Atom Names/Types

This data set gives for various atom names/types the corresponding atomic symbols.

atom.index

Format

A data frame with the following components.

name

a character vector containing atom names/types.

symb

a character vector containing atomic symbols.

See also

elements, atom.index, atom2ele

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

data(atom.index)
atom.index
#>    name symb
#> 1     H    H
#> 2     C    C
#> 3    CA    C
#> 4    CB    C
#> 5    CD    C
#> 6   CD1    C
#> 7   CD2    C
#> 8    CE    C
#> 9   CE1    C
#> 10  CE2    C
#> 11  CE3    C
#> 12   CG    C
#> 13  CG1    C
#> 14  CG2    C
#> 15  CH2    C
#> 16   CZ    C
#> 17  CZ2    C
#> 18  CZ3    C
#> 19    N    N
#> 20  ND1    N
#> 21  ND2    N
#> 22   NE    N
#> 23  NE1    N
#> 24  NE2    N
#> 25  NH1    N
#> 26  NH2    N
#> 27   NZ    N
#> 28    O    O
#> 29  OD1    O
#> 30  OD2    O
#> 31  OE1    O
#> 32  OE2    O
#> 33   OG    O
#> 34  OG1    O
#> 35   OH    O
#> 36  OXT    O
#> 37    S    S
#> 38   SD    S
#> 39   SG    S
#> 40    P    P
#> 41   MG   Mg
#> 42   MN   Mn
#> 43    K    K
#> 44   CL   Cl
#> 45   ZN   Zn
#> 46   SE   Se
#> 47    F    F
#> 48   AL   Al

# Get the atomic symbol of some atoms
atom.names <- c("CA", "O", "N", "OXT")
atom.index[match(atom.names, atom.index$name), "symb"]
#> [1] "C" "O" "N" "O"