alicecomma/vinacarbresults

Assemble various VinaCarb results by listing best binding modes of oxygens into a specific active site.

VinaCarbResults

Windows (.NET/C#) console application to combine .pdbqt results files from a specific folder setup into more convenient collections of formats, taking into account whether oxygens are present inside of a pre-defined sphere.

Use

Can be called from cmd.exe: VinaCarbResults [0] [1] [2]

• [0]: Directory (group of poses) to enter (/*)
• [1]: Enzyme results to check (given *.enzyme, check /dir/pos/*.pdbqt)
• [2]: Pose (element of directory) to enter (/dir/*)

Directory setup

Set up your directories as follows:

VinaCarbResults.exe
[1].enzyme
/[1]
/[0]
/[0]/[2]
/[0]/[2]/[1].log
/[0]/[2]/[1].pdbqt

For example (for PDB: '3KLK', directory 'ENumbers', pose 'E100') after an AutoDock Vina run:

3klk.enzyme
/3klk/
/ENumbers
/ENumbers/E100
/ENumbers/E100/3klk.log
/ENumbers/E100/3klk.pdbqt

[1].enzyme

--radius 1.600 19.829 31.778 74.862

The above defines a sphere [float radius] [float x] [float y] [float z] that is checked to contain oxygens (.endsWith("O") || .endsWith("OA"))

Further reading

Please see the Wiki (to the right)!