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  "Title": "Read, Write, Visualize and Manipulate PDB Files",
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  "_realowner": "discoleo",
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    {
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    {
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    "abc2xyz",
    "addABC",
    "addBBox",
    "addEleLab",
    "addPBCBox",
    "addResLab",
    "addXYZ",
    "angle",
    "as.coords",
    "atoms",
    "basis",
    "basis<-",
    "bbox.pdb",
    "bond",
    "cell.coords",
    "cell.density",
    "cell.volume",
    "centres",
    "chains",
    "connect",
    "connect.nucleic",
    "coords",
    "coords<-",
    "crystal",
    "dihedral",
    "dist.point",
    "distances",
    "dotProd",
    "format.pdb.title",
    "inertia",
    "info3d",
    "is.atoms",
    "is.connect",
    "is.coords",
    "is.crystal",
    "is.distances",
    "is.pdb",
    "lattice.range",
    "Mab",
    "masses",
    "Mbc",
    "Mca",
    "measure",
    "mirror",
    "Mxy",
    "Myz",
    "Mzx",
    "natom",
    "norm",
    "pdb",
    "proj.line3d",
    "R",
    "range.lattice",
    "read.pdb",
    "reindex",
    "replicate",
    "rotVect",
    "Rx",
    "Ry",
    "Rz",
    "select",
    "Ta",
    "Tabc",
    "Tb",
    "Tc",
    "toSymbols",
    "trans",
    "translate",
    "Tx",
    "Txyz",
    "Ty",
    "Tz",
    "unsplit",
    "vectNorm",
    "vectProd",
    "viewAB",
    "viewAxis",
    "viewBC",
    "viewCA",
    "viewInertia",
    "viewXY",
    "viewYZ",
    "viewZX",
    "visualize",
    "wrap",
    "write.pdb",
    "xyz2abc"
  ],
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    {
      "name": "elements",
      "title": "Periodic Table of the Elements",
      "object": "elements",
      "class": [
        "data.frame"
      ],
      "fields": [
        "num",
        "symb",
        "areneg",
        "rcov",
        "rbo",
        "rvdw",
        "maxbnd",
        "mass",
        "elneg",
        "ionization",
        "elaffinity",
        "red",
        "green",
        "blue",
        "name"
      ],
      "rows": 117,
      "table": true,
      "tojson": true
    },
    {
      "name": "universalConstants",
      "title": "Universal Constants",
      "object": "universalConstants",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Quantity",
        "Value",
        "Unit"
      ],
      "rows": 23,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Rpdb-package",
      "title": "Read, Write, Visualize and Manipulate PDB Files",
      "topics": [
        "Rpdb-package"
      ]
    },
    {
      "page": "addAxes",
      "title": "Add Axes or PBC Box to the 'rgl' Scene",
      "topics": [
        "addABC",
        "addAxes",
        "addBBox",
        "addPBCBox",
        "addXYZ",
        "bbox.pdb"
      ]
    },
    {
      "page": "addLabels",
      "title": "Add Labels to the 'rgl' Scene",
      "topics": [
        "addEleLab",
        "addEleLab.atoms",
        "addEleLab.pdb",
        "addLabels",
        "addResLab",
        "addResLab.atoms",
        "addResLab.pdb",
        "info3d",
        "info3d.atoms",
        "info3d.pdb"
      ]
    },
    {
      "page": "atoms",
      "title": "Create 'atoms' Object",
      "topics": [
        "atoms",
        "atoms.atoms",
        "atoms.default",
        "atoms.pdb",
        "is.atoms",
        "[.atoms"
      ]
    },
    {
      "page": "basis",
      "title": "The Basis of an Object",
      "topics": [
        "basis",
        "basis.default",
        "basis.pdb",
        "basis<-",
        "basis<-.default",
        "basis<-.pdb"
      ]
    },
    {
      "page": "bond-angle-dihedral",
      "title": "Atomic Bond Lengths, Angles and Dihedrals",
      "topics": [
        "angle",
        "angle.coords",
        "angle.pdb",
        "bond",
        "bond-angle-dihedral",
        "bond.coords",
        "bond.pdb",
        "dihedral",
        "dihedral.coords",
        "dihedral.pdb",
        "measure",
        "measure.coords",
        "measure.default",
        "measure.pdb"
      ]
    },
    {
      "page": "cellProperties",
      "title": "Properties of a Unit Cell",
      "topics": [
        "cell.coords",
        "cell.coords.crystal",
        "cell.coords.default",
        "cell.coords.pdb",
        "cell.density",
        "cell.density.default",
        "cell.density.pdb",
        "cell.volume",
        "cell.volume.crystal",
        "cell.volume.pdb",
        "cellProperties"
      ]
    },
    {
      "page": "centres",
      "title": "Centres-of-Geometry and Centres-of-Mass",
      "topics": [
        "centres",
        "centres.atoms",
        "centres.coords",
        "centres.pdb"
      ]
    },
    {
      "page": "centres.ppRoll",
      "title": "Centres-of-Geometry: Rolling Window",
      "topics": [
        "centres.ppRoll",
        "centres.ppRoll.atoms",
        "centres.ppRoll.default",
        "centres.ppRoll.pdb"
      ]
    },
    {
      "page": "chains",
      "title": "Extract Chain-Codes from a PDB Molecule Extract the codes of all chains from a PDB object. 'chains' is a generic function to extract the ids of the chains from a PDB molecule.",
      "topics": [
        "chains",
        "chains.atoms",
        "chains.pdb"
      ]
    },
    {
      "page": "connect",
      "title": "Create 'connect' Object",
      "topics": [
        "conect.default",
        "connect",
        "connect.atoms",
        "connect.character",
        "connect.coords",
        "connect.default",
        "connect.pdb",
        "is.connect"
      ]
    },
    {
      "page": "connect.nucleic",
      "title": "Connects atoms in Nucleic acids",
      "topics": [
        "connect.nucleic",
        "connect.nucleic.atoms",
        "connect.nucleic.pdb"
      ]
    },
    {
      "page": "coords",
      "title": "The Atomic Coordinates of an Object",
      "topics": [
        "as.coords",
        "coords",
        "coords.atoms",
        "coords.coords",
        "coords.data.frame",
        "coords.default",
        "coords.matrix",
        "coords.pdb",
        "coords<-",
        "coords<-.atoms",
        "coords<-.pdb",
        "is.coords",
        "print.coords"
      ]
    },
    {
      "page": "crystal",
      "title": "Create 'crystal' Object",
      "topics": [
        "crystal",
        "crystal.default",
        "crystal.pdb",
        "is.crystal"
      ]
    },
    {
      "page": "distances",
      "title": "Inter-Atomic Distances",
      "topics": [
        "dist.point",
        "dist.point.default",
        "distances",
        "distances.atoms",
        "distances.connect",
        "distances.coords",
        "distances.default",
        "distances.pdb",
        "is.distances",
        "norm",
        "norm.connect",
        "norm.distances"
      ]
    },
    {
      "page": "elements",
      "title": "Periodic Table of the Elements",
      "topics": [
        "elements"
      ]
    },
    {
      "page": "format.pdb.title",
      "title": "Format \"Title\" Field of PDB File",
      "topics": [
        "format.pdb.title",
        "format.pdb.title.character"
      ]
    },
    {
      "page": "inertia",
      "title": "Moment of Inertia of a Molecular System",
      "topics": [
        "inertia",
        "inertia.atoms",
        "inertia.coords",
        "inertia.pdb"
      ]
    },
    {
      "page": "masses",
      "title": "Mass of Chemical Elements",
      "topics": [
        "masses",
        "masses.default",
        "masses.pdb"
      ]
    },
    {
      "page": "merge.coords",
      "title": "Merging Molecular Systems",
      "topics": [
        "merge.atoms",
        "merge.coords",
        "merge.pdb",
        "merge.pdb.hetero",
        "merge.pdb.resolution",
        "merge.pdb.structure"
      ]
    },
    {
      "page": "mirror",
      "title": "Reflection of Atomic Coordinates",
      "topics": [
        "mirror",
        "mirror.coords",
        "mirror.pdb"
      ]
    },
    {
      "page": "mirrorHelpers",
      "title": "Helper Functions for reflection of Atomic Coordinates",
      "topics": [
        "Mab",
        "Mab.coords",
        "Mab.pdb",
        "Mbc",
        "Mbc.coords",
        "Mbc.pdb",
        "Mca",
        "Mca.coords",
        "Mca.pdb",
        "mirrorHelpers",
        "Mxy",
        "Mxy.coords",
        "Mxy.pdb",
        "Myz",
        "Myz.coords",
        "Myz.pdb",
        "Mzx",
        "Mzx.coords",
        "Mzx.pdb"
      ]
    },
    {
      "page": "natom",
      "title": "Number of Atoms in an Object Containing Atomic Coordinates",
      "topics": [
        "natom",
        "natom.atoms",
        "natom.coords",
        "natom.pdb"
      ]
    },
    {
      "page": "pdb",
      "title": "Create an Object of Class 'pdb'",
      "topics": [
        "is.pdb",
        "pdb",
        "pdb.default"
      ]
    },
    {
      "page": "proj.line3d",
      "title": "Projections of Objects",
      "topics": [
        "proj.line3d",
        "proj.line3d.matrix",
        "proj.line3d.numeric"
      ]
    },
    {
      "page": "range.coords",
      "title": "Range of Atomic Coordinates",
      "topics": [
        "lattice.range",
        "lattice.range.pdb",
        "range.atoms",
        "range.coords",
        "range.lattice",
        "range.lattice.pdb",
        "range.pdb"
      ]
    },
    {
      "page": "read.pdb",
      "title": "PDB File Reader",
      "topics": [
        "read.pdb"
      ]
    },
    {
      "page": "reindex",
      "title": "Reinitialize Object Indexing",
      "topics": [
        "reindex",
        "reindex.atoms",
        "reindex.pdb"
      ]
    },
    {
      "page": "replicate",
      "title": "Replicate Atomic Coordinates",
      "topics": [
        "replicate",
        "replicate.atoms",
        "replicate.coords",
        "replicate.pdb"
      ]
    },
    {
      "page": "rotation",
      "title": "Rotation of Atomic Coordinates",
      "topics": [
        "R",
        "R.coords",
        "R.pdb",
        "rotation"
      ]
    },
    {
      "page": "rotationHelpers",
      "title": "Helper Functions for Rotation of Atomic Coordinates",
      "topics": [
        "rotationHelpers",
        "Rx",
        "Rx.coords",
        "Rx.pdb",
        "Ry",
        "Ry.coords",
        "Ry.pdb",
        "Rz",
        "Rz.coords",
        "Rz.pdb"
      ]
    },
    {
      "page": "select",
      "title": "Select atoms",
      "topics": [
        "select",
        "select.atoms",
        "select.pdb"
      ]
    },
    {
      "page": "split.pdb",
      "title": "Divide and Reassemble 'pdb' Objects",
      "topics": [
        "split.pdb",
        "unsplit.pdb"
      ]
    },
    {
      "page": "subset.atoms",
      "title": "Subsetting 'atoms' and 'pdb' Objects",
      "topics": [
        "subset.atoms",
        "subset.pdb"
      ]
    },
    {
      "page": "toSymbols",
      "title": "Atomic Symbols Converter",
      "topics": [
        "toSymbols",
        "toSymbols.character",
        "toSymbols.integer",
        "toSymbols.numeric"
      ]
    },
    {
      "page": "translate",
      "title": "Graphics Tools",
      "topics": [
        "trans",
        "translate"
      ]
    },
    {
      "page": "translation",
      "title": "Translation of Atomic Coordinates",
      "topics": [
        "Tabc",
        "Tabc.coords",
        "Tabc.pdb",
        "translation",
        "Txyz",
        "Txyz.coords",
        "Txyz.pdb"
      ]
    },
    {
      "page": "translationHelpers",
      "title": "Helper Functions for Translation of Atomic Coordinates",
      "topics": [
        "Ta",
        "Ta.coords",
        "Ta.pdb",
        "Tb",
        "Tb.coords",
        "Tb.pdb",
        "Tc",
        "Tc.coords",
        "Tc.pdb",
        "translationHelpers",
        "Tx",
        "Tx.coords",
        "Tx.pdb",
        "Ty",
        "Ty.coords",
        "Ty.pdb",
        "Tz",
        "Tz.coords",
        "Tz.pdb"
      ]
    },
    {
      "page": "universalConstants",
      "title": "Universal Constants",
      "topics": [
        "universalConstants"
      ]
    },
    {
      "page": "unsplit",
      "title": "Reassemble Groups",
      "topics": [
        "unsplit",
        "unsplit.default"
      ]
    },
    {
      "page": "vectorialOperations",
      "title": "Basic Vectorial Operations",
      "topics": [
        "dotProd",
        "rotVect",
        "vectNorm",
        "vectorialOperations",
        "vectProd"
      ]
    },
    {
      "page": "viewAxis",
      "title": "Set the View of the 'rgl' Scene",
      "topics": [
        "viewAB",
        "viewAxis",
        "viewBC",
        "viewCA",
        "viewInertia",
        "viewXY",
        "viewYZ",
        "viewZX"
      ]
    },
    {
      "page": "visualize",
      "title": "Visualize a Molecular Structure",
      "topics": [
        "visualize",
        "visualize.atoms",
        "visualize.character",
        "visualize.coords",
        "visualize.data.frame",
        "visualize.matrix",
        "visualize.pdb",
        "windowRect0"
      ]
    },
    {
      "page": "wrap",
      "title": "Wrap Atomic Coordinates",
      "topics": [
        "wrap",
        "wrap.atoms",
        "wrap.coords",
        "wrap.pdb"
      ]
    },
    {
      "page": "write.pdb",
      "title": "PDB File Writer",
      "topics": [
        "write.pdb"
      ]
    },
    {
      "page": "xyz2abc",
      "title": "From Cartesian to Fractional Coordinates and Vice Versa",
      "topics": [
        "abc2xyz",
        "abc2xyz.atoms",
        "abc2xyz.coords",
        "abc2xyz.distances",
        "abc2xyz.pdb",
        "xyz2abc",
        "xyz2abc.atoms",
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