├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── desc-01-AAC.R ├── desc-02-DC.R ├── desc-03-TC.R ├── desc-04-MoreauBroto.R ├── desc-05-Moran.R ├── desc-06-Geary.R ├── desc-07-CTDC.R ├── desc-07-CTDCClass.R ├── desc-08-CTDT.R ├── desc-08-CTDTClass.R ├── desc-09-CTDD.R ├── desc-09-CTDDClass.R ├── desc-10-CTriad.R ├── desc-10-CTriadClass.R ├── desc-11-SOCN.R ├── desc-12-QSO.R ├── desc-13-PAAC.R ├── desc-14-APAAC.R ├── desc-15-PSSM.R ├── desc-15-PSSMAcc.R ├── desc-15-PSSMFeature.R ├── misc-01-readFASTA.R ├── misc-02-readPDB.R ├── misc-03-protcheck.R ├── misc-04-protseg.R ├── misc-05-getUniProt.R ├── misc-06-acc.R ├── misc-07-removeGaps.R ├── par-01-parSeqSim.R ├── par-02-parGOSim.R ├── pcm-01-extractScales.R ├── pcm-01-extractScalesGap.R ├── pcm-02-extractDescScales.R ├── pcm-03-extractProtFP.R ├── pcm-03-extractProtFPGap.R ├── pcm-04-extractFAScales.R ├── pcm-05-extractMDSScales.R ├── pcm-06-extractBLOSUM.R ├── protr-datalist.R ├── protr-package.R └── utils.R ├── README.md ├── _pkgdown.yml ├── data ├── AA2DACOR.rda ├── AA3DMoRSE.rda ├── AAACF.rda ├── AABLOSUM100.rda ├── AABLOSUM45.rda ├── AABLOSUM50.rda ├── AABLOSUM62.rda ├── AABLOSUM80.rda ├── AABurden.rda ├── AACPSA.rda ├── AAConn.rda ├── AAConst.rda ├── AADescAll.rda ├── AAEdgeAdj.rda ├── AAEigIdx.rda ├── AAFGC.rda ├── AAGETAWAY.rda ├── AAGeom.rda ├── AAInfo.rda ├── AAMOE2D.rda ├── AAMOE3D.rda ├── AAMetaInfo.rda ├── AAMolProp.rda ├── AAPAM120.rda ├── AAPAM250.rda ├── AAPAM30.rda ├── AAPAM40.rda ├── AAPAM70.rda ├── AARDF.rda ├── AARandic.rda ├── AATopo.rda ├── AATopoChg.rda ├── AAWHIM.rda ├── AAWalk.rda └── AAindex.rda ├── inst ├── CITATION ├── logo │ └── logo.R ├── protseq │ ├── 4HHB.pdb │ ├── P00750.fasta │ ├── P08218.fasta │ ├── P10323.fasta │ ├── P20160.fasta │ ├── Plasminogen.fasta │ ├── Q9NZP8.fasta │ ├── align.fasta │ ├── extracell.fasta │ └── mitochondrion.fasta └── sysdata │ ├── AAidx.csv │ ├── Grantham.csv │ ├── OptAA3d.sdf │ └── Schneider-Wrede.csv ├── man ├── AA2DACOR.Rd ├── AA3DMoRSE.Rd ├── AAACF.Rd ├── AABLOSUM100.Rd ├── AABLOSUM45.Rd ├── AABLOSUM50.Rd ├── AABLOSUM62.Rd ├── AABLOSUM80.Rd ├── AABurden.Rd ├── AACPSA.Rd ├── AAConn.Rd ├── AAConst.Rd ├── AADescAll.Rd ├── AAEdgeAdj.Rd ├── AAEigIdx.Rd ├── AAFGC.Rd ├── AAGETAWAY.Rd ├── AAGeom.Rd ├── AAInfo.Rd ├── AAMOE2D.Rd ├── AAMOE3D.Rd ├── AAMetaInfo.Rd ├── AAMolProp.Rd ├── AAPAM120.Rd ├── AAPAM250.Rd ├── AAPAM30.Rd ├── AAPAM40.Rd ├── AAPAM70.Rd ├── AARDF.Rd ├── AARandic.Rd ├── AATopo.Rd ├── AATopoChg.Rd ├── AAWHIM.Rd ├── AAWalk.Rd ├── AAindex.Rd ├── ACC.Rd ├── OptAA3d.Rd ├── crossSetSim.Rd ├── crossSetSimDisk.Rd ├── extractAAC.Rd ├── extractAPAAC.Rd ├── extractBLOSUM.Rd ├── extractCTDC.Rd ├── extractCTDCClass.Rd ├── extractCTDD.Rd ├── extractCTDDClass.Rd ├── extractCTDT.Rd ├── extractCTDTClass.Rd ├── extractCTriad.Rd ├── extractCTriadClass.Rd ├── extractDC.Rd ├── extractDescScales.Rd ├── extractFAScales.Rd ├── extractGeary.Rd ├── extractMDSScales.Rd ├── extractMoran.Rd ├── extractMoreauBroto.Rd ├── extractPAAC.Rd ├── extractPSSM.Rd ├── extractPSSMAcc.Rd ├── extractPSSMFeature.Rd ├── extractProtFP.Rd ├── extractProtFPGap.Rd ├── extractQSO.Rd ├── extractSOCN.Rd ├── extractScales.Rd ├── extractScalesGap.Rd ├── extractTC.Rd ├── figures │ └── logo.png ├── getUniProt.Rd ├── parGOSim.Rd ├── parSeqSim.Rd ├── parSeqSimDisk.Rd ├── protcheck.Rd ├── protr-package.Rd ├── protseg.Rd ├── readFASTA.Rd ├── readPDB.Rd ├── removeGaps.Rd ├── twoGOSim.Rd └── twoSeqSim.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── protr.Rproj └── vignettes ├── custom.css ├── figures ├── AAindex.png ├── APAAC.png ├── 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