# nom-pdb
PDB parser implemented in Rust using nom.
## Features
- Parses structural information and a subset of important metadata.
- Able to deal with non-standard residues (not yet mature)
- JSON serialization powered by serde.
# Example (Last Updated 2020-10-17)
```rust
cargo run --example read 1a8o
```
```json
{
"header": {
"classification": "VIRAL PROTEIN",
"deposition_date": "1998-03-27",
"id_code": "1A8O"
},
"title": "HIV CAPSID C-TERMINAL DOMAIN",
"authors": [
"T.R.GAMBLE",
"S.YOO",
"F.F.VAJDOS",
"U.K.VON SCHWEDLER",
"D.K.WORTHYLAKE",
"H.WANG",
"J.P.MCCUTCHEON",
"W.I.SUNDQUIST",
"C.P.HILL"
],
"experimental_techniques": [
"XRayDiffraction"
],
"cryst1": {
"a": 41.98,
"b": 41.98,
"c": 88.92,
"alpha": 90.0,
"beta": 90.0,
"gamma": 90.0,
"lattice_type": "Primitive",
"space_group": [
[
4,
3
],
[
2,
1
],
[
2,
1
]
],
"z": 8
},
"modres": {
"MSE": {
"standard_res": "Met",
"description": "SELENOMETHIONINE",
"occurence": [
[
"A",
151
],
[
"A",
185
],
[
"A",
214
],
[
"A",
215
]
]
}
},
"seqres": [
[
"A",
[
{
"Custom": "MSE"
},
"Asp",
"Ile",
"Arg",
"Gln",
"Gly",
"Pro",
// snip //
]
]
],
"atoms": [
{
"id": 9,
"name": "N",
"id1": " ",
"residue": "Asp",
"chain": "A",
"sequence_number": 152,
"insertion_code": " ",
"x": 21.554,
"y": 34.953,
"z": 27.691,
"occupancy": 1.0,
"temperature_factor": 19.26,
"element": "N",
"charge": 0
},
// snip //
]
"anisou": [
// snip //
]
}
```
# Notes
# References
- http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
- https://proteopedia.org/wiki/index.php/Non-Standard_Residues#cite_note-pdb22-0
# Roadmap
Note: Priority is, and should be placed on parsing structural information instead of metadata, since the latter is more or less disordered free-text and usually not of particular interest to users (even in cases where they are, users can examine the PDB file directly).
### Title Section
- [X] [Header](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER)
- [ ] [Obslte](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#OBSLTE)
- [X] [Title](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#TITLE)
- [ ] [Splt](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SPLIT)
- [ ] [Caveat](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#CAVEAT)
- [ ] [Compnd](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND)
- [ ] [Source](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SOURCE)
- [ ] [Keywds](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#KEYWDS)
- [X] [Expdta](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#EXPDTA)
- [ ] [Nummdl](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#NUMMDL)
- [ ] [Mdltyp](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#MDLTYP)
- [X] [Author](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#AUTHOR)
- [ ] [Sprsde](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SPRSDE)
- [ ] [Revdat](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#REVDAT)
- [ ] [Jrnl](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#JRNL)
- [ ] [Remarks](http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html)
- [ ] [Remarks 3](http://www.wwpdb.org/documentation/file-format-content/format33/remark3.html)
- [ ] [Remarks 0,1,2,4,5-299](http://www.wwpdb.org/documentation/file-format-content/format33/remarks1.html)
- [ ] [REMARK 300-999](http://www.wwpdb.org/documentation/file-format-content/format33/remarks2.html)
### Primary Structure Section
- [ ] [Dbref](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF)
- [ ] [Dbref1](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF1)
- [ ] [Seqadv](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQADV)
- [ ] [Seqres](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQRES)
- [ ] [Modres](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES)
### Heterogen Section
- [ ] [Het](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HET)
- [ ] [Formul](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#FORMUL)
- [ ] [Hetnam](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETNAM)
- [ ] [Hetsyn](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETSYN)
### Secondary Structure Section
- [ ] [Helix](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX)
- [ ] [Sheet](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#SHEET)
### Connectivity Annotation Section
- [ ] [Ssbond](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#SSBOND)
- [ ] [Link](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#LINK)
- [ ] [Cispep](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#CISPEP)
### Miscellaneous Features Section
- [ ] [Site](http://www.wwpdb.org/documentation/file-format-content/format33/sect7.html#SITE)
### Crystallographic and Coordinate Transformation Section
- [X] [Cryst1](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1)
- [ ] [MtrixN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#MTRIXn)
- [ ] [OrigxN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#ORIGXn)
- [ ] [ScaleN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#SCALEn)
### Coordinate Section
- [X] [Model](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL)
- [X] [Atom](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM)
- [X] [Anisou](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ANISOU)
- [X] [Ter](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER)
- [ ] [Hetatm](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM)
- [X] [Endmdl](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL)
### Connectivity Section
- [ ] [Conect](http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT)
### Bookkeeping Section
- [ ] [Master](http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#MASTER)
- [X] [End](http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#END)