I am trying to understand the source code of the AutoDock Vina, but as I am new to the field of Bioinformatics it is a little hard to understand. It seems like they are using a tree data structure to represent the ligand and the receptor. I cannot understand what nodes and branches are in this data structure (Heterotree). I think in order to understand it I should first understand what information the PDBQT file contains. Can you tell me what branch and root is in PDBQT file format?
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1$\begingroup$ For these very specific source code questions, it makes a lot easier if you link the code you talk about as specifically as you can (i.e. as I did in the edit. GitHub allows you to link individual files). Anyway, good luck :-) $\endgroup$– Kamil S JaronCommented Jan 17, 2022 at 11:44
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$\begingroup$ SE is a not a forum for personal opinions, but I feel like I need break the rules here... We see occasionally CS folk ask questions here wherein they are in a wet lab biochem group and are given a computational biochemistry task with little technical supervision and they frequently flounder over and over at the basics. if this premise is correct, I would strongly suggest seeking a relevant collaborator within your institute/department. $\endgroup$– Matteo FerlaCommented Jan 18, 2022 at 10:25
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what information the PDBQT file contains
The PDBQT format is described here: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf —ignore the expired SSL certificate warning as I am pretty sure the Scripps Institute is not a criminal organisation.
what branch and root is in PDBQT file format
It is rather self evident but with a twist and as you have guessed it has to do with trees in graph networks. Lines of text <-> graph networks describing a molecule is a common nuisance in compchemistry. Normally the aim is connectivity, but here it is torisons. But the former is a nice example, a small molecules can be represented with SMILES (strings), where say isopropanol is CC(O)C, in which you have a branch going off in round brackets, whereas everything else is assumed connected sequentially. In the case of the PDBQT format you are describing what atom subsets of the molecule rotate together and actually not how they connect as given away by the fact that you don't have a special syntax for ring closures (in a SMILES you write cyclopropane as C1CC1, where the third carbon connects to C1, which was declared first. This is because the topology is dealt with elsewhere.
Resources
AutoDock 4 and AutoDock Vina are divergent pieces of software, but they have several common elements like the PDBQT format, so you get double the documentation (and papers to read)!
