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A B C D E F G I K L M O P R S T U V W X
| bio3d-package | Biological Structure Analysis |
| aa.index | AAindex: Amino Acid Index Database |
| aa123 | Convert Between 1-letter and 3-letter Aminoacid Codes |
| aa2index | Convert an Aminoacid Sequence to AAIndex Values |
| aa321 | Convert Between 1-letter and 3-letter Aminoacid Codes |
| aln | Bio3d Example Data |
| aln2html | Create a HTML Page For a Given Alignment |
| angle.xyz | Calculate the Angle Between Three Atoms |
| atom.select | Atom Selection From PDB Structure |
| atom2xyz | Convert Between Atom and xyz Indices |
| bio3d | Biological Structure Analysis |
| blast.pdb | NCBI BLAST Sequence Search |
| bounds | Bounds of a Numeric Vector |
| bwr.colors | Color Palettes |
| chain.pdb | Find Possible PDB Chain Breaks |
| cmap | Contact Map |
| consensus | Sequence Consensus for an Alignment |
| conserv | Score Residue Conservation At Each Position in an Alignment |
| convert.pdb | Convert Between Various PDB formats |
| core | Bio3d Example Data |
| core.find | Identification of Invariant Core Positions |
| dccm | DCCM: Dynamical Cross-Correlation Matrix |
| 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 |
| dm.xyz | Distance Matrix Analysis |
| dssp | Secondary Structure Analysis with DSSP |
| entropy | Shannon Entropy Score |
| fit.xyz | Coordinate Superposition |
| gap.inspect | Alignment Gap Summary |
| get.pdb | Download PDB Coordinate Files |
| get.seq | Download FASTA Sequence Files |
| ide.filter | Percent Identity Filter |
| identity | Percent Identity |
| is.gap | Gap Characters |
| kinesin | Bio3d Example Data |
| lbio3d | List all Functions in the bio3d Package |
| mktrj.pca | PCA Atomic Displacement Trajectory |
| mono.colors | Color Palettes |
| motif.find | Find Sequence Motifs. |
| orient.pdb | Orient a PDB Structure |
| overlap | Overlap analysis |
| pairwise | Pair Indices |
| pc.xray | Bio3d Example Data |
| pca.project | Project Data onto Principal Components |
| pca.tor | Principal Component Analysis |
| pca.xyz | Principal Component Analysis |
| pca.xyz2z | Project Data onto Principal Components |
| pca.z2xyz | Project Data onto Principal Components |
| pdb.summary | Atom Selection From PDB Structure |
| pdbaln | Sequence Alignment of PDB Files |
| pdbs | Bio3d Example Data |
| plot.bio3d | Plots with marginal SSE annotation |
| plot.blast | Plot a Summary of BLAST Hit Statistics. |
| plot.core | Plot Core Fitting Progress |
| plot.dccm | DCCM Plot |
| 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 |
| print.core | Printing Core Positions and Returning Indices |
| print.pdb | Read PDB File |
| print.rle2 | Run Length Encoding with Indices |
| read.all | Read Aligned Structure Data |
| read.crd | 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.ncdf | Read AMBER Binary netCDF files |
| read.pdb | Read PDB File |
| read.pdcBD | Read PQR output from pdcBD File |
| read.pqr | Read PQR File |
| rle2 | Run Length Encoding with Indices |
| rmsd | Root Mean Square Deviation |
| rmsd.filter | RMSD Filter |
| rmsf | Atomic RMS Fluctuations |
| rmsip | Root Mean Square Inner Product |
| rot.lsq | Coordinate Superposition |
| seq.pdb | Extract The Aminoacid Sequence From A PDB Object |
| 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 |
| split.pdb | Split a PDB File Into Separate Files, One For Each Chain. |
| sse | Bio3d Example Data |
| store.atom | Store all-atom data from a PDB object |
| stride | Secondary Structure Analysis with STRIDE |
| torsion.pdb | Calculate Mainchain and Sidechain Torsion/Dihedral Angles |
| torsion.xyz | Calculate Torsion/Dihedral Angles |
| trim.pdb | Trim a PDB Object To A Subset of Atoms. |
| unbound | Sequence Generation from a Bounds Vector |
| vec2resno | Replicate Per-residue Vector Values |
| wiki.tbl | Wiki Table |
| wrap.tor | Wrap Torsion Angle Data |
| write.crd | Write CRD File |
| write.fasta | Write FASTA Formated Sequences |
| write.ncdf | Write AMBER Binary netCDF files |
| write.pdb | Write PDB Format Coordinate File |
| write.pqr | Write PQR Format Coordinate File |
| xyz | Bio3d Example Data |