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| | * Analyses/check the molblock (see [[nmredata object structure|possible object structure of NMReDATA]]). Be | | * Analyses/check the molblock (see [[nmredata object structure|possible object structure of NMReDATA]]). Be |
| | | | |
| − | = Reading the NMREDATAT tags = | + | = Determine how to read the NMREDATA tags = |
| | | | |
| | 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 |
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| | First read and analyse the NMREDATA_VERSION to | | First read and analyse the NMREDATA_VERSION to |
| | * determine what character should be ignored (ASCII 10, except for version 1) | | * determine what character should be ignored (ASCII 10, except for version 1) |
| − | * determine the line separator (", except for version 1) | + | * determine the line separator ("\", except for version 1, in which cas the ASCII 10 is the line separator) |
| − | 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)
| + | = read the NMREDATA tags = |
| − |
| |
| − | 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 =
| + | Tags have two parts: |
| − | Information about the sample
| + | * in the first all line start with a variable name followed by the "=" sign followed by the content |
| − | | + | * in the first all line start with a variable name followed by the "=" sign followed by the content |
| − | 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 attributes|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 attributes|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''
| |
Possible structure of the object including NMReDATA reflecting the format of NMReDATA tags of SDF files.
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.
