parse_mol: Parse Molfile (as returned by chemspider) into a R-object.

Description

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

Usage

parse_mol(string)

Arguments

string

molfile as one string

Value

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.
For more information see infochim.u-strasbg.fr/recherche/Download/Fragmentor/MDL_SDF.pdf.

References

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. http://doi.org/10.1186/1751-0473-7-12