Topological Entanglement in Polymers, Proteins and Periodic Systems software
We introduce the Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP) software, that enables to compute the topological and geometrical complexity in such systems. In particular, this software enables the computation of the Writhe, the Average Crossing Number (ACN) and the Jones polynomial of each filament in the system, whether it is open or closed. In particular, the software uses rigorous definitions of the Writhe, ACN and of the Jones polynomial of linear (open) chains that do not require any closure scheme. The software also allows the computation of the Gauss linking integral for all pairs of chains (open or closed) in 3-space and in systems employing Periodic Boundary Conditions.
Copyright 2021 Eleni Panagiotou and Tom Herschberg
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Acknowledging support from NSF CAREER #2047587, NSF DMS #1913180 and NSF #1925603.
Please use the following reference to acknowledge TEPPP:
Herschberg, T. and Panagiotou, E., 2021, A computational package for measuring Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP)