def run_molecular_formula_search(mz, out, parameters_filepath):
mz = [mz]
abundance = [1]
rp, s2n = [[1], [1]]
dataname = Path(str(out))
mass_spectrum_obj = ms_from_array_centroid(mz, abundance, rp, s2n,
dataname)
parameter_from_json.load_and_set_parameters_ms(
mass_spectrum_obj, parameters_path=parameters_filepath)
mass_spectrum_obj.molecular_search_settings.use_min_peaks_filter = False
mass_spectrum_obj.molecular_search_settings.use_min_peaks_filter = 10
mass_spectrum_obj.molecular_search_settings.use_isotopologue_filter = False
click.echo('Searching for molecular formulas within %.3f and %.3f ppm' %
(mass_spectrum_obj.molecular_search_settings.min_ppm_error,
mass_spectrum_obj.molecular_search_settings.max_ppm_error))
SearchMolecularFormulas(mass_spectrum_obj,
find_isotopologues=True).run_worker_ms_peaks(
[mass_spectrum_obj[0]])
ms_peak = mass_spectrum_obj[0]
if ms_peak:
header = [
'Molecular Formula', 'Calculated m/z', 'Mass Error', 'DBE',
'Ion Type'
]
results = []
for formula in ms_peak:
results.append([
formula.to_string, formula.mz_calc, formula.mz_error,
formula.dbe, formula.ion_type
])
click.echo(tabulate(results,
headers=header,
floatfmt=("s", ".5f", ".5f", ".1f", "s")),
file=out)
click.echo('', file=out)
else:
click.echo(
"Could not find a possible molecular formula match for the m/z %.5f"
% mz[0],
file=out)
click.echo('', file=out)
def load_settings(self, mass_spec_obj, output_parameters):
import json
import warnings
settings_file_path = self.file_location.with_suffix('.json')
if settings_file_path.exists():
self._parameters = load_and_set_parameters_class(
'DataInput', self._parameters, parameters_path=settings_file_path)
load_and_set_parameters_ms(
mass_spec_obj, parameters_path=settings_file_path)
else:
warnings.warn(
"auto settings loading is enabled but could not locate the file: %s. Please load the settings manually" % settings_file_path)
def set_parameter_from_json(self, parameters_path):
load_and_set_parameters_ms(self, parameters_path=parameters_path)