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getprop.pl
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Description
This script is used for extracting structural properties for
a set of structures in an ensemble. It requires a tag as argument to
identify the structure set and either one of the options
-show or -prop.
The option -prop is used with a comma-separated list of
property tags to extract the corresponding data written
to standard output. The output consists of data columns
in the same order as the tags are given in the list argument.
The option -show is available to print the tags for
all available properties.
The following tags are commonly available:
| etot | total energy |
| eelec | electrostatic energy |
| evdw | van der Waals energy |
| egb | Generalized Born energy |
| esasa | Hydrophobic solvation energy |
| rgyr | radius of gyration |
| rmsdall | total RMSD from native |
| rmsdca | C-alpha RMSD from native |
| rmsdback | backbone RMSD from native |
| rmsdpol | polar RMS distance from center |
| rmsdhyd | hydrophobic RMS distance from center |
| rmsdchg | charged RMS distance from center |
| rmsdphi | phi dihed. RMSD from native |
| rmsdpsi | psi dihed. RMSD from native |
| rmsdchi1 | chi1 dihed. RMSD from native |
| pphi | percent correct phi |
| ppsi | percent correct psi |
| pchi1 | percent correct chi1 |
| cont | fraction of native contacts |
| rho | fraction of native contacts |
| gdtts | GDT similarity from native |
This script only extracts data that has been previously
calculated. In order to calculate structural properties for
a whole ensemble see <docmark>calcprop.pl</docmark>. Properties
may be set from external data with <docmark>setprop.pl</docmark>.
If the option -score is given a single score is calculated
from the property values of all ensemble structures and written
out instead of the whole list. The most common use would
be to calculate simple averages with -score avg.
Values that lie outside a given multiple
of the standard deviation can be excluded as in
<docmark>bestcluster.pl</docmark> by using avglow or
avgcent as key words instead of avg.
The option -limstd is available to modify the value of
the multiple used in this case.
The option -cluster is available to extract only data for
structures in a certain cluster. Clusters can be calculated with
<docmark>enscluster.pl</docmark>. If cluster information is only
available for a different tag in the same ensemble the tag can
be given with -ctag so that the corresponding cluster
data is used instead. The -cluster
option may be combined with -score to obtain a score for
conformations in a given cluster.
Options
- -help
- usage information
Examples
getprop.pl -dir data -show sample
prints out the available property tags for structures
associated with the sample tag in the
ensemble under the data directory
available properties are: cont etot gdtts pchi1 pphi ppsi rgyr rho rmsdall rmsdback rmsdca rmsdchg rmsdchi1 rmsdhyd rmsdphi rmsdpol rmsdpsi
getprop.pl -dir data -prop rmsdall,cont sample
extracts total RMSD (rmsdall) and fraction of native contacts
(cont) for the sample structures in the
ensemble under the data directory
1 13.483227 0.041667 2 2.994885 0.583333 3 9.699920 0.125000 4 9.598882 0.041667 5 9.066114 0.083333 6 4.274226 0.500000 7 2.733985 0.708333 8 2.774350 0.541667 9 2.788660 0.708333
getprop.pl -dir data -prop rgyr,cont -cluster t.2 sample
extracts the radius of gyration (rgyr) and fraction of native contacts (cont)
for structures in the cluster t.2 associated with the sample tag.
2 9.796450 0.416667 4 9.306858 0.625000 5 9.505148 0.708333 6 9.646953 0.458333 7 10.014612 0.208333 9 9.732428 0.583333 10 12.625645 0.125000 13 9.622869 0.500000 14 9.159078 0.708333 15 9.735043 0.541667 ...
getprop.pl -dir data -prop rmsdall,cont -score avg sample
calculates average values for total RMSD and fraction of native contacts
6.379361 0.370370
getprop.pl -dir data -prop rgyr,cont -score median -cluster t.2 sample
determines median values for the radius of gyration (rgyr) and
fraction of native contacts (cont)
for structures in the cluster t.2 associated with the sample tag.
9.735043 0.416667