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  "Title": "Calculate Indices and Theoretical Physicochemical Properties of\nProtein Sequences",
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  "URL": "https://github.com/dosorio/Peptides/",
  "Description": "Includes functions to calculate several physicochemical\nproperties and indices for amino-acid sequences as well as to\nread and plot 'XVG' output files from the 'GROMACS' molecular\ndynamics package.",
  "License": "GPL-2",
  "RoxygenNote": "7.2.3",
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  "Repository": "https://dosorio.r-universe.dev",
  "Date/Publication": "2023-12-13 17:58:59 UTC",
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  "Author": "Daniel Osorio [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4424-8422>),\nPaola Rondon-Villarreal [aut, ths] (ORCID:\n<https://orcid.org/0000-0001-8209-3885>),\nRodrigo Torres [aut, ths] (ORCID:\n<https://orcid.org/0000-0003-1113-3020>),\nJ. Sebastian Paez [ctb] (ORCID:\n<https://orcid.org/0000-0002-0065-1474>),\nLuis Pedro Coelho [ctb] (ORCID:\n<https://orcid.org/0000-0002-9280-7885>),\nRichèl J.C. Bilderbeek [ctb] (ORCID:\n<https://orcid.org/0000-0003-1107-7049>),\nFlorian C. Sigloch [ctb] (ORCID:\n<https://orcid.org/0000-0001-8130-6885>)",
  "Maintainer": "Daniel Osorio <daniecos@uio.no>",
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    "aaDescriptors",
    "aaList",
    "aaSMILES",
    "aIndex",
    "autoCorrelation",
    "autoCovariance",
    "blosumIndices",
    "boman",
    "charge",
    "crossCovariance",
    "crucianiProperties",
    "fasgaiVectors",
    "hmoment",
    "hydrophobicity",
    "instaIndex",
    "kideraFactors",
    "lengthpep",
    "massShift",
    "membpos",
    "mswhimScores",
    "mw",
    "mz",
    "pI",
    "plotXVG",
    "protFP",
    "readXVG",
    "stScales",
    "tScales",
    "vhseScales",
    "zScales"
  ],
  "_datasets": [
    {
      "name": "AAdata",
      "title": "Properties, scales and indices for the 20 naturally occurring amino acids from various sources",
      "object": "AAdata",
      "file": "AAdata.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "pepdata",
      "title": "Physicochemical properties and indices from 100 amino acid sequences",
      "object": "pepdata",
      "file": "pepdata.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sequence",
        "group",
        "length",
        "mw",
        "tinyAA",
        "smallAA",
        "aliphaticAA",
        "aromaticAA",
        "nonpolarAA",
        "polarAA",
        "chargedAA",
        "basicAA",
        "acidicAA",
        "charge",
        "pI",
        "aindex",
        "instaindex",
        "boman",
        "hydrophobicity",
        "hmoment",
        "transmembrane",
        "globular",
        "surface"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aaComp",
      "title": "Compute the amino acid composition of a protein sequence",
      "topics": [
        "aaComp"
      ]
    },
    {
      "page": "AAdata",
      "title": "Properties, scales and indices for the 20 naturally occurring amino acids from various sources",
      "topics": [
        "AAdata"
      ]
    },
    {
      "page": "aaDescriptors",
      "title": "Compute 66 descriptors for each amino acid of a protein sequence.",
      "topics": [
        "aaDescriptors"
      ]
    },
    {
      "page": "aaList",
      "title": "Return a vector with the 20 standard amino acids in upper case",
      "topics": [
        "aaList"
      ]
    },
    {
      "page": "aaSMILES",
      "title": "Create Smiles String from aminoacid sequences",
      "topics": [
        "aaSMILES"
      ]
    },
    {
      "page": "aIndex",
      "title": "Compute the aliphatic index of a protein sequence",
      "topics": [
        "aIndex"
      ]
    },
    {
      "page": "autoCorrelation",
      "title": "Compute the auto-correlation index of a protein sequence",
      "topics": [
        "autoCorrelation"
      ]
    },
    {
      "page": "autoCovariance",
      "title": "Compute the auto-covariance index of a protein sequence",
      "topics": [
        "autoCovariance"
      ]
    },
    {
      "page": "blosumIndices",
      "title": "Compute the BLOSUM62 derived indices of a protein sequence",
      "topics": [
        "blosumIndices"
      ]
    },
    {
      "page": "boman",
      "title": "Compute the Boman (Potential Protein Interaction) index",
      "topics": [
        "boman"
      ]
    },
    {
      "page": "charge",
      "title": "Compute the theoretical net charge of a protein sequence",
      "topics": [
        "charge"
      ]
    },
    {
      "page": "crossCovariance",
      "title": "Compute the cross-covariance index of a protein sequence",
      "topics": [
        "crossCovariance"
      ]
    },
    {
      "page": "crucianiProperties",
      "title": "Compute the Cruciani properties of a protein sequence",
      "topics": [
        "crucianiProperties"
      ]
    },
    {
      "page": "fasgaiVectors",
      "title": "Compute the FASGAI vectors of a protein sequence",
      "topics": [
        "fasgaiVectors"
      ]
    },
    {
      "page": "hmoment",
      "title": "Compute the hydrophobic moment of a protein sequence",
      "topics": [
        "hmoment"
      ]
    },
    {
      "page": "hydrophobicity",
      "title": "Compute the hydrophobicity index of a protein sequence",
      "topics": [
        "hydrophobicity"
      ]
    },
    {
      "page": "instaIndex",
      "title": "Compute the instability index of a protein sequence",
      "topics": [
        "instaIndex"
      ]
    },
    {
      "page": "kideraFactors",
      "title": "Compute the Kidera factors of a protein sequence",
      "topics": [
        "kideraFactors"
      ]
    },
    {
      "page": "lengthpep",
      "title": "Compute the amino acid length of a protein sequence",
      "topics": [
        "lengthpep"
      ]
    },
    {
      "page": "massShift",
      "title": "Calculate the mass difference of modified peptides.",
      "topics": [
        "massShift"
      ]
    },
    {
      "page": "membpos",
      "title": "Compute theoretically the class of a protein sequence",
      "topics": [
        "membpos"
      ]
    },
    {
      "page": "mswhimScores",
      "title": "Compute the MS-WHIM scores of a protein sequence",
      "topics": [
        "mswhimScores"
      ]
    },
    {
      "page": "mw",
      "title": "Compute the molecular weight of a protein sequence",
      "topics": [
        "mw"
      ]
    },
    {
      "page": "mz",
      "title": "Calculate the m/z for peptides.",
      "topics": [
        "mz"
      ]
    },
    {
      "page": "pepdata",
      "title": "Physicochemical properties and indices from 100 amino acid sequences",
      "topics": [
        "pepdata"
      ]
    },
    {
      "page": "pI",
      "title": "Compute the isoelectic point (pI) of a protein sequence",
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        "pI"
      ]
    },
    {
      "page": "plotXVG",
      "title": "Plot time series from GROMACS XVG files",
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      ]
    },
    {
      "page": "protFP",
      "title": "Compute the protFP descriptors of a protein sequence",
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      ]
    },
    {
      "page": "readXVG",
      "title": "Read output data from a XVG format file.",
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      ]
    },
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      "page": "stScales",
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      ]
    },
    {
      "page": "zScales",
      "title": "Compute the Z-scales of a protein sequence",
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      ]
    }
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