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License: GNU General Public License v3.0
Python script that creates 2D protein-ligand interaction images
License: GNU General Public License v3.0
The domains at the moment can only be specified as range of residues.
In occurrence analysis clock diagrams the total length of interactions is shown, however, nothing is expressed about the character of the interaction - i.e. on/off rate
The ligand selection in the start allows to choose a ligand residue only by resname, which can cause issues if there are several ligands with the same name. Therefore, an additional factors of segid and residue number should be included
I noticed that the configuration file does not get read properly, since I have changed many options. It is time to debug and update the configuration file by adding new features and removing the old ones.
Check user input before asking diagram type, and then offer the disgrams available according to the input
If the figure contains only a few residues or they are all on one side of the ligand, the function for measuring the size of the svg figure fails.
Should the area molecule is drawn in depend on the size of the molecule?
Legends for:
At the moment a mol2 file of the ligand is required. This requirement could be removed by including a software like OpenBabel in the Dockerfile and making a ligand mol2 file as part of the LINTools run.
In case openbabel misbehaves
Need to find a way to make a nicer 2D rendering of the molecule using SMILES instead of mol2 and not loosing track of the atom identities.
Enhance residue placement using more than one atom to determine place on the hull, instead using the 3 closest ones or 2 closest neighbours to the closest ligand atom.
The distance from the hull can be chosen by either sum of all distances or the single closest distance..
Another idea - introduce weighting parameter in this function
For some reason, when LINTools outputs the drawn clock analysis, it output's it to a location 2 directories up from the directory from which it was launched.
Have trajectories with different run lengths to plot appropriately
At the moment spelling the diagram type wrong causes problems.
Sometimes MDAnalysis gives a bug when counting hydrogen bounds by type. I plan to circumvent this problem by writing my own function to deal with this.
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