fraternalilab / dcdencode Goto Github PK

The package provides the functionality to encode a given trajectory into Structural Alphabet (SA) strings.

There are several ways to install the DCDencode package, please choose one of the following. You need to have R installed and the bio3d package.

Download the latest DCDencode release (.tar.gz) and install on the shell with (example for version 0.1):

R CMD INSTALL DCDencode-v.0.1.tar.gz

Download the latest DCDencode release (.tar.gz) and install from the R console (example for version 0.1, assuming it is located in the current directory):

install.packages("./DCDencode-v.0.1.tar.gz")

Install the devtools package and install DCDencode directly from GitHub:

library("devtools")
install_github("Fraternalilab/DCDencode")

Run the script Rscripts/dcdencode.R in the directory containing the DCD trajectory file:

Rscript dcdencode.R <structure_name>.pdb <trajectory_name>.dcd <confInc>

The first argument must be the reference PDB structure. The second argument must be the DCD trajectory. The third argument is an optional conformation increment (integer) that will be added to the number of the first conformation, which is always '1'. The specified DCD trajectory will be encoded into a '<structure_name>.<trajectory_name>.sasta' file containing one SA sequence per trajectory conformation in FASTA-type format. The format of SA sequence headers is <ID>|<conformation>, where ID is a dot-separated structure and trajectory name, while conformations are numbered from 1 to N (= total number of conformations), plus the conformation increment (default = 0).

Trajectories can be large and therefore the encoding routine can be memory hungry. To avoid running out of RAM, a script employing the catdcd program (VMD suite) is included, which facilitates splitting the trajectory into blocks:

Rscript dcdsplit.R <traj_name>.dcd <first> <last> <nConf>

After encoding all blocks, the resulting SA strings can be concatenated to the complete encoded trajectory.

• 2021 Jens Kleinjung (author, maintainer) [email protected]
• 2021 Franca Fraternali (author, maintainer) [email protected]