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 | 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 |