Fix broken NmrParser - Githubissues

As discussed with @maoliyun and @ViktorWeissenborn in #25, the NMR parser was not working.

When running from chemdataextractor.doc import Document, Paragraph from chemdataextractor.model import NmrSpectrum

doc = Document(Paragraph("1H NMR (CDCl3 with 0.05% v/v TMS, 400 MHz): "
            "δH 7.10 (2H, d, J = 8.9 Hz, H2′ and H6′), "
            "7.03-7.07 (3H, m, H3′′, H4′′ and H5′′), "
            "6.83-6.85 (2H, m, H2′′ and H6′′), 6.66 (2H, d, J = 8.9 Hz, H3′ and H5′), "
            "6.42 (1H, d, J = 1.8 Hz, H5), 6.26 (1H, d, J = 1.7 Hz, H7), "
            "5.18 (1H, s, H1′′′), 5.01 (1H, d, J = 6.6 Hz, H1), "
            "4.52 (1H, s, H2′′′), 4.27 (1H, d, J = 14.2 Hz, H3), "
            "4.15 (1H, br d, J = 11.2 Hz, H4′′′), "
            "4.05 (1H, t, J = 11.2 Hz, H3b′′′), "
            "3.88 (1H, J = 14.3, 6.8 Hz, H2), "
            "3.86 (3H, s, OCH38), 3.69 (3H, s, OCH34′), "
            "3.64 (3H, s, COOCH32), 3.49 (3H, br s, H5′′′ and H6′′′), "
            "3.43-3.47 (1H, overlapped, H3a′′′), 3.45 (3H, s, OCH32′′′)."), models = [Compound, NmrSpectrum])
doc.records.serialize()

... the output did not include the NMR data:

[{'Compound': {'names': ['CDCl3']}},
 {'Compound': {'names': ['TMS']}},
 {'Compound': {'names': ['H2 ′']}},
 {'Compound': {'names': ['H6']}},
 {'Compound': {'names': ['3H']}},
 {'Compound': {'names': ['H3']}},
 {'Compound': {'names': ['H4 ′']}},
 {'Compound': {'names': ['H5']}},
 {'Compound': {'names': ['H1']}},
 {'Compound': {'names': ['H2']}},
 {'Compound': {'names': ['OCH38']}},
 {'Compound': {'names': ['OCH34']}},
 {'Compound': {'names': ['COOCH32']}},
 {'Compound': {'names': ['OCH32']}},
 {'Compound': {'labels': ['v']}},
 {'Compound': {'labels': ['3H']}}]

I had to make two small changes in chemdataextractor/parse/nmr.py in order to make it work again.

The NmrParser now inherits everything from BaseSentenceParser instead of BaseParser. If I understand it right, the need for this specification has been introduced with version 2.0, but it has never been applied to the NmrParser.
The interpret method did not return the nmr model data, but the compound. This needed to be changed.

Now, the code above returns the expected output that contains the NMR data:

[{'Compound': {'names': ['CDCl3']}}, {'Compound': {'names': ['TMS']}}, {'Compound': {'names': ['H2 ′']}}, {'Compound': {'names': ['H6']}}, {'Compound': {'names': ['3H']}}, {'Compound': {'names': ['H3']}}, {'Compound': {'names': ['H4 ′']}}, {'Compound': {'names': ['H5']}}, {'Compound': {'names': ['H1']}}, {'Compound': {'names': ['H2']}}, {'Compound': {'names': ['OCH38']}}, {'Compound': {'names': ['OCH34']}}, {'Compound': {'names': ['COOCH32']}}, {'Compound': {'names': ['OCH32']}}, {'Compound': {'labels': ['v']}}, {'Compound': {'labels': ['3H']}}, {'NmrSpectrum': {'nucleus': '1H', 'solvent': 'CDCl3 with 0.05 % v/v TMS', 'frequency': '400', 'frequency_units': 'MHz', 'peaks': [{'NmrPeak': {'shift': '7.10', 'multiplicity': 'd', 'coupling': '8.9', 'coupling_units': 'Hz', 'number': '2H', 'assignment': 'H2 ′'}}, {'NmrPeak': {'shift': '7.03-7.07', 'multiplicity': 'm', 'number': '3H', 'assignment': 'H3 ′ ′'}}, {'NmrPeak': {'shift': '6.83-6.85', 'multiplicity': 'm', 'number': '2H', 'assignment': 'H2 ′ ′'}}, {'NmrPeak': {'shift': '6.66', 'multiplicity': 'd', 'coupling': '8.9', 'coupling_units': 'Hz', 'number': '2H', 'assignment': 'H3 ′'}}, {'NmrPeak': {'shift': '6.42', 'multiplicity': 'd', 'coupling': '1.8', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H5'}}, {'NmrPeak': {'shift': '6.26', 'multiplicity': 'd', 'coupling': '1.7', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H7'}}, {'NmrPeak': {'shift': '5.18', 'multiplicity': 's', 'number': '1H', 'assignment': 'H1 ′ ′ ′'}}, {'NmrPeak': {'shift': '5.01', 'multiplicity': 'd', 'coupling': '6.6', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H1'}}, {'NmrPeak': {'shift': '4.52', 'multiplicity': 's', 'number': '1H', 'assignment': 'H2 ′ ′ ′'}}, {'NmrPeak': {'shift': '4.27', 'multiplicity': 'd', 'coupling': '14.2', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H3'}}, {'NmrPeak': {'shift': '4.15', 'multiplicity': 'br d', 'coupling': '11.2', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H4 ′ ′ ′'}}, {'NmrPeak': {'shift': '4.05', 'multiplicity': 't', 'coupling': '11.2', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H3b ′ ′ ′'}}, {'NmrPeak': {'shift': '3.88', 'coupling': '14.3 , 6.8', 'coupling_units': 'Hz', 'number': '1H', 'assignment': 'H2'}}, {'NmrPeak': {'shift': '3.86', 'multiplicity': 's', 'number': '3H', 'assignment': 'OCH38'}}, {'NmrPeak': {'shift': '3.69', 'multiplicity': 's', 'number': '3H', 'assignment': 'OCH34 ′'}}, {'NmrPeak': {'shift': '3.64', 'multiplicity': 's', 'number': '3H', 'assignment': 'COOCH32'}}, {'NmrPeak': {'shift': '3.49', 'multiplicity': 'br s', 'number': '3H', 'assignment': 'H5 ′ ′ ′'}}, {'NmrPeak': {'shift': '3.43-3.47', 'number': '1H', 'assignment': 'H3a ′ ′ ′'}}, {'NmrPeak': {'shift': '3.45', 'multiplicity': 's', 'number': '3H', 'assignment': 'OCH32 ′ ′ ′'}}], 'compound': {'Compound': {}}}}]

CambridgeMolecularEngineering / chemdataextractor2

Fix broken NmrParser #38