By Martin J. Field
This ebook is aa-ight. it's extra approximately easy methods to use their library for molecular simulation than it's approximately writing your individual from scratch. however it has a couple of sturdy insights. total, it is a stable one for the gathering of molecular simulation books if that is your factor. :)
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Additional info for A Practical Introduction to the Simulation of Molecular Systems
Nevertheless, HETATM and ATOM records have the same format except for the initial record identifier. e. the order of the atom in the molecular sequence. Columns 13–16 hold the atom name. In PDB format, each atom in a residue has a unique name which can consist of, at most, four characters. Atom names start in column 13 if the name is four characters long or if the atom is a hydrogen whose name starts with an integer. Otherwise, the name starts in column 14. Columns 18–20 identify the name of the residue.
This argument is a keyword argument as opposed to the positional arguments that we have met up to now. Keyword arguments have three distinguishing features: (i) they occur after any positional argument in an argument list; (ii) they are passed into a function or method using the keyword = value syntax; and (iii) they are optional and, if absent, will be assigned a default value that is specified in the function or method definition. 45. is the instance of System for which the bonds are to be generated.
Consider, for example, how much easier it is to search databases of molecules if each molecule has a unique identifier. An extension to SMILES, called unique SMILES, permits just this. A project with aims that are, in many respects, similar to those of unique SMILES is the IUPAC (International Union of Pure and Applied Chemistry) chemical identifier or InChI project. This work was underway at the time of writing this book and so no details will be given here. It is probable, however, that InChI will be widely adopted in the future.