bio

Biological data formats and tool output parsers for Golang.

PDB tikz/bio/pdb

https://pkg.go.dev/github.com/tikz/bio/pdb

Fetches and parses PDB files, using the Model/Chain/Residue/Atom architecture.

UniProt tikz/bio/uniprot

https://pkg.go.dev/github.com/tikz/bio/uniprot

Fetches and parses UniProt TXT entries.

Conservation (Pfam) tikz/bio/conservation

https://pkg.go.dev/github.com/tikz/bio/conservation

Fetches a given HMM model from Pfam, aligns it against the given sequence to get the conservation bitscore of each residue.

FoldX tikz/bio/foldx

https://pkg.go.dev/github.com/tikz/bio/foldx

A wrapper for running and parsing FoldX RepairPDB and BuildModel commands.

ClinVar tikz/bio/clinvar

https://pkg.go.dev/github.com/tikz/bio/clinvar

Fetches and loads the summary of all ClinVar variants to query against it.

Interaction tikz/bio/interaction

https://pkg.go.dev/github.com/tikz/bio/interaction

Get all residues that are near het groups or water molecules given a distance threshold from a loaded PDB.

SASA tikz/bio/sasa

https://pkg.go.dev/github.com/tikz/bio/sasa

Parses FreeSASA command line output ran on a single structure.

Fpocket tikz/bio/fpocket

https://pkg.go.dev/github.com/tikz/bio/fpocket

A wrapper for running Fpocket and parsing the resulting residues marked as pockets.

DSSP tikz/bio/dssp

https://pkg.go.dev/github.com/tikz/bio/dssp

A wrapper for running DSSP and parsing the assigned secondary structure to residues.

Tango tikz/bio/tango

https://pkg.go.dev/github.com/tikz/bio/tango

Runner and parser for the Tango tool output.

abSwitch tikz/bio/abswitch

https://pkg.go.dev/github.com/tikz/bio/abswitch

Runner and parser for the abSwitch tool output.