Version 2.2, released in Feb 2015, contains new facilities for sub-optimal path analysis of biomolecular correlation networks, constructing biological units, identification and tidying of malformed PDB files, and improved secondary structure annotation of ‘pdbs’ objects and various plots. We have also updated and enhanced atom selection functionality and developed a new vignette detailing PDB structure manipulation and analysis facilities. For a fine- grained list of changes, or to report a bug, please consult:
Major new functions include:
- cnapath: Suboptimal Path Analysis for Correlation Networks
- biounit: Biological Unit Construction
- clean.pdb: Inspect And Clean Up A PDB Object
- cat.pdb: Concatenate Multiple PDB Objects
- pdb2sse: Obtain An SSE Sequence Vector From A PDB Object
- bounds.sse: Obtain A SSE Object From An SSE Sequence Vector
- aa.table: Updated amino acid reference data that replaces older ‘aa.mass’
- as.fasta: Convert alignment/sequence in matrix/vector format to a FASTA object.
- as.pdb: Convert coordinate data to PDB format
- as.select: Convert atomic indices to a atom.select object
- as.xyz: Convert vectors and matrices to ‘xyz’ class objects
- atom.select.pdb: Atom selection from PDB objects has been extensively updated
- basename.pdb: Utility for manipulation of PDB file names
- check.utility: Check and Report on Missing Bio3D Utility Programs
- cmapt: Update contact map methods for pdb and xyz objects
- cna: Update correlation network analysis methods for dccm and ensmb objects"
- cnapath: Suboptimal Path Analysis for Correlation Networks
- com: Updated center of mass methods for pdb and xyz objects
- combine.select: Combine atom.select objects, renamed from previous ‘combine.sel’
- cov.enma: New method to Calculate Covariance Matrix from Ensemble Normal Modes"
- cov2dccm: Calculates the N-by-N cross-correlation matrix from a 3N-by-3N covariance matrix
- covsoverlap: New methods for nma and enma objects
- dm: Distance matrix gets new methods for pdb and xyz class objects
- dssp: Secondary Structure Analysis with DSSP gets new methods for pdb, xyz and pdbs class objects
- geostas: Geometrically stable domain finder gets new methods for nma, enma, pdb, pdbs and xyz objects.
- is.pdbs: Is an Object of Class pdbs
- mono.colors: New color palette
- pdb2sse: Obtain An SSE Sequence Vector From A PDB Object
- pdbfit: Coordinate superposition gets new methods for multi-model pdb objects and pdbs objects.
- read.crd: Can Now Read Coordinate Data from Amber or CHARMM
- read.prmtop: Read AMBER Parameter/Topology files
- var.pdbs: Pairwise Distance Variance in Cartesian Coordinates
- plot: New or updated plot methods for ‘cmap’, ‘geostas’, and ‘pca’ class objects as well as a new plot.fluct() function that expands on plot.bio3d() for plotting atomic fluctuations from MD and NMA results.
- print: New print methods for cnapath, enma, geostas, mol2, nma, pca, pdb, prmtop, rle2, select and sse objects.