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Package ‘bio3d’ May 11, 2021 Title Biological Structure Analysis Version 2.4-2 Author Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut] VignetteBuilder knitr LinkingTo Rcpp Imports Rcpp, parallel, grid, graphics, grDevices, stats, utils Suggests XML, RCurl, lattice, ncdf4, igraph, bigmemory, knitr, rmarkdown, testthat (>= 0.9.1), httr, msa, Biostrings Depends R (>= 3.1.0) LazyData yes Description Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. Maintainer Barry Grant <[email protected]> License GPL (>= 2) URL http://thegrantlab.org/bio3d/, https://bitbucket.org/Grantlab/bio3d/ RoxygenNote 7.1.1 NeedsCompilation yes Repository CRAN Date/Publication 2021-05-11 07:02:15 UTC 1 2 R topics documented: R topics documented: bio3d-package . .6 aa.index . .7 aa.table . .9 aa123 . 10 aa2index . 11 aa2mass . 12 aanma . 14 aanma.pdbs . 17 aln2html . 19 angle.xyz . 21 as.fasta . 22 as.pdb . 23 as.select . 26 atom.index . 27 atom.select . 28 atom2ele . 31 atom2mass . 33 atom2xyz . 34 basename.pdb . 35 bhattacharyya . 36 binding.site . 38 biounit . 40 blast.pdb . 41 bounds . 44 bounds.sse . 45 bwr.colors . 46 cat.pdb . 47 chain.pdb . 48 check.utility . 50 clean.pdb . 50 cmap............................................. 52 cna.............................................. 54 cnapath . 57 com ............................................. 60 combine.select . 62 community.aln . 64 community.tree . 66 consensus . 68 conserv . 69 convert.pdb . 71 core.cmap . 73 core.find . 74 cov.nma . 78 covsoverlap . 79 dccm............................................. 80 dccm.enma . 81 R topics documented: 3 dccm.gnm . 82 dccm.nma . 84 dccm.pca . 85 dccm.xyz . 87 deformation.nma . 89 diag.ind . 91 difference.vector . 92 dist.xyz . 93 dm.............................................. 94 dssp............................................. 97 elements . 100 entropy . 101 example.data . 104 filter.cmap . 105 filter.dccm . 106 filter.identity . 108 filter.rmsd . 110 fit.xyz . 111 fluct.nma . 114 formula2mass . 115 gap.inspect . 116 geostas . 118 get.pdb . 122 get.seq . 124 gnm............................................. 125 hclustplot . 127 hmmer . 129 identify.cna . 132 inner.prod . 133 inspect.connectivity . 135 is.gap . 136 is.mol2 . 137 is.pdb . 138 is.select . 139 is.xyz . 140 layout.cna . 140 lbio3d . 142 load.enmff . ..

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