<commit_before># Emolsion
A pdb and dcd reading/writing molecular mechanics evaluation program.

## Quickstart:
1. DCD reading: To read a pdb with corresponding dcd (from frames 6 - 27, stepping by 3 frames) ..

        make dcdr
        emol_dcdreader mt.ref.pdb mt_partial.dcd 6 27 3

2. DCD writing: To write a dcd from the pdb with corresponding dcd (from frames 4 - 30,
stepping by 2 frames)..

        make dcdw
        emol_dcdwriter mt.ref.pdb mt_partial.dcd 4 30 2



## Dependencies:
Other softwares I often use with this project include:
* cscope - developer's tool for browsing program code. Run `./scope.sh`, creates cscope.files and cscope.out.
* [Boost] (http://www.boost.org/) - provides free peer-reviewed portable C++ source libraries.

## Microtubules' Contacts:
# The microtubule map: the diagram
            West
            4  7
         2  0  1  5
            3  6
            East
# Figure of microtubule:
[[https://github.com/dmerz75/repository/blob/master/fig/microtubule.png|alt=octocat]]

If 0 is alpha, 1 is beta, then, 9 situations from the 2 monomers in the dimer and their 6 neighbors arise:
* 0    intra-alpha
* 1    intra-beta
* 0-1  intra-dimer
* 0-2  alpha-south
* 0-3  alpha-east
* 0-4  alpha-west
* 1-5  beta-north
* 1-6  beta-east
* 1-7  beta-west2



## Notes/ Disclaimer/ Acknowledgements:
Six header files are not mine. They are currently used because I believe permission was given
provided the copyrights were retained and credit/notice given. They are:

* [<NAME>'s] (https://learncodethehardway.org/c/) awesome debug macros.
  * debug.h
* These 5 headers are from UIUC, for use with their proprietary 'dcd' format. Information is
provided [here.] (http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/files.html)

        (C) Copyright 1995-2006 The Board of Trustees of the<commit_msg>adding the microtubule picture, round 2<commit_after># Emolsion
A pdb and dcd reading/writing molecular mechanics evaluation program.

## Quickstart:
1. DCD reading: To read a pdb with corresponding dcd (from frames 6 - 27, stepping by 3 frames) ..

        make dcdr
        emol_dcdreader mt.ref.pdb mt_partial.dcd 6 27 3

2. DCD writing: To write a dcd from the pdb with corresponding dcd (from frames 4 - 30,
stepping by 2 frames)..

        make dcdw
        emol_dcdwriter mt.ref.pdb mt_partial.dcd 4 30 2



## Dependencies:
Other softwares I often use with this project include:
* cscope - developer's tool for browsing program code. Run `./scope.sh`, creates cscope.files and cscope.out.
* [Boost] (http://www.boost.org/) - provides free peer-reviewed portable C++ source libraries.

## Microtubules' Contacts:
# The microtubule map: the diagram
            West
            4  7
         2  0  1  5
            3  6
            East
# Figure of microtubule:
<!-- [[https://github.com/dmerz75/repository/blob/master/fig/microtubule.png|alt=octocat]] -->
[[https://github.com/dmerz75/emolsion/blob/master/fig/microtubule.png]]

If 0 is alpha, 1 is beta, then, 9 situations from the 2 monomers in the dimer and their 6 neighbors arise:
* 0    intra-alpha
* 1    intra-beta
* 0-1  intra-dimer
* 0-2  alpha-south
* 0-3  alpha-east
* 0-4  alpha-west
* 1-5  beta-north
* 1-6  beta-east
* 1-7  beta-west2



## Notes/ Disclaimer/ Acknowledgements:
Six header files are not mine. They are currently used because I believe permission was given
provided the copyrights were retained and credit/notice given. They are:

* [<NAME>'s] (https://learncodethehardway.org/c/) awesome debug macros.
  * debug.h
* These 5 headers are from UIUC, for use with their proprietary 'dcd' format. Information is
provided [here.] (http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/files.html)

        (C) Copyright 1995-2006 The Board of Trustees of the
{'fraction_non_alphanumeric': 0.09578137436985938, 'fraction_numerical': 0.0321040063677368, 'mean_word_length': 2.9894179894179893, 'pattern_counts': {'":': 0, '<': 6, '<?xml version=': 0, '>': 6, 'https://': 5, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '695614', 'n_tokens_mistral': 1337, 'n_tokens_neox': 1179, 'n_words': 449}