spectrum_utils
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Spectrum annotating
Spectrum visualization
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spectrum_utils
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Index
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__init__() (spectrum_utils.fragment_annotation.FragmentAnnotation method)
(spectrum_utils.fragment_annotation.PeakInterpretation method)
(spectrum_utils.proforma.Charge method)
(spectrum_utils.proforma.CvEntry method)
(spectrum_utils.proforma.Formula method)
(spectrum_utils.proforma.Glycan method)
(spectrum_utils.proforma.Info method)
(spectrum_utils.proforma.Ion method)
(spectrum_utils.proforma.Label method)
(spectrum_utils.proforma.Mass method)
(spectrum_utils.proforma.Modification method)
(spectrum_utils.proforma.Monosaccharide method)
(spectrum_utils.proforma.ProFormaTransformer method)
(spectrum_utils.proforma.Proteoform method)
(spectrum_utils.spectrum.MsmsSpectrum method)
_abc_impl (spectrum_utils.proforma.CvEntry attribute)
(spectrum_utils.proforma.Formula attribute)
(spectrum_utils.proforma.Glycan attribute)
(spectrum_utils.proforma.Mass attribute)
(spectrum_utils.proforma.ModificationSource attribute)
_annotate_ion() (in module spectrum_utils.plot)
_global_modifications (spectrum_utils.proforma.ProFormaTransformer attribute)
_import_cv() (in module spectrum_utils.proforma)
_load_from_cache() (in module spectrum_utils.proforma)
_mass (spectrum_utils.proforma.Formula attribute)
(spectrum_utils.proforma.Glycan attribute)
(spectrum_utils.proforma.Modification attribute)
_modification_sort_key() (in module spectrum_utils.proforma)
_modifications (spectrum_utils.proforma.ProFormaTransformer attribute)
_parse_obo() (in module spectrum_utils.proforma)
_preferred_labels (spectrum_utils.proforma.ProFormaTransformer attribute)
_range_pos (spectrum_utils.proforma.ProFormaTransformer attribute)
_read_from_cv() (spectrum_utils.proforma.CvEntry method)
_sequence (spectrum_utils.proforma.ProFormaTransformer attribute)
_store_in_cache() (in module spectrum_utils.proforma)
_unknown (spectrum_utils.fragment_annotation.PeakInterpretation attribute)
A
AA() (spectrum_utils.proforma.ProFormaTransformer method)
aa() (spectrum_utils.proforma.ProFormaTransformer method)
accession (spectrum_utils.proforma.CvEntry property)
ACCESSION (spectrum_utils.proforma.LookupType attribute)
annotate_ion_type() (in module spectrum_utils.plot)
annotate_proforma() (spectrum_utils.spectrum.MsmsSpectrum method)
annotation (spectrum_utils.spectrum.MsmsSpectrum property)
B
BRANCH (spectrum_utils.proforma.LabelType attribute)
C
Charge (class in spectrum_utils.proforma)
charge (spectrum_utils.fragment_annotation.FragmentAnnotation property)
(spectrum_utils.proforma.Charge attribute)
(spectrum_utils.proforma.Proteoform attribute)
charge() (spectrum_utils.proforma.ProFormaTransformer method)
clear_cache() (in module spectrum_utils.proforma)
composition (spectrum_utils.proforma.Glycan attribute)
controlled_vocabulary (spectrum_utils.proforma.CvEntry property)
(spectrum_utils.proforma.Mass attribute)
count (spectrum_utils.proforma.Monosaccharide attribute)
CV_ABBREV() (spectrum_utils.proforma.ProFormaTransformer method)
CV_ABBREV_OPT() (spectrum_utils.proforma.ProFormaTransformer method)
CV_NAME() (spectrum_utils.proforma.ProFormaTransformer method)
CvEntry (class in spectrum_utils.proforma)
F
filter_intensity() (spectrum_utils.spectrum.MsmsSpectrum method)
Formula (class in spectrum_utils.proforma)
formula (spectrum_utils.proforma.Formula attribute)
FORMULA() (spectrum_utils.proforma.ProFormaTransformer method)
FragmentAnnotation (class in spectrum_utils.fragment_annotation)
from_usi() (spectrum_utils.spectrum.MsmsSpectrum class method)
G
GENERAL (spectrum_utils.proforma.LabelType attribute)
get_mass() (spectrum_utils.proforma.CvEntry method)
(spectrum_utils.proforma.Formula method)
(spectrum_utils.proforma.Glycan method)
(spectrum_utils.proforma.Mass method)
(spectrum_utils.proforma.ModificationSource method)
get_theoretical_fragments() (in module spectrum_utils.fragment_annotation)
Glycan (class in spectrum_utils.proforma)
I
identifier (spectrum_utils.spectrum.MsmsSpectrum property)
Info (class in spectrum_utils.proforma)
info() (spectrum_utils.proforma.ProFormaTransformer method)
intensity (spectrum_utils.spectrum.MsmsSpectrum property)
Ion (class in spectrum_utils.proforma)
ion (spectrum_utils.proforma.Ion attribute)
ion() (spectrum_utils.proforma.ProFormaTransformer method)
ions (spectrum_utils.proforma.Charge attribute)
ISOTOPE() (spectrum_utils.proforma.ProFormaTransformer method)
isotopes (spectrum_utils.proforma.Formula attribute)
L
Label (class in spectrum_utils.proforma)
label (spectrum_utils.proforma.Label attribute)
(spectrum_utils.proforma.Modification attribute)
LabelType (class in spectrum_utils.proforma)
LookupType (class in spectrum_utils.proforma)
M
Mass (class in spectrum_utils.proforma)
MASS (spectrum_utils.proforma.LookupType attribute)
mass (spectrum_utils.proforma.Mass attribute)
(spectrum_utils.proforma.Modification property)
mass_diff() (in module spectrum_utils.utils)
message (spectrum_utils.proforma.Info attribute)
mirror() (in module spectrum_utils.iplot)
(in module spectrum_utils.plot)
mod() (spectrum_utils.proforma.ProFormaTransformer method)
mod_accession() (spectrum_utils.proforma.ProFormaTransformer method)
mod_c_term() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_COUNT() (spectrum_utils.proforma.ProFormaTransformer method)
mod_formula() (spectrum_utils.proforma.ProFormaTransformer method)
mod_global() (spectrum_utils.proforma.ProFormaTransformer method)
mod_glycan() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_LABEL() (spectrum_utils.proforma.ProFormaTransformer method)
mod_label() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_LABEL_BRANCH() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_LABEL_XL() (spectrum_utils.proforma.ProFormaTransformer method)
mod_labile() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_MASS() (spectrum_utils.proforma.ProFormaTransformer method)
mod_mass() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_MASS_OBS() (spectrum_utils.proforma.ProFormaTransformer method)
mod_n_term() (spectrum_utils.proforma.ProFormaTransformer method)
mod_name() (spectrum_utils.proforma.ProFormaTransformer method)
mod_range() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_RANGE_L() (spectrum_utils.proforma.ProFormaTransformer method)
mod_range_pos() (spectrum_utils.proforma.ProFormaTransformer method)
MOD_SCORE() (spectrum_utils.proforma.ProFormaTransformer method)
mod_unknown_pos() (spectrum_utils.proforma.ProFormaTransformer method)
Modification (class in spectrum_utils.proforma)
modifications (spectrum_utils.proforma.Proteoform attribute)
ModificationSource (class in spectrum_utils.proforma)
module
spectrum_utils.fragment_annotation
spectrum_utils.iplot
spectrum_utils.plot
spectrum_utils.proforma
spectrum_utils.utils
Monosaccharide (class in spectrum_utils.proforma)
monosaccharide (spectrum_utils.proforma.Monosaccharide attribute)
monosaccharide() (spectrum_utils.proforma.ProFormaTransformer method)
MsmsSpectrum (class in spectrum_utils.spectrum)
mz (spectrum_utils.spectrum.MsmsSpectrum property)
mz_delta (spectrum_utils.fragment_annotation.FragmentAnnotation property)
N
name (spectrum_utils.proforma.CvEntry property)
NAME (spectrum_utils.proforma.LookupType attribute)
P
parse() (in module spectrum_utils.proforma)
PeakInterpretation (class in spectrum_utils.fragment_annotation)
peptide() (spectrum_utils.proforma.ProFormaTransformer method)
position (spectrum_utils.proforma.Modification attribute)
precursor_charge (spectrum_utils.spectrum.MsmsSpectrum property)
precursor_mz (spectrum_utils.spectrum.MsmsSpectrum property)
proforma() (spectrum_utils.proforma.ProFormaTransformer method)
ProFormaTransformer (class in spectrum_utils.proforma)
Proteoform (class in spectrum_utils.proforma)
proteoform() (spectrum_utils.proforma.ProFormaTransformer method)
R
remove_precursor_peak() (spectrum_utils.spectrum.MsmsSpectrum method)
retention_time (spectrum_utils.spectrum.MsmsSpectrum property)
round() (spectrum_utils.spectrum.MsmsSpectrum method)
S
scale_intensity() (spectrum_utils.spectrum.MsmsSpectrum method)
score (spectrum_utils.proforma.Label attribute)
sequence (spectrum_utils.proforma.Proteoform attribute)
set_mz_range() (spectrum_utils.spectrum.MsmsSpectrum method)
source (spectrum_utils.proforma.Modification attribute)
spectrum() (in module spectrum_utils.iplot)
(in module spectrum_utils.plot)
spectrum_utils.fragment_annotation
module
spectrum_utils.iplot
module
spectrum_utils.plot
module
spectrum_utils.proforma
module
spectrum_utils.utils
module
T
TEXT() (spectrum_utils.proforma.ProFormaTransformer method)
type (spectrum_utils.proforma.Label attribute)
X
XL (spectrum_utils.proforma.LabelType attribute)
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