Scripting & Batching
The Poky Suite has been written in different computer languages and library kits exhibiting the maximum efficiency and performance in each program. C++ with QT for the Poky main, Easy NMRPIPE2UCSF, Easy BRUKER2UCSF, Easy NMRVIEW2UCSF, and Poky Structure Builder programs (https://qt.io), Python and Tcl/Tk for the scripting and plugins, Free Pascal with LCL (Lazarus Component Library) for Easy UCSFDATA, NDP-Plot and Poky Structure Analyzer. All the programs in the Poky suite are cross-platform supporting Windows, Mac, and Linux.
A low-level interface has been written to glue the Python interpreter and QT’s modern graphical user interfaces (GUIs). Users can make use of the interface to write their own script and batch files.
Introduction to Poky Notepad
Poky Notepad (two-letter-code Pn) is a powerful text editor that allows you write your own script to do many things. In this video, you'll see how to open the Notepad, load and run a sample script that shows current data information. You'll also see how you can change the existing template and re-run the script.
Detailed reference documentation is available from Poky Notepad's File menu, Poky Scripts and Poky Script Reference.
Poky Notepad Showing Yes No Dialog
In this video, you'll see how you can show a yes/no question dialog to the user. You'll also see how you can use a conditional statement in your code to evaluate the user's response.
Poky Notepad DNN Based NUS Reconstruction
In this video, you'll see how you can use one of the already available scripts in Poky Notepad to use Deep Neural Network method to reconstruct a non-uniformly sampled data. In the video, data was downloaded and processed on the command-line, but the user can just click Run Python Module right away. Poky will download and process everything automatically.
D.F. Hansen's web page: https://www.ucl.ac.uk/hansen-lab/deep-nus.html
D. Flemming Hansen. Using Deep Neural Networks to Reconstruct Non-uniformly Sampled NMR Spectra. J. Biomol. NMR (2019)
Poky Notepad Wavelet Denoising
In this video, you'll see how you can use the Poky Notepad for wavelet denoising using one of the already available scripts. We'll first add noise to a spectra, and then denoise it using the script. Finally, we compare the results.
You can find the Scikit-Image restoration module documentation from here:
https://scikit-image.org/docs/dev/api/skimage.restoration.html
https://scikit-image.org/docs/dev/auto_examples/filters/plot_denoise_wavelet.html
Poky Notepad TV Bregman Denoising
In this video, you'll see how you can use the Poky Notepad for implementing TV-Bregman denoising using one of the already available scripts. We'll modify the wavelet denoising script for TV-Bregman denoising.
TV-Bregman reference from Scikit-Image:
Poky Notepad TALOS Results Plotting
In this video, you'll see how you can plot the result of TALOS using the script that is already available in the Poky Notepad.
TALOS-N webserver:
https://spin.niddk.nih.gov/bax/nmrserver/talosn/
Yang Shen, and Ad Bax. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J. Biomol. NMR 56, 227-241(2013).
Poky Notepad Drag and Drop
In this video, you'll see how you can open files in the Poky Notepad by simply dragging and dropping the files. You'll also see how you can get the path for the file.
Poky Notepad Batching
In this video, you'll see how you can use the batching feature of Poky. This allows you to process many files quickly from the terminal without even opening Poky.