Function reference • Bio3D

Input/Output Read and Write Common Biomolecular Data Types
`read.pdb()` `read.pdb2()` `print(<pdb>)` `summary(<pdb>)`	Read PDB File
`read.fasta()`	Read FASTA formated Sequences
`read.fasta.pdb()`	Read Aligned Structure Data
`read.ncdf()`	Read AMBER Binary netCDF files
`read.dcd()`	Read CHARMM/X-PLOR/NAMD Binary DCD files
`read.crd()`	Read Coordinate Data from Amber or Charmm
`read.pqr()`	Read PQR File
`read.mol2()` `print(<mol2>)`	Read MOL2 File
`read.all()`	Read Aligned Structure Data
`read.pdcBD()`	Read PQR output from pdcBD File
`read.cif()`	Read mmCIF File
`read.crd(<amber>)`	Read AMBER Coordinate files
`read.crd(<charmm>)`	Read CRD File
`read.prmtop()` `print(<prmtop>)`	Read AMBER Parameter/Topology files
`aln2html()`	Create a HTML Page For a Given Alignment
`get.pdb()`	Download PDB Coordinate Files
`get.seq()`	Download FASTA Sequence Files
`load.enmff()` `ff.calpha()` `ff.anm()` `ff.pfanm()` `ff.sdenm()` `ff.reach()` `ff.aaenm()` `ff.aaenm2()`	ENM Force Field Loader
`write.pdb()`	Write PDB Format Coordinate File
`write.crd()`	Write CRD File
`write.fasta()`	Write FASTA Formated Sequences
`write.ncdf()`	Write AMBER Binary netCDF files
`write.pqr()`	Write PQR Format Coordinate File
`write.pir()`	Write PIR Formated Sequences
`write.mol2()`	Write MOL2 Format Coordinate File
`mktrj()`	PCA / NMA Atomic Displacement Trajectory
`pymol()`	Biomolecular Visualization with PyMOL
`vmd()`	View CNA Protein Structure Network Community Output in VMD
Sequence Analysis Do Interesting Things with Protein Sequence
`consensus()`	Sequence Consensus for an Alignment
`conserv()`	Score Residue Conservation At Each Position in an Alignment
`blast.pdb()` `get.blast()` `plot(<blast>)`	NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
`hmmer()`	HMMER Sequence Search
`pfam()`	Download Pfam FASTA Sequence Alignment
`uniprot()`	Fetch UniProt Entry Data.
`entropy()`	Shannon Entropy Score
`filter.identity()`	Percent Identity Filter
`seqidentity()`	Percent Identity
`motif.find()`	Find Sequence Motifs.
`pdbaln()`	Sequence Alignment of PDB Files
`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
Structure Analysis Do Interesting Things with Protein Structure
`angle.xyz()`	Calculate the Angle Between Three Atoms
`biounit()`	Biological Units Construction
`blast.pdb()` `get.blast()` `plot(<blast>)`	NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
`atom.select()` `print(<select>)`	Atom Selection from PDB and PRMTOP Structure Objects
`combine.select()`	Combine Atom Selections From PDB Structure
`cmap()`	Contact Map
`filter.cmap()`	Contact Map Consensus Filtering
`core.find()`	Identification of Invariant Core Positions
`core.cmap()`	Identification of Contact Map Core Positions
`com()`	Center of Mass
`dccm()`	DCCM: Dynamical Cross-Correlation Matrix
`filter.dccm()`	Filter for Cross-correlation Matrices (Cij)
`dist.xyz()`	Calculate the Distances Between the Rows of Two Matrices
`dm()`	Distance Matrix Analysis
`dssp()` `stride()` `print(<sse>)`	Secondary Structure Analysis with DSSP or STRIDE
`geostas()` `amsm.xyz()` `print(<geostas>)`	GeoStaS Domain Finder
`mustang()`	Structure-based Sequence Alignment with MUSTANG
`fit.xyz()` `rot.lsq()`	Coordinate Superposition
`binding.site()`	Binding Site Residues
`mktrj()`	PCA / NMA Atomic Displacement Trajectory
`overlap()`	Overlap analysis
`pca()`	Principal Component Analysis
`pca(<xyz>)` `print(<pca>)`	Principal Component Analysis
`pca(<pdbs>)`	Principal Component Analysis
`pca(<array>)`	Principal Component Analysis of an array of matrices
`pca(<tor>)`	Principal Component Analysis
`dccm(<pca>)`	Dynamical Cross-Correlation Matrix from Principal Component Analysis
`project.pca()` `z2xyz.pca()` `xyz2z.pca()`	Project Data onto Principal Components
`pdbaln()`	Sequence Alignment of PDB Files
`pdb.annotate()` `pdb.pfam()`	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
`pdbs2sse()`	SSE annotation for a PDBs Object
`pdbfit()`	PDB File Coordinate Superposition
`chain.pdb()`	Find Possible PDB Chain Breaks
`convert.pdb()`	Renumber and Convert Between Various PDB formats
`rgyr()`	Radius of Gyration
`rmsd()`	Root Mean Square Deviation
`filter.rmsd()`	RMSD Filter
`rmsf()`	Atomic RMS Fluctuations
`rmsip()`	Root Mean Square Inner Product
`struct.aln()`	Structure Alignment Of Two PDB Files
`torsion.pdb()`	Calculate Mainchain and Sidechain Torsion/Dihedral Angles
`torsion.xyz()`	Calculate Torsion/Dihedral Angles
`wrap.tor()`	Wrap Torsion Angle Data
`aa2mass()`	Amino Acid Residues to Mass Converter
`aa.table`	Table of Relevant Amino Acids
`atom.index`	Atom Names/Types
`atom2mass()`	Atom Names/Types to Mass Converter
`atom2ele()`	Atom Names/Types to Atomic Symbols Converter
`cov(<nma>)` `cov(<enma>)`	Calculate Covariance Matrix from Normal Modes
`dccm(<enma>)`	Cross-Correlation for Ensemble NMA (eNMA)
`dccm(<nma>)`	Dynamic Cross-Correlation from Normal Modes Analysis
`dccm(<xyz>)`	Dynamical Cross-Correlation Matrix from Cartesian Coordinates
`deformation.nma()`	Deformation Analysis
`fluct.nma()`	NMA Fluctuations
`inner.prod()`	Mass-weighted Inner Product
`load.enmff()` `ff.calpha()` `ff.anm()` `ff.pfanm()` `ff.sdenm()` `ff.reach()` `ff.aaenm()` `ff.aaenm2()`	ENM Force Field Loader
`nma()`	Normal Mode Analysis
`nma(<pdb>)` `build.hessian()` `print(<nma>)`	Normal Mode Analysis
`nma(<pdbs>)` `print(<enma>)`	Ensemble Normal Mode Analysis
`normalize.vector()`	Mass-Weighted Normalized Vector
`pdbs2pdb()`	PDBs to PDB Converter
`plot(<enma>)`	Plot eNMA Results
`plot(<nma>)`	Plot NMA Results
`plot(<rmsip>)`	Plot RMSIP Results
`sdENM`	Index for the sdENM ff
`sse.bridges()`	SSE Backbone Hydrogen Bonding
`var.xyz()` `var.pdbs()`	Pairwise Distance Variance in Cartesian Coordinates
`inspect.connectivity()`	Check the Connectivity of Protein Structures
Trajectory Analysis Do Interesting Things with Simulation Data
`angle.xyz()`	Calculate the Angle Between Three Atoms
`cmap()`	Contact Map
`filter.cmap()`	Contact Map Consensus Filtering
`core.find()`	Identification of Invariant Core Positions
`dccm()`	DCCM: Dynamical Cross-Correlation Matrix
`dccm(<pca>)`	Dynamical Cross-Correlation Matrix from Principal Component Analysis
`filter.dccm()`	Filter for Cross-correlation Matrices (Cij)
`dist.xyz()`	Calculate the Distances Between the Rows of Two Matrices
`dm()`	Distance Matrix Analysis
`dssp()` `stride()` `print(<sse>)`	Secondary Structure Analysis with DSSP or STRIDE
`geostas()` `amsm.xyz()` `print(<geostas>)`	GeoStaS Domain Finder
`fit.xyz()` `rot.lsq()`	Coordinate Superposition
`mktrj()`	PCA / NMA Atomic Displacement Trajectory
`overlap()`	Overlap analysis
`project.pca()` `z2xyz.pca()` `xyz2z.pca()`	Project Data onto Principal Components
`pca(<tor>)`	Principal Component Analysis
`pca(<xyz>)` `print(<pca>)`	Principal Component Analysis
`pdbaln()`	Sequence Alignment of PDB Files
`rgyr()`	Radius of Gyration
`rmsd()`	Root Mean Square Deviation
`filter.rmsd()`	RMSD Filter
`rmsf()`	Atomic RMS Fluctuations
`rmsip()`	Root Mean Square Inner Product
`torsion.pdb()`	Calculate Mainchain and Sidechain Torsion/Dihedral Angles
`torsion.xyz()`	Calculate Torsion/Dihedral Angles
`wrap.tor()`	Wrap Torsion Angle Data
Normal Mode Analysis Probe Large-Scale Protein Motions
`aa2mass()`	Amino Acid Residues to Mass Converter
`aa.table`	Table of Relevant Amino Acids
`atom.index`	Atom Names/Types
`atom2mass()`	Atom Names/Types to Mass Converter
`atom2ele()`	Atom Names/Types to Atomic Symbols Converter
`bhattacharyya()`	Bhattacharyya Coefficient
`cov(<nma>)` `cov(<enma>)`	Calculate Covariance Matrix from Normal Modes
`covsoverlap()`	Covariance Overlap
`dccm(<enma>)`	Cross-Correlation for Ensemble NMA (eNMA)
`dccm(<nma>)`	Dynamic Cross-Correlation from Normal Modes Analysis
`dccm(<xyz>)`	Dynamical Cross-Correlation Matrix from Cartesian Coordinates
`deformation.nma()`	Deformation Analysis
`geostas()` `amsm.xyz()` `print(<geostas>)`	GeoStaS Domain Finder
`fluct.nma()`	NMA Fluctuations
`inner.prod()`	Mass-weighted Inner Product
`load.enmff()` `ff.calpha()` `ff.anm()` `ff.pfanm()` `ff.sdenm()` `ff.reach()` `ff.aaenm()` `ff.aaenm2()`	ENM Force Field Loader
`mktrj()`	PCA / NMA Atomic Displacement Trajectory
`nma()`	Normal Mode Analysis
`nma(<pdb>)` `build.hessian()` `print(<nma>)`	Normal Mode Analysis
`nma(<pdbs>)` `print(<enma>)`	Ensemble Normal Mode Analysis
`aanma()` `rtb()`	All Atom Normal Mode Analysis
`aanma(<pdbs>)`	Ensemble Normal Mode Analysis with All-Atom ENM
`gnm()`	Gaussian Network Model
`dccm(<gnm>)` `dccm(<egnm>)`	Dynamic Cross-Correlation from Gaussian Network Model
`normalize.vector()`	Mass-Weighted Normalized Vector
`pdbs2pdb()`	PDBs to PDB Converter
`plot(<enma>)`	Plot eNMA Results
`plot(<nma>)`	Plot NMA Results
`plot(<rmsip>)`	Plot RMSIP Results
`sdENM`	Index for the sdENM ff
`sse.bridges()`	SSE Backbone Hydrogen Bonding
`sip()`	Square Inner Product
`var.xyz()` `var.pdbs()`	Pairwise Distance Variance in Cartesian Coordinates
Correlation Network Analysis Network analysis of protein structure and dynamic coupling
`cna()`	Protein Dynamic Correlation Network Construction and Community Analysis.
`cnapath()` `summary(<cnapath>)` `print(<cnapath>)` `plot(<cnapath>)` `plot(<ecnapath>)`	Suboptimal Path Analysis for Correlation Networks
`dccm()`	DCCM: Dynamical Cross-Correlation Matrix
`filter.dccm()`	Filter for Cross-correlation Matrices (Cij)
`cmap()`	Contact Map
`community.tree()`	Reconstruction of the Girvan-Newman Community Tree for a CNA Class Object.
`network.amendment()`	Amendment of a CNA Network According To A Input Community Membership Vector.
`plot(<cna>)` `plot(<ecna>)`	Protein Structure Network Plots in 2D and 3D.
`print(<cna>)` `summary(<cna>)`	Summarize and Print Features of a cna Network Graph
`identify(<cna>)`	Identify Points in a CNA Protein Structure Network Plot
`layout.cna()`	Protein Structure Network Layout
`prune.cna()`	Prune A cna Network Object
`community.aln()`	Align communities from two or more networks
Graphics Plotting and Graphic Display
`bwr.colors()` `mono.colors()`	Color Palettes
`vmd_colors()`	VMD Color Palette
`plotb3()` `plot(<bio3d>)`	Plots with marginal SSE annotation
`blast.pdb()` `get.blast()` `plot(<blast>)`	NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
`plot(<cmap>)`	Plot Contact Matrix
`plot(<core>)`	Plot Core Fitting Progress
`plot(<dccm>)`	DCCM Plot
`plot(<dmat>)`	Plot Distance Matrix
`plot(<fluct>)`	Plot Fluctuations
`plot(<geostas>)`	Plot Geostas Results
`plot(<pca>)` `plot(<pca.scree>)` `plot(<pca.score>)`	Plot PCA Results
`plot(<pca.loadings>)`	Plot Residue Loadings along PC1 to PC3
`hclustplot()`	Dendrogram with Clustering Annotation
`plot(<cna>)` `plot(<ecna>)`	Protein Structure Network Plots in 2D and 3D.
`plot(<fasta>)`	Plot a Multiple Sequence Alignment
`plot(<hmmer>)`	Plot a Summary of HMMER Hit Statistics.
`plot(<matrix.loadings>)`	Plot Residue-Residue Matrix Loadings
Utilities Convert and Manipulate Data
`aa.index`	AAindex: Amino Acid Index Database
`aa123()` `aa321()`	Convert Between 1-letter and 3-letter Aminoacid Codes
`aa2index()`	Convert an Aminoacid Sequence to AAIndex Values
`aln2html()`	Create a HTML Page For a Given Alignment
`as.fasta()`	Alignment to FASTA object
`as.pdb()`	Convert to PDB format
`as.select()`	Convert Atomic Indices to a Select Object
`is.xyz()` `as.xyz()`	Is an Object of Class ‘xyz’?
`atom.select()` `print(<select>)`	Atom Selection from PDB and PRMTOP Structure Objects
`combine.select()`	Combine Atom Selections From PDB Structure
`atom2xyz()` `xyz2atom()`	Convert Between Atom and xyz Indices
`basename.pdb()`	Manipulate PDB File Names
`bio3d-package`	Biological Structure Analysis
`biounit()`	Biological Units Construction
`bounds()`	Bounds of a Numeric Vector
`bounds.sse()`	Obtain A SSE Object From An SSE Sequence Vector
`cat.pdb()`	Concatenate Multiple PDB Objects
`check.utility()`	Check on Missing Utility Programs
`clean.pdb()`	Inspect And Clean Up A PDB Object
`chain.pdb()`	Find Possible PDB Chain Breaks
`convert.pdb()`	Renumber and Convert Between Various PDB formats
`diag.ind()`	Diagonal Indices of a Matrix
`difference.vector()`	Difference Vector
`gap.inspect()`	Alignment Gap Summary
`blast.pdb()` `get.blast()` `plot(<blast>)`	NCBI BLAST Sequence Search and Summary Plot of Hit Statistics
`inspect.connectivity()`	Check the Connectivity of Protein Structures
`filter.identity()`	Percent Identity Filter
`is.gap()`	Gap Characters
`is.pdb()` `is.pdbs()`	Is an Object of Class ‘pdb(s)’?
`is.select()`	Is an Object of Class ‘select’?
`is.mol2()`	Is an Object of Class ‘mol2’?
`lbio3d()`	List all Functions in the bio3d Package
`mask()`	Mask a Subset of Atoms in a DCCM Object.
`orient.pdb()`	Orient a PDB Structure
`pairwise()`	Pair Indices
`plotb3()` `plot(<bio3d>)`	Plots with marginal SSE annotation
`print(<core>)`	Printing Core Positions and Returning Indices
`print(<cna>)` `summary(<cna>)`	Summarize and Print Features of a cna Network Graph
`print(<fasta>)` `.print.fasta.ali()`	Printing Sequence Alignments
`print(<xyz>)`	Printing XYZ coordinates
`cnapath()` `summary(<cnapath>)` `print(<cnapath>)` `plot(<cnapath>)` `plot(<ecnapath>)`	Suboptimal Path Analysis for Correlation Networks
`nma(<pdbs>)` `print(<enma>)`	Ensemble Normal Mode Analysis
`geostas()` `amsm.xyz()` `print(<geostas>)`	GeoStaS Domain Finder
`read.mol2()` `print(<mol2>)`	Read MOL2 File
`nma(<pdb>)` `build.hessian()` `print(<nma>)`	Normal Mode Analysis
`pca(<xyz>)` `print(<pca>)`	Principal Component Analysis
`read.pdb()` `read.pdb2()` `print(<pdb>)` `summary(<pdb>)`	Read PDB File
`read.prmtop()` `print(<prmtop>)`	Read AMBER Parameter/Topology files
`rle2()` `print(<rle2>)`	Run Length Encoding with Indices
`dssp()` `stride()` `print(<sse>)`	Secondary Structure Analysis with DSSP or STRIDE
`filter.rmsd()`	RMSD Filter
`pdbseq()`	Extract The Aminoacid Sequence From A PDB Object
`seqbind()`	Combine Sequences by Rows Without Recycling
`pdbsplit()`	Split a PDB File Into Separate Files, One For Each Chain.
`store.atom()`	Store all-atom data from a PDB object
`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
`vec2resno()`	Replicate Per-residue Vector Values
`setup.ncore()`	Setup for Running Bio3D Functions using Multiple CPU Cores
`elements`	Periodic Table of the Elements
`formula2mass()`	Chemical Formula to Mass Converter
Example Data Bio3d Example Data
`kinesin` `transducin` `hivp`	Bio3d Example Data

Reference

Input/Output

Sequence Analysis

Structure Analysis

Trajectory Analysis

Normal Mode Analysis

Correlation Network Analysis

Graphics

Utilities

Example Data