Entry: aa.index
Aliases: aa.index
Keywords: datasets
Description: AAindex: Amino Acid Index Database
URL: ../../../library/bio3d/html/aa.index.html

Entry: aa123
Aliases: aa123 aa321
Keywords: utilities
Description: Convert Between 1-letter and 3-letter Aminoacid Codes
URL: ../../../library/bio3d/html/aa123.html

Entry: aa2index
Aliases: aa2index
Keywords: utilities
Description: Convert an Aminoacid Sequence to AAIndex Values
URL: ../../../library/bio3d/html/aa2index.html

Entry: aln2html
Aliases: aln2html
Keywords: IO
Description: Create a HTML Page For a Given Alignment
URL: ../../../library/bio3d/html/aln2html.html

Entry: angle.xyz
Aliases: angle.xyz
Keywords: utilities
Description: Calculate the Angle Between Three Atoms
URL: ../../../library/bio3d/html/angle.xyz.html

Entry: atom.select
Aliases: atom.select pdb.summary
Keywords: utilities
Description: Atom Selection From PDB Structure
URL: ../../../library/bio3d/html/atom.select.html

Entry: atom2xyz
Aliases: atom2xyz
Keywords: utilities
Description: Convert Between Atom and xyz Indices
URL: ../../../library/bio3d/html/atom2xyz.html

Entry: bio3d-package
Aliases: bio3d-package bio3d
Keywords: documentation
Description: Biological Structure Analysis
URL: ../../../library/bio3d/html/bio3d.package.html

Entry: blast.pdb
Aliases: blast.pdb
Keywords: utilities
Description: NCBI BLAST Sequence Search
URL: ../../../library/bio3d/html/blast.pdb.html

Entry: bounds
Aliases: bounds
Keywords: utilities
Description: Bounds of a Numeric Vector
URL: ../../../library/bio3d/html/bounds.html

Entry: bwr.colors
Aliases: bwr.colors mono.colors
Keywords: utilities
Description: Color Palettes
URL: ../../../library/bio3d/html/bwr.colors.html

Entry: chain.pdb
Aliases: chain.pdb
Keywords: utilities
Description: Find Possible PDB Chain Breaks
URL: ../../../library/bio3d/html/chain.pdb.html

Entry: cmap
Aliases: cmap
Keywords: utilities
Description: Contact Map
URL: ../../../library/bio3d/html/cmap.html

Entry: consensus
Aliases: consensus
Keywords: utilities
Description: Sequence Consensus for an Alignment
URL: ../../../library/bio3d/html/consensus.html

Entry: conserv
Aliases: conserv
Keywords: utilities
Description: Score Residue Conservation At Each Position in an Alignment
URL: ../../../library/bio3d/html/conserv.html

Entry: convert.pdb
Aliases: convert.pdb
Keywords: utilities
Description: Convert Between Various PDB formats
URL: ../../../library/bio3d/html/convert.pdb.html

Entry: core.find
Aliases: core.find
Keywords: utilities
Description: Identification of Invariant Core Positions
URL: ../../../library/bio3d/html/core.find.html

Entry: dccm
Aliases: dccm
Keywords: utilities
Description: DCCM: Dynamical Cross-Correlation Matrix
URL: ../../../library/bio3d/html/dccm.html

Entry: diag.ind
Aliases: diag.ind
Keywords: utilities
Description: Diagonal Indices of a Matrix
URL: ../../../library/bio3d/html/diag.ind.html

Entry: dist.xyz
Aliases: dist.xyz
Keywords: utilities
Description: Calculate the Distances Between the Rows of Two Matrices
URL: ../../../library/bio3d/html/dist.xyz.html

Entry: dm
Aliases: dm dm.xyz
Keywords: utilities
Description: Distance Matrix Analysis
URL: ../../../library/bio3d/html/dm.html

Entry: dssp
Aliases: dssp
Keywords: utilities
Description: Secondary Structure Analysis with DSSP
URL: ../../../library/bio3d/html/dssp.html

Entry: entropy
Aliases: entropy
Keywords: utilities
Description: Shannon Entropy Score
URL: ../../../library/bio3d/html/entropy.html

Entry: fit.xyz
Aliases: fit.xyz rot.lsq
Keywords: utilities
Description: Coordinate Superposition
URL: ../../../library/bio3d/html/fit.xyz.html

Entry: gap.inspect
Aliases: gap.inspect
Keywords: utilities
Description: Alignment Gap Summary
URL: ../../../library/bio3d/html/gap.inspect.html

Entry: get.pdb
Aliases: get.pdb
Keywords: utilities
Description: Download PDB Coordinate Files
URL: ../../../library/bio3d/html/get.pdb.html

Entry: get.seq
Aliases: get.seq
Keywords: IO utilities
Description: Download FASTA Sequence Files
URL: ../../../library/bio3d/html/get.seq.html

Entry: ide.filter
Aliases: ide.filter
Keywords: utilities
Description: Percent Identity Filter
URL: ../../../library/bio3d/html/ide.filter.html

Entry: identity
Aliases: identity
Keywords: utilities
Description: Percent Identity
URL: ../../../library/bio3d/html/identity.html

Entry: is.gap
Aliases: is.gap
Keywords: utilities
Description: Gap Characters
URL: ../../../library/bio3d/html/is.gap.html

Entry: kinesin
Aliases: kinesin pdbs aln core xyz core pc.xray sse
Keywords: datasets
Description: Bio3d Example Data
URL: ../../../library/bio3d/html/kinesin.html

Entry: lbio3d
Aliases: lbio3d
Keywords: utilities
Description: List all Functions in the bio3d Package
URL: ../../../library/bio3d/html/lbio3d.html

Entry: mktrj.pca
Aliases: mktrj.pca
Keywords: utilities
Description: PCA Atomic Displacement Trajectory
URL: ../../../library/bio3d/html/mktrj.pca.html

Entry: orient.pdb
Aliases: orient.pdb
Keywords: manip
Description: Orient a PDB Structure
URL: ../../../library/bio3d/html/orient.pdb.html

Entry: pairwise
Aliases: pairwise
Keywords: utilities
Description: Pair Indices
URL: ../../../library/bio3d/html/pairwise.html

Entry: pca.project
Aliases: pca.project pca.z2xyz pca.xyz2z
Keywords: utilities
Description: Project Data onto Principal Components
URL: ../../../library/bio3d/html/pca.project.html

Entry: pca.tor
Aliases: pca.tor
Keywords: utilities multivariate
Description: Principal Component Analysis
URL: ../../../library/bio3d/html/pca.tor.html

Entry: pca.xyz
Aliases: pca.xyz
Keywords: utilities multivariate
Description: Principal Component Analysis
URL: ../../../library/bio3d/html/pca.xyz.html

Entry: plot.bio3d
Aliases: plot.bio3d
Keywords: hplot
Description: Plots with marginal SSE annotation
URL: ../../../library/bio3d/html/plot.bio3d.html

Entry: plot.blast
Aliases: plot.blast
Keywords: hplot
Description: Plot BLAST Hit Statistics.
URL: ../../../library/bio3d/html/plot.blast.html

Entry: plot.core
Aliases: plot.core
Keywords: hplot
Description: Plot Core Fitting Progress
URL: ../../../library/bio3d/html/plot.core.html

Entry: plot.dmat
Aliases: plot.dmat
Keywords: hplot
Description: Plot Distance Matrix
URL: ../../../library/bio3d/html/plot.dmat.html

Entry: plot.pca
Aliases: plot.pca plot.pca.score plot.pca.scree
Keywords: hplot
Description: Plot PCA Results
URL: ../../../library/bio3d/html/plot.pca.html

Entry: plot.pca.loadings
Aliases: plot.pca.loadings
Keywords: hplot
Description: Plot Residue Loadings along PC1 to PC3
URL: ../../../library/bio3d/html/plot.pca.loadings.html

Entry: print.core
Aliases: print.core
Keywords: utilities
Description: Printing Core Positions and Returning Indices
URL: ../../../library/bio3d/html/print.core.html

Entry: read.all
Aliases: read.all
Keywords: IO
Description: Read Aligned Structure Data
URL: ../../../library/bio3d/html/read.all.html

Entry: read.crd
Aliases: read.crd
Keywords: IO
Description: Read CRD File
URL: ../../../library/bio3d/html/read.crd.html

Entry: read.dcd
Aliases: read.dcd
Keywords: IO
Description: Read CHARMM/X-PLOR/NAMD Binary DCD files
URL: ../../../library/bio3d/html/read.dcd.html

Entry: read.fasta
Aliases: read.fasta
Keywords: IO
Description: Read FASTA formated Sequences
URL: ../../../library/bio3d/html/read.fasta.html

Entry: read.fasta.pdb
Aliases: read.fasta.pdb
Keywords: IO
Description: Read Aligned Structure Data
URL: ../../../library/bio3d/html/read.fasta.pdb.html

Entry: read.ncdf
Aliases: read.ncdf
Keywords: IO
Description: Read AMBER Binary netCDF files
URL: ../../../library/bio3d/html/read.ncdf.html

Entry: read.pdb
Aliases: read.pdb
Keywords: IO
Description: Read PDB File
URL: ../../../library/bio3d/html/read.pdb.html

Entry: read.pqr
Aliases: read.pqr
Keywords: IO
Description: Read PQR File
URL: ../../../library/bio3d/html/read.pqr.html

Entry: rmsd
Aliases: rmsd
Keywords: utilities
Description: Root Mean Square Deviation
URL: ../../../library/bio3d/html/rmsd.html

Entry: rmsd.filter
Aliases: rmsd.filter
Keywords: utilities
Description: RMSD Filter
URL: ../../../library/bio3d/html/rmsd.filter.html

Entry: rmsf
Aliases: rmsf
Keywords: utilities
Description: Atomic RMS Fluctuations
URL: ../../../library/bio3d/html/rmsf.html

Entry: seq.pdb
Aliases: seq.pdb
Keywords: utilities
Description: Extract The Aminoacid Sequence From A PDB Object
URL: ../../../library/bio3d/html/seq.pdb.html

Entry: seqaln
Aliases: seqaln
Keywords: utilities
Description: Sequence Alignment with MUSCLE
URL: ../../../library/bio3d/html/seqaln.html

Entry: seqaln.pair
Aliases: seqaln.pair
Keywords: utilities
Description: Sequence Alignment of Identical Protein Sequences
URL: ../../../library/bio3d/html/seqaln.pair.html

Entry: seqbind
Aliases: seqbind
Keywords: utilities
Description: Combine Sequences by Rows Without Recycling
URL: ../../../library/bio3d/html/seqbind.html

Entry: split.pdb
Aliases: split.pdb
Keywords: utilities
Description: Split a PDB File Into Separate Files, One For Each Chain.
URL: ../../../library/bio3d/html/split.pdb.html

Entry: store.atom
Aliases: store.atom
Keywords: utilities
Description: Store all-atom data from a PDB object
URL: ../../../library/bio3d/html/store.atom.html

Entry: stride
Aliases: stride
Keywords: utilities
Description: Secondary Structure Analysis with STRIDE
URL: ../../../library/bio3d/html/stride.html

Entry: torsion.pdb
Aliases: torsion.pdb
Keywords: utilities
Description: Calculate Mainchain and Sidechain Torsion/Dihedral Angles
URL: ../../../library/bio3d/html/torsion.pdb.html

Entry: torsion.xyz
Aliases: torsion.xyz
Keywords: utilities
Description: Calculate Torsion/Dihedral Angles
URL: ../../../library/bio3d/html/torsion.xyz.html

Entry: trim.pdb
Aliases: trim.pdb
Keywords: utilities
Description: Trim a PDB Object To A Subset of Atoms.
URL: ../../../library/bio3d/html/trim.pdb.html

Entry: unbound
Aliases: unbound
Keywords: utilities
Description: Sequence Generation from a Bounds Vector
URL: ../../../library/bio3d/html/unbound.html

Entry: wiki.tbl
Aliases: wiki.tbl
Keywords: utilities
Description: Wiki Table
URL: ../../../library/bio3d/html/wiki.tbl.html

Entry: wrap.tor
Aliases: wrap.tor
Keywords: utilities
Description: Wrap Torsion Angle Data
URL: ../../../library/bio3d/html/wrap.tor.html

Entry: write.crd
Aliases: write.crd
Keywords: IO
Description: Write CRD File
URL: ../../../library/bio3d/html/write.crd.html

Entry: write.fasta
Aliases: write.fasta
Keywords: IO
Description: Write FASTA Formated Sequences
URL: ../../../library/bio3d/html/write.fasta.html

Entry: write.ncdf
Aliases: write.ncdf
Keywords: IO
Description: Write AMBER Binary netCDF files
URL: ../../../library/bio3d/html/write.ncdf.html

Entry: write.pdb
Aliases: write.pdb
Keywords: IO
Description: Write PDB Format Coordinate File
URL: ../../../library/bio3d/html/write.pdb.html

Entry: write.pqr
Aliases: write.pqr
Keywords: IO
Description: Write PQR Format Coordinate File
URL: ../../../library/bio3d/html/write.pqr.html
