hqs_nmr.spectrumio
Deserialization and serialization from varios NMR spectrum formats.
Functions
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Read spectral data from a Bruker directory and write it to a JCAMP-DX file. |
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Read spectral data from Bruker directory. |
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Read spectral data from a JCAMP-DX (JDX) file. |
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Parses JDX spectral data from string. |
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Write a JCAMP-DX file. |
- hqs_nmr.spectrumio._extract_solvent_jcampdx(data: dict[str, Any]) list[str][source]
Extracts solvent string from a JCAMP-DX data dictionary if available.
With JCAMP-DX version 5.01 a new optional “.SOLVENT NAME” key has been added to store a description of the solvent. According to the specification this may include pH, ionic strength, if relevant. This function does not distinguish the solvent name from such additional data.
A few notes regarding the parsing via the nmrglue package: Since a JCAMP-DX file may contain more than one block (ends with “##END”), nmrglue collects all values of a key in a list. Furthermore, nmrglue normalizes the key in the data dictionary, i.e. while the JCAMP-DX file may contain “##.SOLVENTNAME” or “##.SOLVENT NAME”, the resulting data dictionary only contains a “.SOLVENTNAME” key in both cases.
- Parameters:
data – Data dictionary resulting from parsing with nmrglue.
- Returns:
Solvent string(s) or an empty list if no solvent information was found.
- hqs_nmr.spectrumio._extract_solvent_bruker(data: dict[str, Any]) str[source]
Extracts solvent string from a Bruker data dictionary if available.
The Bruker directory format stores the solvent name in the acquisition file (acqus or acqu) under the non-standard key “##$SOLVENT”. The solvent name is usually enclosed in angle brackets (e.g. <DMSO>), which are stripped of with this function.
- Parameters:
data – Data dictionary resulting from parsing with nmrglue.
- Returns:
Solvent string or an empty string if no solvent information was found.
- hqs_nmr.spectrumio._extract_temperature_jcampdx(data: dict[str, Any]) list[float][source]
Extracts temperature (in Kelvin) from a JCAMP-DX data dictionary if available.
JCAMP-DX files store the temperature in degrees Celsius in the “##TEMPERATURE” field. Note that this function returns the temperature in Kelvin.
A few notes regarding the parsing via the nmrglue package: Since a JCAMP-DX file may contain more than one block (ends with “##END”), nmrglue collects all values of a key in a list.
- Parameters:
data – Data dictionary resulting from parsing with nmrglue.
- Returns:
Temperature(s) in Kelvin or an empty list if no temperature was found.
- hqs_nmr.spectrumio._extract_temperature_bruker(data: dict[str, Any]) float | None[source]
Extracts temperature (in Kelvin) from a Bruker data dictionary if available.
The Bruker directory format stores the temperature (in Kelvin) in the acquisition file (acqus or acqu) under the non-standard key “##$TE”. The data dictionary produced by nmrglue.bruker.read_pdata holds the temperature already as a float.
- Parameters:
data – Data dictionary resulting from parsing with nmrglue.
- Returns:
Temperature in Kelvin or None if no solvent information was found.
- hqs_nmr.spectrumio._extract_isotope_jcampdx(data: dict[str, Any]) list[Isotope][source]
Extracts isotope from a JCAMP-DX data dictionary.
JCAMP-DX files store the isotope in the “##.OBSERVE NUCLEUS” field. The corresponding value usually contains a leading caret (e.g. ^13C), which is removed in this function.
A few notes regarding the parsing via the nmrglue package: Since a JCAMP-DX file may contain more than one block (ends with “##END”), nmrglue collects all values of a key in a list. Furthermore, nmrglue normalizes the key in the data dictionary, i.e. while the JCAMP-DX file may contain “##.OBSERVENUCLEUS” or “##.OBSERVE NUCLEUS”, the resulting data dictionary only contains a “.OBSERVENUCLEUS” key in both cases.
- Parameters:
data – Data dictionary resulting from parsing with nmrglue.
- Returns:
Isotope of observed nucleus.
- hqs_nmr.spectrumio._extract_isotope_bruker(data: dict[str, Any]) Isotope[source]
Extracts isotope from a Bruker data dictionary.
The Bruker directory format stores the isotope in the processing file (procs or proc) “##$AXNUC”. The isotope string is usually enclosed in angle brackets (e.g. <1H>). Contrary to the solvent name, the isotope string stored in the data dictionary does not include the angle brackets.
- Parameters:
data – Data dictionary resulting from parsing with nmrglue.
- Returns:
Isotope of observed nucleus.
- hqs_nmr.spectrumio.read_jdx(file: Path | str, source: str = 'Unknown', license_id: str = 'Unknown') NMRExperimentalSpectrum1D[source]
Read spectral data from a JCAMP-DX (JDX) file.
NOTE: it is assumed that the JCAMP-DX file contains only one block, i.e. one spectrum and one isotope.
- Parameters:
file – Path to the JDX file.
source – Owner or producer of the spectrum.
license_id – License associated with the spectrum (as SPDX identifier if possible).
- Raises:
RuntimeError – Parsing failed.
NotImplementedError – Unsupported spectral data.
ValueError – Inconsistent JDX parameters.
- Returns:
A NMRExperimentalSpectrum1D object with chemical shifts (in ppm) and intensities.
- hqs_nmr.spectrumio.read_jdx_string(file_content: str, source: str = 'Unknown', license_id: str = 'Unknown') tuple[ndarray, ndarray][source]
Parses JDX spectral data from string.
Note this function creates a temporary file in order to match the function interface of nmrglue.jcampdx.read.
- Parameters:
file_content – Content of a JCAMP-DX file.
source – Owner or producer of the spectrum.
license_id – License associated with the spectrum (as SPDX identifier if possible).
- Returns:
A tuple of chemical shifts (in ppm) and intensities.
- hqs_nmr.spectrumio.read_bruker_dir(directory: Path | str, source: str = 'Unknown', license_id: str = 'Unknown') NMRExperimentalSpectrum1D[source]
Read spectral data from Bruker directory.
- Parameters:
directory – Path to the Bruker directory.
source – Owner or producer of the spectrum.
license_id – License associated with the spectrum (as SPDX identifier if possible).
- Returns:
A NMRExperimentalSpectrum1D object containing chemical shifts (in ppm) and intensities.
- hqs_nmr.spectrumio.write_jdx(x_data: ndarray, y_data: ndarray, frequency_MHz: float, molecule_name: str, solvent: str = 'CDCl3', isotope: str = '1H', manual_shift: float | None = None) None[source]
Write a JCAMP-DX file.
This function writes a JCAMP-DX file from given x and y data. It is able of moving the x-axis by a specified amount. This is useful when the experimental spectrum is wrong referenced.
- Parameters:
x_data – X data, shifts in ppm.
y_data – Y data, intensity.
frequency_MHz – Observation frequency in MHz (depends on the isotope).
molecule_name – Molecule name.
solvent – Solvent name. Defaults to “CDCl3”.
isotope – String representation of the isotope as [atomic mass number][symbol]. Defaults to “1H”.
manual_shift – Manual shift in ppm. Defaults to None.