Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea:
* added program options to pdbdistance-vineyard
* pdbdistance-vineyard takes frame list in a file
* more logging
* verification of pairing after vertex transpositions (commented out)
From: Dmitriy Morozov <morozov@cs.duke.edu>
Date: Thu, 28 Feb 2008 05:33:34 -0500
State: fixed
Subject: Two simulators
Message-Id: <c664b2f69b5f6ea3-0-artemis@metatron>
Consider using two simulators instead of one to make sure that trajectory
changes are processed before simplex swaps.