tmscore(1) [debian man page]

TMSCORE(1)						      General Commands Manual							TMSCORE(1)

NAME

       TM-score - an algorithm to calculate the similarity of topologies of two protein structures

VERSION

       This documentation refers to TM-score version released on 2011/01/30

SYNOPSIS

       1. Run TM-score to compare 'model' and 'native':

	   TMscore model native

       2. Run TM-score with an assigned d0, e.g. 5 Angstroms:

	   TMscore model native -d 5

       3. Run TM-score with superposition output, e.g. 'TM.sup', and view in Rasmol:

	   TMscore model native -o TM.sup
	   rasmol -script TM.sup

DESCRIPTION

       This program is to compare two protein structures and identify the best superposition that has the highest TM-score. Input structures must
       be in the PDB format. By default, TM-score is normalized by the second protein. Users can obtain a brief instruction by simply running the
       program without arguments.

OPTIONS

	   -o filename.sup Outputs the superposition to the specified file,
	      suitable for use in rasmol.

	   -d value Sets d0 to the specified number of angstroms.

SEE ALSO

       TMalign, rasmol

       When  using  this proram and for more detailed information, please refer to the publication in NucleicAcidsRes.	(2005) Volume 33 page
       2303ff. by Zhang and Skolnick.

AUTHOR

       For comments/suggestions,please contact email: zhng@umich.edu.

       This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk)

.								    2011-02-03								TMSCORE(1)

Mail::SpamAssassin::AutoWhitelist(3)			User Contributed Perl Documentation		      Mail::SpamAssassin::AutoWhitelist(3)

NAME

       Mail::SpamAssassin::AutoWhitelist - auto-whitelist handler for SpamAssassin

SYNOPSIS

	 (see Mail::SpamAssassin)

DESCRIPTION

       Mail::SpamAssassin is a module to identify spam using text analysis and several internet-based realtime blacklists.

       This class is used internally by SpamAssassin to manage the automatic whitelisting functionality.  Please refer to the "Mail::SpamAssassin"
       documentation for public interfaces.

METHODS

       $meanscore = awl->check_address($addr, $originating_ip, $signedby);
	   This method will return the mean score of all messages associated with the given address, or undef if the address hasn't been seen
	   before.

	   If $originating_ip is supplied, it will be used in the lookup.

       awl->count();
	   This method will return the count of messages used in determining the whitelist correction.

       awl->add_score($score);
	   This method will add half the score to the current entry.  Half the score is used, so that repeated use of the same From and IP address
	   combination will gradually reduce the score.

       awl->add_known_good_address($addr);
	   This method will add a score of -100 to the given address -- effectively "bootstrapping" the address as being one that should be
	   whitelisted.

       awl->add_known_bad_address($addr);
	   This method will add a score of 100 to the given address -- effectively "bootstrapping" the address as being one that should be
	   blacklisted.

perl v5.16.3							    2011-06-06				      Mail::SpamAssassin::AutoWhitelist(3)