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)!
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)!
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.
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 asC1CC1, 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)!
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.
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 asC1CC1, 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)!
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