Read e-book online A Practical Introduction to the Simulation of Molecular PDF

By Martin J. Field

ISBN-10: 0521852528

ISBN-13: 9780521852524

This booklet is aa-ight. it really is 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 strong insights. total, it is a strong 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

Example text

5 Example 2 29 Alanyl N Cα C N-Methyl Acetyl Fig. 3. N-Methyl-alanyl-acetamide. 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 # .

Function PruneByAtom Create a new instance of a class by pruning atoms from an existing instance of the class. Usage: old selection new Remarks: new = PruneByAtom ( old, selection ) is the old instance. specifies the atoms that are to be kept in the pruning process. Most usually this argument is an instance of the class Selection that contains the indices of the atoms to be retained. is the new, smaller instance. Pruning by atom is similar to merging in that only classes with the notion of an atom can be pruned.

It has been simplified somewhat by removing lines not directly concerned with the molecule and its atom and bond definitions. 75" z3="0"/> 6 7 8 9 10 11 1 2 Lines 1 and 11 mark the beginning and the end of the molecule specification. In XML all data are expressed in terms of elements, so molecule is the CML element that represents a molecule. The beginning and the end of the element are given by start and end tags – lines 1 and 11, respectively – and the elements in between are its child elements.

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A Practical Introduction to the Simulation of Molecular Systems by Martin J. Field

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