By Martin J. Field
This ebook is aa-ight. it truly is extra approximately the best way to use their library for molecular simulation than it's approximately writing your individual from scratch. however it has a couple of reliable insights. total, it is a reliable one for the gathering of molecular simulation books if that is your factor. :)
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Additional resources for A Practical Introduction to the Simulation of Molecular Systems
Function SMILES_FromSystem Generate a SMILES representation of a system. Usage: system smiles smiles = SMILES_FromSystem ( system ) is the system whose SMILES is to be generated. is a string containing the SMILES. It is convenient at this stage to introduce two functions that read and write XPK files, as files in XPK format are employed quite extensively in this book. The function definitions are: Function XMLPickle Write Python objects in XPK format to a file. Usage: filename objects XMLPickle ( filename, objects ) is the name of the file to which data are to be written.
The atom elements are empty but they have attributes that give the atom’s identifier, id, its elemental type, elementType, and its coordinates in three dimensions, x3, y3 and z3. Lines 7–10 define the bonds in the molecule using a syntax that is very similar to that of the atoms. The attributes of the bond elements are atomRefs2 which lists the identifiers of the two atoms in the bond and order which gives the bond order. A bond order of 1 indicates a single bond. CML is not the only markup language that pDynamo supports.
The aim of the example in this section is to make use of the functions defined above. The program creates different representations of the bALA molecule by reading files in various formats and by converting a SMILES string. Summaries of each of the representations are then printed. """ 2 3 from Definitions import * 4 5 6 # . Initialize a list to contain the molecules. molecules =  7 8 # . Read all molecules. xyz" ) ) ) 9 12 13 14 15 16 17 18 # . Generate a molecule from a SMILES string. append ( SMILES_ToSystem ( "CC(=O)NC(C)C(=O)NC" ) ) # .
A Practical Introduction to the Simulation of Molecular Systems by Martin J. Field