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HHProfileParser hhmake compatibility

HHMs created with HHsuite 2.0's hhmake can have a number of features that will cause an exception while loading with HHProfileParser. The issues I noticed are: the master sequence of the profile,...

Id #32 | Release: None | Updated: Jan 30, 2015 at 3:01 PM by kalev | Created: Jan 21, 2015 at 10:13 AM by jbassler

Tests fail in Debian package when trying to write to the install directory

Please see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=732945 Would it be possible to write a patch/new version that would create a temporary directory for the test-generated files? Thanks!

Id #31 | Release: csb 1.2.2 | Updated: Dec 10 at 11:22 AM by kalev | Created: Dec 23, 2013 at 10:18 AM by tdido

AbstractDensity is not generic

The current implementation of AbstractDensity assumes that all parameters are simple float values. While this assumption makes sense and covers most cases, there is no reason why AbstractDensity sh...

Id #30 | Release: None | Updated: Dec 10 at 11:22 AM by kalev | Created: Oct 24, 2013 at 5:48 PM by kalev

Support PDFs with chained and shared parameters

The idea is to allow PDFs to use shared and chained/virtual/computed parameters, which . Chained parameters should support lazy evaluation - updating a base parameter should trigger implicit update...

Id #29 | Release: None | Updated: Dec 10 at 11:22 AM by kalev | Created: Oct 24, 2013 at 5:43 PM by kalev

Comma in exception breaks python3 compatibility

While building the new 1.2.1 package for Debian, I got an error when installing the python3 version of the package: Setting up python3-csb (1.2.1+dfsg-1) ... File "/usr/lib/python3/dist-package...

Id #28 | Release: csb 1.2.1 | Updated: Dec 10 at 11:22 AM by kalev | Created: Oct 9, 2013 at 3:20 PM by tdido

ContactMapComparsonInfo

Should be replaced with ContactMapComparisonInfo?

Id #27 | Release: None | Updated: Dec 10 at 11:22 AM by kalev | Created: Oct 4, 2013 at 7:08 AM by mhabeck

buildhmm.py calls the deprecated buildali.pl

csb.apps.buildhmm fails with recent HHsuite versions. This is because it calls the deprecated buildali.pl script from the old HHsuite. We need to migrate to the new HHsuite interface (hhblits + add...

Id #26 | Release: None | Updated: Dec 10 at 11:22 AM by kalev | Created: Sep 3, 2013 at 10:26 AM by kalev

Bug in statistics.samplers.mc.multichain.HMCStepRENS

statistics.samplers.mc.multichain.HMCStepRENS._setup_propagations() produces HMCPropagation instances with identical parameters (namely, the parameters corresponding to the last propagation step in...

Id #24 | Release: None | Updated: Jul 4 at 10:06 PM by kalev | Created: Apr 22, 2013 at 3:00 PM by simeoncarstens

Refactor _run_traj_generator() of statistics.samplers.mc.multichain.AbstractRENS

Refactoring the _run_traj_generator() method of statistics.samplers.mc.multichain.AbstractRENS and derived classes avoids code duplication and allows for easier unit testing.

Id #23 | Release: None | Updated: Jul 4 at 10:06 PM by kalev | Created: Apr 17, 2013 at 4:21 PM by simeoncarstens

Bug in numeric.InvertibleMatrix._check_diagonal()

The check numeric.InvertibleMatrix whether the matrix is diagonal or not is erroneous.

Id #22 | Release: None | Updated: Jul 4 at 10:06 PM by kalev | Created: Mar 29, 2013 at 5:11 PM by simeoncarstens