psm_utils
v0.7.2
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psm_utils
psm_utils.io
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Command line interface
psm_utils
Index
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Index
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C
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E
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F
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G
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X
A
add_fixed_modifications() (psm_utils.peptidoform.Peptidoform method)
(psm_utils.psm_list.PSMList method)
add_note() (psm_utils.io.idxml.IdXMLException method)
(psm_utils.io.idxml.IdXMLReaderEmptyListException method)
(psm_utils.io.ionbot.InvalidIonbotModificationError method)
(psm_utils.io.maxquant.MSMSParsingError method)
(psm_utils.io.msamanda.MSAmandaParsingError method)
(psm_utils.io.mzid.UnknownMzidScore method)
(psm_utils.io.peptide_record.InvalidPeprecError method)
(psm_utils.io.peptide_record.InvalidPeprecModificationError method)
(psm_utils.io.xtandem.XTandemException method)
(psm_utils.io.xtandem.XTandemModificationException method)
AmbiguousResidueException
append() (psm_utils.psm_list.PSMList method)
apply_fixed_modifications() (psm_utils.peptidoform.Peptidoform method)
(psm_utils.psm_list.PSMList method)
C
calculate_qvalues() (psm_utils.psm_list.PSMList method)
collections (psm_utils.psm_list.PSMList property)
composition (psm_utils.peptidoform.Peptidoform property)
convert() (in module psm_utils.io)
E
extend() (psm_utils.psm_list.PSMList method)
F
find_decoys() (psm_utils.psm_list.PSMList method)
from_dataframe() (in module psm_utils.io.peptide_record)
G
get_precursor_charge() (psm_utils.psm.PSM method)
get_psm_dict() (psm_utils.psm_list.PSMList method)
get_rank1_psms() (psm_utils.psm_list.PSMList method)
get_usi() (psm_utils.psm.PSM method)
I
IdXMLException
IdXMLReader (class in psm_utils.io.idxml)
IdXMLReaderEmptyListException
IdXMLWriter (class in psm_utils.io.idxml)
InvalidIonbotModificationError
InvalidPeprecError
InvalidPeprecModificationError
IonbotReader (class in psm_utils.io.ionbot)
is_modified (psm_utils.peptidoform.Peptidoform property)
J
join_pout_files() (in module psm_utils.io.percolator)
M
mass_to_mz() (in module psm_utils.utils)
model_config (psm_utils.psm.PSM attribute)
(psm_utils.psm_list.PSMList attribute)
model_fields (psm_utils.psm.PSM attribute)
(psm_utils.psm_list.PSMList attribute)
ModificationException
module
psm_utils
psm_utils.__main__
psm_utils.io
psm_utils.io.idxml
psm_utils.io.ionbot
psm_utils.io.maxquant
psm_utils.io.msamanda
psm_utils.io.mzid
psm_utils.io.peptide_record
psm_utils.io.pepxml
psm_utils.io.percolator
psm_utils.io.proteome_discoverer
psm_utils.io.sage
psm_utils.io.tsv
psm_utils.io.xtandem
psm_utils.peptidoform
psm_utils.psm
psm_utils.psm_list
psm_utils.utils
MSAmandaParsingError
MSAmandaReader (class in psm_utils.io.msamanda)
MSFReader (class in psm_utils.io.proteome_discoverer)
MSMSParsingError
MSMSReader (class in psm_utils.io.maxquant)
mz_to_mass() (in module psm_utils.utils)
MzidReader (class in psm_utils.io.mzid)
MzidWriter (class in psm_utils.io.mzid)
P
parsed_sequence (psm_utils.peptidoform.Peptidoform attribute)
peprec_to_proforma() (in module psm_utils.io.peptide_record)
PeptideRecordReader (class in psm_utils.io.peptide_record)
PeptideRecordWriter (class in psm_utils.io.peptide_record)
Peptidoform (class in psm_utils.peptidoform)
PeptidoformException
PepXMLReader (class in psm_utils.io.pepxml)
PercolatorTabReader (class in psm_utils.io.percolator)
PercolatorTabWriter (class in psm_utils.io.percolator)
precursor_charge (psm_utils.peptidoform.Peptidoform property)
precursor_mz_error (psm_utils.psm.PSM property)
proforma (psm_utils.peptidoform.Peptidoform property)
proforma_to_peprec() (in module psm_utils.io.peptide_record)
properties (psm_utils.peptidoform.Peptidoform attribute)
PSM (class in psm_utils.psm)
psm_utils
module
psm_utils.__main__
module
psm_utils.io
module
psm_utils.io.idxml
module
psm_utils.io.ionbot
module
psm_utils.io.maxquant
module
psm_utils.io.msamanda
module
psm_utils.io.mzid
module
psm_utils.io.peptide_record
module
psm_utils.io.pepxml
module
psm_utils.io.percolator
module
psm_utils.io.proteome_discoverer
module
psm_utils.io.sage
module
psm_utils.io.tsv
module
psm_utils.io.xtandem
module
psm_utils.peptidoform
module
psm_utils.psm
module
psm_utils.psm_list
module
psm_utils.utils
module
PSMList (class in psm_utils.psm_list)
R
read_file() (in module psm_utils.io)
(psm_utils.io.idxml.IdXMLReader method)
(psm_utils.io.ionbot.IonbotReader method)
(psm_utils.io.maxquant.MSMSReader method)
(psm_utils.io.msamanda.MSAmandaReader method)
(psm_utils.io.mzid.MzidReader method)
(psm_utils.io.peptide_record.PeptideRecordReader method)
(psm_utils.io.pepxml.PepXMLReader method)
(psm_utils.io.percolator.PercolatorTabReader method)
(psm_utils.io.proteome_discoverer.MSFReader method)
(psm_utils.io.sage.SageReader method)
(psm_utils.io.tsv.TSVReader method)
(psm_utils.io.xtandem.XTandemReader method)
rename_modifications() (psm_utils.peptidoform.Peptidoform method)
(psm_utils.psm_list.PSMList method)
runs (psm_utils.psm_list.PSMList property)
S
SageReader (class in psm_utils.io.sage)
sequence (psm_utils.peptidoform.Peptidoform property)
sequential_composition (psm_utils.peptidoform.Peptidoform property)
sequential_theoretical_mass (psm_utils.peptidoform.Peptidoform property)
set_ranks() (psm_utils.psm_list.PSMList method)
T
theoretical_mass (psm_utils.peptidoform.Peptidoform property)
theoretical_mz (psm_utils.peptidoform.Peptidoform property)
to_dataframe() (in module psm_utils.io.peptide_record)
(psm_utils.psm_list.PSMList method)
TSVReader (class in psm_utils.io.tsv)
TSVWriter (class in psm_utils.io.tsv)
U
UnknownMzidScore
W
with_traceback() (psm_utils.io.idxml.IdXMLException method)
(psm_utils.io.idxml.IdXMLReaderEmptyListException method)
(psm_utils.io.ionbot.InvalidIonbotModificationError method)
(psm_utils.io.maxquant.MSMSParsingError method)
(psm_utils.io.msamanda.MSAmandaParsingError method)
(psm_utils.io.mzid.UnknownMzidScore method)
(psm_utils.io.peptide_record.InvalidPeprecError method)
(psm_utils.io.peptide_record.InvalidPeprecModificationError method)
(psm_utils.io.xtandem.XTandemException method)
(psm_utils.io.xtandem.XTandemModificationException method)
write_file() (in module psm_utils.io)
(psm_utils.io.idxml.IdXMLWriter method)
(psm_utils.io.mzid.MzidWriter method)
(psm_utils.io.peptide_record.PeptideRecordWriter method)
(psm_utils.io.percolator.PercolatorTabWriter method)
(psm_utils.io.tsv.TSVWriter method)
write_psm() (psm_utils.io.idxml.IdXMLWriter method)
(psm_utils.io.mzid.MzidWriter method)
(psm_utils.io.peptide_record.PeptideRecordWriter method)
(psm_utils.io.percolator.PercolatorTabWriter method)
(psm_utils.io.tsv.TSVWriter method)
X
XTandemException
XTandemModificationException
XTandemReader (class in psm_utils.io.xtandem)
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