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%YAML 1.2
---
# PDB syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: pdb
# YAML for PDB files
file_extensions: [pdb]
scope: source.pdb
contexts:
main:
#Header line
- match: '^HEADER.*$'
scope: invalid.pdb
#Title line
- match: '^TITLE.*$'
scope: constant.character.pdb
#COMPND line
- match: '^COMPND.*$'
scope: markup.deleted.pdb
#SOURCE line
- match: '^SOURCE.*$'
scope: constant.language.pdb
#KEYWDS line
- match: '^KEYWDS.*$'
scope: entity.name.pdb
#EXPDTA line
- match: '^EXPDTA.*$'
scope: storage.type.pdb
#AUTHOR line
- match: '^AUTHOR.*$'
scope: string.pdb
#REVDAT line
- match: "^REVDAT.*$"
scope: constant.character.pdb
#JRNL section
- match: '^JRNL.*$'
push: journal
#REMARK section
- match: '^REMARK[\s\t]+[0-9]+'
push: remark
#SEQRES section
- match: '^SEQRES'
#scope: storage.type.pdb
push: seqres
#HELIX section
- match: "^HELIX.*$"
scope: storage.type.pdb
#HELIX section
- match: "^SHEET.*$"
scope: entity.name.tag.pdb
#SITE section
- match: "^SITE.*$"
scope: string.pdb
#ATOM section
- match: '^(ATOM|ANISOU)[\s\t]+[0-9]+[\s\t]+[A-Z0-9]+'
#scope: constant.character.pdb
push: atom
#HETATM section
- match: "^HETATM.*$"
scope: markup.deleted.pdb
journal:
- meta_scope: string.pdb #colour everything in this section
- match: '[\s\t]+TITL\b.*'
scope: entity.name.pdb #colour the title of the paper
- match: '(?!JRNL\b)\b.*' #when new string starts with no JRNL header, go out
pop: true
remark:
- meta_scope: constant.character.pdb #meta.structure.dictionary.json.pdb
- match: '[\s\t]+RESOLUTION.*$' #'[\s\t]+(?=RESOLUTION).*'
scope: entity.name.pdb #string.unquoted.yaml.pdb
- match: '.*(?=:)'
push: remark_value
- match: '((?!REMARK).)*$' #'(?!REMARK\b)\b.*'
pop: true
remark_value:
- meta_scope: constant.character.pdb
- match: ':[\s\t]+NULL' #':([\s\t]+NULL[\s\t]+.*)+'
#scope: markup.deleted.pdb
push: semicolon_NULL
- match: ':'
#scope: entity.name.pdb
push: semicolon
- match: '$'
pop: true
semicolon:
- meta_scope: entity.name.pdb
- match: '[\s\t]?;[\s\t]?'
scope: constant.language.pdb
- match: '$'
pop: true
semicolon_NULL:
- meta_scope: markup.deleted.pdb
- match: '[\s\t]?;[\s\t]?'
scope: constant.language.pdb
- match: '$'
pop: true
seqres:
#different chanes should be coloured differently (focus on A-H)
#don't care about colours for now, but they should be different
- meta_scope: constant.character.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[AP].*'
scope: ntA.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[BQ].*'
scope: ntT.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[CR].*'
scope: ntG.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[DS].*'
scope: ntC.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[ET].*'
scope: ntU.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[FU].*'
scope: ntR.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[GV].*'
scope: ntY.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[HW].*'
scope: ntS.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[IX].*'
scope: ntW.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[JY].*'
scope: ntM.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[KZ].*'
scope: ntK.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[L].*'
scope: ntD.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[M].*'
scope: ntB.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[N].*'
scope: ntV.pdb
- match: '[\s\t]+[0-9]+[\s\t]+[O].*'
scope: ntH.pdb
- match: '$'
pop: true
atom:
- meta_scope: constant.character.pdb
#residue number
- match: '(?<=[A-Z])[\s\t]+[0-9]+'
scope: storage.type.pdb
#amino acids
- match: '[\s\t]+ALA'
scope: aaA
- match: '[\s\t]+ARG'
scope: aaR
- match: '[\s\t]+ASN'
scope: aaN
- match: '[\s\t]+ASP'
scope: aaD
- match: '[\s\t]+CYS'
scope: aaC
- match: '[\s\t]+GLN'
scope: aaQ
- match: '[\s\t]+GLU'
scope: aaE
- match: '[\s\t]+GLY'
scope: aaG
- match: '[\s\t]+HIS'
scope: aaH
- match: '[\s\t]+ILE'
scope: aaI
- match: '[\s\t]+LEU'
scope: aaL
- match: '[\s\t]+LYS'
scope: aaK
- match: '[\s\t]+MET'
scope: aaM
- match: '[\s\t]+PHE'
scope: aaF
- match: '[\s\t]+PRO'
scope: aaP
- match: '[\s\t]+SER'
scope: aaS
- match: '[\s\t]+THR'
scope: aaT
- match: '[\s\t]+TRP'
scope: aaW
- match: '[\s\t]+TYR'
scope: aaY
- match: '[\s\t]+VAL'
scope: aaV
#define chains (different colours for different chains from A-H)
- match: '(?<=[\s\t])[AP](?=[\s\t]+[0-9])'
scope: ntA.pdb
- match: '(?<=[\s\t])[BQ](?=[\s\t]+[0-9])'
scope: ntT.pdb
- match: '(?<=[\s\t])[CR](?=[\s\t]+[0-9])'
scope: ntG.pdb
- match: '(?<=[\s\t])[DS](?=[\s\t]+[0-9])'
scope: ntC.pdb
- match: '(?<=[\s\t])[ET](?=[\s\t]+[0-9])'
scope: ntU.pdb
- match: '(?<=[\s\t])[FU](?=[\s\t]+[0-9])'
scope: ntR.pdb
- match: '(?<=[\s\t])[GV](?=[\s\t]+[0-9])'
scope: ntY.pdb
- match: '(?<=[\s\t])[HW](?=[\s\t]+[0-9])'
scope: ntS.pdb
- match: '(?<=[\s\t])[IX](?=[\s\t]+[0-9])'
scope: ntW.pdb
- match: '(?<=[\s\t])[JY](?=[\s\t]+[0-9])'
scope: ntM.pdb
- match: '(?<=[\s\t])[KZ](?=[\s\t]+[0-9])'
scope: ntK.pdb
- match: '(?<=[\s\t])L(?=[\s\t]+[0-9])'
scope: ntD.pdb
- match: '(?<=[\s\t])M(?=[\s\t]+[0-9])'
scope: ntB.pdb
- match: '(?<=[\s\t])N(?=[\s\t]+[0-9])'
scope: ntV.pdb
- match: '(?<=[\s\t])O(?=[\s\t]+[0-9])'
scope: ntH.pdb
- match: '$'
pop: true
#aa_chain_resnumber:
#- meta_scope: string.pdb
#- match: '[A-Z]{3}'
#scope: storage.type.pdb'
#- match: '[\s\t]+'
#pop: true
|
