Difference between revisions of "Nmredata object structure"
From NMReDATA
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m (Protected "Nmredata object structure" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))) |
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| − | Possible structure of the object including NMReDATA: | + | 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 = | = Chemical structure = | ||
For the structure part originating from the .mol part of the SDF file: | For the structure part originating from the .mol part of the SDF file: | ||
| Line 6: | Line 9: | ||
object.structure.atom[''n''] (for each atom ''n'') | object.structure.atom[''n''] (for each atom ''n'') | ||
| − | object.structure.atom[''n''].N '''''integer''''' atomic | + | 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''].X '''''float''''' x coordinate in A | ||
object.structure.atom[''n''].Y '''''float''''' y coordinate in A | object.structure.atom[''n''].Y '''''float''''' y coordinate in A | ||
| Line 12: | Line 15: | ||
object.structure.bond[''m''] (for each bond ''m'') | object.structure.bond[''m''] (for each bond ''m'') | ||
| − | object.structure.bond[''m''].a1 '''''int''''' first atom | + | object.structure.bond[''m''].a1 '''''int''''' first atom (1 to number of atoms) |
| − | object.structure.bond[''m''].a2 '''''int''''' second atom | + | 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 | object.structure.bond[''m''].type '''''int''''' 1:for single bond, 2: for double bond, 3: for triple bond | ||
| − | = | + | = Sample data = |
| − | For the <NMR_SIGNALS> of the SDF file: | + | 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) | The signals of all isotopes are listed together, they compile the information from the tag describing the spectra (see below) | ||
| − | object. | + | object.assignment[''n''] (for each assignment ''n'') |
| − | object. | + | object.assignment[''n''].label '''''string''''' label given to the atom or set of atoms |
| − | object. | + | object.assignment[''n''].cs '''''float''''' chemical shift (single value, no range accepted!) |
| − | object. | + | object.assignment[''n''].atom[''m''] '''''integer''''' atom number(s) assigned to the signal (start numbering at 1) |
= J couplings = | = J couplings = | ||
| Line 33: | Line 48: | ||
object.J[''n''].label2 '''''string''''' label of the second signal | object.J[''n''].label2 '''''string''''' label of the second signal | ||
object.J[''n''].value '''''float''''' coupling constant between label1 and label2 | 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 = | = 1D spectra = | ||
| + | See also [[1D attributes|1D spectra attributes page]]. | ||
object.spectrum1d[''n''] (for each 1D spectrum ''n'') | 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 = | = 2D spectra = | ||
| − | + | See also [[2D attributes|2D spectra attributes page]]. | |
| − | object. | + | 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'' | ||
Latest revision as of 10:54, 13 April 2018
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 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
