_pkgdown.yml

url: https://nanx.me/protr/

template:
  bootstrap: 5
  bslib:
    preset: "bootstrap"

reference:
  - title: "Protein sequence descriptors"
    desc: >
      Calculate protein and peptide sequence descriptors.
    contents:
    - extractAAC
    - extractDC
    - extractTC
    - extractMoreauBroto
    - extractMoran
    - extractGeary
    - extractCTDC
    - extractCTDCClass
    - extractCTDDClass
    - extractCTDTClass
    - extractCTDT
    - extractCTDD
    - extractCTriad
    - extractCTriadClass
    - extractSOCN
    - extractQSO
    - extractPAAC
    - extractAPAAC
  - title: "PSSM descriptors"
    desc: >
      Calculate PSSM (profile-based) protein and peptide sequence descriptors.
    contents:
    - extractPSSM
    - extractPSSMAcc
    - extractPSSMFeature
    - acc
  - title: "PCM descriptors"
    desc: >
      Calculate PCM (proteochemometric modeling) descriptors.
    contents:
    - extractScales
    - extractScalesGap
    - extractProtFP
    - extractProtFPGap
    - extractDescScales
    - extractFAScales
    - extractMDSScales
    - extractBLOSUM
  - title: "Similarity measures between proteins"
    desc: >
      Calculate protein sequence alignment based
      similarity measures and GO-based semantic similarity measures.
    contents:
    - parSeqSim
    - parSeqSimDisk
    - crossSetSim
    - crossSetSimDisk
    - twoSeqSim
    - parGOSim
    - twoGOSim
  - title: "Pre-process protein sequences"
    desc: >
      Helper functions for pre-processing protein sequences.
    contents:
    - getUniProt
    - readFASTA
    - readPDB
    - protcheck
    - protseg
    - removeGaps
    - protr-package
  - title: "Precomputed molecular descriptors"
    desc: >
      Precomputed molecular descriptors for the 20 amino acids.
    contents:
    - AAindex
    - AAMetaInfo
    - OptAA3d
    - AA2DACOR
    - AA3DMoRSE
    - AAACF
    - AABurden
    - AAConn
    - AAConst
    - AACPSA
    - AADescAll
    - AAEdgeAdj
    - AAEigIdx
    - AAFGC
    - AAGeom
    - AAGETAWAY
    - AAInfo
    - AAMOE2D
    - AAMOE3D
    - AAMolProp
    - AARandic
    - AARDF
    - AATopo
    - AATopoChg
    - AAWalk
    - AAWHIM
  - title: "BLOSUM and PAM matrices"
    desc: >
      BLOSUM and PAM matrices for the 20 amino acids.
    contents:
    - AABLOSUM45
    - AABLOSUM50
    - AABLOSUM62
    - AABLOSUM80
    - AABLOSUM100
    - AAPAM30
    - AAPAM40
    - AAPAM70
    - AAPAM120
    - AAPAM250