# Macro to copy the peak assignments from one peak to another
 
from ccpn.core.lib.ContextManagers import undoBlock
 
with undoBlock():
    assignmentsToCopy = None
    # Check only one peak is fully or partially assigned and get the assignments to copy
    for peak in current.peaks:
        if len(peak.assignments) != 0 and assignmentsToCopy is None:
            assignmentsToCopy = peak.assignmentsByDimensions
        elif len(peak.assignments) != 0 and assignmentsToCopy is not None:
            print("You have more than one assigned peak.")
            assignmentsToCopy = None
 
    if assignmentsToCopy is not None:
        for peak in current.peaks:
            if len(peak.assignments) == 0:  # only copy assignments to unassigned peaks
                peak.dimensionNmrAtoms = assignmentsToCopy
    else:
        print("Please make sure you have one assigned peak.")

(01-29-2020, 02:02 PM)VickyH Wrote: Here is a macro to copy assignments from one peak to one or more others. This would be useful if you have two spectra recorded under different conditions where some or all of the peaks have moved (e.g with/without ligand, different temperature, buffer etc.) and want to copy the assignments from one spectrum to another.

Select one (fully or partially) assigned peak and one or more unassigned peaks. The assignments from the assigned peak will be copied to the unassigned peaks. This will work both within and between peak lists, spectra and spectrum displays.

The macro works in a similar way to the V2 "Propagate Assignment" function. However, note that the peak dimensions are matched by their Axis Codes and there is no checking of chemical shifts. This is deliberate, so that you can copy assignments in situations where the chemical shift has changed. But this does mean that you might encounter unexpected behaviour for spectra with at least two dimensions belonging to the same isotope (e.g. when copying assignments across the diagonal of a homonuclear spectrum), or for two spectra where the peaks' Axis Codes and Assignments don't line up. But this should hopefully only be a minority of cases.

Python

def copyAssignment(peak, assignmentsToCopy, axisCodesToUse):
    assignDone = 0
    count = 0
    for assignment in assignmentsToCopy:
        temp = str(assignment)
        assignmentLabels = temp.split(',')
        assignmentLabels[0] = assignmentLabels[0][1:]
        assignmentLabels[-1] = assignmentLabels[-1][0:-1]
        axCodes = dict(zip(assignmentLabels, axisCodesToUse))
        for label in assignmentLabels:
            count = count+1
            if 'None' not in label:
                temp = str(label)
                assignmentComponents = temp.split(':')
                assignmentComponents[0] = 'NA'
                assignmentComponents[1] = assignmentComponents[1][0:-1]
                axCde = axCodes[label]
                newAssignment = ':'.join(assignmentComponents)
                if axCde in peak.axisCodes:
                    peak.assignDimension(axCde, newAssignment)
                    assignDone = 1
    if assignDone == 0:
        print('Your peaks have to have matching Axis Codes in at least one assigned dimension in order to copy an assignment.')
 
 
assignmentsToCopy = None
axisCodesToUse = None
# Check only one peak is fully or partially assigned and get the assignments and Axis Codes to copy
for peak in current.peaks:
    if len(peak.assignments) != 0 and assignmentsToCopy is None:
        assignmentsToCopy = peak.assignments
        axisCodesToUse = peak.axisCodes
    elif len(peak.assignments) != 0 and assignmentsToCopy is not None:
        print("You have more than one assigned peak.")
        assignmentsToCopy = None
 
 
if assignmentsToCopy is not None:
    for peak in current.peaks:
        if len(peak.assignments) == 0:  # only copy assignments to unassigned peaks
            copyAssignment(peak, assignmentsToCopy, axisCodesToUse)
else:
    print("Please make sure you have one assigned peak.")

Any problems, let me know.

Vicky

(12-11-2020, 02:25 PM)VickyH Wrote: Hi Gina,

you can access the Chemical Shift Mapping tutorial either in the Help Menu in the programme: Help / Tutorials / Chemical Shift Perturbation Tutorial or from the website: https://www.ccpn.ac.uk/v3-software/tutorials/chemical-shift-perturbation-analysis-tutorial/view
This will take you through how to set up a titration series and analyse the data. The macro above is just an alternative way to transfer the assignments from one peak to another, if (like me) you are not so keen to do it with the system outlined in the tutorial.
It is worth pointing out, though, that V2 does have a "Follow Shift Changes" routine which we don't yet have in V3. So transferring the assignments from one spectrum to another is slightly less automated in V3 compared to V2 at the moment.

Best wishes,

Vicky

(03-10-2021, 02:27 PM)VickyH Wrote: Hi Gina,

when you drop a peak lists onto another spectrum you simply invoke the "Copy Peak List" function. So you are not moving it from one spectrum to another, but copying it - you will retain your apo peak list if you drop it on another spectrum. But by copying it to another spectrum you will have it as a starting point in the other spectrum.

Yes, all you need is a series of peak lists (one for each spectrum) and the peaks need to be correlated.
We correlate the peaks by giving them the same assignment (technically the same NmrAtoms). If you don't yet have your assignments, then you can use place holders. So in your case I would take the first spectrum and run Assignment / Set up NmrResidues (SN for short). This will create random NmrResidues and NmrAtoms for you for each NH peak.
You are then left with having to peak pick the other spectra and assign the peaks (either using the real assignments if you have those, or the randomly generated NmrAtoms). It is really simply a matter of preference whether you prefer to copy the peak list from one spectrum to another and then move the peaks to their true positions (the system described in the tutorial), or whether you prefer to peak pick each spectrum and then copy over the assignments (the system enabled by the macro here).

Yes, we will certainly be implementing the "Follow Shift Changes" function from V2 at some point, though there are other things higher up on the priority list at the moment, so it will be a little while yet, I would have thought.

Best wishes,

Vicky

---------------------------------

Hi Vicky OK thanks for the explanation I will try that. G