Difference between revisions of "Parser"

From NMReDATA
Jump to: navigation, search
Line 22: Line 22:
 
Scan the tags and list the index of the ones including NMREDATA_ in their name  
 
Scan the tags and list the index of the ones including NMREDATA_ in their name  
  
Read the NMReDATA tag. Keep in mind the end of line problem  
+
Read the NMReDATA tag. Keep in mind the [[end-of-line | end of line problem ]].
  
  First read and analyse the "NMREDATA_VERSION"  
+
  First read and analyse the NMREDATA_VERSION to
  and NMREDATA_LEVEL tags because the define how the rest will be read/stored.
+
* determine what character should be ignored (ASCII 10, except for version 1)
 +
* determine the line separator (", except for version 1)
 +
  and NMREDATA_LEVEL tags because they define how the rest will be read/stored.
 
analyse the NMREDATA_ASSIGNMENT and NMREDATA_J
 
analyse the NMREDATA_ASSIGNMENT and NMREDATA_J
  

Revision as of 07:26, 29 January 2019

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.

Reading the SDF file

Libraries for divers languages exist to read SDF files. This paragraph is only relevant if you write your own reader/writer

We recommend having in mind, when reading, that an SDF file will have to be written at some point later. We recommend to write them in the same oder, but I don't think that this suggerstion is followed by all writer, so be ready for the TAGS to appear in any order.

If not too large, the content of the input should be kept in memory so that it can be written later. Since SDF files may contain divers TAGS (not only the NMREDATA tags) they should all be written in the output SDF file.

We recommend to

  • Open the SDF file
  • Read/store the molblock as chain of characters
  • Read/store the TAGS as chain of characters
  • Close the file
  • Analyses/check the molblock (see possible object structure of NMReDATA). Be

Reading the NMREDATAT tags

Scan the tags and list the index of the ones including NMREDATA_ in their name

Read the NMReDATA tag. Keep in mind the end of line problem .

First read and analyse the NMREDATA_VERSION to 
  • determine what character should be ignored (ASCII 10, except for version 1)
  • determine the line separator (", except for version 1)
and NMREDATA_LEVEL tags because they define how the rest will be read/stored.

analyse the NMREDATA_ASSIGNMENT and NMREDATA_J

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 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 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