Bio.NMR.xpktools module

Tools to manipulate data from nmrview .xpk peaklist files.

class Bio.NMR.xpktools.XpkEntry(entry, headline)

Bases: object

Provide dictionary access to single entry from nmrview .xpk file.

This class is suited for handling single lines of non-header data from an nmrview .xpk file. This class provides methods for extracting data by the field name which is listed in the last line of the peaklist header.

Parameters

xpkentrystr

The line from an nmrview .xpk file.

xpkheadlinestr

The line from the header file that gives the names of the entries. This is typically the sixth line of the header, 1-origin.

Attributes

fieldsdict

Dictionary of fields where key is in header line, value is an entry. Variables are accessed by either their name in the header line as in self.field[“H1.P”] will return the H1.P entry for example. self.field[“entrynum”] returns the line number (1st field of line)

__init__(entry, headline)

Initialize the class.

class Bio.NMR.xpktools.Peaklist(infn)

Bases: object

Provide access to header lines and data from a nmrview xpk file.

Header file lines and file data are available as attributes.

Parameters

infnstr

The input nmrview filename.

Examples

>>> from Bio.NMR.xpktools import Peaklist
>>> peaklist = Peaklist('../Doc/examples/nmr/noed.xpk')
>>> peaklist.firstline
'label dataset sw sf '
>>> peaklist.dataset
'test.nv'
>>> peaklist.sf
'{599.8230 } { 60.7860 } { 60.7860 }'
>>> peaklist.datalabels
' H1.L  H1.P  H1.W  H1.B  H1.E  H1.J  15N2.L  15N2.P  15N2.W  15N2.B  15N2.E  15N2.J  N15.L  N15.P  N15.W  N15.B  N15.E  N15.J  vol  int  stat '

Attributes

firstlinestr

The first line in the header.

axislabelsstr

The axis labels.

datasetstr

The label of the dataset.

swstr

The sw coordinates.

sfstr

The sf coordinates.

datalabelsstr

The labels of the entries.

datalist

File data after header lines.

__init__(infn)

Initialize the class.

residue_dict(index)

Return a dict of lines in ‘data’ indexed by residue number or a nucleus.

The nucleus should be given as the input argument in the same form as it appears in the xpk label line (H1, 15N for example)

Parameters

indexstr

The nucleus to index data by.

Returns

resdictdict

Mappings of index nucleus to data line.

Examples

>>> from Bio.NMR.xpktools import Peaklist
>>> peaklist = Peaklist('../Doc/examples/nmr/noed.xpk')
>>> residue_d = peaklist.residue_dict('H1')
>>> sorted(residue_d.keys())
['10', '3', '4', '5', '6', '7', '8', '9', 'maxres', 'minres']
>>> residue_d['10']
['8  10.hn   7.663   0.021   0.010   ++   0.000   10.n   118.341   0.324   0.010   +E   0.000   10.n   118.476   0.324   0.010   +E   0.000  0.49840 0.49840 0']

write_header(outfn)

Write header lines from input file to handle outfn.

Bio.NMR.xpktools.replace_entry(line, fieldn, newentry)

Replace an entry in a string by the field number.

No padding is implemented currently. Spacing will change if the original field entry and the new field entry are of different lengths.

Bio.NMR.xpktools.data_table(fn_list, datalabel, keyatom)

Generate a data table from a list of input xpk files.

Parameters

fn_listlist

List of .xpk file names.

datalabelstr

The data element reported.

keyatomstr

The name of the nucleus used as an index for the data table.

Returns

outlistlist

List of table rows indexed by keyatom.