Atom Types

In addition to the partial charges, Rosetta AtomTypes are defined. These basically control hydrogen-bonding and atom size. In some cases the assignment may have gone wrong and it is worth checking.

These are added to the rdkit.Chem.Mol Property via (atom.SetProp('_rType', 'xxx')) and to the params.ATOM[n].rtype string.

Example:

from rdkit import Chem
from rdkit_to_params import Params

for smiles in ('CC[NH3+]','CC[NH2]','C=C[NH2]','CC[OH]','CC[OH2+]','CC[O-]','C=CO','CC=O'):
    p = Params.from_smiles(smiles)
    i = 2
    print(smiles, p.mol.GetAtomWithIdx(i).GetHybridization().name, p.ATOM[i].rtype)

SMILES	Hybridisation	AtomType
CC[NH3+]	SP3	Nlys
CC[NH2]	SP3	Npro
C=C[NH2]	SP2	NH2O
CC[OH]	SP3	OH
CC[OH2+]	SP3	Oet3
CC[O-]	SP3	Oet3
C=CO	SP2	OH
CC=O	SP2	OOC

To see what the different atom type properties one could inspect a residue in pyrosetta

at = pose.residue(1).atom_type(1)
at.get_all_properties()

Or look at the file rosetta/main/database/chemical/atom_type_sets/fa_standard/atom_properties.txt but briefly these are the accepted atom types.

AtomType options

	AtomType	Element	Properties
0	aroC	C	AROMATIC ORBITALS
1	Ntrp	N	DONOR AROMATIC ORBITALS
2	Nhis	N	ACCEPTOR AROMATIC RING_HYBRID ORBITALS
3	NtrR	N	DONOR AROMATIC ORBITALS
4	NH2O	N	DONOR
5	Narg	N	DONOR ORBITALS
6	OH	O	ACCEPTOR SP3_HYBRID DONOR ORBITALS
7	OW	O	ACCEPTOR SP3_HYBRID DONOR ORBITALS
8	ONH2	O	ACCEPTOR SP2_HYBRID ORBITALS
9	OOC	O	ACCEPTOR SP2_HYBRID ORBITALS
10	Oaro	O	ACCEPTOR AROMATIC RING_HYBRID ORBITALS
11	Oet2	O	ACCEPTOR SP2_HYBRID ORBITALS
12	Oet3	O	ACCEPTOR SP3_HYBRID DONOR ORBITALS
13	Nbb	N	DONOR
14	OCbb	O	ACCEPTOR SP2_HYBRID ORBITALS
15	Hpol	H	POLAR_HYDROGEN
16	HS	H	POLAR_HYDROGEN
17	HNbb	H	POLAR_HYDROGEN
18	Hwat	H	POLAR_HYDROGEN
19	Owat	O	ACCEPTOR DONOR SP3_HYBRID
20	HOH	O	ACCEPTOR DONOR SP3_HYBRID
21	F	F	SP3_HYBRID
22	Cl	CL	SP3_HYBRID
23	Br	BR	SP3_HYBRID
24	I	I	SP3_HYBRID
25	#Zn2p	ZN	SP3_HYBRID
26	Zn2p	ZN	SP3_HYBRID
27	Co2p	CO	SP3_HYBRID
28	Cu2p	CU	SP3_HYBRID
29	Fe2p	FE	SP3_HYBRID
30	Fe3p	FE	SP3_HYBRID
31	Mg2p	MG	SP3_HYBRID
32	Ca2p	CA	SP3_HYBRID
33	Pha	P	SP3_HYBRID
34	OPha	O	ACCEPTOR SP3_HYBRID
35	OHha	O	ACCEPTOR DONOR SP3_HYBRID
36	Hha	H	POLAR_HYDROGEN
37	CO3	C	SP2_HYBRID
38	OC3	O	ACCEPTOR SP2_HYBRID
39	Si	Si	SP3_HYBRID
40	OSi	O	ACCEPTOR SP3_HYBRID
41	Oice	O	ACCEPTOR SP3_HYBRID
42	Hice	H	POLAR_HYDROGEN
43	Na1p	NA	SP3_HYBRID
44	K1p	K	SP3_HYBRID
45	REPL	Z	REPULSIVE
46	REPLS	Z	REPULSIVE
47	HREPS	Z	REPULSIVE
48	VIRT	X	VIRTUAL