load_hbond {MDplot}

Loading hydrogen bond data

Description

This function loads hydrogen bond information from a text file and stores it in a table. See functions hbond() and hbond_ts() for usage of the return value.

Usage

load_hbond( path,
            GROMACShbondlogfile = NA,
            mdEngine = "GROMOS" ) 

Arguments

path

Specifies the path of the text input file.

GROMACShbondlogfile

Additional file path required in case GROMACS format is specified.

mdEngine

Argument distinguishes between input formats based on the molecular dynamics engine used. Currently available: "GROMOS", "GROMACS" and "AMBER". Note, that load_hbond() is able to load both summary and time-series data for the AMBER simulation package.

Value

Returns a table, where the hydrogen bonds are stored in a row-wise fashion and the columns hold the following information (note, that information not available e.g. because the MD analysis tool output does not provide it, is represented by NA values):

• hbondID The identifier number of the hydrogen bonds (if not given by the input, they are numbered ascendingly).

• resDonor Number of the donor residue.

• resDonorName Name of the donor residue.

• resAcceptor Number of the acceptor residue.

• resAcceptorName Name of the acceptor residue.

• atomDonor Number of atom, that is the hydrogen bond donor.

• atomDonorName Name of atom, that is the hydrogen bond donor.

• atomH Number of atom (proton) that is forming the hydrogen bond.

• atomAcceptor Number of atom, that is the hydrogen bond acceptor.

• atomAcceptorName Name of atom, that is the hydrogen bond acceptor.

• percentage Number between 0 and 100 in percent representing the occurence rate of a particular hydrogen bond over the trajectory.

Author(s)

Christian Margreitter

Examples

# GROMOS
load_hbond( system.file( "extdata/hbond_example.txt.gz", package = "MDplot" ) )

# GROMACS
load_hbond( system.file( "extdata/hbond_ts_example_GROMACS.xpm.gz",
                         package = "MDplot" ),
            system.file( "extdata/hbond_example_GROMACS.txt.gz",
                         package = "MDplot" ),
            mdEngine = "GROMACS" )

# AMBER (summary)
load_hbond( system.file( "extdata/hbond_example_AMBER.txt.gz",
            package = "MDplot" ), mdEngine = "AMBER" )

# AMBER (time-series)
load_hbond( system.file( "extdata/hbond_ts_example_AMBER.txt.gz",
            package = "MDplot" ), mdEngine = "AMBER" )