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Base classes for DSD design

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Copyright (c) 2017 Stefan Badelt and contributors <badelt@caltech.edu>

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Download-URL: https://github.com/DNA-and-Natural-Algorithms-Group/dsdobjects/archive/v0.6.tar.gz
Description: # dsdobjects - base classes for DSD design

This module provides standardized Python parent classes for
domain-level strand displacement programming:

- SequenceConstraint
- DL_Domain
- SL_Domain
- DSD_Complex
- DSD_Reaction
- DSD_RestingSet

An example is shown below:

```py
from dsdobjects import DL_Domain

# A personalized domain that extends the DL_Domain base class.
class MyDomain(DL_Domain):

def __init__(self, name, dtype=None, length=None):
super(MyDomain, self).__init__(name, dtype, length)

@property
def complement(self):
# Automatically initialize or return the complementary domain.
if self._complement is None:
cname = self._name[:-1] if self.is_complement else self._name + '*'
if cname in DL_Domain.MEMORY:
self._complement = DL_Domain.MEMORY[cname]
else :
self._complement = MyDomain(cname, self.dtype, self.length)
return self._complement

```

Inheriting from the DL_Domain base class enables standardized built in
functions such as '~', '==', '!=', and provides a built-in memory management
raising the DSDDuplicationError when conflicting domain names are chosen.


```py
>>> # Initialize a Domain.
>>> x = MyDomain('hello', dtype='short')
>>> # The '~' operator calls x.complement
>>> y = ~x
>>> (y == ~x)
True

```

These and many more functionalities and sanity checks are also available for
other objects. See the respective docstrings for details.

## Install
To install this library, use the following command in the root directory:
```
$ python ./setup.py install
```
or use local installation:
```
$ python ./setup.py install --user
```

## Version
0.6 -- PIL parser supports concentration format
* "non-equal" bugfixes in base_classes.py
* supports rate-error bars when parsing PIL format

0.5 -- improved canonical forms

## Author
Stefan Badelt

### Contributors
This library contains adapted code from various related Python packages coded
in the [DNA and Natural Algorithms Group], Caltech:
* "DNAObjecs" coded by Joseph Berleant and Joseph Schaeffer
* [peppercornenumerator] coded by Kathrik Sarma, Casey Grun and Erik Winfree
* [nuskell] coded by Seung Woo Shin

## Projects depending on dsdobjects
* [peppercornenumerator]
* [nuskell]


## License
MIT

[nuskell]: <http://www.github.com/DNA-and-Natural-Algorithms-Group/nuskell>
[peppercornenumerator]: <http://www.github.com/DNA-and-Natural-Algorithms-Group/peppercornenumerator>
[DNA and Natural Algorithms Group]: <http://dna.caltech.edu>

Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 2.7

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