Merge remote-tracking branch 'origin/master' into cmake_misc

# from https://github.com/github/gitignore/blob/master/Python.gitignore

# Byte-compiled / optimized / DLL files

__pycache__/

*.py[cod]

*$py.class

# C extensions

*.so

# Distribution / packaging

.Python

env/

build/

develop-eggs/

dist/

downloads/

eggs/

.eggs/

lib/

lib64/

parts/

sdist/

var/

wheels/

*.egg-info/

.installed.cfg

*.egg

# PyInstaller

#  Usually these files are written by a python script from a template

#  before PyInstaller builds the exe, so as to inject date/other infos into it.

*.manifest

*.spec

# Installer logs

pip-log.txt

pip-delete-this-directory.txt

# Unit test / coverage reports

htmlcov/

.tox/

.coverage

.coverage.*

.cache

nosetests.xml

coverage.xml

*,cover

.hypothesis/

# Translations

*.mo

*.pot

# Django stuff:

*.log

local_settings.py

# Flask stuff:

instance/

.webassets-cache

# Scrapy stuff:

.scrapy

# Sphinx documentation

docs/_build/

# PyBuilder

target/

# Jupyter Notebook

.ipynb_checkpoints

# pyenv

.python-version

# celery beat schedule file

celerybeat-schedule

# dotenv

.env

# virtualenv

.venv/

venv/

ENV/

# Spyder project settings

.spyderproject

# Rope project settings

.ropeproject

# text-editor temporary files:

*~

# misc rubbish

deleteme*

DELETEME*

######## files specific to moltemplate and lammps ########

# latex/bibtex temporary files for the moltemplate manual:

moltemplate_manual*.aux

moltemplate_manual*.bbl

moltemplate_manual*.blg

moltemplate_manual*.log

moltemplate_manual*.out

moltemplate_manual*.toc

######## files created by running LAMMPS: ########

log.lammps

log.cite

traj*.lammpstrj

######## files generated by running moltemplate: ########

system.data

system.in

system.in.init

system.in.settings

system.in.charges

system.psf

ttree_assignments.txt

output_ttree/

# Sections from the LAMMPS data file generated by moltemplate.sh

"Data Header"*

"Data Atoms"*

"Data Masses"*

"Data Velocities"*

"Data Bonds"*

"Data Bond List"*

"Data Bonds AtomId AtomId"*

"Data Angles"*

"Data Dihedrals"*

"Data Impropers"*

"Data Bond Coeffs"*

"Data Angle Coeffs"*

"Data Dihedral Coeffs"*

"Data Improper Coeffs"*

"Data Pair Coeffs"*

"Data PairIJ Coeffs"*

# interactions-by-type (not id. This is not part of the LAMMPS standard.)

"Data Charge By Bond"*

"Data Bonds By Type"*

"Data Angles By Type"*

"Data Dihedrals By Type"*

"Data Impropers By Type"*

# class2 data sections

"Data BondBond Coeffs"*

"Data BondAngle Coeffs"*

"Data MiddleBondTorsion Coeffs"*

"Data EndBondTorsion Coeffs"*

"Data AngleTorsion Coeffs"*

"Data AngleAngleTorsion Coeffs"*

"Data BondBond13 Coeffs"*

"Data AngleAngle Coeffs"*

# sections for non-point-like particles:

"Data Ellipsoids"*

"Data Lines"*

"Data Triangles"*

# periodic boundary conditions

"Data Boundary"*

# Sections from the LAMMPS input script(s) generated by moltemplate.sh

"In Init"*

"In Settings"*

"In Coords"*

"In Charges"*

#temporary file created by moltemplate.sh for storing coordinates

tmp_atom_coords.dat

[![Build Status](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)

Moltemplate

===========

##  Description

Moltemplate is a cross-platform text-based molecule builder for LAMMPS.

Moltemplate is a *general* cross-platform text-based molecule builder for **LAMMPS** and **ESPResSo**.  Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well.  It currently supports the **OPLS**, **COMPASS**, **AMBER**(GAFF,GAFF2), **MARTINI**, **SDK**, **LOPLS**(2015), and **TraPPE**(1998) force fields, and includes approximately 40 examples.  (New force fields and examples are added continually by users.)

## Typical usage

    pip uninstall moltemplate

If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "virtualenv", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands:

If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "*virtualenv*", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands:

    cd ~/moltemplate

    virtualenv venv

    pip install .

    #(now do something useful with moltemplate...)

(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate.)  If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable.  Instructions for doing that are included below.

(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate.

The *virtualenv* tool is

[explained in detail here](http://docs.python-guide.org/en/latest/dev/virtualenvs/))  If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable.  Instructions for doing that are included below.

## Manual installation: