Skip to contents

Parse Molfile (as returned by ChemSpider) into a R-object.





molfile as one string


A list with of four entries: header (eh), counts line (cl), atom block (ab) and bond block (bb).

header: a = number of atoms, b = number of bonds, l = number of atom lists, f = obsolete, c = chiral flag (0=not chiral, 1 = chiral), s = number of stext entries, x, r, p, i = obsolete, m = 999, v0 version

atom block: x, y, z = atom coordinates, a = mass difference, c= charge, s= stereo parity, h = hydrogen count 1, b = stereo care box, v = valence, h = h0 designator, r, i = not used, m = atom-atom mapping number, n = inversion/retention flag, e = exact change flag

bond block: 1 = first atom, 2 = second atom, t = bond type, s = stereo type, x = not used, r = bond typology, c = reacting center status.


Grabner, M., Varmuza, K., & Dehmer, M. (2012). RMol: a toolset for transforming SD/Molfile structure information into R objects. Source Code for Biology and Medicine, 7, 12. doi:10.1186/1751-0473-7-12