"""
Module Documentation here
"""
#=========================================================================================
# Licence, Reference and Credits
#=========================================================================================
__copyright__ = "Copyright (C) CCPN project (http://www.ccpn.ac.uk) 2014 - 2019"
__credits__ = ("Ed Brooksbank, Luca Mureddu, Timothy J Ragan & Geerten W Vuister")
__licence__ = ("CCPN licence. See http://www.ccpn.ac.uk/v3-software/downloads/license")
__reference__ = ("Skinner, S.P., Fogh, R.H., Boucher, W., Ragan, T.J., Mureddu, L.G., & Vuister, G.W.",
"CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis",
"J.Biomol.Nmr (2016), 66, 111-124, http://doi.org/10.1007/s10858-016-0060-y")
#=========================================================================================
# Last code modification
#=========================================================================================
__modifiedBy__ = "$modifiedBy: Luca Mureddu $"
__dateModified__ = "$dateModified: 2017-07-07 16:32:55 +0100 (Fri, July 07, 2017) $"
__version__ = "$Revision: 3.0.0 $"
#=========================================================================================
# Created
#=========================================================================================
__author__ = "$Author: Luca Mureddu $"
__date__ = "$Date: 2017-03-23 16:50:22 +0000 (Thu, March 23, 2017) $"
#=========================================================================================
# Start of code
#=========================================================================================
tempQueryCode = """
Below the script from BMRB website.
Copied for understanding how it worked only.
history.replaceState('data', '', '/search/multiple_peak_search.php?' + $("#search_form").serialize());
$("#loading").show();
$("#results").hide();
$("body").css("cursor", "progress");
$("#shift_body").empty();
// Make the parameter data packet
var data = {
s: shifts,
database: $('#database').val()
}
// Perform the query
$.ajax({
type: "get",
data: data,
traditional: true,
url: "http://webapi.bmrb.wisc.edu/v2/search/multiple_shift_search",
success: function(response){
$("#loading").hide();
$("body").css("cursor", "default");
if (response["data"].length == 0){
alert("No matching peaks found.");
return;
}
$.each(response["data"], function(i, item) {
$('<tr>').append(
$('<td>').append($('<a>',{text: item.Entry_ID, title: item.Entry_ID, href: item.Link})),
$('<td>').text(item.Title),
$('<td>').text(item.Peaks_matched),
$('<td>').text(item.Combined_offset),
$('<td>').text(item.Assigned_chem_shift_list_ID),
$('<td>').text(item.Val.join(", "))
).appendTo('#shifts_table');
});
$("#results").show();
}, error: function(xhr){
$("#loading").hide();
$("body").css("cursor", "default");
alert($.parseJSON(xhr.responseText)["error"]);
}
});
"""
# import pynmrstar
import pandas as pd
import urllib.request, json
BMRB_API_URL = "http://webapi.bmrb.wisc.edu/v2"
Shift_search_URL = '/search/multiple_shift_search?'
Database = '&database='
Metabolomics = 'metabolomics'
AND = '&'
S = 's='
csData = 'data'
# DataFrame column titles from BMRB database
Title = 'Title'
EntryID = 'Entry_ID'
AssignedshiftID = 'Assigned_chem_shift_list_ID'
CombinedOffset = 'Combined_offset'
ShiftLink = 'Link'
PeaksMatched = 'Peaks_matched'
ShiftColumns = [
AssignedshiftID,
CombinedOffset,
EntryID,
ShiftLink,
PeaksMatched,
Title,
]
"""
Full address to be:
- for a single chemical shift query (e.g. 3.136), database=metabolomics
>> "http://webapi.bmrb.wisc.edu/v2/search/multiple_shift_search?s=3.136&database=metabolomics"
- for multiple chemical shift searches (e.g. 3.136,7):
>> "http://webapi.bmrb.wisc.edu/v2/search/multiple_shift_search?s=3.136&s=7.0&database=metabolomics"
"""
[docs]def bmrbMultiShiftSearch(shifts: list, databaseType=Metabolomics):
bmrbUrl = BMRB_API_URL + Shift_search_URL
shiftAsStr = ''
for shift in shifts:
shiftAsStr += S + str(shift) + AND
fullUrl = bmrbUrl + shiftAsStr + Database + databaseType
with urllib.request.urlopen(fullUrl) as url:
data = json.loads(url.read().decode())
d = data[csData]
df = pd.DataFrame.from_dict(d)
return d
[docs]def peaksToShifts1D(objs):
'''
:param objs: peaks or multiplets
:return: a list of peak positions
'''
return [x.position[0] for x in objs]
[docs]def testAla():
ala = [3.771, 1.471]
df = bmrbMultiShiftSearch(ala)
print(df[Title], df[PeaksMatched])