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https://github.com/fogleman/ribbon
Ribbon diagrams of proteins in #golang.
https://github.com/fogleman/ribbon
3d biochemistry chemistry go protein protein-data-bank
Last synced: 7 days ago
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Ribbon diagrams of proteins in #golang.
- Host: GitHub
- URL: https://github.com/fogleman/ribbon
- Owner: fogleman
- License: mit
- Created: 2017-02-21T02:38:57.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2022-02-19T16:08:32.000Z (almost 3 years ago)
- Last Synced: 2024-04-17T05:17:05.505Z (10 months ago)
- Topics: 3d, biochemistry, chemistry, go, protein, protein-data-bank
- Language: Go
- Homepage:
- Size: 778 KB
- Stars: 242
- Watchers: 10
- Forks: 24
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# Protein Ribbon Diagrams
Parse PDB files and render ribbon diagrams of proteins in pure Go.
### Installation
[Go](https://golang.org/) should be installed and your `GOPATH` should be set (defaults to `$HOME/go` in Go 1.8+). `$GOPATH/bin` should be on your `$PATH` if you want to run the binaries easily.
$ go get -u github.com/fogleman/ribbon/cmd/rcsb
### Example Usage
Provide a 4-digit RCSB Structure ID. The PDB file will automatically be downloaded and an image will be rendered. The triangle mesh will also be saved.
```bash
$ rcsb 4hhb # generates 4hhb.png and 4hhb.stl
```
### Resources
[RCSB Protein Data Bank](http://www.rcsb.org/) - Find PDB files of proteins here. Over 100,000 in the database.
[PDB File Format](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html) - Details on the PDB file format.
### Package `pdb`
[Documentation](https://godoc.org/github.com/fogleman/ribbon/pdb)
The `pdb` package parses PDB files. The following entities are currently parsed:
```
ATOM => *pdb.Atom
HETATM => *pdb.Atom
CONECT => *pdb.Connection
HELIX => *pdb.Helix
SHEET => *pdb.Strand
BIOMT => pdb.Matrix
SMTRY => pdb.Matrix
```
Additionally, some higher-level constructs are produced:
```
*pdb.Residue
*pdb.Chain
```
### Package `ribbon`
[Documentation](https://godoc.org/github.com/fogleman/ribbon/ribbon)
The `ribbon` package generates 3D meshes given a `pdb.Model`. It can produce the following types of meshes:
- Ribbon
- Ball & stick (for ligands)
- Space filling
- Backbone
### Package `fauxgl`
The [fauxgl](https://github.com/fogleman/fauxgl) library is used for rendering the 3D meshes in pure Go.
### Samples
