Man pages for bio3d
Biological Structure Analysis
| 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 |
| aa.index | AAindex: Amino Acid Index Database |
| aanma.pdb | All Atom Normal Mode Analysis |
| aanma.pdbs | Ensemble Normal Mode Analysis with All-Atom ENM |
| aa.table | Table of Relevant Amino Acids |
| 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 |
| atom2ele | Atom Names/Types to Atomic Symbols Converter |
| atom2mass | Atom Names/Types to Mass Converter |
| atom2xyz | Convert Between Atom and xyz Indices |
| atom.index | Atom Names/Types |
| atom.select | Atom Selection from PDB and PRMTOP Structure Objects |
| 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... |
| 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... |
| 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.cmap | Identification of Contact Map Core Positions |
| 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 | Dynamical Cross-Correlation Matrix from Principal Component... |
| dccm.xyz | Dynamical Cross-Correlation Matrix from Cartesian Coordinates |
| 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 |
| load.enmff | ENM Force Field Loader |
| mask.dccm | 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... |
| 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 |
| 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 |
| pdb.annotate | Get Customizable Annotations From PDB Or PFAM Databases |
| 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.mol2 | Trim a MOL2 Object To A Subset of Atoms. |
| trim.pdb | Trim a PDB 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.cna | 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 |
