_pkgdown.yml

url: https://nanx.me/Rcpi/

template:
  bootstrap: 5

reference:
  - title: "Protein sequence retrieval"
    desc: >
      Retrieve protein sequence data from online databases.
    contents:
    - getProt
    - getFASTAFromUniProt
    - getFASTAFromKEGG
    - getPDBFromRCSBPDB
    - getSeqFromUniProt
    - getSeqFromKEGG
    - getSeqFromRCSBPDB
  - title: "Drug molecular data retrieval"
    desc: >
      Retrieve drug molecular data from online databases.
    contents:
    - getDrug
    - getMolFromDrugBank
    - getMolFromPubChem
    - getMolFromChEMBL
    - getMolFromKEGG
    - getMolFromCAS
    - getSmiFromDrugBank
    - getSmiFromPubChem
    - getSmiFromChEMBL
    - getSmiFromKEGG
  - title: "Protein sequence descriptors"
    desc: >
      Compute commonly used protein sequence derived descriptors.
    contents:
    - extractProtAAC
    - extractProtDC
    - extractProtTC
    - extractProtMoreauBroto
    - extractProtMoran
    - extractProtGeary
    - extractProtCTDC
    - extractProtCTDT
    - extractProtCTDD
    - extractProtCTriad
    - extractProtSOCN
    - extractProtQSO
    - extractProtPAAC
    - extractProtAPAAC
    - AAindex
  - title: "Profile-based protein sequence descriptors"
    desc: >
      Generate profile-based protein representations.
    contents:
    - extractProtPSSM
    - extractProtPSSMFeature
    - extractProtPSSMAcc
  - title: "Scales-based descriptors for proteochemometrics modeling"
    desc: >
      Generate scales-based descriptors for proteochemometrics (PCM) modeling.
    contents:
    - extractPCMScales
    - extractPCMPropScales
    - extractPCMDescScales
    - extractPCMFAScales
    - extractPCMMDSScales
    - extractPCMBLOSUM
    - acc
  - title: "Molecular descriptor sets for generating scales-based descriptors"
    desc: >
      Molecular descriptor sets of the 20 amino acids for
      generating scales-based descriptors.
    contents:
    - OptAA3d
    - AAMetaInfo
    - AA2DACOR
    - AA3DMoRSE
    - AAACF
    - AABurden
    - AAConn
    - AAConst
    - AAEdgeAdj
    - AAEigIdx
    - AAFGC
    - AAGeom
    - AAGETAWAY
    - AAInfo
    - AAMolProp
    - AARandic
    - AARDF
    - AATopo
    - AATopoChg
    - AAWalk
    - AAWHIM
    - AACPSA
    - AADescAll
    - AAMOE2D
    - AAMOE3D
    - AABLOSUM45
    - AABLOSUM50
    - AABLOSUM62
    - AABLOSUM80
    - AABLOSUM100
    - AAPAM30
    - AAPAM40
    - AAPAM70
    - AAPAM120
    - AAPAM250
  - title: "Molecular descriptors"
    desc: >
      Compute commonly used molecular descriptors.
    contents:
    - extractDrugAIO
    - extractDrugALOGP
    - extractDrugAminoAcidCount
    - extractDrugApol
    - extractDrugAromaticAtomsCount
    - extractDrugAromaticBondsCount
    - extractDrugAtomCount
    - extractDrugAutocorrelationCharge
    - extractDrugAutocorrelationMass
    - extractDrugAutocorrelationPolarizability
    - extractDrugBCUT
    - extractDrugBondCount
    - extractDrugBPol
    - extractDrugCarbonTypes
    - extractDrugChiChain
    - extractDrugChiCluster
    - extractDrugChiPath
    - extractDrugChiPathCluster
    - extractDrugCPSA
    - extractDrugDescOB
    - extractDrugECI
    - extractDrugFMF
    - extractDrugFragmentComplexity
    - extractDrugGravitationalIndex
    - extractDrugHBondAcceptorCount
    - extractDrugHBondDonorCount
    - extractDrugHybridizationRatio
    - extractDrugIPMolecularLearning
    - extractDrugKappaShapeIndices
    - extractDrugKierHallSmarts
    - extractDrugLargestChain
    - extractDrugLargestPiSystem
    - extractDrugLengthOverBreadth
    - extractDrugLongestAliphaticChain
    - extractDrugMannholdLogP
    - extractDrugMDE
    - extractDrugMomentOfInertia
    - extractDrugPetitjeanNumber
    - extractDrugPetitjeanShapeIndex
    - extractDrugRotatableBondsCount
    - extractDrugRuleOfFive
    - extractDrugTPSA
    - extractDrugVABC
    - extractDrugVAdjMa
    - extractDrugWeight
    - extractDrugWeightedPath
    - extractDrugWHIM
    - extractDrugWienerNumbers
    - extractDrugXLogP
    - extractDrugZagrebIndex
  - title: "Molecular fingerprints"
    desc: >
      Compute commonly used molecular fingerprints.
    contents:
    - extractDrugStandard
    - extractDrugStandardComplete
    - extractDrugExtended
    - extractDrugExtendedComplete
    - extractDrugGraph
    - extractDrugGraphComplete
    - extractDrugHybridization
    - extractDrugHybridizationComplete
    - extractDrugMACCS
    - extractDrugMACCSComplete
    - extractDrugEstate
    - extractDrugEstateComplete
    - extractDrugPubChem
    - extractDrugPubChemComplete
    - extractDrugKR
    - extractDrugKRComplete
    - extractDrugShortestPath
    - extractDrugShortestPathComplete
    - extractDrugOBFP2
    - extractDrugOBFP3
    - extractDrugOBFP4
    - extractDrugOBMACCS
  - title: "PPI and CPI descriptors"
    desc: >
      Compute protein-protein and compound-protein interaction descriptors.
    contents:
    - getPPI
    - getCPI
  - title: "Similarity and similarity searching"
    desc: >
      Compute sequence/molecular similarities and similarity searching.
    contents:
    - calcDrugFPSim
    - calcDrugMCSSim
    - searchDrug
    - calcTwoProtSeqSim
    - calcParProtSeqSim
    - calcTwoProtGOSim
    - calcParProtGOSim
  - title: "Protein sequence data processing"
    desc: >
      Process protein sequence data.
    contents:
    - readFASTA
    - readPDB
    - segProt
    - checkProt
  - title: "Molecular data processing"
    desc: >
      Process molecular data.
    contents:
    - readMolFromSDF
    - readMolFromSmi
    - convMolFormat