libBioLCCC v1.3.0
Anton Goloborodko
libBioLCCC v1.3.0 has been released! The list of changes:
General:
======
- Add a general expression for the rod model. The previously used
special expression did not account for bridge conformations of a
polymer, in which both its ends are adsorbed to the opposite walls of
a pore. The special expression is valid only when polymerLength <
slitWidth - 2 * layerWidth. The newly introduced general expression is
valid for polymers of any length, but requires more computational
resources. The general expression is disabled by default and can be
enabled by setting specialRodModel variable of a ChemicalBasis to
false.
- Add bindArea variable to ChemicalGroup class. This variable contains
the size of the chemical group. This size is defined as a number of
binary solvent molecules which are desorbed when the chemical group is
adsorbed to the surface. By default every chemical group has a size of
1.0, except for the terminal groups, which has zero size.
- Add experimental option neglectPartiallyDesorbedStates.
Corresponding citation from the documentation: “In BioLCCC model, the
distribution coefficient of a polymer is calculated by integration
over all its possible conformations. These could be differentiated
into three distinct groups: totally adsorbed, totally desorbed and
partially desorbed states. The latter are of particular interest,
because these conformations give rise to sequence specificity of
BioLCCC model. Using setNeglectPartiallyDesorbedStates function, these
conformations can be excluded from calculation. This option is
intended for study of BioLCCC properties, and should not be used in
routine applications.”
- Code refactoring: biolccc.cpp/.h was splitted into biolccc.cpp/.h,
parsing.cpp/.h, rod_model.cpp/.h and chain_model.cpp/.h.
API changes:
==========
- Parsing functionality is now available through parsing.cpp.
The new version of pyBioLCCC may be downloaded via pip package
manager. On Ubuntu, just execute: sudo pip install pyBioLCCC --upgrade
.
The easiest way to obtain the new pyBioLCCC version for Windows is a
precompiled package at http://pypi.python.org/pypi/pyBioLCCC/.
Don't hesitate to ask questions - we need your feedback!
Anton Goloborodko.