https://github.com/yanganto/nestingblock
https://github.com/yanganto/nestingblock
Last synced: 12 months ago
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- Host: GitHub
- URL: https://github.com/yanganto/nestingblock
- Owner: yanganto
- License: other
- Created: 2015-02-02T03:17:02.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2015-02-03T09:03:18.000Z (over 11 years ago)
- Last Synced: 2025-06-08T13:43:39.000Z (about 1 year ago)
- Language: Python
- Size: 164 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# NestingBlock
This is program of modeling side-chain interaction of peptides in helix/coil states.
It can be easy to calculate the fraction helix of peptides based on Lifson-Roig theory by using following command:
$ python3 NestingBlock.py test-LifsonRoig
It also can list the equation of equilibrium constant with special force in the block within helix state by using following command:
$ python3 NestingBlock.py test-NestingBlock
=========
| SNOPSIS |
=========
$ python3 NestingBlock.py [-p protocol modified] [-c change wnc value] [-v] protocol_file
==================
| FUNCTION LETTERS |
==================
-p protocol modified, --protocol=protocol modified
The is an python command written in the protocol file.
Use this option can over write the the setting already in the protocol file.
-c change wnc value, --chwnc=change wnc value
is format like this A.w=1.44, which means change the w value of Ala to 1.44
-v
verbose.
=========
| Example |
=========
Calculating the fraction helix of peptie, and override the w value of Ala to 1.2
$ python3 NestingBlock.py -c A.w=1.2 test-LifsonRoig
List the equation of equilibrium constant with special force in the block within helix state,
and change the mode to basic lifson roig (without concering dipole and cap issue)
$ python3 NestingBlock.py -p mod=\"\" test-NestingBlock