Python Programming for Biology: Bioinformatics and Beyond

1

http://www.wwpdb.org

.

2

We decided against using the name Molecule to emphasise the fact that this class is a

container for a series of smaller chemical entities.

3

See

Chapter 11

for a description of why these are called residues.

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4

 Several  other  molecular  structure  data  models  use  the  term  ‘model’  instead  of

‘conformation’,  but  we  avoided  it  here  because  in  a  chapter  about  data  models,  talking

about other kinds of ‘model’ would be needlessly confusing.

5

The wwPDB offers a web service to fetch structural data, which can be accessed using

Python.

6

 From  Python  2.7  we  also  have  the  option  of  using  an  ordered  dictionary,  which  is  a

special collection type in the collections module.

7

See

Chapter 9

for discussion of NumPy.

8

Technically a single space, in some older files.

9

Strictly, such a cache should be reset, as part of the model implementation, when any

atom is added or removed.

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