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aa.table Table of Relevant Amino Acids
aa123 Convert Between 1-letter and 3-letter Aminoacid
Codes
aa2index Convert an Aminoacid Sequence to AAIndex Values
aa2mass Amino Acid Residues to Mass Converter
aanma All Atom Normal Mode Analysis
aanma.pdbs Ensemble Normal Mode Analysis with All-Atom ENM
aln2html Create a HTML Page For a Given Alignment
angle.xyz Calculate the Angle Between Three Atoms
as.fasta Alignment to FASTA object
as.pdb Convert to PDB format
as.select Convert Atomic Indices to a Select Object
atom.index Atom Names/Types
atom.select Atom Selection from PDB and PRMTOP Structure
Objects
atom2ele Atom Names/Types to Atomic Symbols Converter
atom2mass Atom Names/Types to Mass Converter
atom2xyz Convert Between Atom and xyz Indices
basename.pdb Manipulate PDB File Names
bhattacharyya Bhattacharyya Coefficient
binding.site Binding Site Residues
bio3d-package Biological Structure Analysis
biounit Biological Units Construction
blast.pdb NCBI BLAST Sequence Search and Summary Plot of
Hit Statistics
bounds Bounds of a Numeric Vector
bounds.sse Obtain A SSE Object From An SSE Sequence Vector
bwr.colors Color Palettes
cat.pdb Concatenate Multiple PDB Objects
chain.pdb Find Possible PDB Chain Breaks
check.utility Check on Missing Utility Programs
clean.pdb Inspect And Clean Up A PDB Object
cmap Contact Map
cna Protein Dynamic Correlation Network
Construction and Community Analysis.
cnapath Suboptimal Path Analysis for Correlation
Networks
com Center of Mass
combine.select Combine Atom Selections From PDB Structure
community.aln Align communities from two or more networks
community.tree Reconstruction of the Girvan-Newman Community
Tree for a CNA Class Object.
consensus Sequence Consensus for an Alignment
conserv Score Residue Conservation At Each Position in
an Alignment
convert.pdb Renumber and Convert Between Various PDB
formats
core.find Identification of Invariant Core Positions
cov.nma Calculate Covariance Matrix from Normal Modes
covsoverlap Covariance Overlap
dccm DCCM: Dynamical Cross-Correlation Matrix
dccm.enma Cross-Correlation for Ensemble NMA (eNMA)
dccm.gnm Dynamic Cross-Correlation from Gaussian Network
Model
dccm.nma Dynamic Cross-Correlation from Normal Modes
Analysis
dccm.pca Dynamic Cross-Correlation from Principal
Component Analysis
dccm.xyz DCCM: Dynamical Cross-Correlation Matrix
deformation.nma Deformation Analysis
diag.ind Diagonal Indices of a Matrix
difference.vector Difference Vector
dist.xyz Calculate the Distances Between the Rows of Two
Matrices
dm Distance Matrix Analysis
dssp Secondary Structure Analysis with DSSP or
STRIDE
elements Periodic Table of the Elements
entropy Shannon Entropy Score
example.data Bio3d Example Data
filter.cmap Contact Map Consensus Filtering
filter.dccm Filter for Cross-correlation Matrices (Cij)
filter.identity Percent Identity Filter
filter.rmsd RMSD Filter
fit.xyz Coordinate Superposition
fluct.nma NMA Fluctuations
formula2mass Chemical Formula to Mass Converter
gap.inspect Alignment Gap Summary
geostas GeoStaS Domain Finder
get.pdb Download PDB Coordinate Files
get.seq Download FASTA Sequence Files
gnm Gaussian Network Model
hclustplot Dendrogram with Clustering Annotation
hmmer HMMER Sequence Search
identify.cna Identify Points in a CNA Protein Structure
Network Plot
inner.prod Mass-weighted Inner Product
inspect.connectivity Check the Connectivity of Protein Structures
is.gap Gap Characters
is.mol2 Is an Object of Class 'mol2'?
is.pdb Is an Object of Class 'pdb(s)'?
is.select Is an Object of Class 'select'?
is.xyz Is an Object of Class 'xyz'?
layout.cna Protein Structure Network Layout
lbio3d List all Functions in the bio3d Package
lmi LMI: Linear Mutual Information Matrix
load.enmff ENM Force Field Loader
mask Mask a Subset of Atoms in a DCCM Object.
mktrj PCA / NMA Atomic Displacement Trajectory
motif.find Find Sequence Motifs.
mustang Structure-based Sequence Alignment with MUSTANG
network.amendment Amendment of a CNA Network According To A Input
Community Membership Vector.
nma Normal Mode Analysis
nma.pdb Normal Mode Analysis
nma.pdbs Ensemble Normal Mode Analysis
normalize.vector Mass-Weighted Normalized Vector
orient.pdb Orient a PDB Structure
overlap Overlap analysis
pairwise Pair Indices
pca Principal Component Analysis
pca.array Principal Component Analysis of an array of
matrices
pca.pdbs Principal Component Analysis
pca.tor Principal Component Analysis
pca.xyz Principal Component Analysis
pdb.annotate Get Customizable Annotations From PDB Or PFAM
Databases
pdb2aln Align a PDB structure to an existing alignment
pdb2aln.ind Mapping from alignment positions to PDB atomic
indices
pdb2sse Obtain An SSE Sequence Vector From A PDB Object
pdbaln Sequence Alignment of PDB Files
pdbfit PDB File Coordinate Superposition
pdbs2pdb PDBs to PDB Converter
pdbs2sse SSE annotation for a PDBs Object
pdbseq Extract The Aminoacid Sequence From A PDB
Object
pdbsplit Split a PDB File Into Separate Files, One For
Each Chain.
pfam Download Pfam FASTA Sequence Alignment
plot.bio3d Plots with marginal SSE annotation
plot.cmap Plot Contact Matrix
plot.cna Protein Structure Network Plots in 2D and 3D.
plot.core Plot Core Fitting Progress
plot.dccm DCCM Plot
plot.dmat Plot Distance Matrix
plot.enma Plot eNMA Results
plot.fasta Plot a Multiple Sequence Alignment
plot.fluct Plot Fluctuations
plot.geostas Plot Geostas Results
plot.hmmer Plot a Summary of HMMER Hit Statistics.
plot.matrix.loadings Plot Residue-Residue Matrix Loadings
plot.nma Plot NMA Results
plot.pca Plot PCA Results
plot.pca.loadings Plot Residue Loadings along PC1 to PC3
plot.rmsip Plot RMSIP Results
print.cna Summarize and Print Features of a cna Network
Graph
print.core Printing Core Positions and Returning Indices
print.fasta Printing Sequence Alignments
print.xyz Printing XYZ coordinates
project.pca Project Data onto Principal Components
prune.cna Prune A cna Network Object
pymol Biomolecular Visualization with PyMOL
read.all Read Aligned Structure Data
read.cif Read mmCIF File
read.crd Read Coordinate Data from Amber or Charmm
read.crd.amber Read AMBER Coordinate files
read.crd.charmm Read CRD File
read.dcd Read CHARMM/X-PLOR/NAMD Binary DCD files
read.fasta Read FASTA formated Sequences
read.fasta.pdb Read Aligned Structure Data
read.mol2 Read MOL2 File
read.ncdf Read AMBER Binary netCDF files
read.pdb Read PDB File
read.pdcBD Read PQR output from pdcBD File
read.pqr Read PQR File
read.prmtop Read AMBER Parameter/Topology files
rgyr Radius of Gyration
rle2 Run Length Encoding with Indices
rmsd Root Mean Square Deviation
rmsf Atomic RMS Fluctuations
rmsip Root Mean Square Inner Product
sdENM Index for the sdENM ff
seq2aln Add a Sequence to an Existing Alignmnet
seqaln Sequence Alignment with MUSCLE
seqaln.pair Sequence Alignment of Identical Protein
Sequences
seqbind Combine Sequences by Rows Without Recycling
seqidentity Percent Identity
setup.ncore Setup for Running Bio3D Functions using
Multiple CPU Cores
sip Square Inner Product
sse.bridges SSE Backbone Hydrogen Bonding
store.atom Store all-atom data from a PDB object
struct.aln Structure Alignment Of Two PDB Files
torsion.pdb Calculate Mainchain and Sidechain
Torsion/Dihedral Angles
torsion.xyz Calculate Torsion/Dihedral Angles
trim Trim a PDB Object To A Subset of Atoms.
trim.mol2 Trim a MOL2 Object To A Subset of Atoms.
trim.pdbs Filter or Trim a PDBs Object
trim.xyz Trim a XYZ Object of Cartesian Coordinates.
unbound Sequence Generation from a Bounds Vector
uniprot Fetch UniProt Entry Data.
var.xyz Pairwise Distance Variance in Cartesian
Coordinates
vec2resno Replicate Per-residue Vector Values
vmd View CNA Protein Structure Network Community
Output in VMD
vmd_colors VMD Color Palette
wrap.tor Wrap Torsion Angle Data
write.crd Write CRD File
write.fasta Write FASTA Formated Sequences
write.mol2 Write MOL2 Format Coordinate File
write.ncdf Write AMBER Binary netCDF files
write.pdb Write PDB Format Coordinate File
write.pir Write PIR Formated Sequences
write.pqr Write PQR Format Coordinate File
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