<commit_before>genpoly_lt.py
===========


## Description

Generate a moltemplate file containing a definition of a Polymer
molecule containing monomers located at the positions specified in
"coords.raw" (a 3-column text file).  Monomers will be rotated so
that they point along the polymer axis direction (see "-dir-indices")<commit_msg>updated the documentation for genpoly_lt.py  (I added links to a few pictures to demonstrate what it does.  The documentation still could use some improvement.)<commit_after>genpoly_lt.py
===========

![DNA model](https://raw.githubusercontent.com/jewettaij/ndmansfield/master/doc/images/moltemplate_usage/CG_dsDNA_gold_turquoise.gif)
![](https://raw.githubusercontent.com/jewettaij/ndmansfield/master/doc/images/plus.png)
![space-filling curve](https://raw.githubusercontent.com/jewettaij/ndmansfield/master/doc/images/hamiltonian_paths_16x16x16.gif)
![](https://raw.githubusercontent.com/jewettaij/ndmansfield/master/doc/images/rightarrow.png)
![DNA wrapped along curve](https://raw.githubusercontent.com/jewettaij/ndmansfield/master/doc/images/moltemplate_usage/wrap_CG_dsDNA_around_a_curve_from_ndmansfield_LLR.png)

## Description

*genpoly_lt.py* is a program for preparing simulations containing polymers.
It is useful for wrapping polymers around an arbitrary curve.
(An example of its use is provided
[here](examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/confined_viral_DNA).)
*genpoly_lt.py* generates a moltemplate file (.LT file) containing a definition
of a polymer molecule containing monomers located at the positions specified
in a 3-column text file ("coords.raw" in the example below).  Monomers will be
rotated so that they point along the polymer axis direction (see "-dir-indices")
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{'dir': 'git-commits-cleaned', 'id': '3787943', 'n_tokens_mistral': 555, 'n_tokens_neox': 508, 'n_words': 148}