read.pdb() behavior with het2atom=TRUE

[Barry Grant]

I propose that if read.pdb() has het2atom=TRUE then the $het output component should be NULL.

Note that currently when you set het2atom=TRUE in read.pdb() all $het data gets put in $atom however we also keep this data in $het. Therefore we store duplicate data.

This is not usually a problem as we don't typically do much with $het. But the output from summary.pdb()/print.pdb() will be confusing... e.g.

> summary( read.pdb("4q21") )
##  Note: Accessing online PDB file
##  HEADER    ONCOGENE PROTEIN                        25-SEP-91   4Q21
##
## Call:  read.pdb(file = "4q21")
##
##  Atom Count: 1447
##
##   Total ATOMs#: 1340
##     Protein ATOMs#: 1340   ( Calpha ATOMs#: 168 )
##     Non-protein ATOMs#: 0   ( residues:  )
##
##   Total HETATOMs: 107
##     Residues HETATOMs#: 80   ( residues: MG GDP HOH )
##
##+ attr: atom, het, helix, sheet, seqres,
##        xyz, xyz.models, calpha, call

> summary( read.pdb("4q21", het2atom=T) )
##  Note: Accessing online PDB file
##  HEADER    ONCOGENE PROTEIN                        25-SEP-91   4Q21
##
## Call:  read.pdb(file = "4q21", het2atom = T)
##
##  Atom Count: 1554
##
##   Total ATOMs#: 1447
##     Protein ATOMs#: 1340   ( Calpha ATOMs#: 168 )
##     Non-protein ATOMs#: 107   ( residues: MG GDP HOH )
##
##   Total HETATOMs: 107
##     Residues HETATOMs#: 80   ( residues: MG GDP HOH )
##
##+ attr: atom, het, helix, sheet, seqres,
##        xyz, xyz.models, calpha, call

Note the duplicate 107 non-protein and HETATOM report in the second case above. I propose that if het2atom=TRUE we should blank-out the $het records

[Barry Grant]

Made this change, see more sensible output below:

> library(bio3d)
> read.pdb("4q21")
  Note: Accessing online PDB file
  HEADER    ONCOGENE PROTEIN                        25-SEP-91   4Q21

 Call:  read.pdb(file = "4q21")

  Atom Count: 1447

   Total ATOMs#: 1340
     Protein ATOMs#: 1340   ( Calpha ATOMs#: 168 )
     Non-protein ATOMs#: 0   ( residues:  )
     Chains#: 1   ( values: A )

   Total HETATOMs: 107
     Residues HETATOMs#: 80   ( residues: MG GDP HOH )
     Chains#: 1   ( values: A )

   Sequence:
      MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
      QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
      AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKL

+ attr: atom, het, helix, sheet, seqres,
        xyz, xyz.models, calpha, call
>
>
> read.pdb("4q21", het2atom=T)
  Note: Accessing online PDB file
  HEADER    ONCOGENE PROTEIN                        25-SEP-91   4Q21

 Call:  read.pdb(file = "4q21", het2atom = T)

  Atom Count: 1447

   Total ATOMs#: 1447
     Protein ATOMs#: 1340   ( Calpha ATOMs#: 168 )
     Non-protein ATOMs#: 107   ( residues: MG GDP HOH )
     Chains#: 1   ( values: A )

   Total HETATOMs: 0
     Residues HETATOMs#: 0   ( residues: none )
     Chains#: 1   ( values: 0 )

   Sequence:
      MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
      QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
      AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKL

+ attr: atom, het, helix, sheet, seqres,
        xyz, xyz.models, calpha, call
>