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Interfacing to MarvinSketch - the "API-free" solution. Jan Holst Jensen CEO, Biochemfusion. - Enabling biochemformatics. A need for chemistry ? Yes. PLN text H-QC(1)IC(1)SLYC(3)N-OH. H-A[Gla]LVC(3)GER-OH name="Example protein." id=EXA_PROT. Biochemfusion's Proteax

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slide1

Interfacing to MarvinSketch

- the "API-free" solution

Jan Holst Jensen

CEO, Biochemfusion

- Enabling biochemformatics

a need for chemistry yes
A need for chemistry ? Yes.

PLN text

H-QC(1)IC(1)SLYC(3)N-OH.

H-A[Gla]LVC(3)GER-OH

name="Example protein." id=EXA_PROT

  • Biochemfusion's Proteax
    • Registration and analysis of modified protein structures
    • Oracle cartridge + spreadsheet solution (Excel or OpenOffice Calc)
  • Sequence format transforms
  • Sequence to chemical structure translation
mapping sequence to structure
Mapping sequence to structure
  • Each residue code mapped to a residue structure
    • Standard amino acids - built-in
    • Custom residues - defined by modification database
  • Stitch resulting residue structures together, add terminals, add crosslinks - done.

H-QC(1)IC(1)SLYC(3)N-OH.

H-A[Gla]LVC(3)GER-OH

normal edit workflow
Normal edit workflow
  • Write molecule to temporary molfile
  • Start editor (MarvinSketch.exe)
    • Passing temporary molfile on command line
    • Use CreateProcess(), save returned process id
  • Wait for editor process exit...
  • ...or temporary file change (editor saved file)
    • in this case: request editor close (see next slide)
  • Read molecule back in from temporary file
cancelling edits
Cancelling edits
  • Post WM_CLOSE message to main window of editor process
    • Main window of editor process is found by
      • Enumerating all windows
      • Choosing the first window that belongs to editor process and
        • is visible, has a title and is not a child window
      • Probably not fool-proof but is observed to work in general
  • Rely on editor's normal WM_CLOSE response
    • Just like an end-user closing the main window