helenginn / mabscape Goto Github PK

Currently it is possible to create antibodies that do not have a name, and there can be antibodies with the same name multiple times.
There probably should be a warning about this and requirement to have a non-empty, unique name for the antibody.

It seems that some part in the process of showing all the Labels is very inefficient, because it takes a few seconds to even show 5 labels. If this function should stay, this should be improved.

A legend for the highlighting of the different antibodies could be very usefull and might enable other features like colored connections between the antibodies upon selecting an antibody.

This may be caused by alt-tabbing out of the window and back in again.
Also happend after refining the mesh.

Some combination of commands changed the input style of the program to a form where one can draw a rectangle by left/right clicking and dragging the mouse. The command line will prompt Found 0 after this. Before opening this view a bunch of 3D vectors was printed to the command line as well. It seems these were the coordinates of the antibodies since it was a list of 290 vectors.

When opening the results of monte carlo calculations in cluster4x, in the terminal there is the promtp, "no screen...". If the "Datasets to cluster4x" button is pressed, cluster4x opens up with the selected datasets as expected.
When the cluster4x window is closed, and a result is selected the following text is promted to the terminal:

Calculating averages from 1 datasets...
AveCSV vector list = 0
Average vec: 
Inter-correlations against average...
find intercorrel Vectorlist: 0

Calculating SVD...
Clustering success.
Job complete.
QObject::moveToThread: Current thread (0x55bf6a1b0c40) is not the object's thread (0x7f2ee4004680).
Cannot move to target thread (0x55bf6a1b0c40)

(0, 0, 0)
0
Refreshing.
Repopulating the SVD

Furthermore, the "Datasets to cluster4x" button does no longer work and only prompts

Copying from original...

to the terminal.

If the file selection window, shown upon clicking "Read selected results", is closed with the cross, the program terminates with the message:
Could not get file contents for file
terminate called after throwing an instance of 'int'

It would be nice if the mousewheel could also zoom in and out of the rendered structure.

When opening the results window of the monte carlo section, or the entailing cluster4x window, these windows do not close after the main window is closed, and the program is still running in the terminal.
This disconnection might be the reason of the "No screen" prompt that is shown when opening the results window.

After manipulations of the mesh, including triangulations and mesh refinements etc. the cursor position and the highlighted/selected position on the protein do no longer overlap

show.sh: line 20: 13058 Segmentation fault (core dumped) LD_LIBRARY_PATH=~/install/lib/x86_64-linux-gnu/ ~/HiWi/Helen/test/mabscape/build/current/mabscape load-structure=rbd.obj load-data=data_27012021.csv load-positions=positions.csv load-metadata=metachains.csv load-metadata=indian_kds.csv load-metadata=ic50.csv load-metadata=p1_ic50.csv load-metadata=p1_kd.csv load-metadata=sa_kd_ratio.csv load-metadata=kd.csv load-metadata=strains.csv load-metadata=sequences.csv read-results=good.results refine-mesh triangulate-mesh triangulate-mesh select-all average-positions

When opening the results of the monte carlo, it would be nice if there was a clear indication of how many datasets are opened in cluster4x, because if you just select a single set by clicking on it, there will be only one dataset sent to cluster4x.
A change of the button with the current number of selected elements in the results list would probably be easiest.
e.g. "25 Datasets to cluster4x", instead of the current "Datasets to cluster4x" which doesnt change.

When selecting an antibody, it is highlighted in light grey, which could be changed to the color of the selected antigen when showing competition etc. which is yellow.
Furthermore, the name and the connections of a selected antibody could be displayed when selected, a second click on the same antigen would deselect in that case, to clean up the view again.
If selecting an antibody from the explorer, the protein could rotate in such a way, that the antigen is displayed in the middle of the screen, currently it can be in the back of the protein and because of the very subtle selection color it is almost impossible to see which antigen was selected.