Molecular Dynamics Trajectory Analysis Tools
MIT License
A command line tool for Mjolnir/CafeMol users.
mill
has the following modes.
help
modecalc
modetraj
modedcd
modepdb
modeninfo
modeAnd each mode has its own commands.
To see the usage and explanation of each command, run the following command.
$ mill help [mode] [command]
or
$ mill [mode] [command] help
E.g.
$ mill calc rmsd help
Info : ___ __ __ __ __ _ _ _
Info : / __| ___ / _|/ _| ___ ___ | \ / |(_)| || |
Info : | | / _ \| |_| |_ / _ \/ _ \ | \/ || || || |
Info : | |__| (_) | _| _| __| __/ | |\/| || || || |
Info : \___|\___/|_| |_| \___|\___| |_| |_||_||_||_|
Info : Copyright 2016-now Toru Niina)
Info : usage: mill calc rmsd [traj file] [ref file]
: optinal args:
: --align=(true|false) [by default, true]
: If true (default), perform alignment by minimizing RMSD.
: otherwise, it calculates RMSD without minimization.
: --output=<filename> [by default, "mill_rmsd.dat"]
: output data file.
: --only=<begin>:<end>
: --ref-only=<begin>:<end>
: use [begin, end) region only.
calc
modeAll the .dcd
, .pdb
, .trr
, and .xyz
formats are supported in calc
mode.
rmsd
dist
angle
wham
aabb
obb
autocorrelation
mean
pca
export OMP_NUM_THREADS=N
.help
traj
modeAll the .dcd
, .pdb
, .trr
, and .xyz
formats are supported in traj
mode.
You can use any of it, and even mix them in a single command.
convert
impose
join
split
extract
translate
rotate
running-average
projection
help
dcd
modeAs the name suggests, dcd
mode only supports .dcd
format.
info
help
pdb
modeAs the name suggests, pdb
mode only supports .pdb
format.
seq
help
ninfo
modeAs the name suggests, ninfo
mode only supports .ninfo
format that is specific to CafeMol.
split
help
$ git clone https://github.com/ToruNiina/Coffee-mill.git --recursive
$ cd build
$ cmake ..
$ make
To find Eigen3, you can use cmake .. -DEigen3_DIR=/path/to/eigen-3.y.z/
.