Bio3D in R

 

WhatsNew

Page history last edited by barry 2 yrs ago

Whats New

New features and bug fixes of the latest release of the bio3d package are listed here. For more general information see the package homepage and online documentation.

  1. Whats New
    1. Version 1.0-4 (May 07)
      1. Additions since last release
    2. Version 1.0-3 (Nov 06)
      1. Additions since last release
    3. Version 1.0-2
      1. Additions since last release
    4. Version 1.0-1
      1. Fist released version

Version 1.0-4 (May 07)

Additions since last release

New Functions:

Function Name:Description:
aln2htmlCreate a HTML Page For a Given Alignment
plot.bio3dPlots with marginal SSE annotation
conservScore Residue Conservation At Each Position in an Alignment
seqaln.pairPairwise Alignment of Identical Protein Sequences

 

 

The function dssp has a new input paramater (resno=TRUE) to give output in terms of residue numbers and optionaly, when FALSE, in terms of residue index (position in sequence).

The function read.fasta has been completely re-writen.

A new package manual in PDF format is available for download

 

 

Version 1.0-3 (Nov 06)

Additions since last release

New Functions:

Function Name:Description:
torsion.pdbCalculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyzCalculate Torsion/Dihedral Angles
pca.torPrincipal components analysis (PCA) on torsion angle data
pca.projectProject Data onto Principal Components
wrap.torWrap Torsion Angle Data
aa.indexAAindex: Amino Acid Index Database
aa2indexConverts sequences to aminoacid indeces from the AAindex database
angle.xyzA function for basic bound angle determination

 

 

Version 1.0-2

Additions since last release

New Functions:

Function Name:Description:
read.crdRead a CHARMM CRD Format Coordinate File
write.crdWrite a CHARMM CRD Format Coordinate File
dsspSecondary Structure Analysis with DSSP
strideSecondary Structure Analysis with STRIDE
rmsfAtomic RMS Fluctuations
seqalnSequence Alignment
ide.filterPercent Identity Filter
rmsd.filterRMSD Filter
seqbindCombine Sequences by Rows Without Recycling
unboundSequence Generation from a Bounds Vector
convert.pdbConvert between CHARMM, Amber, Gromacs and Brookhaven PDB formats
atom2xyzConvert Between atom and xyz Indices
wiki.tblWIKI Table

Version 1.0-1

Fist released version

Functions include:

Function Name:Description:
aa123Convert Between 1-letter and 3-letter Aminoacid Codes
aa321Convert Between 1-letter and 3-letter Aminoacid Codes
alnBio3d Example Data
atom.selectAtom Selection From PDB Structure
bio3dBiological Structure Analysis
bio3d-packageBiological Structure Analysis
boundsBounds of a Numeric Vector
bwr.colorsColor Palettes
consensusSequence Consensus for an Alignment
coreBio3d Example Data
core.findIdentification of Invariant Core Positions
dmDistance Matrix Analysis
entropyShannon Entropy Score
fit.xyzCoordinate Superposition
gap.inspectAlignment Gap Summary
identityPercent Identity
kinesinBio3d Example Data
lbio3dList all Functions in the bio3d Package
mktrj.pcaPCA Atomic Displacement Trajectory
mono.colorsColor Palettes
orient.pdbOrient a PDB Structure
pairwisePair Indices
pc.xrayBio3d Example Data
pca.xyzPrincipal Component Analysis
pdb.summaryAtom Selection From PDB Structure
pdbsBio3d Example Data
plot.corePlot Core Fitting Progress
plot.dmatPlot Distance Matrix
plot.pcaPlot PCA Results
plot.pca.loadingsPlot Residue Loadings along PC1 to PC3
plot.pca.scorePlot PCA Results
plot.pca.screePlot PCA Results
read.dcdRead CHARMM/X-PLOR/NAMD Binary DCD files
read.fastaRead FASTA formated Sequences
read.fasta.pdbRead Aligned Structure Data
read.pdbRead PDB File
rmsdRoot Mean Square Deviation
rot.lsqCoordinate Superposition
write.fastaWrite FASTA Formated Sequences
write.pdbWrite PDB Format Coordinate File
xyzBio3d Example Data

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