campari: Original campari run

In CampaR1: Trajectory Analysis

Description

campari will call the original campari software, specified in the directory camp_home. It is possible to use this function following the instructions in http://campari.sourceforge.net/tutorial11.html. For that purpose a keyfile and sequence file are present inside this package as an example (in CampaR1/inst/extdata).

Usage

campari(nsnaps, wd, data_file, base_name, camp_home, ...)

Arguments

nsnaps	Number of snapshots in the trajectory file.
wd	Working directory.
data_file	Input file (e.g. trajectory.dcd) location.
base_name	This name should be used for the input files (base_name.key and base_name.in) in order to run campari.
camp_home	Location of the installed campari software.
...	Analysis variables (similarly to mst_from_trj).

Details

For details, please refer to the main documentation of the original campari software http://campari.sourceforge.net/documentation.html.

See Also

mst_from_trj, gen_progindex, gen_annotation.

Examples

## Not run: 
campari(nsnaps = 100, wd = "./", data_file = "file_dcd", camp_home = "/campari_home/",
        base_name = "nbu", pdb_format = 4,
        cprogindstart = 2,distance_met = 5, birch_height = 5, cmaxrad = 1, cradius = 0.1,
        cprogindwidth = 10,search_attempts = 10, methodst = 2)

## End(Not run)

CampaR1 documentation built on May 30, 2017, 2:51 a.m.