import logging
import os
from typing import IO, Dict, List, Union
from ..Fragments import Fragments
from ..Spectrum import Spectrum
from ..utils import fingerprint_export_warning
logger = logging.getLogger("matchms")
_extentions_not_allowed = ["mzml", "mzxml", "json", "mgf"]
[docs]def save_as_msp(spectrums: List[Spectrum], filename: str,
write_peak_comments: bool = True,
mode: str = "a", style: str = "matchms"):
"""Save spectrum(s) as msp file.
:py:attr:`~matchms.Spectrum.losses` of spectrum will not be saved.
Example:
.. code-block:: python
import numpy as np
from matchms import Spectrum
from matchms.exporting import save_as_msp
# Create dummy spectrum
spectrum = Spectrum(mz=np.array([100, 200, 300], dtype="float"),
intensities=np.array([10, 10, 500], dtype="float"),
metadata={"charge": -1,
"inchi": '"InChI=1S/C6H12"',
"precursor_mz": 222.2})
# Write spectrum to test file
save_as_msp(spectrum, "test.msp")
Parameters
----------
spectrums:
Expected input are match.Spectrum.Spectrum() objects.
filename:
Provide filename to save spectrum(s).
write_peak_comments:
Writes peak comments to individual peaks after the respective mz/intensity pair
when set to True. Default is True.
mode:
Mode on how to write to file. One of ["w", "a"] (write/append). Default is append.
style:
Converts the keys to required Export style. One of ["massbank", "nist", "riken", "gnps"].
Default is "matchms"
"""
file_extension = filename.split(".")[-1]
assert file_extension.lower() not in _extentions_not_allowed, \
f"File extension '.{file_extension}' not allowed."
if not filename.endswith(".msp"):
logger.warning("Spectrum(s) will be stored as msp file with extension .%s",
filename.split(".")[-1])
spectrums = _ensure_list(spectrums)
fingerprint_export_warning(spectrums)
with open(filename, mode, encoding="utf-8") as outfile:
for spectrum in spectrums:
_write_spectrum(spectrum, outfile, write_peak_comments, style)
def _write_spectrum(spectrum: Spectrum,
outfile: IO,
write_peak_comments: bool,
export_style: str = "matchms"):
_write_metadata(spectrum.metadata_dict(export_style), outfile)
if write_peak_comments is True:
_write_peaks(spectrum.peaks, spectrum.peak_comments, outfile)
else:
_write_peaks(spectrum.peaks, None, outfile)
outfile.write(os.linesep)
def _write_peaks(peaks: Fragments, peak_comments: Spectrum.peak_comments, outfile: IO):
outfile.write(f"NUM PEAKS: {len(peaks)}\n")
for mz, intensity in zip(peaks.mz, peaks.intensities):
peak_comment = _format_peak_comment(mz, peak_comments)
outfile.write(f"{mz}\t{intensity}{peak_comment}\n".expandtabs(12))
def _write_metadata(metadata: dict, outfile: IO):
for key, value in metadata.items():
if not (_is_num_peaks(key) or _is_peak_comments(key) or _is_fingerprint(key)):
outfile.write(f"{key.upper()}: {value}\n")
def _format_peak_comment(mz: Union[int, float], peak_comments: Dict):
"""Format peak comment for given mz to return the quoted comment or empty string if no peak comment is present."""
if not isinstance(peak_comments, dict):
return ""
peak_comment = peak_comments.get(mz, None)
if peak_comment is None:
return ""
return f"\t\"{peak_comment}\""
def _is_num_peaks(key: str) -> bool:
return key.lower().startswith("num peaks") or key.lower().startswith("num_peaks")
def _is_peak_comments(key: str) -> bool:
return key.lower().startswith("peak_comments")
def _is_fingerprint(key: str) -> bool:
return key.lower().startswith("fingerprint")
def _ensure_list(spectrums) -> List[Spectrum]:
if not isinstance(spectrums, list):
# Assume that input was single Spectrum
spectrums = [spectrums]
return spectrums
