hbond_ts
(Package: MDplot) :
Plot hydrogen bond timeseries
Timeseries plot of hydrogen bonds (various selections possible). In addition to the timeseries file, the summary file is also necessary.
● Data Source:
CranContrib
● Keywords: hbond, hydrogen bond, timeseries
● Alias: hbond_ts
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1 images
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load_rmsd
(Package: MDplot) :
Loading function for code{link{rmsd
Returns a list of vector pairs of datapoint indices and RMSD values.
● Data Source:
CranContrib
● Keywords: rmsd
● Alias: load_rmsd
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0 images
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load_clusters
(Package: MDplot) :
Loading cluster information
This function loads clusters from a plain text file and stores them in a matrix. The trajectories can be named by the user.
● Data Source:
CranContrib
● Keywords: Clusters
● Alias: load_clusters
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0 images
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Loads DSSP output files from a specified directory and combines it into a list suited for dssp_ts().
● Data Source:
CranContrib
● Keywords: DSSP
● Alias: load_dssp_ts
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0 images
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translate_aminoacids
(Package: MDplot) :
Function to translate between canonical and GROMOS amino acid abbreviations
Converts an aminoacid naming scheme in the context of GROMOS (e.g. containing HISH) into canonical three- or one-letter codes.
● Data Source:
CranContrib
● Keywords: aminoacids
● Alias: translate_aminoacids
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0 images
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xrmsd
(Package: MDplot) :
XRMSD plot in heatmap style
Plots an heatmap according to the RMSD values for a 2D snapshot matrix, based on molecular dynamics trajectories.
● Data Source:
CranContrib
● Keywords: xrmsd
● Alias: xrmsd
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0 images
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dssp_summary
(Package: MDplot) :
DSSP summary plot for secondary structure elements (proteins)
Plots summary plot for secondary structure motifs based on the output of the widely used classification program DSSP, which takes hydrogen bonds into account. The default order is: "3-Helix", "4-Helix", "5-Helix", "Bend", "Beta-Bridge", "Beta-Strand", "Turn".
● Data Source:
CranContrib
● Keywords: dssp
● Alias: dssp_summary
●
1 images
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load_TIcurve
(Package: MDplot) :
Loading function for thermodynamic integration function code{link{TIcurve
Returns a list of matrices holding three columns (lambda state point, value and error) for every file.
● Data Source:
CranContrib
● Keywords: thermodynamic integration
● Alias: load_TIcurve
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0 images
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load_rmsf
(Package: MDplot) :
Loading function for code{link{rmsf
Returns a list of vector pairs of datapoint indices and RMSF values.
● Data Source:
CranContrib
● Keywords: rmsf
● Alias: load_rmsf
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0 images
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load_timeseries
(Package: MDplot) :
Loading function for code{link{timeseries
Returns a list of vector pairs of datapoint indices and values.
● Data Source:
CranContrib
● Keywords: timeseries
● Alias: load_timeseries
●
0 images
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