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Nmredata_object_structure.md

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title Nmredata object structure
permalink /Nmredata_object_structure/

Possible structure of the object including NMReDATA reflecting the format of NMReDATA tags of SDF files.

Note: This is not designed to include ambiguities in the assignment. This is therefore only for use with Level=0.

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 `***`integer`***` atomic number of atom N) 
object.structure.atom[`*`n`*`].X `***`float`***` x coordinate in A 
object.structure.atom[`*`n`*`].Y `***`float`***` y coordinate in A 
object.structure.atom[`*`n`*`].Z `***`float`***` z coordinate in A 

object.structure.bond[`*`m`*`] (for each bond `*`m`*`)
object.structure.bond[`*`m`*`].a1 `***`int`***` first atom (1 to number of atoms)
object.structure.bond[`*`m`*`].a2 `***`int`***` second atom (1 to number of atoms)
object.structure.bond[`*`m`*`].type `***`int`***` 1:for single bond, 2: for double bond, 3: for triple bond

Sample data

Information about the sample

object.version string version (content of the NMREDATA_VERSION tag) object.level int level (content of the NMREDATA_LEVEL tag) object.SMILE String smile code

When H are explicit in the structure, the SMILE code must also include all the H atoms in the smile code. The reason to include the smiles in the NMReDATA is that it can be used to generate pure text MNR description of spectra (This is under elaboration but it is very important for stability of the format to include them in SDF files!)

object.concentration float concentration in mM object.temp float temperature in K

Assignment

For the <NMR_ASSIGNMENT> (previously named 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.assignment[n] (for each assignment n) object.assignment[n].label string label given to the atom or set of atoms object.assignment[n].cs float chemical shift (single value, no range accepted!) object.assignment[n].atom[m] integer atom number(s) assigned to the signal (start numbering at 1)

J couplings

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 stringlabel of the first signal object.J[n].label2 stringlabel of the second signal object.J[n].value float coupling constant between label1 and label2

optional because possibly involving difficulties:

object.J[n].nb[m] intnumber of bonds between the atoms corresponding to the labels.

In most cases, m = 1, but when the two labels correspond to more than one spin (for example in AA'XX' systems is described using a single lable for A and A' and a single label for X and X') the number of bonds depends on whether we consider A-X and A-X', this is why we need two elements in the tabel.

1D spectra

See also 1D spectra attributes page.

object.spectrum1d[n] (for each 1D spectrum n) object.spectrum1d[n].S Multiplicity (string) object.spectrum1d[n].J Scalar coupling (string) This is a string because it contains the description of the coupling, assignment, etc. object.spectrum1d[n].N number of nuclei (int) object.spectrum1d[n].L Label of the signal (string) object.spectrum1d[n].E Integral (float) object.spectrum1d[n].I Intensity (float) object.spectrum1d[n].T1 T1 relaxation time (float) object.spectrum1d[n].T2 T2 relaxation time (float) object.spectrum1d[n].Diff diffusion rate (float)

2D spectra

See also 2D spectra attributes page.

object.spectrum2d[n] (for each 2D spectrum n) object.spectrum2d[n].L1 Label of the signal in F1(string) (if the signal is not assigned, the chemical shift is given as a string) object.spectrum2d[n].L2 Label of the signal in F2(string) (if the signal is not assigned, the chemical shift is given as a string) object.spectrum2d[n].I Intensity (float) object.spectrum2d[n].E Signal volume (float) object.spectrum2d[n].Ja Active scalar coupling (float) ``i.e.`` ``from`` ``a`` ``COSY`` ``spectrum object.spectrum2d[n].J1[m] Passive scalar coupling(s) in F1 (float)i.e.`` ``from`` ``a`` ``high-resolution`` ``COSY`` ``spectrum object.spectrum2d[n].J2[m] Passive scalar coupling(s) in F2 (float)i.e.`` ``from`` ``a`` ``high-resolution`` ``COSY`` ``spectrum object.spectrum2d[n].JL1[m] Label of the assigned passive coupling in F1 (string)i.e.`` ``from`` ``a`` ``high-resolution`` ``COSY`` ``spectrum object.spectrum2d[n].JL2[m] Label of the assigned passive coupling in F2 (string')i.e.`` ``from`` ``a`` ``high-resolution`` ``COSY`` ``spectrum