summary.pdb() nucleotide sequence format printing

[Barry Grant]

The update for nucleic acid printing added to summary.pdb() and reported by print.pdb() is not consistent with width format.

> pdb <- read.pdb("1BPX")
  Note: Accessing on-line PDB file
  HEADER    TRANSFERASE/DNA                         11-APR-97   1BPX
> pdb

 Call:  read.pdb(file = "1BPX")

   Total Models#: 1
     Total Atoms#: 3368,  XYZs#: 10104  Chains#: 4  (values: T P D A)

     Protein Atoms#: 2653  (residues/Calpha atoms#: 331)
     Nucleic acid Atoms#: 632  (residues/phosphate atoms#: 29)

     Non-protein/nucleic Atoms#: 83  (residues: 83)
     Non-protein/nucleic resid values: [HOH (81), NA (2) ]

   Protein sequence:
      KAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPG
      VGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLED
      LRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRG
      AESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLS...<cut>...DRSE

   Nucleic acid sequence:
      DCDGDADCDGDGDCDGDCDADTDCDADGDCDCDTDGDADTDGDCDGDCDGDTDCDGDGNANANANANANANANANANANA
      NANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANA
      NANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANA
      NANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANA
      NANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANA
      NANANANANANANANANANANANANANANANANANANANANANANANANA...<cut>...NANANANA

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

Something is quite weird there.

[Lars Skjærven]

right... fixed by introducing a function .aa321.na() which is called from within summary.pdb(). see commit 7a85fd6. Certainly not ideal to have a specific function for nucleic acid sequences, but revising aa321() could potentially affect other other functions.

> pdb

 Call:  read.pdb(file = "1BPX")

   Total Models#: 1
     Total Atoms#: 3368,  XYZs#: 10104  Chains#: 4  (values: T P D A)

     Protein Atoms#: 2653  (residues/Calpha atoms#: 331)
     Nucleic acid Atoms#: 632  (residues/phosphate atoms#: 29)

     Non-protein/nucleic Atoms#: 83  (residues: 83)
     Non-protein/nucleic resid values: [HOH (81), NA (2) ]

   Protein sequence:
      KAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPG
      VGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLED
      LRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRG
      AESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLS...<cut>...DRSE

   Nucleic acid sequence:
      CGACGGCGCATCAGCCTGATGCGCGTCGG

+ attr: atom, helix, sheet, seqres, xyz,
        calpha, call

[Barry Grant]

Fixed