Bio3D in R

 

WhatsNew

Page history last edited by Barry Grant 3 mos 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 1.0-5 (July 09)
      1. Additions since last release
    2. Version 1.0-4 (May 07)
      1. Additions since last release
    3. Version 1.0-3 (Nov 06)
      1. Additions since last release
    4. Version 1.0-2
      1. Additions since last release
    5. Version 1.0-1
      1. Fist released version

 

Version 1.0-5 (July 09)

Additions since last release

New Functions:

 

Function Name: Description:
  C
   
   

 

 

Version 1.0-4 (May 07)

Additions since last release

New Functions:

 

Function Name: Description:
aln2html Create a HTML Page For a Given Alignment
plot.bio3d Plots with marginal SSE annotation
conserv Score Residue Conservation At Each Position in an Alignment
seqaln.pair Pairwise 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.pdb Calculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyz Calculate Torsion/Dihedral Angles
pca.tor Principal components analysis (PCA) on torsion angle data
pca.project Project Data onto Principal Components
wrap.tor Wrap Torsion Angle Data
aa.index AAindex: Amino Acid Index Database
aa2index Converts sequences to aminoacid indeces from the AAindex database
angle.xyz A function for basic bound angle determination

 

 

Version 1.0-2

Additions since last release

New Functions:

 

Function Name: Description:
read.crd Read a CHARMM CRD Format Coordinate File
write.crd Write a CHARMM CRD Format Coordinate File
dssp Secondary Structure Analysis with DSSP
stride Secondary Structure Analysis with STRIDE
rmsf Atomic RMS Fluctuations
seqaln Sequence Alignment
ide.filter Percent Identity Filter
rmsd.filter RMSD Filter
seqbind Combine Sequences by Rows Without Recycling
unbound Sequence Generation from a Bounds Vector
convert.pdb Convert between CHARMM, Amber, Gromacs and Brookhaven PDB formats
atom2xyz Convert Between atom and xyz Indices
wiki.tbl WIKI Table

 

Version 1.0-1

Fist released version

Functions include:

 

Function Name: Description:
aa123 Convert Between 1-letter and 3-letter Aminoacid Codes
aa321 Convert Between 1-letter and 3-letter Aminoacid Codes
aln Bio3d Example Data
atom.select Atom Selection From PDB Structure
bio3d Biological Structure Analysis
bio3d-package Biological Structure Analysis
bounds Bounds of a Numeric Vector
bwr.colors Color Palettes
consensus Sequence Consensus for an Alignment
core Bio3d Example Data
core.find Identification of Invariant Core Positions
dm Distance Matrix Analysis
entropy Shannon Entropy Score
fit.xyz Coordinate Superposition
gap.inspect Alignment Gap Summary
identity Percent Identity
kinesin Bio3d Example Data
lbio3d List all Functions in the bio3d Package
mktrj.pca PCA Atomic Displacement Trajectory
mono.colors Color Palettes
orient.pdb Orient a PDB Structure
pairwise Pair Indices
pc.xray Bio3d Example Data
pca.xyz Principal Component Analysis
pdb.summary Atom Selection From PDB Structure
pdbs Bio3d Example Data
plot.core Plot Core Fitting Progress
plot.dmat Plot Distance Matrix
plot.pca Plot PCA Results
plot.pca.loadings Plot Residue Loadings along PC1 to PC3
plot.pca.score Plot PCA Results
plot.pca.scree Plot PCA Results
read.dcd Read CHARMM/X-PLOR/NAMD Binary DCD files
read.fasta Read FASTA formated Sequences
read.fasta.pdb Read Aligned Structure Data
read.pdb Read PDB File
rmsd Root Mean Square Deviation
rot.lsq Coordinate Superposition
write.fasta Write FASTA Formated Sequences
write.pdb Write PDB Format Coordinate File
xyz Bio3d Example Data

 

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