Package: MDaRes
Title: MD Analysis of Residue Properties Using Structural Alphabets
Version: 0.0.2
Authors@R: 
    c(
      person(given = "Nancy",
             family = "D'Arminio",
             role = c("aut"),
             email = "nancydarminio67@gmail.com",
             comment = c(ORCID = "0000-0002-8065-2142")),
      person(given = "Anna",
             family = "Marabotti",
             role = "aut",
             email = "amarabotti@unisa.it",
             comment = c(ORCID = "0000-0002-9510-5205")),
      person(given = "Alessandro",
             family = "Pandini",
             role = c("aut", "cph", "cre"),
             email = "alessandro.pandini@gmail.com",
             comment = c(ORCID = "0000-0002-4158-233X"))
    )
Description: Analyze molecular dynamics (MD) simulation data using
        structural alphabets. Protein local conformations from
        molecular simulations are encoded in a compressed string
        representation. Residue-level UniProt annotations can be
        directly retrieved. Comparative analysis tools are available to
        investigate conformational variability, coordinated motions,
        and differences between systems (e.g. wild-type vs mutant;
        bound vs unbound). Methodological details for the structural
        alphabet analysis can be found in Pandini et al. (2013)
        <doi:10.1093/bioinformatics/btt326>.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.3
Depends: R (>= 4.1.0)
Imports: bio3d, DescTools, SOMMD, tools, dplyr, tidyr, stringr,
        UniprotR, Rcpp
LinkingTo: Rcpp, RcppArmadillo
Suggests: httr, future, future.apply, curl, testthat (>= 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2026-09-25 08:59:00 UTC; root
Author: Nancy D'Arminio [aut] (ORCID:
        <https://orcid.org/0000-0002-8065-2142>), Anna Marabotti [aut]
        (ORCID: <https://orcid.org/0000-0002-9510-5205>), Alessandro
        Pandini [aut, cph, cre] (ORCID:
        <https://orcid.org/0000-0002-4158-233X>)
Maintainer: Alessandro Pandini <alessandro.pandini@gmail.com>
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libmagick++-dev
        gsfonts libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev
        libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://alepandini.r-universe.dev
Date/Publication: 2026-08-25 15:10:09 UTC
RemoteUrl: https://github.com/cran/MDaRes
RemoteRef: HEAD
RemoteSha: 4f28c3367a3128a2905ac4378469d336664ee704