{
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  "Description": "Utilities to process, organize and explore protein\nstructure, sequence and dynamics data. Features include the\nability to read and write structure, sequence and dynamic\ntrajectory data, perform sequence and structure database\nsearches, data summaries, atom selection, alignment,\nsuperposition, rigid core identification, clustering, torsion\nanalysis, distance matrix analysis, structure and sequence\nconservation analysis, normal mode analysis, principal\ncomponent analysis of heterogeneous structure data, and\ncorrelation network analysis from normal mode and molecular\ndynamics data. In addition, various utility functions are\nprovided to enable the statistical and graphical power of the R\nenvironment to work with biological sequence and structural\ndata. Please refer to the URLs below for more information.",
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      "page": "as.select",
      "title": "Convert Atomic Indices to a Select Object",
      "topics": [
        "as.select"
      ]
    },
    {
      "page": "atom.index",
      "title": "Atom Names/Types",
      "topics": [
        "atom.index"
      ]
    },
    {
      "page": "atom.select",
      "title": "Atom Selection from PDB and PRMTOP Structure Objects",
      "topics": [
        "atom.select",
        "atom.select.mol2",
        "atom.select.pdb",
        "atom.select.pdbs",
        "atom.select.prmtop",
        "print.select"
      ]
    },
    {
      "page": "atom2ele",
      "title": "Atom Names/Types to Atomic Symbols Converter",
      "topics": [
        "atom2ele",
        "atom2ele.default",
        "atom2ele.pdb"
      ]
    },
    {
      "page": "atom2mass",
      "title": "Atom Names/Types to Mass Converter",
      "topics": [
        "atom2mass",
        "atom2mass.default",
        "atom2mass.pdb"
      ]
    },
    {
      "page": "atom2xyz",
      "title": "Convert Between Atom and xyz Indices",
      "topics": [
        "atom2xyz",
        "xyz2atom"
      ]
    },
    {
      "page": "basename.pdb",
      "title": "Manipulate PDB File Names",
      "topics": [
        "basename.pdb"
      ]
    },
    {
      "page": "bhattacharyya",
      "title": "Bhattacharyya Coefficient",
      "topics": [
        "bhattacharyya",
        "bhattacharyya.array",
        "bhattacharyya.enma",
        "bhattacharyya.matrix",
        "bhattacharyya.nma",
        "bhattacharyya.pca"
      ]
    },
    {
      "page": "binding.site",
      "title": "Binding Site Residues",
      "topics": [
        "binding.site"
      ]
    },
    {
      "page": "biounit",
      "title": "Biological Units Construction",
      "topics": [
        "biounit"
      ]
    },
    {
      "page": "blast.pdb",
      "title": "NCBI BLAST Sequence Search and Summary Plot of Hit Statistics",
      "topics": [
        "blast.pdb",
        "get.blast",
        "plot.blast"
      ]
    },
    {
      "page": "bounds",
      "title": "Bounds of a Numeric Vector",
      "topics": [
        "bounds"
      ]
    },
    {
      "page": "bounds.sse",
      "title": "Obtain A SSE Object From An SSE Sequence Vector",
      "topics": [
        "bounds.sse"
      ]
    },
    {
      "page": "bwr.colors",
      "title": "Color Palettes",
      "topics": [
        "bwr.colors",
        "mono.colors"
      ]
    },
    {
      "page": "cat.pdb",
      "title": "Concatenate Multiple PDB Objects",
      "topics": [
        "cat.pdb"
      ]
    },
    {
      "page": "chain.pdb",
      "title": "Find Possible PDB Chain Breaks",
      "topics": [
        "chain.pdb"
      ]
    },
    {
      "page": "check.utility",
      "title": "Check on Missing Utility Programs",
      "topics": [
        "check.utility"
      ]
    },
    {
      "page": "clean.pdb",
      "title": "Inspect And Clean Up A PDB Object",
      "topics": [
        "clean.pdb"
      ]
    },
    {
      "page": "cmap",
      "title": "Contact Map",
      "topics": [
        "cmap",
        "cmap.default",
        "cmap.pdb",
        "cmap.pdbs",
        "cmap.xyz"
      ]
    },
    {
      "page": "cna",
      "title": "Protein Dynamic Correlation Network Construction and Community Analysis.",
      "topics": [
        "cna",
        "cna.dccm",
        "cna.ensmb"
      ]
    },
    {
      "page": "cnapath",
      "title": "Suboptimal Path Analysis for Correlation Networks",
      "topics": [
        "cnapath",
        "plot.cnapath",
        "plot.ecnapath",
        "print.cnapath",
        "summary.cnapath"
      ]
    },
    {
      "page": "com",
      "title": "Center of Mass",
      "topics": [
        "com",
        "com.pdb",
        "com.xyz"
      ]
    },
    {
      "page": "combine.select",
      "title": "Combine Atom Selections From PDB Structure",
      "topics": [
        "combine.select"
      ]
    },
    {
      "page": "community.aln",
      "title": "Align communities from two or more networks",
      "topics": [
        "community.aln"
      ]
    },
    {
      "page": "community.tree",
      "title": "Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.",
      "topics": [
        "community.tree"
      ]
    },
    {
      "page": "consensus",
      "title": "Sequence Consensus for an Alignment",
      "topics": [
        "consensus"
      ]
    },
    {
      "page": "conserv",
      "title": "Score Residue Conservation At Each Position in an Alignment",
      "topics": [
        "conserv"
      ]
    },
    {
      "page": "convert.pdb",
      "title": "Renumber and Convert Between Various PDB formats",
      "topics": [
        "convert.pdb"
      ]
    },
    {
      "page": "core.cmap",
      "title": "Identification of Contact Map Core Positions",
      "topics": [
        "core.cmap"
      ]
    },
    {
      "page": "core.find",
      "title": "Identification of Invariant Core Positions",
      "topics": [
        "core.find",
        "core.find.default",
        "core.find.pdb",
        "core.find.pdbs"
      ]
    },
    {
      "page": "cov.nma",
      "title": "Calculate Covariance Matrix from Normal Modes",
      "topics": [
        "cov.enma",
        "cov.nma"
      ]
    },
    {
      "page": "covsoverlap",
      "title": "Covariance Overlap",
      "topics": [
        "covsoverlap",
        "covsoverlap.enma",
        "covsoverlap.nma"
      ]
    },
    {
      "page": "dccm",
      "title": "DCCM: Dynamical Cross-Correlation Matrix",
      "topics": [
        "dccm"
      ]
    },
    {
      "page": "dccm.enma",
      "title": "Cross-Correlation for Ensemble NMA (eNMA)",
      "topics": [
        "dccm.enma"
      ]
    },
    {
      "page": "dccm.gnm",
      "title": "Dynamic Cross-Correlation from Gaussian Network Model",
      "topics": [
        "dccm.egnm",
        "dccm.gnm"
      ]
    },
    {
      "page": "dccm.nma",
      "title": "Dynamic Cross-Correlation from Normal Modes Analysis",
      "topics": [
        "dccm.nma"
      ]
    },
    {
      "page": "dccm.pca",
      "title": "Dynamical Cross-Correlation Matrix from Principal Component Analysis",
      "topics": [
        "dccm.pca"
      ]
    },
    {
      "page": "dccm.xyz",
      "title": "Dynamical Cross-Correlation Matrix from Cartesian Coordinates",
      "topics": [
        "dccm.xyz"
      ]
    },
    {
      "page": "deformation.nma",
      "title": "Deformation Analysis",
      "topics": [
        "deformation.nma"
      ]
    },
    {
      "page": "diag.ind",
      "title": "Diagonal Indices of a Matrix",
      "topics": [
        "diag.ind"
      ]
    },
    {
      "page": "difference.vector",
      "title": "Difference Vector",
      "topics": [
        "difference.vector"
      ]
    },
    {
      "page": "dist.xyz",
      "title": "Calculate the Distances Between the Rows of Two Matrices",
      "topics": [
        "dist.xyz"
      ]
    },
    {
      "page": "dm",
      "title": "Distance Matrix Analysis",
      "topics": [
        "dm",
        "dm.pdb",
        "dm.pdbs",
        "dm.xyz"
      ]
    },
    {
      "page": "dssp",
      "title": "Secondary Structure Analysis with DSSP or STRIDE",
      "topics": [
        "dssp",
        "dssp.pdb",
        "dssp.pdbs",
        "dssp.xyz",
        "print.sse",
        "stride"
      ]
    },
    {
      "page": "elements",
      "title": "Periodic Table of the Elements",
      "topics": [
        "elements"
      ]
    },
    {
      "page": "entropy",
      "title": "Shannon Entropy Score",
      "topics": [
        "entropy"
      ]
    },
    {
      "page": "example.data",
      "title": "Bio3d Example Data",
      "topics": [
        "annotation",
        "core",
        "example.data",
        "hivp",
        "kinesin",
        "pdbs",
        "transducin"
      ]
    },
    {
      "page": "filter.cmap",
      "title": "Contact Map Consensus Filtering",
      "topics": [
        "filter.cmap"
      ]
    },
    {
      "page": "filter.dccm",
      "title": "Filter for Cross-correlation Matrices (Cij)",
      "topics": [
        "filter.dccm"
      ]
    },
    {
      "page": "filter.identity",
      "title": "Percent Identity Filter",
      "topics": [
        "filter.identity"
      ]
    },
    {
      "page": "filter.rmsd",
      "title": "RMSD Filter",
      "topics": [
        "filter.rmsd"
      ]
    },
    {
      "page": "fit.xyz",
      "title": "Coordinate Superposition",
      "topics": [
        "fit.xyz",
        "rot.lsq"
      ]
    },
    {
      "page": "fluct.nma",
      "title": "NMA Fluctuations",
      "topics": [
        "fluct.nma"
      ]
    },
    {
      "page": "formula2mass",
      "title": "Chemical Formula to Mass Converter",
      "topics": [
        "formula2mass"
      ]
    },
    {
      "page": "gap.inspect",
      "title": "Alignment Gap Summary",
      "topics": [
        "gap.inspect"
      ]
    },
    {
      "page": "geostas",
      "title": "GeoStaS Domain Finder",
      "topics": [
        "amsm.xyz",
        "geostas",
        "geostas.default",
        "geostas.enma",
        "geostas.nma",
        "geostas.pdb",
        "geostas.pdbs",
        "geostas.xyz",
        "print.geostas"
      ]
    },
    {
      "page": "get.pdb",
      "title": "Download PDB Coordinate Files",
      "topics": [
        "get.pdb"
      ]
    },
    {
      "page": "get.seq",
      "title": "Download FASTA Sequence Files",
      "topics": [
        "get.seq"
      ]
    },
    {
      "page": "gnm",
      "title": "Gaussian Network Model",
      "topics": [
        "gnm",
        "gnm.pdb",
        "gnm.pdbs"
      ]
    },
    {
      "page": "hclustplot",
      "title": "Dendrogram with Clustering Annotation",
      "topics": [
        "hclustplot"
      ]
    },
    {
      "page": "hmmer",
      "title": "HMMER Sequence Search",
      "topics": [
        "hmmer"
      ]
    },
    {
      "page": "identify.cna",
      "title": "Identify Points in a CNA Protein Structure Network Plot",
      "topics": [
        "identify.cna"
      ]
    },
    {
      "page": "inner.prod",
      "title": "Mass-weighted Inner Product",
      "topics": [
        "inner.prod"
      ]
    },
    {
      "page": "inspect.connectivity",
      "title": "Check the Connectivity of Protein Structures",
      "topics": [
        "inspect.connectivity"
      ]
    },
    {
      "page": "is.gap",
      "title": "Gap Characters",
      "topics": [
        "is.gap"
      ]
    },
    {
      "page": "is.mol2",
      "title": "Is an Object of Class 'mol2'?",
      "topics": [
        "is.mol2"
      ]
    },
    {
      "page": "is.pdb",
      "title": "Is an Object of Class 'pdb(s)'?",
      "topics": [
        "is.pdb",
        "is.pdbs"
      ]
    },
    {
      "page": "is.select",
      "title": "Is an Object of Class 'select'?",
      "topics": [
        "is.select"
      ]
    },
    {
      "page": "is.xyz",
      "title": "Is an Object of Class 'xyz'?",
      "topics": [
        "as.xyz",
        "is.xyz"
      ]
    },
    {
      "page": "layout.cna",
      "title": "Protein Structure Network Layout",
      "topics": [
        "layout.cna"
      ]
    },
    {
      "page": "lbio3d",
      "title": "List all Functions in the bio3d Package",
      "topics": [
        "lbio3d"
      ]
    },
    {
      "page": "load.enmff",
      "title": "ENM Force Field Loader",
      "topics": [
        "ff.aaenm",
        "ff.aaenm2",
        "ff.anm",
        "ff.calpha",
        "ff.pfanm",
        "ff.reach",
        "ff.sdenm",
        "load.enmff"
      ]
    },
    {
      "page": "mask.dccm",
      "title": "Mask a Subset of Atoms in a DCCM Object.",
      "topics": [
        "mask",
        "mask.dccm"
      ]
    },
    {
      "page": "mktrj",
      "title": "PCA / NMA Atomic Displacement Trajectory",
      "topics": [
        "mktrj",
        "mktrj.enma",
        "mktrj.nma",
        "mktrj.pca"
      ]
    },
    {
      "page": "motif.find",
      "title": "Find Sequence Motifs.",
      "topics": [
        "motif.find"
      ]
    },
    {
      "page": "mustang",
      "title": "Structure-based Sequence Alignment with MUSTANG",
      "topics": [
        "mustang"
      ]
    },
    {
      "page": "network.amendment",
      "title": "Amendment of a CNA Network According To A Input Community Membership Vector.",
      "topics": [
        "network.amendment"
      ]
    },
    {
      "page": "nma",
      "title": "Normal Mode Analysis",
      "topics": [
        "nma"
      ]
    },
    {
      "page": "nma.pdb",
      "title": "Normal Mode Analysis",
      "topics": [
        "build.hessian",
        "nma.pdb",
        "print.nma"
      ]
    },
    {
      "page": "nma.pdbs",
      "title": "Ensemble Normal Mode Analysis",
      "topics": [
        "nma.pdbs",
        "print.enma"
      ]
    },
    {
      "page": "normalize.vector",
      "title": "Mass-Weighted Normalized Vector",
      "topics": [
        "normalize.vector"
      ]
    },
    {
      "page": "orient.pdb",
      "title": "Orient a PDB Structure",
      "topics": [
        "orient.pdb"
      ]
    },
    {
      "page": "overlap",
      "title": "Overlap analysis",
      "topics": [
        "overlap"
      ]
    },
    {
      "page": "pairwise",
      "title": "Pair Indices",
      "topics": [
        "pairwise"
      ]
    },
    {
      "page": "pca",
      "title": "Principal Component Analysis",
      "topics": [
        "pca"
      ]
    },
    {
      "page": "pca.array",
      "title": "Principal Component Analysis of an array of matrices",
      "topics": [
        "pca.array"
      ]
    },
    {
      "page": "pca.pdbs",
      "title": "Principal Component Analysis",
      "topics": [
        "pca.pdbs"
      ]
    },
    {
      "page": "pca.tor",
      "title": "Principal Component Analysis",
      "topics": [
        "pca.tor"
      ]
    },
    {
      "page": "pca.xyz",
      "title": "Principal Component Analysis",
      "topics": [
        "pca.xyz",
        "print.pca"
      ]
    },
    {
      "page": "pdb.annotate",
      "title": "Get Customizable Annotations From PDB Or PFAM Databases",
      "topics": [
        "pdb.annotate",
        "pdb.pfam"
      ]
    },
    {
      "page": "pdb2aln",
      "title": "Align a PDB structure to an existing alignment",
      "topics": [
        "pdb2aln"
      ]
    },
    {
      "page": "pdb2aln.ind",
      "title": "Mapping from alignment positions to PDB atomic indices",
      "topics": [
        "pdb2aln.ind"
      ]
    },
    {
      "page": "pdb2sse",
      "title": "Obtain An SSE Sequence Vector From A PDB Object",
      "topics": [
        "pdb2sse"
      ]
    },
    {
      "page": "pdbaln",
      "title": "Sequence Alignment of PDB Files",
      "topics": [
        "pdbaln"
      ]
    },
    {
      "page": "pdbfit",
      "title": "PDB File Coordinate Superposition",
      "topics": [
        "pdbfit",
        "pdbfit.pdb",
        "pdbfit.pdbs"
      ]
    },
    {
      "page": "pdbs2pdb",
      "title": "PDBs to PDB Converter",
      "topics": [
        "pdbs2pdb"
      ]
    },
    {
      "page": "pdbs2sse",
      "title": "SSE annotation for a PDBs Object",
      "topics": [
        "pdbs2sse"
      ]
    },
    {
      "page": "pdbseq",
      "title": "Extract The Aminoacid Sequence From A PDB Object",
      "topics": [
        "pdbseq"
      ]
    },
    {
      "page": "pdbsplit",
      "title": "Split a PDB File Into Separate Files, One For Each Chain.",
      "topics": [
        "pdbsplit"
      ]
    },
    {
      "page": "pfam",
      "title": "Download Pfam FASTA Sequence Alignment",
      "topics": [
        "pfam"
      ]
    },
    {
      "page": "plot.bio3d",
      "title": "Plots with marginal SSE annotation",
      "topics": [
        "plot.bio3d",
        "plotb3"
      ]
    },
    {
      "page": "plot.cmap",
      "title": "Plot Contact Matrix",
      "topics": [
        "plot.cmap"
      ]
    },
    {
      "page": "plot.cna",
      "title": "Protein Structure Network Plots in 2D and 3D.",
      "topics": [
        "plot.cna",
        "plot.ecna"
      ]
    },
    {
      "page": "plot.core",
      "title": "Plot Core Fitting Progress",
      "topics": [
        "plot.core"
      ]
    },
    {
      "page": "plot.dccm",
      "title": "DCCM Plot",
      "topics": [
        "plot.dccm"
      ]
    },
    {
      "page": "plot.dmat",
      "title": "Plot Distance Matrix",
      "topics": [
        "plot.dmat"
      ]
    },
    {
      "page": "plot.enma",
      "title": "Plot eNMA Results",
      "topics": [
        "plot.enma"
      ]
    },
    {
      "page": "plot.fasta",
      "title": "Plot a Multiple Sequence Alignment",
      "topics": [
        "plot.fasta"
      ]
    },
    {
      "page": "plot.fluct",
      "title": "Plot Fluctuations",
      "topics": [
        "plot.fluct"
      ]
    },
    {
      "page": "plot.geostas",
      "title": "Plot Geostas Results",
      "topics": [
        "plot.geostas"
      ]
    },
    {
      "page": "plot.hmmer",
      "title": "Plot a Summary of HMMER Hit Statistics.",
      "topics": [
        "plot.hmmer"
      ]
    },
    {
      "page": "plot.matrix.loadings",
      "title": "Plot Residue-Residue Matrix Loadings",
      "topics": [
        "plot.matrix.loadings"
      ]
    },
    {
      "page": "plot.nma",
      "title": "Plot NMA Results",
      "topics": [
        "plot.nma"
      ]
    },
    {
      "page": "plot.pca",
      "title": "Plot PCA Results",
      "topics": [
        "plot.pca",
        "plot.pca.score",
        "plot.pca.scree"
      ]
    },
    {
      "page": "plot.pca.loadings",
      "title": "Plot Residue Loadings along PC1 to PC3",
      "topics": [
        "plot.pca.loadings"
      ]
    },
    {
      "page": "plot.rmsip",
      "title": "Plot RMSIP Results",
      "topics": [
        "plot.rmsip"
      ]
    },
    {
      "page": "print.cna",
      "title": "Summarize and Print Features of a cna Network Graph",
      "topics": [
        "print.cna",
        "summary.cna"
      ]
    },
    {
      "page": "print.core",
      "title": "Printing Core Positions and Returning Indices",
      "topics": [
        "print.core"
      ]
    },
    {
      "page": "print.fasta",
      "title": "Printing Sequence Alignments",
      "topics": [
        ".print.fasta.ali",
        "print.fasta"
      ]
    },
    {
      "page": "print.xyz",
      "title": "Printing XYZ coordinates",
      "topics": [
        "print.xyz"
      ]
    },
    {
      "page": "project.pca",
      "title": "Project Data onto Principal Components",
      "topics": [
        "project.pca",
        "xyz2z.pca",
        "z2xyz.pca"
      ]
    },
    {
      "page": "prune.cna",
      "title": "Prune A cna Network Object",
      "topics": [
        "prune.cna"
      ]
    },
    {
      "page": "pymol",
      "title": "Biomolecular Visualization with PyMOL",
      "topics": [
        "pymol",
        "pymol.dccm",
        "pymol.modes",
        "pymol.nma",
        "pymol.pca",
        "pymol.pdbs"
      ]
    },
    {
      "page": "read.all",
      "title": "Read Aligned Structure Data",
      "topics": [
        "read.all"
      ]
    },
    {
      "page": "read.cif",
      "title": "Read mmCIF File",
      "topics": [
        "read.cif"
      ]
    },
    {
      "page": "read.crd",
      "title": "Read Coordinate Data from Amber or Charmm",
      "topics": [
        "read.crd"
      ]
    },
    {
      "page": "read.crd.amber",
      "title": "Read AMBER Coordinate files",
      "topics": [
        "read.crd.amber"
      ]
    },
    {
      "page": "read.crd.charmm",
      "title": "Read CRD File",
      "topics": [
        "read.crd.charmm"
      ]
    },
    {
      "page": "read.dcd",
      "title": "Read CHARMM/X-PLOR/NAMD Binary DCD files",
      "topics": [
        "read.dcd"
      ]
    },
    {
      "page": "read.fasta",
      "title": "Read FASTA formated Sequences",
      "topics": [
        "read.fasta"
      ]
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