Difference between revisions of "Nmredata object structure"

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(J couplings)
(J couplings)
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  object.J[''n''].nb[''m''] '''''int''''' number of bonds between the atoms corresponding to the labels.  
 
  object.J[''n''].nb[''m''] '''''int''''' number 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 bond depends whether we consider A-X and A-X')
+
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 bond depends whether we consider A-X and A-X', this is why we need two elements in the tabel.
  
 
= Sample data =
 
= Sample data =

Revision as of 14:53, 8 August 2017

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 threfore 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 mumber 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

NMR isolated signals

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 string label of the first signal 
object.J[n].label2 string label 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] int number 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 bond depends whether we consider A-X and A-X', this is why we need two elements in the tabel.

Sample data

Information about the sample

object.version string verions (content of the NMREDATA_VERSION)
object.level int level (content of the NMREDATA_LEVEL)
object.ID[n] String ID n (line n of the NMREDATA_ID tag)

When using list of signals including interchangeable assignments (see .... for examples), set to 1.

When using ambiguously assigned signals in 1D or 2D spectra (see .... for examples), set to 2.

When using interchangeable and ambiguous assignment, set to 3.

<NMREDATA_ID> (for database)

This tag is optional but very much encouraged, in particular when data are originating from a stable database. When copied from database to database, multiple ID's may be included. These will be defined by database manager and software producers.

DB_ID= the code or number is assigned by the hosting database
Title= Full analysis of whatever from methanol extract of leafs  
Comment= Here more details could be given on the record.
Comment1= Here more details could be given on the record.
Comment2= Here more details could be given on the record.
Comment3= Here more details could be given on the record.
AUTHOR=John Doe, University of Tougalpa, Swiniland (optional)
Title_L1=after sep. hplc (this could be extracted from the first line of the title in the 1H spectrum)

One or more identifier can be given under "ID". The ID will be generated by the software generating data and/or the database storing the data, etc. There may be more than one ID (for example one from the software generating it, one from the university labelling the origin of the data, one from the database, one from the publisher of the associated data, etc.) it is to the “generator” of the file to decide if/how to make it unique if desired. InChIKey/SMILES could be given if the soft generating the data is able to specify it. CAS-number if it already exists.

<NMREDATA_SMILES> Very strongly encourage

SMILE code of the molecules. When H are explicit in the structure, the SMILE code muss also include all the H atoms in the smile code. The reason to includ 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!)

<NMREDATA_SOLVENT>

The solvent is specified using this tag.

>  <NMREDATA_SOLVENT>
CDCl3

For mixture of solvents, the most abundant is first and they are separated by "/" followed by the raio in % separated by ":"

>  <NMREDATA_SOLVENT>
CDCl3/DMSO 80:20
>  <NMREDATA_SOLVENT>
CDCl3/DMSO/D2O 80:10:10

The proportions are given in % volumes.

In the case of RDC measurements, the medium used can be specified in the line following the name of the solvent.

>  <NMREDATA_SOLVENT>
CDCl3
PBLG

The quantity of the orientation medium should be given using usual units (this is vague, but we cannot do better). Agarose used at 1% mass ratio:

>  <NMREDATA_SOLVENT>
D2O
Agarose 1%

For solid-states samples:

>  <NMREDATA_SOLVENT >
solid

<NMREDATA_CONCENTRATION> (optional)

When known, the concentration should be given. Only “mM” are allowed, but the unit is specified.

<NMREDATA_CONCENTRATION>
12.3 mM

<NMREDATA_TEMPERATURE> (optional)

When available the temperature of the sample should be given (only K are allowed, but the unit is given)

>  <NMREDATA_TEMPERATURE>
298.0 K

1D spectra

object.spectrum1d[n] (for each 1D spectrum n)
object.spectrum1d[n].S Multiplicity (string)
object.spectrum1d[n].J Scalar coupling (string)
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

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