MMTSB
Tool Set Documentation

Difference between revisions of "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
 
<B>-show</B> or <B>-prop</B>.<BR>
 
The option <B>-prop</B> 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 <B>-show</B> is available to print the tags for
 
all available properties.<BR>
 
The following tags are commonly available:<BR><BR>
 
<TABLE CELLPADDING=1 CELLSPACING=1>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>etot</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>total energy</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>eelec</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>electrostatic energy</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>evdw</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>van der Waals energy</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>egb</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>Generalized Born energy</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>esasa</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>Hydrophobic solvation energy</FONT></TD>
 
</TR>
 
<TR><TD></TD></TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rgyr</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>radius of gyration</FONT></TD>
 
</TR>
 
<TR><TD></TD></TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdall</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>total RMSD from native</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdca</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>C-alpha RMSD from native</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdback</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>backbone RMSD from native</FONT></TD>
 
</TR>
 
<TR><TD></TD></TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdpol</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>polar RMS distance from center</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdhyd</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>hydrophobic RMS distance from center</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdchg</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>charged RMS distance from center</FONT></TD>
 
</TR>
 
<TR><TD></TD></TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdphi</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>phi dihed. RMSD from native</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdpsi</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>psi dihed. RMSD from native</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rmsdchi1</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>chi1 dihed. RMSD from native</FONT></TD>
 
</TR>
 
<TR><TD></TD></TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>pphi</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>percent correct phi</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>ppsi</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>percent correct psi</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>pchi1</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>percent correct chi1</FONT></TD>
 
</TR>
 
<TR><TD></TD></TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>cont</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>fraction of native contacts</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>rho</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>fraction of native contacts</FONT></TD>
 
</TR>
 
<TR>
 
  <TD><FONT FACE=courier SIZE=3>gdtts</FONT></TD>
 
  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>GDT similarity from native</FONT></TD>
 
</TR>
 
</TABLE>
 
<BR>
 
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>.
 
<BR><BR>
 
If the option <B>-score</B> 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 <B>-score avg</B>.
 
Values that lie outside a given multiple
 
of the standard deviation can be excluded as in
 
<docmark>bestcluster.pl</docmark> by using <font color=#508060>avglow</font> or
 
<font color=#508060>avgcent</font> as key words instead of <font color=#508060>avg</font>.
 
The option <B>-limstd</B> is available to modify the value of
 
the multiple used in this case.<BR><BR>
 
The option <B>-cluster</B> 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 <B>-ctag</B> so that the corresponding cluster
 
data is used instead. The <B>-cluster</B>
 
option may be combined with <B>-score</B> to obtain a score for
 
conformations in a given cluster.
 
 
 
== Options ==
 
 
 
; -help : usage information
 
 
 
 
 
== Examples ==
 
 
 
<mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test1"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test2"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test3"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test4"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test5"></mmtsbToolExample>
 

Revision as of 12:06, 24 October 2008

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