TRATES is a tool that prepares all of the files that are necessary for molecular dynamics simulations and provides analysis of simulation data for glucose transporter termini.
TRATES can be easily installed with:pip3 install git+git://github.com/Kobie-Kirven/tratesTRATES is made up of several subpackages including
- trates-prepare
- trates-rmsd
- trates-contacts
- trates-plot
Trates Prepare:
usage: trates-prepare [-h] -1 IN1 -s1 S1 -2 IN2 -s2 S2 -o OUT_PATH -nc NC -vmd
VMD -n OUT_NAME -a ANCHOR -d DISTANCE [-t TIME]
TRAnsporter TErmani Simulations
optional arguments:
-h, --help show this help message and exit
-1 IN1, --input-1 IN1
First FASTA input file
-s1 S1, --slice-1 S1 The positons of the start and stop residue (inclusive)
for the first terminus seperated by a dash (start-
stop)
-2 IN2, --input-2 IN2
Second FASTA input file
-s2 S2, --slice-2 S2 The positons of the start and stop residue (inclusive)
for the second terminus seperated by a dash (start-
stop)
-o OUT_PATH, --output-path OUT_PATH
Path and name of output folder (Ex. ~/Desktop/output
-nc NC, --n-and-c NC Boolean (T/F) if the simulation is for a combination
of the N-terminus and C-terminus
-vmd VMD, --vmd-path VMD
Path to VMD
-n OUT_NAME, --out-name OUT_NAME
Name of output files
-a ANCHOR, --anchoring-residues ANCHOR
Anchoring residue for each terminus in comma-seperated
format
-d DISTANCE, --distance-apart DISTANCE
Distance between alpha carbons of anchoring residues
in angstroms
-t TIME, --simulation-time TIME
How long to run the simulation in nanoseconds
usage: trates-rmsd [-h] [-psf PSF] [-dcd DCD] [-o OUT] [-vmd VMD]
RMSD calculations
optional arguments:
-h, --help show this help message and exit
-psf PSF, --psf-file PSF
PSF file
-dcd DCD, --dcd-file DCD
DCD file
-o OUT, --out-file OUT
Output Data File
-vmd VMD, --vmd-path VMD
Path to vmd
usage: trates-native-contacts [-h] [-psf PSF] [-dcd DCD] [-vmd VMD] [-o OUT]
[-f FRAME] [-d DISTANCE] [-t TYPE] [-r CUTOFF]
[-c CHAIN]
Calculate native contacts
optional arguments:
-h, --help show this help message and exit
-psf PSF, --psf-file PSF
Protein structure (PSF) file
-dcd DCD, --dcd-file DCD
Trajectory (DCD) file
-vmd VMD, --vmd-path VMD
Path to vmd
-o OUT, --out-file OUT
Name of output file (.txt)
-f FRAME, --frame-span FRAME
Begining and ending frame of simulation
-d DISTANCE, --contact-distance DISTANCE
Cutoff distance in angstroms for native contacts
-t TYPE, --contact-type TYPE
Type of native coontact (options: inter, intra, all)
-r CUTOFF, --residue-cut-off CUTOFF
Intramolecular: Cutoff for native contacts (only
interactions more than a specified distance apart
-c CHAIN, --chain-number CHAIN
Intramolecular: Chain number (1 or 2)
usage: trates-plot [-h] [-i INPUT] [-o IMAGE] [-s SMOOTH] [-d TYPE]
Plot the output data
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input-file INPUT
Input data file
-o IMAGE, --image-file IMAGE
Output image
-s SMOOTH, --sliding-widow SMOOTH
Sliding window length for smoothing
-d TYPE, --data-type TYPE
Data type (rmsd, conacts)