The bio3d Package February 24, 2015 Title Biological Structure Analysis Version 2.2-0 Author Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide VignetteBuilder knitr Imports parallel, grid Suggests XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) Depends R (>= 3.1.0) LazyData yes Description Utilities to process, organize and explore protein structure, sequence and dynam- ics data. Features include the ability to read and write structure, sequence and dynamic trajec- tory data, perform sequence and structure database searches, data summaries, atom selec- tion, alignment, superposition, rigid core identification, clustering, torsion analysis, distance ma- trix analysis, structure and sequence conservation analysis, normal mode analysis, principal com- ponent analysis of heterogeneous structure data, and correlation network analysis from nor- mal mode and molecular dynamics data. In addition, various utility functions are provided to en- able the statistical and graphical power of the R environment to work with biological se- quence 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/, http://bitbucket.org/Grantlab/bio3d R topics documented: bio3d-package . .5 aa.index . .7 aa.table . .8 aa123 . .9 aa2index . 10 1 2 R topics documented: aa2mass . 11 aln2html . 13 angle.xyz . 14 as.fasta . 15 as.pdb . 16 as.select . 19 atom.index . 20 atom.select . 20 atom2ele . 23 atom2mass . 25 atom2xyz . 26 basename.pdb . 27 bhattacharyya . 28 binding.site . 29 biounit . 31 blast.pdb . 32 bounds . 35 bounds.sse . 36 bwr.colors . 37 cat.pdb . 38 chain.pdb . 39 check.utility . 40 clean.pdb . 41 cmap............................................. 42 cna.............................................. 44 cnapath . 47 com ............................................. 49 combine.select . 51 community.tree . 52 consensus . 54 conserv . 55 convert.pdb . 57 core.find . 59 cov.nma . 62 covsoverlap . 63 dccm............................................. 64 dccm.enma . 65 dccm.nma . 66 dccm.pca . 67 dccm.xyz . 69 deformation.nma . 71 diag.ind . 72 difference.vector . 73 dist.xyz . 74 dm.............................................. 76 dssp............................................. 78 elements . 81 entropy . 82 example.data . 84 filter.cmap . 85 filter.dccm . 86 filter.identity . 88 R topics documented: 3 filter.rmsd . 90 fit.xyz . 91 fluct.nma . 93 formula2mass . 95 gap.inspect . 95 geostas . 97 get.pdb . 101 get.seq . 102 hclustplot . 103 hmmer . 105 identify.cna . 108 inner.prod . 109 inspect.connectivity . 110 is.gap . 111 is.pdb . 113 is.select . 113 is.xyz . 114 layout.cna . 115 lbio3d . 116 lmi.............................................. 117 load.enmff . 118 mktrj . 120 motif.find . 122 mustang . 123 network.amendment . 124 nma ............................................. 126 nma.pdb . 127 nma.pdbs . 131 normalize.vector . ..