BUG: atom.select() with 'operator = "OR"'

[Xinqiu Yao]

I've made a little bit update of test-atom.select.R for a more complete test for the atom.select() function. It failed at 'operator="OR"'. Digging into more details gives following information:

 > atom.select(pdb, chain="B")

 Call:  atom.select.pdb(pdb = pdb, chain = "B")

   Atom Indices#: 77  ($atom)
   XYZ  Indices#: 231  ($xyz)

+ attr: atom, xyz, call


> atom.select(pdb, resid="GDP")

 Call:  atom.select.pdb(pdb = pdb, resid = "GDP")

   Atom Indices#: 40  ($atom)
   XYZ  Indices#: 120  ($xyz)

+ attr: atom, xyz, call

> atom.select(pdb, resid="GDP", chain="B", operator="OR")

 Call:  atom.select.pdb(pdb = pdb, resid = "GDP", chain = "B", operator = "OR")

   Atom Indices#: 175  ($atom)
   XYZ  Indices#: 525  ($xyz)

+ attr: atom, xyz, call

Note that the correct number in the last atom select should be 177 (a union of first two selects). I used the examples/test.pdb for the test.

[Lars Skjærven]

bugfix in 302e53. thanks for spotting Xinqiu. this is getting embarrassing...

> file <- system.file("examples/test.pdb", package="bio3d")
> pdb=read.pdb(file)
> atom.select(pdb, chain="B")

 Call:  atom.select.pdb(pdb = pdb, chain = "B")

   Atom Indices#: 77  ($atom)
   XYZ  Indices#: 231  ($xyz)

+ attr: atom, xyz, call
> 
> atom.select(pdb, resid="GDP")

 Call:  atom.select.pdb(pdb = pdb, resid = "GDP")

   Atom Indices#: 40  ($atom)
   XYZ  Indices#: 120  ($xyz)

+ attr: atom, xyz, call
> 
> atom.select(pdb, resid="GDP", chain="B", operator="OR")

 Call:  atom.select.pdb(pdb = pdb, resid = "GDP", chain = "B", operator = "OR")

   Atom Indices#: 117  ($atom)
   XYZ  Indices#: 351  ($xyz)

+ attr: atom, xyz, call

[Xinqiu Yao]

Thanks!