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Currently, the recreation of the coordinates (PD |$\rightarrow $| Mathematica) is not possible, if the coordinates were not given.
PDB |$\rightarrow $| Mathematica, or to obtain the abstract representation, e.g. In particular, this option can be used to translate between the formats, e.g. The coordinates and the codes for the structures are stored in the memory and can be written out in the desired format. identification of topologies with more than eight crossings and theoretical research of topological invariants. We recommend usage of other invariants only for more specific goals, e.g. The user may also supply the spatial graphs (with branching points) with each arc separated by a line without coordinates.ĭecision tree with our proposition of choosing optimal invariant for topology check. directly from the RCSB database), the coordinates of |$C_\alpha $| atoms are extracted. In case the structure is given as PDB or mmCIF file (e.g.
#UW PYTHON DOWNLOAD MAC CODE#
The main function of Topoly is to analyze the topology of the structure given either as 3D coordinates (PDB, mmCIF, XYZ, Mathematica formats) or as an abstract code (Planar Diagram or Ewing–Millett code). Topoly features Input files and format translation The easiest way to get started with Topoly is to download or clone the tutorial project that we provide at and follow the three-step instructions in the README.
#UW PYTHON DOWNLOAD MAC INSTALL#
It is distributed using the standard Python package manager-PyPI-and can be easily installed by invoking pip install topoly, provided a recent version of the pip installer is used.
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Topoly is available for Python3 running on 64-bit Linux or Mac OS X.
#UW PYTHON DOWNLOAD MAC MANUAL#
Topoly comes with a thorough manual (including the description of all functions) and a tutorial project ( ) that includes real-life examples of its usage. As usual in case of a Python package, Topoly’s results can be easily captured and parsed further according to the needs of the user. For open structures (such as protein chains), the package provides the option of chain closure with various methods. The schemes present (from left to right) |$3_1$| knot, Hopf link, |$3_1$| slipknot, |$L_1$| lasso, |$\theta 5_1$| |$\theta $|-curve, |$H6_1$| handcuff graph and a random polymer with 20 steps.Īpart from self-generated structures, Topoly as a versatile tool accepts structures provided as a set of coordinates in various formats (XYZ, PDB, mmCIF, Mathematica and other) or as an abstract code (Planar Diagram or Ewing–Millett code). The exemplary structures, which can be identified using the Topoly package, and the methods suitable for their detection (below the schemes). To study statistics, or simply to test the behavior of the functions provided, the user may also generate random loops and lassos (tadpoles), |$\theta $|-curves, two-component links and handcuff graphs (dumbbells). Exemplary structures, which can be analyzed with Topoly, are presented in Figure 1.
Apart from standard knot-determining techniques (Alexander, Conway, Jones and HOMFLY-PT polynomials ) it includes less-known methods (Kauffman and APS Brackets, Kauffman and BLM/Ho polynomials ), a polynomial for the analysis of spatial graphs (Yamada polynomial ), minimal surface analysis to identify the lasso topology or the Gauss linking number (GLN). Topoly is a Python3 package, allowing one to identify and analyze any polymers’ topology studied so far. To address this need, we have developed a flexible and powerful tool-the Topoly package ( ). However, such an approach is not sufficient when one needs to perform a meticulous analysis of the whole library of polymer structures, use non-standard methods or analyze new topologies (such as branched polymers). For some topologies (usually knots or links), one may use some dedicated web servers, plugins or stand-alone packages. Therefore, a tool automatically identifying the nontrivial topology is required. However, for complex structures, the identification of the topologically nontrivial motif becomes a time-consuming and hard task even for specialists. The inclusion of branching points showed the existence of the |$\theta $|-curve topology, lasso motif or cystine knots, where the depth of the piercing affects the properties of the polymer. In particular, the effect of knots, slipknots and links in linear polymers was studied in designed compounds, DNA and proteins. Recently, researchers moved one step further and focused on the analysis of the influence of the topology on the properties of polymers. In the 20th century, great attention was paid to monitor the chirality of the compounds. The history of science provides dozens of cases when the properties of matter were dictated not by its composition, but rather by its spatial arrangements. Knot, lasso, graph, cyclotide, protein, DNA Introduction
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