen atom with with no lone pairs (valance 5) and two benzene bonds (one of the lone pairs also participates in the aromatic bond) and up to one single bond
N5bd	nitrogen atom with with no lone pairs (valance 5), two benzene bonds, and one double bond
Oxygen atom types
O	oxygen atom with any local bond structure
Oa	oxygen atom with three lone pairs and no bonds
O0sc	charged oxygen with three lone pairs (valance 0) and up to one single bond
O0dc	charged oxygen atom with three lone pairs (valance 0) and one double bond
O2s	oxygen atom with two lone pairs (valance 2) and up to two single bonds
O2sc	charged oxygen atom with two lone pairs (valance 2) and up to one single bond
O2d	oxygen atom with two lone pairs (valance 2) and one doubel bond
O4sc	charged oxygen atom with one one pair (valance 4) and up to three single bonds
O4dc	charged oxygen atom with one one pair (valance 4), one double bond and up to one single bond
O4tc	charged oxygen atom with one one pair (valance 4) and one triple bond
O4b	oxygen atom with one one pair (valance 4) and and two benzene bonds
Silicon atom types
Si	silicon atom with any local bond structure
Sis	silicon atom with four single bonds
Sid	silicon atom with one double bond (to carbon) and two single bonds
SiO	silicon atom with one double bond (to oxygen) and two single bonds
Sidd	silicon atom with two double bonds
Sit	silicon atom with one triple bond and one single bond
Sib	silicon atom with two benzene bonds and one single bond
Sibf	silicon atom with three benzene bonds
Phosphorus atom types
P	phosphorus atom with any local bond structure
P0sc	charged phosphorus atom with three lone pairs (valence 0) and up to 1 single bond
P1s	phosphorus atom with two lone pairs (valence 1) and up to 1 single bond
P1sc	charged phosphorus atom with two lone pairs (valence 1) and up to 2 single bonds
P1dc	charged phosphorus atom with two lone pairs (valence 1) and 1 double bond
P3s	phosphorus atom with one lone pair (valence 3) and up to 3 single bonds
P3d	phosphorus atom with one lone pair (valence 3), 1 double bond and up to 1 single bond
P3t	phosphorus atom with one lone pair (valence 3) and 1 triple bond
P3b	phosphorus atom with one lone pair (valence 3) and 2 benzene bonds
P5s	phosphorus atom with no lone pairs (valence 5) and up to 5 single bonds
P5sc	charged phosphorus atom with no lone pairs (valence 5) and up to 6 single bonds
P5d	phosphorus atom with no lone pairs (valence 5), 1 double bond and up to 3 single bonds
P5dd	phosphorus atom with no lone pairs (valence 5), 2 double bonds and up to 1 single bond
P5dc	charged phosphorus atom with no lone pairs (valence 5), 1 double bond and up to 2 single bonds
P5ddc	charged phosphorus atom with no lone pairs (valence 5) and 2 double bonds
P5t	phosphorus atom with no lone pairs (valence 5), 1 triple bond and up to 2 single bonds
P5td	phosphorus atom with no lone pairs (valence 5), 1 triple bond and 1 double bond
P5tc	charged phosphorus atom with no lone pairs (valence 5), 1 triple bond and up to 1 single bond
P5b	phosphorus atom with no lone pairs (valence 5), 2 benzene bonds and up to 1 single bond
P5bd	phosphorus atom with no lone pairs (valence 5), 2 benzene bonds and 1 double bond
Sulfur atom types
S	sulfur atom with any local bond structure
Sa	sulfur atom with three lone pairs and no bonds
S0sc	charged sulfur atom with three lone pairs (valance 0) and up to one single bonds
S2s	sulfur atom with two lone pairs (valance 2) and up to two single bonds
S2sc	charged sulfur atom with two lone pairs (valance 2) and up to three single bonds
S2d	sulfur atom with two lone pairs (valance 2) and one double bond
S2dc	charged sulfur atom with two lone pairs (valance 2), one double bond and up to one single bond
S2tc	charged sulfur atom with two lone pairs (valance 2) and one triple bond
S4s	sulfur atom with one lone pair (valance 4) and up to four single bonds
S4sc	charged sulfur atom with one lone pair (valance 4) and up to five single bonds
S4d	sulfur atom with one lone pair (valance 4), one double bond and up to two single bonds
S4dd	sulfur atom with one lone pair (valance 4) and two double bonds
S4dc	charged sulfur atom with one lone pair (valance 4), one to three double bonds and up to three single bonds
S4b	sulfur atom with one lone pair (valance 4) and two benzene bonds (one of the lone pairs also participates in the aromatic bond)
S4t	sulfur atom with one lone pair (valance 4), one triple bond and up to one single bond
S4tdc	charged sulfur atom with one lone pair (valance 4) one to two triple bonds, up to two double bonds, and up to three single bonds
S6s	sulfur atom with no lone pairs (valance 6) and up to six single bonds
S6sc	charged sulfur atom with no lone pairs (valance 6) and up to seven single bonds
S6d	sulfur atom with no lone pairs (valance 6), one double bond and up to four single bonds
S6dd	sulfur atom with no lone pairs (valance 6), two double bonds and up to two single bonds
S6ddd	sulfur atom with no lone pairs (valance 6) and three double bonds
S6dc	charged sulfur atom with no lone pairs (valance 6), one to three double bonds and up to five single bonds
S6t	sulfur atom with no lone pairs (valance 6), one triple bond and up to three single bonds
S6td	sulfur atom with no lone pairs (valance 6), one triple bond, one double bond and up to one single bond
S6tt	sulfur atom with no lone pairs (valance 6) and two triple bonds
S6tdc	charged sulfur atom with no lone pairs (valance 6), one to two triple bonds, up to two double bonds, and up to four single bonds
Chlorine atom types
Cl	chlorine atom with any local bond structure
Cl1s	chlorine atom with three lone pairs and zero to one single bonds
Bromine atom types
Br	bromine atom with any local bond structure
Br1s	bromine atom with three lone pairs and zero to one single bonds
Iodine atom types
I	iodine atom with any local bond structure
I1s	iodine atom with three lone pairs and zero to one single bonds
Fluorine atom types
F	fluorine atom with any local bond structure
F1s	fluorine atom with three lone pairs and zero to one single bonds