Version 2.0, released in Nov 2013, contains over 30 new functions including enhanced Normal Mode Analysis facilities as well extensive improvements to existing code and documentation. For a fine-grained list of changes or to report a bug, please consult:
Major new functions include:
- aa2mass: Amino Acid Residues to Mass Converter
- atom.index: Index of Atomic Masses
- atom2mass(atom2ele, formula2mass): Atom Names to Mass Converter
- binding.site: Binding Site Residues
- com(com.xyz): Center of Mass
- combine.sel: Combine Atom Selections From PDB Structure
- dccm.enma: Cross-Correlation for Ensemble NMA (eNMA)
- dccm.mean: Filter DCCM matrices
- dccm.nma: Dynamic Cross-Correlation from Normal Modes Analysis
- dccm.xyz: DCCM: Dynamical Cross-Correlation Matrix
- deformation.nma: Deformation Analysis
- dssp.trj: Secondary Structure Analysis of Trajectories with DSSP
- fluct.nma: NMA Fluctuations
- inner.prod: Mass-weighted Inner Product
- is.pdb: Is an Object of Class pdb
- is.select: Is an Object of Class atom.select
- load.enmff(ff.calpha, ff.calphax, ff.anm, ff.pfanm, ff.sdenm, ff.reach): ENM Force Field Loader
- mktrj.nma: NMA Atomic Displacement Trajectory
- nma(build.hessian, print.nma): Normal Mode Analysis
- nma.pdbs(print.enma): Ensemble Normal Mode Analysis
- normalize.vector: Mass-Weighted Normalized Vector
- pdb.annotate: Get Customizable Annotations From PDB
- pdb2aln: Align a PDB structure to an existing alignment
- pdb2aln.ind: Mapping between PDB atomic indices and alignment positions
- pdbfit: PDB File Coordinate Superposition
- pdbs2pdb: PDBs to PDB Converter
- plot.enma: Plot eNMA Results
- plot.nma: Plot NMA Results
- plot.rmsip: Plot RMSIP Results
- read.mol2: Read MOL2 File
- sdENM: Index for the sdENM ff
- sse.bridges: SSE Backbone Hydrogen Bonding
- struct.aln: Structure Alignment Of Two PDB Files
- view.dccm: Visualization of Dynamic Cross-Correlation
- view.modes: Vector Field Visualization of Modes
- vmd.colors: Color as in VMD Molecular Viewer