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Software Design Overview

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Jens Kleinjung edited this page Feb 22, 2020 · 8 revisions

POPSC

A C program 'pops' that computes the solvent accessible surface area (SASA) for a given PDB or PDBML structure. The input structure can be compressed. The output is either a ASCII table, a JSON file or an R-compatible table. For the purpose of POPScomp, the R-compatible output is created. A detailed description of POPSC is given in Software Design POPSC.

POPSR

An R-package containing routines to process input PDB structures and to plot result data. The core function popscomp.R detects whether the input structure is a complex, splits complexes into single chains, creates all possible chain pairs and runs 'pops' over those newly created single- and paired-chain structures.

Shiny App

The R Shiny App provides a convenient interface to the PDB database, the POPSC program and the POPSR functions. It runs 'pops' over the input structure, launches popscomp.R and shows the ouput SASA tables. Download buttons are provided for individual tables and for the bundled output as tar file.

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