Documentation for Chemicals.py

Chemicals

Provides implementation of Chemicals objects that are used as input to the simulation.

Adducts

Adducts(
    formula,
    adduct_proportion_cutoff=0.05,
    adduct_prior_dict=None,
    adduct_profile=None,
    adduct_concentration=15.0,
)

A class to represent an adduct of a chemical

Create an Adduct class

Parameters:

Name	Type	Description	Default
formula		the formula of this adduct	required
adduct_proportion_cutoff		proportion cut-off of the adduct	0.05
adduct_prior_dict		custom adduct dictionary or callable, if any	None
adduct_profile		preset profile name or dict of adduct priors	None
adduct_concentration		dirichlet concentration for adduct sampling	15.0

Source code in vimms/Chemicals.py

def __init__(
    self,
    formula,
    adduct_proportion_cutoff=0.05,
    adduct_prior_dict=None,
    adduct_profile=None,
    adduct_concentration=15.0,
):
    """
    Create an Adduct class

    Args:
        formula: the formula of this adduct
        adduct_proportion_cutoff: proportion cut-off of the adduct
        adduct_prior_dict: custom adduct dictionary or callable, if any
        adduct_profile: preset profile name or dict of adduct priors
        adduct_concentration: dirichlet concentration for adduct sampling
    """
    if callable(adduct_prior_dict):
        adduct_prior_dict = adduct_prior_dict(formula)

    if adduct_prior_dict is None and adduct_profile is not None:
        if isinstance(adduct_profile, str):
            adduct_prior_dict = ADDUCT_PROFILE_PRESETS.get(adduct_profile)
            if adduct_prior_dict is None:
                raise ValueError(f"Unknown adduct profile '{adduct_profile}'")
        else:
            adduct_prior_dict = adduct_profile

    if adduct_prior_dict is None:
        self.adduct_names = {POSITIVE: ADDUCT_NAMES_POS, NEGATIVE: ADDUCT_NAMES_NEG}
        self.adduct_prior = {
            POSITIVE: np.array([ADDUCT_PRIOR_POS.get(name, 0.05) for name in ADDUCT_NAMES_POS]),
            NEGATIVE: np.array([ADDUCT_PRIOR_NEG.get(name, 0.05) for name in ADDUCT_NAMES_NEG]),
        }
    else:
        assert POSITIVE in adduct_prior_dict or NEGATIVE in adduct_prior_dict
        self.adduct_names = {k: list(adduct_prior_dict[k].keys()) for k in adduct_prior_dict}
        self.adduct_prior = {
            k: np.array(list(adduct_prior_dict[k].values())) for k in adduct_prior_dict
        }
    self.formula = formula
    self.adduct_proportion_cutoff = adduct_proportion_cutoff
    self.adduct_concentration = adduct_concentration
    self._validate_adduct_names()

get_adducts

get_adducts()

Get the adducts Returns: adducts in the correct proportion

Source code in vimms/Chemicals.py

def get_adducts(self):
    """
    Get the adducts
    Returns: adducts in the correct proportion
    """
    adducts = {}
    proportions = self._get_adduct_proportions()
    for k in self.adduct_names:
        adducts[k] = []
        for j in range(len(self.adduct_names[k])):
            if proportions[k][j] != 0:
                adducts[k].extend([(self._get_adduct_names()[k][j], proportions[k][j])])
    return adducts

BaseChemical

BaseChemical(ms_level, children)

The base class for Chemical objects across all MS levels. Chemicals at MS level = 1 is special and should be instantiated as either Known or Unknown chemicals. For other MS levels, please use the MSN class.

Defines a base chemical object Args: ms_level: the MS level of this chemical children: any children of this chemical

Source code in vimms/Chemicals.py

def __init__(self, ms_level, children):
    """
    Defines a base chemical object
    Args:
        ms_level: the MS level of this chemical
        children: any children of this chemical
    """
    self.ms_level = ms_level
    self.children = children

Chemical

Chemical(rt, max_intensity, chromatogram, children, base_chemical)

Bases: BaseChemical

The class that represents a Chemical object of MS-level 1. Should be realised as either Known or Unknown chemicals.

Create a Chemical object Args: rt: the starting RT value of this chemical max_intensity: the maximum intensity of this chemical chromatogram: the chromatogram of this chemical children: any children of this chemical base_chemical: the base chemical from which this chemical is derived

Source code in vimms/Chemicals.py

def __init__(self, rt, max_intensity, chromatogram, children, base_chemical):
    """
    Create a Chemical object
    Args:
        rt: the starting RT value of this chemical
        max_intensity: the maximum intensity of this chemical
        chromatogram: the chromatogram of this chemical
        children: any children of this chemical
        base_chemical: the base chemical from which this chemical is derived
    """
    ms_level = 1
    super().__init__(ms_level, children)

    self.rt = rt
    self.max_intensity = max_intensity
    self.chromatogram = chromatogram
    self.mz_diff = 0
    self.base_chemical = base_chemical

get_apex_rt

get_apex_rt()

Get the apex (highest point) RT of the chromatogram of this chemical Returns: the apex RT of the chromatogram

Source code in vimms/Chemicals.py

def get_apex_rt(self):
    """
    Get the apex (highest point) RT of the chromatogram of this chemical
    Returns: the apex RT of the chromatogram

    """

    return self.rt + self.chromatogram.get_apex_rt()

get_original_parent

get_original_parent()

Get the original base chemical in a recursive manner. This is necessary if the parent chemical also has another parent. Returns: the original base chemical

Source code in vimms/Chemicals.py

def get_original_parent(self):
    """
    Get the original base chemical in a recursive manner.
    This is necessary if the parent chemical also has another parent.
    Returns: the original base chemical

    """
    return self if self.base_chemical is None else self.base_chemical.get_original_parent()

ChemicalMixtureCreator

ChemicalMixtureCreator(
    formula_sampler,
    rt_and_intensity_sampler=UniformRTAndIntensitySampler(),
    chromatogram_sampler=GaussianChromatogramSampler(),
    ms2_sampler=UniformMS2Sampler(),
    adduct_proportion_cutoff=0.05,
    adduct_prior_dict=None,
    adduct_profile=None,
    adduct_concentration=15.0,
)

A class to create a list of known chemical objects using simplified, cleaned methods.

Create a mixture of vimms.Chemicals.KnownChemical objects. Args: formula_sampler: an instance of vimms.ChemicalSamplers.FormulaSampler to sample chemical formulae. rt_and_intensity_sampler: an instance of vimms.ChemicalSamplers.RTAndIntensitySampler to sample RT and intensity values. chromatogram_sampler: an instance of vimms.ChemicalSamplers.ChromatogramSampler to sample chromatograms. ms2_sampler: an instance of vimms.ChemicalSamplers.MS2Sampler to sample MS2 fragmentation spectra. adduct_proportion_cutoff: proportion of adduct cut-off adduct_prior_dict: custom adduct dictionary adduct_profile: preset name or dict of adduct priors adduct_concentration: dirichlet concentration for adduct sampling

Source code in vimms/Chemicals.py

def __init__(
    self,
    formula_sampler,
    rt_and_intensity_sampler=UniformRTAndIntensitySampler(),
    chromatogram_sampler=GaussianChromatogramSampler(),
    ms2_sampler=UniformMS2Sampler(),
    adduct_proportion_cutoff=0.05,
    adduct_prior_dict=None,
    adduct_profile=None,
    adduct_concentration=15.0,
):
    """
    Create a mixture of [vimms.Chemicals.KnownChemical][] objects.
    Args:
        formula_sampler: an instance of [vimms.ChemicalSamplers.FormulaSampler][] to sample
                         chemical formulae.
        rt_and_intensity_sampler: an instance of
                                  [vimms.ChemicalSamplers.RTAndIntensitySampler][] to sample
                                  RT and intensity values.
        chromatogram_sampler: an instance of
                              [vimms.ChemicalSamplers.ChromatogramSampler][] to sample
                              chromatograms.
        ms2_sampler: an instance of
                     [vimms.ChemicalSamplers.MS2Sampler][] to sample MS2
                     fragmentation spectra.
        adduct_proportion_cutoff: proportion of adduct cut-off
        adduct_prior_dict: custom adduct dictionary
        adduct_profile: preset name or dict of adduct priors
        adduct_concentration: dirichlet concentration for adduct sampling
    """
    self.formula_sampler = formula_sampler
    self.rt_and_intensity_sampler = rt_and_intensity_sampler
    self.chromatogram_sampler = chromatogram_sampler
    self.ms2_sampler = ms2_sampler
    self.adduct_proportion_cutoff = adduct_proportion_cutoff
    self.adduct_prior_dict = adduct_prior_dict
    self.adduct_profile = adduct_profile
    self.adduct_concentration = adduct_concentration

sample

sample(n_chemicals, ms_levels, include_adducts_isotopes=True)

Samples chemicals.

Parameters:

Name	Type	Description	Default
n_chemicals		the number of chemicals	required
ms_levels		the highest MS level to generate. Typically this is 2.	required
include_adducts_isotopes		whether to include adduct and isotopes or not.	True

Returns: a list of vimms.Chemicals.KnownChemical objects.

Source code in vimms/Chemicals.py

def sample(self, n_chemicals, ms_levels, include_adducts_isotopes=True):
    """
    Samples chemicals.

    Args:
        n_chemicals: the number of chemicals
        ms_levels: the highest MS level to generate. Typically this is 2.
        include_adducts_isotopes: whether to include adduct and isotopes or not.

    Returns: a list of [vimms.Chemicals.KnownChemical][] objects.

    """

    formula_list = self.formula_sampler.sample(n_chemicals)
    rt_list = []
    intensity_list = []
    chromatogram_list = []
    for formula, db_accession in formula_list:
        rt, intensity = self.rt_and_intensity_sampler.sample(formula)
        rt_list.append(rt)
        intensity_list.append(intensity)
        chromatogram_list.append(self.chromatogram_sampler.sample(formula, rt, intensity))
    logger.debug("Sampled rt and intensity values and chromatograms")

    # make into known chemical objects
    chemicals = []
    for i, (formula, db_accession) in enumerate(formula_list):
        rt = rt_list[i]
        max_intensity = intensity_list[i]
        chromatogram = chromatogram_list[i]
        if isinstance(formula, Formula):
            isotopes = Isotopes(formula)
            adducts = Adducts(
                formula,
                self.adduct_proportion_cutoff,
                adduct_prior_dict=self.adduct_prior_dict,
                adduct_profile=self.adduct_profile,
                adduct_concentration=self.adduct_concentration,
            )

            chemicals.append(
                KnownChemical(
                    formula,
                    isotopes,
                    adducts,
                    rt,
                    max_intensity,
                    chromatogram,
                    include_adducts_isotopes=include_adducts_isotopes,
                    database_accession=db_accession,
                )
            )
        elif isinstance(formula, DummyFormula):
            chemicals.append(UnknownChemical(formula.mass, rt, max_intensity, chromatogram))
        else:
            logger.warning("Unkwown formula object: {}".format(type(formula)))

        if ms_levels == 2:
            parent = chemicals[-1]
            child_mz, child_intensity, parent_proportion = self.ms2_sampler.sample(parent)

            children = []
            for mz, intensity in zip(child_mz, child_intensity):
                child = MSN(mz, 2, intensity, parent_proportion, None, parent)
                children.append(child)
            children.sort(key=lambda x: x.isotopes[0])
            parent.children = children

    return chemicals

ChemicalMixtureFromMZML

ChemicalMixtureFromMZML(
    mzml_file_name, ms2_sampler=UniformMS2Sampler(), roi_params=None
)

A class to create a list of known chemical objects from an mzML file using simplified, cleaned methods.

Create a ChemicalMixtureFromMZML class. Args: mzml_file_name: the mzML filename to extract vimms.Chemicals.UnknownChemical objects from. ms2_sampler: the MS2 sampler to use. Should be an instance of vimms.ChemicalSamplers.MS2Sampler. roi_params: parameters for ROI building, as defined in vimms.Roi.RoiBuilderParams.

Source code in vimms/Chemicals.py

def __init__(self, mzml_file_name, ms2_sampler=UniformMS2Sampler(), roi_params=None):
    """
    Create a ChemicalMixtureFromMZML class.
    Args:
        mzml_file_name: the mzML filename to extract [vimms.Chemicals.UnknownChemical][]
                        objects from.
        ms2_sampler: the MS2 sampler to use. Should be an instance of
                     [vimms.ChemicalSamplers.MS2Sampler][].
        roi_params: parameters for ROI building, as defined in [vimms.Roi.RoiBuilderParams][].
    """
    self.mzml_file_name = mzml_file_name
    self.ms2_sampler = ms2_sampler
    self.roi_params = roi_params

    if roi_params is None:
        self.roi_params = RoiBuilderParams()

    self.good_rois = self._extract_rois()
    assert len(self.good_rois) > 0

sample

sample(n_chemicals, ms_levels, source_polarity=POSITIVE)

Generate a dataset of Chemicals from the mzml file Args: n_chemicals: the number of Chemical objects. Set to None to get all the ROIs. ms_levels: the maximum MS level source_polarity: either POSITIVE or NEGATIVE

Returns: the list of Chemicals from the mzML file.

Source code in vimms/Chemicals.py

def sample(self, n_chemicals, ms_levels, source_polarity=POSITIVE):
    """
    Generate a dataset of Chemicals from the mzml file
    Args:
        n_chemicals: the number of Chemical objects. Set to None to get all the ROIs.
        ms_levels: the maximum MS level
        source_polarity: either POSITIVE or NEGATIVE

    Returns: the list of Chemicals from the mzML file.

    """
    if n_chemicals is None:
        rois_to_use = range(len(self.good_rois))
    elif n_chemicals > len(self.good_rois):
        rois_to_use = range(len(self.good_rois))
        logger.warning("Requested more chemicals than ROIs")
    else:
        rois_to_use = np.random.permutation(len(self.good_rois))[:n_chemicals]
    chemicals = []
    for roi_idx in rois_to_use:
        r = self.good_rois[roi_idx]
        mz = r.mean_mz
        if source_polarity == POSITIVE:
            mz -= PROTON_MASS
        elif source_polarity == NEGATIVE:
            mz += PROTON_MASS
        else:
            logger.warning("Unknown source polarity {}".format(source_polarity))
        rt = r.rt_list[0]  # this is in seconds
        max_intensity = max(r.intensity_list)

        # make a chromatogram object
        chromatogram = EmpiricalChromatogram(
            np.array(r.rt_list),
            np.array(r.mz_list),
            np.array(r.intensity_list),
            single_point_length=0.9,
        )

        # make a chemical
        new_chemical = UnknownChemical(mz, rt, max_intensity, chromatogram, children=None)
        chemicals.append(new_chemical)

        if ms_levels == 2:
            parent = chemicals[-1]
            child_mz, child_intensity, parent_proportion = self.ms2_sampler.sample(parent)

            children = []
            for mz, intensity in zip(child_mz, child_intensity):
                child = MSN(mz, 2, intensity, parent_proportion, None, parent)
                children.append(child)
            children.sort(key=lambda x: x.isotopes[0])
            parent.children = children

    return chemicals

DatabaseCompound

DatabaseCompound(
    name,
    chemical_formula,
    monisotopic_molecular_weight,
    smiles,
    inchi,
    inchikey,
)

A class to represent a compound stored in a database, e.g. HMDB

Creates a DatabaseCompound object Args: name: the compound name chemical_formula: the formula of that compound monisotopic_molecular_weight: the monoisotopic weight of the compound smiles: SMILES of the compound inchi: InCHI of the compound inchikey: InCHI key of the compound

Source code in vimms/Chemicals.py

def __init__(
    self, name, chemical_formula, monisotopic_molecular_weight, smiles, inchi, inchikey
):
    """
    Creates a DatabaseCompound object
    Args:
        name: the compound name
        chemical_formula: the formula of that compound
        monisotopic_molecular_weight: the monoisotopic weight of the compound
        smiles: SMILES of the compound
        inchi: InCHI of the compound
        inchikey: InCHI key of the compound
    """
    self.name = name
    self.chemical_formula = chemical_formula
    self.monisotopic_molecular_weight = monisotopic_molecular_weight
    self.smiles = smiles
    self.inchi = inchi
    self.inchikey = inchikey

Isotopes

Isotopes(
    formula, min_prob=1e-12, max_peaks=None, max_states=4000, mass_precision=8
)

A class to represent an isotope of a chemical

Create an Isotope object Args: formula: the formula for the given isotope

Source code in vimms/Chemicals.py

def __init__(
    self, formula, min_prob=1e-12, max_peaks=None, max_states=4000, mass_precision=8
):
    """
    Create an Isotope object
    Args:
        formula: the formula for the given isotope
    """
    self.formula = formula
    self.min_prob = min_prob
    self.max_peaks = max_peaks
    self.max_states = max_states
    self.mass_precision = mass_precision

get_isotopes

get_isotopes(
    total_proportion,
    min_prob=None,
    max_peaks=None,
    max_states=None,
    mass_precision=None,
)

Gets the isotope total proportion

Parameters:

Name	Type	Description	Default
total_proportion		the total proportion to compute	required

Returns: the computed isotope total proportion

Source code in vimms/Chemicals.py

def get_isotopes(
    self, total_proportion, min_prob=None, max_peaks=None, max_states=None, mass_precision=None
):
    """
    Gets the isotope total proportion

    Args:
        total_proportion: the total proportion to compute

    Returns: the computed isotope total proportion

    """
    peaks = []
    distributions = self._get_isotope_distribution(
        total_proportion=total_proportion,
        min_prob=self.min_prob if min_prob is None else min_prob,
        max_peaks=self.max_peaks if max_peaks is None else max_peaks,
        max_states=self.max_states if max_states is None else max_states,
        mass_precision=self.mass_precision if mass_precision is None else mass_precision,
    )
    base_mz = self.formula._get_mz()
    for idx, (mass_shift, proportion) in enumerate(distributions):
        name = MONO if idx == 0 else f"M+{idx}"
        peaks.append((base_mz + mass_shift, proportion, name))
    return peaks

KnownChemical

KnownChemical(
    formula,
    isotopes,
    adducts,
    rt,
    max_intensity,
    chromatogram,
    children=None,
    include_adducts_isotopes=True,
    total_proportion=0.99,
    database_accession=None,
    base_chemical=None,
)

Bases: Chemical

A Chemical representation from a known chemical formula. Known chemicals have formula which are defined during creation.

Initialises a Known chemical object

Parameters:

Name	Type	Description	Default
formula		the formula of this chemical object.	required
isotopes		the isotope of this chemical object	required
adducts		the adduct of this chemical object	required
rt		the starting retention time value of this chemical object	required
max_intensity		the maximum intensity value in the chromatogram	required
chromatogram		the chromatogram of the chemical	required
children		any children of the chemical	None
include_adducts_isotopes		whether to include adducts and isotopes of this chemical	True
total_proportion		total proportion of this chemical	0.99
database_accession		database accession number, if any	None
base_chemical		parent chemica, if any	None

Source code in vimms/Chemicals.py

def __init__(
    self,
    formula,
    isotopes,
    adducts,
    rt,
    max_intensity,
    chromatogram,
    children=None,
    include_adducts_isotopes=True,
    total_proportion=0.99,
    database_accession=None,
    base_chemical=None,
):
    """
    Initialises a Known chemical object

    Args:
        formula: the formula of this chemical object.
        isotopes: the isotope of this chemical object
        adducts: the adduct of this chemical object
        rt: the starting retention time value of this chemical object
        max_intensity: the maximum intensity value in the chromatogram
        chromatogram: the chromatogram of the chemical
        children: any children of the chemical
        include_adducts_isotopes: whether to include adducts and isotopes of this chemical
        total_proportion: total proportion of this chemical
        database_accession: database accession number, if any
        base_chemical: parent chemica, if any
    """
    super().__init__(rt, max_intensity, chromatogram, children, base_chemical)
    self.formula = formula
    self.mz_diff = C13_MZ_DIFF
    if include_adducts_isotopes is True:
        self.isotopes = isotopes.get_isotopes(total_proportion)
        self.adducts = adducts.get_adducts()
    else:
        mz = isotopes.get_isotopes(total_proportion)[0][0]
        self.isotopes = [(mz, 1, MONO)]
        self.adducts = {POSITIVE: [("M+H", 1)], NEGATIVE: [("M-H", 1)]}
    self.mass = self.formula.mass
    self.database_accession = database_accession

MSN

MSN(mz, ms_level, prop_ms2_mass, parent_mass_prop, children=None, parent=None)

Bases: BaseChemical

A chemical that represents an MS2+ fragment.

Initialises an MSN object

Parameters:

Name	Type	Description	Default
mz		the m/z value of this fragment peak	required
ms_level		the MS level of this fragment peak	required
prop_ms2_mass		proportion of MS2 mass	required
parent_mass_prop		proportion from the parent MS1 mass	required
children		any children	None
parent		parent MS1 peak	None

Source code in vimms/Chemicals.py

def __init__(self, mz, ms_level, prop_ms2_mass, parent_mass_prop, children=None, parent=None):
    """
    Initialises an MSN object

    Args:
        mz: the m/z value of this fragment peak
        ms_level: the MS level of this fragment peak
        prop_ms2_mass: proportion of MS2 mass
        parent_mass_prop: proportion from the parent MS1 mass
        children: any children
        parent: parent MS1 peak
    """
    super().__init__(ms_level, children)
    self.isotopes = [(mz, None, "MSN")]
    self.prop_ms2_mass = prop_ms2_mass
    self.parent_mass_prop = parent_mass_prop
    self.parent = parent

MultipleMixtureCreator

MultipleMixtureCreator(
    master_chemical_list,
    group_list,
    group_dict,
    intensity_noise=GaussianPeakNoise(sigma=0.001, log_space=True),
    overall_missing_probability=0.0,
)

A class to create a list of known chemical objects in multiple samples (mixtures)

Create a chemical mixture creator. example

Parameters:

Name	Type	Description	Default
master_chemical_list		the master list of Chemicals to create each sample (mixture)	required
group_list		a list of different groups, e.g. group_list = ['control', 'control', 'case', 'case']	required
group_dict		a dictionary of parameters for each group, e.g. group_dict = { 'control': { 'missing_probability': 0.0, 'changing_probability': 0.0 }, 'case': { 'missing_probability': 0.0, 'changing_probability': 0.0 } }	required
intensity_noise		intensity noise. Should be an instance of vimms.Noise.NoPeakNoise.	GaussianPeakNoise(sigma=0.001, log_space=True)
overall_missing_probability		overall missing probability across all mixtures.	0.0

Source code in vimms/Chemicals.py

def __init__(
    self,
    master_chemical_list,
    group_list,
    group_dict,
    intensity_noise=GaussianPeakNoise(sigma=0.001, log_space=True),
    overall_missing_probability=0.0,
):
    """
    Create a chemical mixture creator.
    example

    Args:
        master_chemical_list: the master list of Chemicals to create each sample (mixture)
        group_list: a list of different groups, e.g.
                    group_list = ['control', 'control', 'case', 'case']
        group_dict: a dictionary of parameters for each group, e.g.
                    group_dict = {
                        'control': {
                            'missing_probability': 0.0,
                            'changing_probability': 0.0
                        }, 'case': {
                            'missing_probability': 0.0,
                            'changing_probability': 0.0
                        }
                    }
        intensity_noise: intensity noise. Should be an instance of [vimms.Noise.NoPeakNoise][].
        overall_missing_probability: overall missing probability across all mixtures.
    """
    self.master_chemical_list = master_chemical_list
    self.group_list = group_list
    self.group_dict = group_dict
    self.intensity_noise = intensity_noise
    self.overall_missing_probability = overall_missing_probability

    if "control" not in self.group_dict:
        self.group_dict["control"] = {}
        self.group_dict["control"]["missing_probability"] = 0.0
        self.group_dict["control"]["changing_probability"] = 0.0

    self._generate_changes()

generate_chemical_lists

generate_chemical_lists()

Generates list of chemicals across mixtures (samples)

Returns: the list of chemicals across mixtures (samples)

Source code in vimms/Chemicals.py

def generate_chemical_lists(self):
    """
    Generates list of chemicals across mixtures (samples)

    Returns: the list of chemicals across mixtures (samples)

    """
    chemical_lists = []
    for group in self.group_list:
        new_list = []
        for chemical in self.master_chemical_list:
            if (
                np.random.rand() < self.overall_missing_probability
                or self.group_multipliers[group][chemical] == 0.0
            ):
                continue  # chemical is missing overall
            new_intensity = chemical.max_intensity * self.group_multipliers[group][chemical]
            new_intensity = self.intensity_noise.get(new_intensity, 1)

            # make a new known chemical
            new_chemical = copy.deepcopy(chemical)
            new_chemical.max_intensity = new_intensity
            new_chemical.base_chemical = chemical
            new_list.append(new_chemical)
        chemical_lists.append(new_list)
    return chemical_lists

UnknownChemical

UnknownChemical(
    mz, rt, max_intensity, chromatogram, children=None, base_chemical=None
)

Bases: Chemical

A Chemical representation from an unknown chemical formula. Unknown chemicals are typically created by extracting Regions-of-Interest from an existing mzML file.

Initialises an UnknownChemical object.

Parameters:

Name	Type	Description	Default
mz		the m/z value of this chemical. Unlike vimms.Chemicals.KnownChemical here we know the m/z value but do not known the formula that generates this chemical.	required
rt		the starting RT value of this chemical	required
max_intensity		the maximum intensity of this chemical	required
chromatogram		the chromatogram of this chemical	required
children		any children of this chemical	None
base_chemical		the base chemical from which this chemical is derived	None

Source code in vimms/Chemicals.py

def __init__(self, mz, rt, max_intensity, chromatogram, children=None, base_chemical=None):
    """
    Initialises an UnknownChemical object.

    Args:
        mz: the m/z value of this chemical. Unlike [vimms.Chemicals.KnownChemical][] here we
            know the m/z value but do not known the formula that generates this chemical.
        rt: the starting RT value of this chemical
        max_intensity: the maximum intensity of this chemical
        chromatogram: the chromatogram of this chemical
        children: any children of this chemical
        base_chemical: the base chemical from which this chemical is derived
    """
    super().__init__(rt, max_intensity, chromatogram, children, base_chemical)
    self.isotopes = [(mz, 1, "Mono")]  # [(mz, intensity_proportion, isotope,name)]
    self.adducts = {POSITIVE: [("M+H", 1)], NEGATIVE: [("M-H", 1)]}
    self.mass = mz

get_pooled_sample

get_pooled_sample(dataset_list)

Takes a list of datasets and creates a pooled dataset from them

Parameters:

Name	Type	Description	Default
dataset_list		a list of datasets, each containing Chemical objects	required

Returns: combined list where the datasets have been pooled

Source code in vimms/Chemicals.py

def get_pooled_sample(dataset_list):
    """
    Takes a list of datasets and creates a pooled dataset from them

    Args:
        dataset_list: a list of datasets, each containing Chemical objects

    Returns: combined list where the datasets have been pooled

    """
    n_datasets = len(dataset_list)
    all_chems = np.array([item for sublist in dataset_list for item in sublist])
    unique_parents = list(set([chem.base_chemical for chem in all_chems]))
    # create dataset
    dataset = []
    for chem in unique_parents:
        matched_chemicals = all_chems[np.where(all_chems == chem)[0]]
        new_intensity = sum([mchem.max_intensity for mchem in matched_chemicals]) / n_datasets
        new_chem = copy.deepcopy(chem)
        new_chem.max_intensity = new_intensity
        dataset.append(new_chem)
    return dataset