three-digit mapping numbers disrupt the column structure in the output

[anastasiiaNG]

Hi, when using RDT to map reactions with compounds that have more than 99 atoms, the output .rxn file has corrupted column structure. Specifically, it locates three-digit mapping numbers into preceding column and thus in these rows there are not 16 columns but 15. It makes it impossible to process such output .rxn files automatically.

ECBLAST_R01492_AAM.txt

[johnmay]

Is the ECBLAST_R01492_AAM.txt the output? That looks correct, it's fixed width not a TSV you can't open it in Excel which it looks like you've done.

[johnmay]

Please see bottom of Page 40: "The Atom Block" http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/direct/reference/ctfileformats2016.pdf

[anastasiiaNG]

Ok, I see, thank you.

Probably you could advise me is there any way to automatically extract these atomblocks as separate R/python objects with atom mapping numbers always in the same column?

I try to read ECBLAST_R01492_AAM.txt automatically by the means of R package ChemmineR and even this specialized library fails to read such files correctly. Below is how ChemmineR interprets this file:

ttt <- ChemmineR::read.SDFindex("ECBLAST_R01492_AAM.txt", 
                                index=data.frame(A=1, 
                                                 B=length(readr::read_lines("ECBLAST_R01492_AAM.txt"))))
ChemmineR::atomblock(ttt)

[johnmay]

Then this looks like it might be a bug in ChemmieR... RDKit/CDK will handle it correctly but you will have to manually by iterating over the atoms.

Because it's a fix width format (dates back to fortran days) you can just grabs the chars you need using simple command line utilities.

 $ grep -F '.' ~/Downloads/ECBLAST_R01492_AAM.txt | cut -c1-49,61-63
...
  -18.8182   -5.0468    0.0000 C   0  0  0  0  0  61
  -17.7257   -4.0189    0.0000 C   0  0  0  0  0  62
  -18.0704   -2.5582    0.0000 C   0  0  0  0  0  63
  -19.5074   -2.1254    0.0000 C   0  0  0  0  0  64
  -16.2893   -4.4509    0.0000 C   0  0  0  0  0  65
  -18.4745   -6.5069    0.0000 C   0  0  0  0  0  66
  -12.6166    0.2957    0.0000 C   0  0  0  0  0  67
   -3.6837    0.0740    0.0000 C   0  0  1  0  0  68
   -3.9578   -1.4007    0.0000 C   0  0  0  0  0  69
   -2.8177   -2.3755    0.0000 C   0  0  0  0  0  70
   -1.4035   -1.8755    0.0000 O   0  0  0  0  0  71
   -3.0918   -3.8502    0.0000 N   0  0  0  0  0  72
    1.6146   -0.0598    0.0000 C   0  0  1  0  0  73
    6.0587    1.6342    0.0000 O   0  0  0  0  0  92
    5.3087    0.3351    0.0000 P   0  0  0  0  0  93
    6.7183   -0.1779    0.0000 O   0  0  0  0  0  94
    5.0483   -1.1421    0.0000 O   0  0  0  0  0  95
    3.8087    0.3351    0.0000 O   0  0  0  0  0  96
    3.0587    1.6342    0.0000 P   0  0  0  0  0  97
    4.4683    2.1472    0.0000 O   0  0  0  0  0  98
    2.7983    3.1114    0.0000 O   0  0  0  0  0  99
    1.5587    1.6342    0.0000 O   0  0  0  0  0 100
    0.8087    0.3351    0.0000 P   0  0  0  0  0 101
    2.2183   -0.1779    0.0000 O   0  0  0  0  0 102
   -0.6913    0.3351    0.0000 O   0  0  0  0  0 103
    0.5483   -1.1421    0.0000 O   0  0  0  0  0 104

Let's roll back though, what are you actually trying to do? see: http://xyproblem.info/

[anastasiiaNG]

Thanks for the help, no questions to you anymore.