Combine Atom Selections From PDB Structure

Do "and", "or", or "not" set operations between two or more atom selections made by atom.select

combine.select(sel1=NULL, sel2=NULL, ..., operator="AND", verbose=TRUE)

Arguments

sel1

an atom selection object of class "select", obtained from atom.select.
sel2

a second atom selection object of class "select", obtained from atom.select.
...

more select objects for the set operation.
operator

name of the set operation.
verbose

logical, if TRUE details of the selection combination are printed.

Details

The value of operator should be one of following: (1) "AND", "and", or "&" for set intersect, (2) "OR", "or", "|", or "+" for set union, (3) "NOT", "not", "!", or "-" for set difference sel1 - sel2 - sel3 ....

Value

Returns a list of class "select" with components:

atom

atom indices of selected atoms.

xyz

xyz indices of selected atoms.

call

the matched call.

References

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

Author

Xin-Qiu Yao

See also

atom.select, as.select read.pdb, trim.pdb

Examples


# Read a PDB file
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

## - Build atom selections to be operated
# Select C-alpha atoms of entire system
ca.global.inds <- atom.select(pdb, "calpha")

# Select C-beta atoms of entire protein
cb.global.inds <- atom.select(pdb, "protein", elety="CB")

# Select backbone atoms of entire system
bb.global.inds <- atom.select(pdb, "backbone")

# Select all atoms with residue number from 46 to 50
aa.local.inds <- atom.select(pdb, resno=46:50)


# Do set intersect:
# - Return C-alpha atoms with residue number from 46 to 50
ca.local.inds <- combine.select(ca.global.inds, aa.local.inds)
#>  Intersect of selects
#>  *  Selected a total of: 5 atoms  *
print( pdb$atom[ ca.local.inds$atom, ] )
#>     type eleno elety  alt resid chain resno insert      x      y      z o     b
#> 359 ATOM   359    CA <NA>   ASN     A    46   <NA> 15.247 22.135 24.062 1 12.92
#> 367 ATOM   367    CA <NA>   THR     A    47   <NA> 18.108 23.768 25.931 1 39.90
#> 374 ATOM   374    CA <NA>   ASP     A    48   <NA> 16.626 22.832 29.261 1  9.90
#> 382 ATOM   382    CA <NA>   GLY     A    49   <NA> 16.950 19.205 28.182 1 10.24
#> 386 ATOM   386    CA <NA>   SER     A    50   <NA> 13.311 18.716 27.712 1  7.32
#>     segid elesy charge
#> 359  <NA>     C   <NA>
#> 367  <NA>     C   <NA>
#> 374  <NA>     C   <NA>
#> 382  <NA>     C   <NA>
#> 386  <NA>     C   <NA>

# Do set subtract:
# - Return side-chain atoms with residue number from 46 to 50
sc.local.inds <- combine.select(aa.local.inds, bb.global.inds, operator="-")
#>  Select 2 (, 3, ...) is subtracted from select 1
#>  *  Selected a total of: 13 atoms  *
print( pdb$atom[ sc.local.inds$atom, ] )
#>     type eleno elety  alt resid chain resno insert      x      y      z o     b
#> 362 ATOM   362    CB <NA>   ASN     A    46   <NA> 13.989 22.699 24.735 1 11.70
#> 363 ATOM   363    CG <NA>   ASN     A    46   <NA> 12.659 22.418 24.007 1 21.14
#> 364 ATOM   364   OD1 <NA>   ASN     A    46   <NA> 11.762 21.669 24.459 1 23.29
#> 365 ATOM   365   ND2 <NA>   ASN     A    46   <NA> 12.508 23.062 22.886 1 24.99
#> 370 ATOM   370    CB <NA>   THR     A    47   <NA> 18.506 25.250 25.905 1 47.42
#> 371 ATOM   371   OG1 <NA>   THR     A    47   <NA> 17.376 26.053 26.142 1 38.53
#> 372 ATOM   372   CG2 <NA>   THR     A    47   <NA> 19.115 25.572 24.552 1 58.08
#> 377 ATOM   377    CB <NA>   ASP     A    48   <NA> 15.349 23.377 29.887 1 14.78
#> 378 ATOM   378    CG <NA>   ASP     A    48   <NA> 14.119 22.821 29.267 1 19.04
#> 379 ATOM   379   OD1 <NA>   ASP     A    48   <NA> 14.160 21.981 28.422 1 28.31
#> 380 ATOM   380   OD2 <NA>   ASP     A    48   <NA> 13.002 23.315 29.717 1 28.61
#> 389 ATOM   389    CB <NA>   SER     A    50   <NA> 12.113 19.490 28.182 1  4.67
#> 390 ATOM   390    OG <NA>   SER     A    50   <NA> 12.074 20.716 27.461 1  9.76
#>     segid elesy charge
#> 362  <NA>     C   <NA>
#> 363  <NA>     C   <NA>
#> 364  <NA>     O   <NA>
#> 365  <NA>     N   <NA>
#> 370  <NA>     C   <NA>
#> 371  <NA>     O   <NA>
#> 372  <NA>     C   <NA>
#> 377  <NA>     C   <NA>
#> 378  <NA>     C   <NA>
#> 379  <NA>     O   <NA>
#> 380  <NA>     O   <NA>
#> 389  <NA>     C   <NA>
#> 390  <NA>     O   <NA>

# Do set union:
# - Return C-alpha and side-chain atoms with residue number from 46 to 50
casc.local.inds <- combine.select(ca.local.inds, sc.local.inds, operator="+")
#>  Union of selects
#>  *  Selected a total of: 18 atoms  *
print( pdb$atom[ casc.local.inds$atom, ] )
#>     type eleno elety  alt resid chain resno insert      x      y      z o     b
#> 359 ATOM   359    CA <NA>   ASN     A    46   <NA> 15.247 22.135 24.062 1 12.92
#> 362 ATOM   362    CB <NA>   ASN     A    46   <NA> 13.989 22.699 24.735 1 11.70
#> 363 ATOM   363    CG <NA>   ASN     A    46   <NA> 12.659 22.418 24.007 1 21.14
#> 364 ATOM   364   OD1 <NA>   ASN     A    46   <NA> 11.762 21.669 24.459 1 23.29
#> 365 ATOM   365   ND2 <NA>   ASN     A    46   <NA> 12.508 23.062 22.886 1 24.99
#> 367 ATOM   367    CA <NA>   THR     A    47   <NA> 18.108 23.768 25.931 1 39.90
#> 370 ATOM   370    CB <NA>   THR     A    47   <NA> 18.506 25.250 25.905 1 47.42
#> 371 ATOM   371   OG1 <NA>   THR     A    47   <NA> 17.376 26.053 26.142 1 38.53
#> 372 ATOM   372   CG2 <NA>   THR     A    47   <NA> 19.115 25.572 24.552 1 58.08
#> 374 ATOM   374    CA <NA>   ASP     A    48   <NA> 16.626 22.832 29.261 1  9.90
#> 377 ATOM   377    CB <NA>   ASP     A    48   <NA> 15.349 23.377 29.887 1 14.78
#> 378 ATOM   378    CG <NA>   ASP     A    48   <NA> 14.119 22.821 29.267 1 19.04
#> 379 ATOM   379   OD1 <NA>   ASP     A    48   <NA> 14.160 21.981 28.422 1 28.31
#> 380 ATOM   380   OD2 <NA>   ASP     A    48   <NA> 13.002 23.315 29.717 1 28.61
#> 382 ATOM   382    CA <NA>   GLY     A    49   <NA> 16.950 19.205 28.182 1 10.24
#> 386 ATOM   386    CA <NA>   SER     A    50   <NA> 13.311 18.716 27.712 1  7.32
#> 389 ATOM   389    CB <NA>   SER     A    50   <NA> 12.113 19.490 28.182 1  4.67
#> 390 ATOM   390    OG <NA>   SER     A    50   <NA> 12.074 20.716 27.461 1  9.76
#>     segid elesy charge
#> 359  <NA>     C   <NA>
#> 362  <NA>     C   <NA>
#> 363  <NA>     C   <NA>
#> 364  <NA>     O   <NA>
#> 365  <NA>     N   <NA>
#> 367  <NA>     C   <NA>
#> 370  <NA>     C   <NA>
#> 371  <NA>     O   <NA>
#> 372  <NA>     C   <NA>
#> 374  <NA>     C   <NA>
#> 377  <NA>     C   <NA>
#> 378  <NA>     C   <NA>
#> 379  <NA>     O   <NA>
#> 380  <NA>     O   <NA>
#> 382  <NA>     C   <NA>
#> 386  <NA>     C   <NA>
#> 389  <NA>     C   <NA>
#> 390  <NA>     O   <NA>

# More than two selections:
# - Return side-chain atoms (but not C-beta) with residue number from 46 to 50
sc2.local.inds <- combine.select(aa.local.inds, bb.global.inds, cb.global.inds, operator="-")
#>  Select 2 (, 3, ...) is subtracted from select 1
#>  *  Selected a total of: 9 atoms  *
print( pdb$atom[ sc2.local.inds$atom, ] )
#>     type eleno elety  alt resid chain resno insert      x      y      z o     b
#> 363 ATOM   363    CG <NA>   ASN     A    46   <NA> 12.659 22.418 24.007 1 21.14
#> 364 ATOM   364   OD1 <NA>   ASN     A    46   <NA> 11.762 21.669 24.459 1 23.29
#> 365 ATOM   365   ND2 <NA>   ASN     A    46   <NA> 12.508 23.062 22.886 1 24.99
#> 371 ATOM   371   OG1 <NA>   THR     A    47   <NA> 17.376 26.053 26.142 1 38.53
#> 372 ATOM   372   CG2 <NA>   THR     A    47   <NA> 19.115 25.572 24.552 1 58.08
#> 378 ATOM   378    CG <NA>   ASP     A    48   <NA> 14.119 22.821 29.267 1 19.04
#> 379 ATOM   379   OD1 <NA>   ASP     A    48   <NA> 14.160 21.981 28.422 1 28.31
#> 380 ATOM   380   OD2 <NA>   ASP     A    48   <NA> 13.002 23.315 29.717 1 28.61
#> 390 ATOM   390    OG <NA>   SER     A    50   <NA> 12.074 20.716 27.461 1  9.76
#>     segid elesy charge
#> 363  <NA>     C   <NA>
#> 364  <NA>     O   <NA>
#> 365  <NA>     N   <NA>
#> 371  <NA>     O   <NA>
#> 372  <NA>     C   <NA>
#> 378  <NA>     C   <NA>
#> 379  <NA>     O   <NA>
#> 380  <NA>     O   <NA>
#> 390  <NA>     O   <NA>