Revision as of 10:10, 2 August 2017

Possible structure of the object including nmredata:

Chemical structure

For the structure part originating from the .mol part of the SDF file:

object.structure (from the .mol part of the file)
object.structure.atom[n] (for each atom n) 
object.structure.atom[n].N atomic mumber of atom N) 
object.structure.atom[n].X x coordinate in A 
object.structure.atom[n].Y y coordinate in A 
object.structure.atom[n].Z z coordinate in A 

object.structure.bond[m] (for each bond m)
object.structure.bond[m].a1 first atom
object.structure.bond[m].a2 second atom
object.structure.bond[m].type 1:for single bond, 2: for double bond, 3: for triple bond

NMR signals

For the <NMR_SIGNALS> of the SDF file: The signals of all isotopes are listed together, they compile the information from the tag describing the spectra (see below)

object.signal[n] (for each signal n)
object.signal[n].label  string including the label give to the atom or set of atoms
object.signal[n].cs  chemical shift of
object.signal[n].atom[m]  list of the m atomnumber the signal is assigned to (from 1 to number of atom in the object.structure.atom)

J

For the <NMR_J> of the SDF file: This includes all the coupling extracted from the spectra (see below)

object.J[n] (for each coupling n listed)
object.J[n].label1  label of the first signal 
object.J[n].label2  label of the second signal 
object.J[n].value coupling constant between label1 and label2

sample data

Information about the sample

object.solvent...

1D spectra

object.spectrum1d[n] (for each 1D spectrum n)
...

2D spectra

object.spectrumdd[n] (for each 2D spectrum n)
...