Vectorization of hydrophobicity

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: Peptides
-Version: 1.1.1
-Date: 2015-11-26
-Title: Calculate Indices and Theoretical Properties of Protein
-        Sequences
+Version: 1.1.2
+Date: 2016-05-24
+Title: Calculate Indices and Theoretical Properties of Protein Sequences
 Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
 Maintainer: Daniel Osorio <daniel.osorio@correo.uis.edu.co>
 URL: https://github.com/dosorio/Peptides/
+Imports: stringi
 Suggests: RUnit
 Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot output files from the 'GROMACS' molecular dynamics package.
 License: GPL-2

NAMESPACE

@@ -2,4 +2,5 @@ exportPattern("^[[:alpha:]]+")
 importFrom("graphics", "legend", "plot")
 importFrom("stats", "embed")
 importFrom("utils", "data")
+importFrom("stringi", "stri_count_fixed")
 S3method(plot,xvg)

R/aindex.R

@@ -3,17 +3,20 @@
 # Thermostability and aliphatic index of globular proteins.
 # Journal of Biochemistry, 88(6), 1895-1898.
 
-aindex<-function(seq){
-  seq<-gsub("[\r\n ]","",seq)
-  # Divide the amino acid sequence and extracts the relative frequency of Alanine, Valine, Leucine and Isoleucine
-  p<-table(strsplit(toupper(seq),"")[[1]])/nchar(seq)
+aindex <- function(seq){
+  seq <- .remove_spaces(seq)
+  # Extract the frequency of Alanine, Valine, Leucine and Isoleucine
+  A <- stri_count_fixed(seq, "A")
+  V <- stri_count_fixed(seq, "V")
+  L <- stri_count_fixed(seq, "L")
+  I <- stri_count_fixed(seq, "I")
 
   # Aliphatic index = X(Ala) + a * X(Val) + b * ( X(Ile) + X(Leu) )
   # where X(Ala), X(Val), X(Ile), and X(Leu) are mole percent (100 X mole fraction)
   # of alanine, valine, isoleucine, and leucine.
   # The coefficients a and b are the relative volume of valine side chain (a = 2.9)
   # and of Leu/Ile side chains (b = 3.9) to the side chain of alanine.
 
-  # Return the result as percentage rounded to 2 decimals
-  sum(c(p["A"],(2.9*p["V"]),3.9*p[c("L","I")]),na.rm=T)*100
+  # Return the result as percentage
+  100 * sum(c(A + 2.9 * V + 3.9 * (L + I))) / nchar(seq)
 }

R/boman.R

@@ -5,12 +5,21 @@
 # Boman, H. G. (2003). Antibacterial peptides: basic facts and emerging concepts.
 # Journal of Internal Medicine, 254(3), 197-215.
 
-boman<-function(seq){
-  seq<-gsub("[\r\n ]","",seq)
+boman <- function(seq){
+  seq <- .remove_spaces(seq)
   # Create the Boman scale vector
   boman<-c(L=4.92, I=4.92, V=4.04, F=2.98, M=2.35, W=2.33, A=1.81, C=1.28, G=0.94, Y=-0.14, T=-2.57, S=-3.40,
            H=-4.66, Q=-5.54, K=-5.55, N=-6.64, E=-6.81, D=-8.72, R=-14.92)
-  # Asign a value to each amino acids in the sequence, sum the values and divide on amino acid sequence length
+  amino_acid_scores <- vapply(
+    names(boman),
+    function(aa)
+    {
+      boman[aa] * stri_count_fixed(seq, aa)
+    },
+    numeric(length(seq))
+  )
+  # Assign a value to each amino acids in the sequence, sum the values and divide on amino acid sequence length
   # Report the index rounded to 2 decimals
-  return(-1*sum(boman[strsplit(toupper(seq),"")[[1]]],na.rm=T)/nchar(seq))
+  sum_fn <- if(is.matrix(amino_acid_scores)) rowSums else sum
+  -sum_fn(amino_acid_scores) / nchar(seq)
 }

R/hydrophobicity.R

@@ -5,15 +5,26 @@
 # A simple method for displaying the hydropathic character of a protein.
 # Journal of Molecular Biology, 157(1), 105-32.
 
-hydrophobicity<-function(seq,scale="KyteDoolittle"){
-  seq<-gsub("[\r\n ]","",seq)
+hydrophobicity <- function(seq, scale="KyteDoolittle"){
+  seq <- .remove_spaces(seq)
   # Loading hydrophobicity scales
-  data(H, envir = environment())
-  H<-H
+  e <- new.env()
+  data(list = "H", package = "Peptides", envir = e)
   # Setting the hydrophobicity scale
-  M<-names(H)
-  scale<-match.arg(scale,M)
+  scale <- match.arg(scale, names(e$H))
+  hydrophobicity_scores <- e$H[[scale]]
+  # For each amino acid, its score is the hydro. score times the number of 
+  # occurences
+  amino_acid_scores <- vapply(
+    names(hydrophobicity_scores),
+    function(aa)
+    {
+      hydrophobicity_scores[aa] * stri_count_fixed(seq, aa)
+    },
+    numeric(length(seq))
+  )
   # Sum the hydrophobicity of each amino acid and divide them between the sequence length
   # Return the GRAVY value
-  sum(H[[scale]][strsplit(seq,"")[[1]]],na.rm = TRUE)/nchar(seq)
+  sum_fn <- if(is.matrix(amino_acid_scores)) rowSums else sum
+  sum_fn(amino_acid_scores) / nchar(seq)
 }

R/utilities.R

@@ -0,0 +1,22 @@
+#' Remove spaces from strings
+#' 
+#' A utility function to remove spaces from strings.
+#' @param x A character vector.
+#' @return A character vector without spaces.
+#' @noRd
+.remove_spaces <- function(x)
+{
+  gsub("[\r\n ]", "", x)
+}
+
+#' Convert a string to upper case chars
+#' 
+#' A utility to convert a character vector to a list of character vectors of
+#' upper case strings.
+#' @param x A character vector.
+#' @return A list of character vectors. 
+#' @noRd
+.to_upper_chars <- function(x)
+{
+  strsplit(toupper(x), "")
+}

inst/tests/runit.hydrophobicity.R

@@ -9,4 +9,206 @@ test.hydrophobicity <- function(){
 
   # CHECK OUTPUT CLASS
   checkTrue(is.numeric(hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Kyte")))
-}
+}
+
+test.hydrophobicity.B6SF67 <- function(){
+  # A long sequence, from
+  # http://www.uniprot.org/uniprot/B6SF67.fasta
+  seq_B6SF67 <- "MSRMPQGAARRNDCVSEHQGTTDLEDIVRFWERHLDGVNASAFPALSSSLVVPKPKLQTE
+HRISLGTAVSDQWSDAVICRAALAVILARYTHATEALYGIVVEQPSVSNAQKRSADDASS
+IVVPIRVQCASGQFGNDILAAIATHDASCRSLSAIGLDGIRCLDDAKTVARGLQTVLTVT
+SRKSVDASSPNILDLENIASSHGRALMIECQMSTTSACLRAQYDAGILRNEQVVRLLKQL
+ALSIQHFRGNAANDLLRDFCFISPGEEMEIAYWNRRSIRTNEVCIHDVIFKRATYMPTDT
+AVSAWDGEWTYADLDVVSSCLADYVRSLDLRSGQAIPLCFEKSRNTIAAMVAVLKAGHPF
+CLIDPSTPSARITQMCEQMSATVAFASRALCSIMQAGVSRCIAVDDDLFQSLSSVIGCPQ
+MSMTRPQDLAYVIFTSGSTGIPKGSMIEHRGFASCALEFGPQLLIDRNTRALQFASHAFG
+ACLLEVLVTLMLGGCVCVPSENDRLNNLSGFIEQSGVNWTLFTPSFIGALTPETIRGVHT
+VVLGGEPMTPFIRDVWASKVQLLSIYGQSESSTVCSVVKIKPDTTDLSSLGHAIGARFWI
+VDAENPSRLAPIGCIGELMVESPGIAREYLSAQEAQMSPFITKTPAWYPMKQRCSPVKFY
+MTGDLACYGRDGTVMNLGRKDSQVKIRGQRVELGDVETNLRSVLPKHIIPVVEAIDSIHA
+SGSKFLVAILIGANHGMKNEFDTEPRREVSILDETAVIRIRKSMQDLVPSYCIPTQYICM
+ERLLTTTTGKADRKRLRAICVDLLKPSRRAMVPESSDGPTLKLTAGQVLDEAWHRYLRFD
+SVLDGSKSKFFDLNGDSITAIKIANAARKHGVMLKVADILANPTLADLRAQFQIDFTPQN
+SILRTSYRGPIQQSFAQNRLWFLDQLNVGASWYIVPVAVRLQGTVHVDALVTALCALEQR
+HETLRTTFEESDGEGIQRIQPSGLEQLRLIDVDCVDSRDYQRVLEEEQTTPFELSREPGW
+RVALLRLGDDDHVLSIVMHHIISDGWSVDVLRHELGQFYSAALRGQDPLSQISPLPIQYR
+DFALWQRQDEQVAEHQRQLEHWTEQLADSSPAELLSDHPRPSILSGQAGAIPVNVQGSLY
+QALRAFCRAHQVTSFVVLLTAFRIAHYRLTGAEDATIGTPIANRNRPELENMIGFFVNTQ
+CMRIVIGSDDTFEGLVQQVRSITAAAHENQDVPFERIVSALLPGSRDTSRNPLVQLMFAV
+HSQRNLGQISLEGLQGELLGVASPTRFDVEFHLFQEENMLSGRVLFSDDLFEQKTMQGMV
+DVFQEVLSRGLEQPQIPLATLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAAC
+SEAIAVKDSSAQLTYSELDRQSDELAGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKA
+NLAYLPLDVNVPATRLESILSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPG
+APGDNEAPVVQPSATSLAYVIFTSGSTGKPKGVMVEHRGVVRLVKQSNVVYHLPSTSRVA
+HLSNLAFDASAWEIYAALLNGGTLICIDYFTTLDCSALGAKFIKEKIVATMIPPALLKQC
+LAIFPTALSELVLLFAAGDRFSSGDAVEVQRHTKGAVCNAYGPTENTILSTIYEVKQNEN
+FPNGVPIGRAVSNSGAYVMDPQQQLVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSV
+NGQLVRAYRTGDRVRCRPCDGQIEFFGRMDRQVKIRGHRIELAEVEHAVLGLEDVQDAAV
+IAFDNVDSEEPEMVGFVTITEDNPVREDETSGQVEDWANHFEISTYTDIAAIDQGSIGSD
+FVGWTSMYDGSEIDKAEMQEWLADTMASMLDGQAPGNVLEIGTGTGMVLFNLGDGLQSYV
+GLEPSRSAAAFVNQTIKSLPTLAGNAEVHIGTATDVARLDGLRPDLVVVNSVVQYFPSPE
+YLMEVVEALARLPGVERIFFGDVRSYAINRDFLAARALHELGDRATKHEIRRKMLEMEER
+EEELLVDPAFFTMLTSSLPGLIQHVEILPKLMRATNELSAYRYTAVVHVCRAGQEPRSVH
+TIDDDAWVNLGASRLSRPTLSSLLQTSEGASAVAVSNIPYSKTITERALVSALDEDDMQD
+SSDWLLAVRETGRSCSSFSATDLVELARETGWRVELSWARQYSQKGALDAVFHRHPVSAG
+SGRVMFQFPVETEDRPHISRTNRPLQRLQKKRTETHVHEQLRALLPRYMVPTRIVALDKL
+PVNANGKVDRQQLARTAQVLPASKAPSACVAPRNELEMTLCEEFSQVLGVEVGITDNFFH
+LGGHSLMATKFAARISRRLNAIVSVKNVFDHPVPMDLAATIQEGSKLHTPIPRTAYSGPV
+EQSFAQGRLWFLDQFNPSSIGYVMPFAARLHGQLQIEALTAALFALEQRHEILRTTLDAH
+DGVGMQIVHAEHPQQLRIIDVSAKASSSYAQTLRDEQASPFDLSKEPGWRVSLLQLSEID
+YVLSIVMHHTIYDGWSLDVLRRELSQFYAAAIRGREPLSTIEPLPIQYRDFSVWQKQEDQ
+VAEHRRQLHYWIEQLDGSSPAEFLNDKPRPTLLSGKAGVVEIAVKGTVYQRLLEFCRLHQ
+VTSFMVLLAAFRATHYRLTGTEDATVGTPIANRNRPELENMIGLFVNTQCIRLKIEDNDT
+LEELVQHVRATITASISNQDVPFEQVVSALLPGSRDTSRNPLVQLTFAVHSQRNLADIQL
+ENVETNAMPICPSTRFDAEFHLFQEENMLSGRVLFSDDLFEQKTMQGMVDVFQEVLSRGL
+EQPQIPLATLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAVKDSSA
+QLTYSELDRQSDELAGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKANLAYLPLDVNV
+PATRLESILSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNEAPVVQ
+PSATSLAYVIFTSGSTGKPKGVMVEHRSIVRLMRHSNVSSRLLLHPRMTHLSNLAFDASV
+WEIFLTLLNGGTLICIDYLSSLDCRALGVSILEHQVDASVLPPALLKQCLANVPEALASL
+QVLLSAGDRLDSRDAIESCALVRGSVYNGYGPTENGIQSTIYEVKADAEFVNGVPIGRAV
+SNSGAYVMDPQQQLVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSVNGQLVRAYRTG
+DRVRCRPCDGQIEFFGRMDRQVKIRGHRIELAEVEHAVLGLEDVQDAAVLIAQTAENEEL
+VGFFTLRQTQAVQSNGAAGVVPEHSDSELAQSCSCTQTERRVRNRLQSCLPRYMVPSRMV
+LLDRLPVNPNGKVDRQELTRRAQDLPISESSPVHVKPRTELERSLCEEFADVIGLEVGVT
+DNFFDLGGHSLMAMKLAARISRRSNAHISVKDIFDHPLIADLAMKIREGSDLHTPIPHRM
+YVGPIQLSFAQGRLWFLDQLNLGASWYVMPLAMRLQGSLQLDALETALFAIEQRHETLRM
+TFAEQDGVAVQVVHAAHYKHIKMIDKPLRQKIDVLKMLEEERTTPFELSREPGWRVALLR
+LGDDDHVLSIVMHHIISDGWSVDVLRHELGQFYSAALRGQDPLSQISPLPIQYRDFALWQ
+RQDEQVAEHQRQLEHWTEQLADSSPAELLSDHPRPSILSGQAGAIPVNVQGSLYQALRAF
+CRAHQVTSFVVLLTAFRIAHYRLTGAEDATIGTPIANRNRPELENMIGFFVNTQCMRIVI
+GSDDTFEGLVQQVRSITAAAHENQDVPFERIVSALLPGSRDTSRNPLVQLMFAVHSQRNL
+GQISLEGLQGELLGVAATTRFDVEFHLFQDDDKLSGNVLFATELFEQKTMQGMVDVFQEV
+LSRGLEQPQIPLATLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAV
+KDSSAQLTYSELDRQSDELAGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKANLAYLP
+LDVNVPATRLESILSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNE
+APVVQPSATSLAYVIFTSGSTGKPKGVMVEHRSIVRLMRHSNVSSRLLLHPRMTHLSNLA
+FDASVWEIFLTLLNGGTLICIDYLSSLDCRALGVSILEHQVDASVLPPALLKQCLANVPE
+ALASLQVLLSAGDRLDSRDAIESCALVRGSVYNGYGPTENGIQSTIYEVKADAEFVNGVP
+IGRAVSNSGAYVMDPQQQLVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSVNGQLVR
+AYRTGDRVRCRPCDGQIEFFGRMDRQVKIRGHRIELAEVEHAVLGLEDVQDAAVIAFDNV
+DSEEPEMVGFVTITEDNPVREDETSGQVEDWANHFEISTYTDIAAIDQGSIGSDFVGWTS
+MYDGSEIDKAEMQEWLADTMASMLDGQAPGNVLEIGTGTGMVLFNLGDGLQSYVGLEPSR
+SAAAFVNQTIKSLPTLAGNAEVHIGTATDVARLDGLRPDLVVVNSVVQYFPSPEYLMEVV
+EALARLPGVERIFFGDVRSYAINRDFLAARALHELGDRATKHEIRRKMLEMEEREEELLV
+DPAFFTMLTSSLPGLIQHVEILPKLMRATNELSAYRYTAVVHVCRAGQEPRSVHTIDDDA
+WVNLGASRLSRPTLSSLLQTSEGASAVAVSNIPYSKTITERALVSALDEDDMQDSSDWLL
+AVRETGRSCSSFSATDLVELARETGWRVELSWARQYSQKGALDAVFHRHPVSAGSGRVMF
+QFPVETEDRPHISRTNRPLQRLQKKRTETHVHEQLRALLPRYMVPTRIVALDKLPVNANG
+KVDRQQLARTAQVLPASKAPSACVAPRNELEMTLCEEFSQVLGVEVGITDNFFHLGGHSL
+MATKLAARISHRLHTRISVKHIFDHPLIGDLSVHIADSPVPLLTITRAQHAGAVEQSFAQ
+ARLWFLVQLGLESPSYIIPIVLRLHGSLSKTAIEGALSALMERHEVLRTTFEDHKGIGMQ
+VVQDHRHQDLVVIDVAGQGSLDYKQHLYMEHVKPFDLTRDPGWRVALLRLGDDDHVLSIV
+MHHIISDGWSIDILLRELGQFYSAALRGQDPLSQTSPLPIQYRDFALWQKQDHQLADHEK
+QLRYWEEQLAESSPAELLCDHARPTTPSGQAGSIPVNVQGSLYQALRAFCRAHQVTSFVV
+LLTAFRIAHYRLTGAEDATIGTPIANRNRPELENMIGFFVNTQCMRIVIGSDDTFEGLVQ
+QVRSITAAAHENQDVPFERIVSALLPGSRDTSRNPLVQLLFAVHAYQEVENFAIPGVHSE
+LVQGTTFTRFDVEFHLLEDPDKLSGNVLFATELFEQKTMQGMVDVFQEVLSRGLEQPQIP
+LATLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAVKDSSAQLTYSE
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+SILSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNEAPVVQPSATSL
+AYVIFTSGSTGKPKGVMVEHRSILRVVTSPPARALLPSTIIMAHLTNIAFDVSLWEICTA
+LLHGGTLICIQYLASLDVRGLQTTFSREAINVAVFPPALLKTCLAKIPSALASLSAMFSS
+GDRLDSRDASEGATLVRQGIHNAYGPTENGIQSTIYEVKADAEFVNGVPIGRAVSNSGAY
+VMDPQQQLVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSVNGQLVRAYRTGDRVRCR
+PCDGQIEFFGRMDRQVKIRGHRIELAEVEHAILSLDYVIDAAVLLRQLIDQEPQVVGFVI
+VSTKRAYSRHNSGYASEVSAFCIKDQIAWRIRQHLCRMLPSYMVPYQIAILDEMPINANG
+KVDRQNLASRTVNVQRILAAPYMAPRNEVEISLCEQYAALLEHDVGILDDFFELGGHSLM
+ATRLASRISSRFSAPVSVRDIFDHPRIMDLASIIRAGDIQWSRILPSAYERPVEQSFAQN
+RLWFLYKLDIGTTQYNLPLAIHLRGPLDISALFIAFKALTERHELLRTTFDEDDGTCLQM
+LLPEYQHEVRITDLQGSHKGSLLDILNNNQKTPFELSREPGWRVALLRLGDDDHVLSIVM
+HHIISDGWSVDVLRHELGQFYSAALRGQDPLSQISPLPIQYRDFALWQRQDEQVAEHQRQ
+LEHWTEQLADSSPAELLSDHPRPSILSGQAGAIPVNVQGSLYQALRAFCRAHQVTSFVVL
+LTAFRIAHYRLTGAEDATIGTPIANRNRPELENMIGFFVNTQCMRIVIGSDDTFEGLVQQ
+VRSITAAAHENQDVPFERIVSALLPGSRDTSRNPLVQLMFAVHSQRNLGQISLEGLQGEL
+LGVAATTRFDVEFHLFQDDDKLSGNVLFATELFEQKTMQGMVDVFQEVLSRGLEQPQIPL
+ATLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAVKDSSAQLTYSEL
+DRQSDELAGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKANLAYLPLDVNVPATRLES
+ILSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNEAPVVQPSATSLA
+YVIFTSGSTGKPKGVMVEHRGVVRLVKQSNVVYHLPSTSRVAHLSNLAFDASVLEIYAAL
+LNGGTVYCIDYLTTLDPHALESVFIDADLNTAVLPPALLKQVLASSPSTLHALDLLFIGG
+DRLDARDALYANRLVRGSLYNVYGPTENTVLSVVYLFNDDDACINGVPIGQVVSNSGVYV
+MDSEQKLVPPGVMGEIVVTGDGLARGYTDSTLNTDRFVQISVNGRVLQAYRTGDRGRYRP
+TDARLEFFGRLDQQIKLRGHRVELKEIEQAMLGHNAVDDAGVVALEISECQELEMVGFVT
+LRNLGTMEATNNLAHTSWNPVTLKTPLASQIVAEVRGRLQRNLPLYMVPATIVVLHTMPV
+NANGKLDRQALVKAAMTLPKTAPLVWMAPRNEGETSLCEELTDILGVNVGITDNFFDLGG
+HSLLATRVAARISRRLDALVTVKQIFDHPVIGDLAAAIQGGSVRHLPITASEVDGPVQQS
+FAQNRLWFLEQMNIGATWYIVPLAVRLYGTLRVEALNIALRTIQQRHETLRTTFEELNGI
+AVQRCDSTCQGQLRVVDLVGQGPDRYREILDVQQTTPFELSQEPGWRVALLRLGDDDHVL
+SIVMHHIISDGWSVDVLLREIGQFYSAALRGQDPLSQISPLPIQYRDFALWQRQDEQVAE
+HQRQLEHWTEQLADSSPAELLSDHPRPSILSGQAGAIPVNVQGSLYQALRAFCRAHQVTS
+FVVLLTAFRIAHYRLTGAEDATIGTPIANRNRPELENMIGFFVNTQCMRIVIGSDDTFEG
+LVQQVRSITAAAHENQDVPFERIVSALLPGSRDTSRNPLVQLMFAVHSQRNLGQISLEGL
+QGELLGVAATTRFDVEFHLFQDDDKLSGNVLFATELFEQKTMQGMVDVFQEVLSRGLEQP
+QIPLATLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAVKDSSAQLT
+YSELDRQSDELAGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKANLAYLPLDVNVPAT
+RLESILSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNEAPVVQPSA
+TSLAYVIFTSGSTGKPKGVMVEHRGVVRLVKQSNVVYHLPSTSRVAHLSNLAFDASAWEI
+YAALLNGGTLICIDYFTTLDCSALGAKFIKEKIVATMIPPALLKQCLAIFPTALSELVLL
+FAAGDRFSSGDAVEVQRHTKGAVCNAYGPTENTILSTIYEVKQNENFPNGVPIGRAVSNS
+GAYVMDPQQQLVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSVNGQLVRAYRTGDRV
+RCRPCDGQIEFFGRMDRQVKIRGHRIELAEVEHAVLGLEDVQDAAVIAFDNVDSEEPEMV
+GFVTITEDNPVREDETSGQVEDWANHFEISTYTDIAAIDQGSIGSDFVGWTSMYDGSEID
+KAEMQEWLADTMASMLDGQAPGNVLEIGTGTGMVLFNLGDGLQSYVGLEPSRSAAAFVNQ
+TIKSLPTLAGNAEVHIGTATDVARLDGLRPDLVVVNSVVQYFPSPEYLMEVVEALARLPG
+VERIFFGDVRSYAINRDFLAARALHELGDRATKHEIRRKMLEMEEREEELLVDPAFFTML
+TSSLPGLIQHVEILPKLMRATNELSAYRYTAVVHVCRAGQEPRSVHTIDDDAWVNLGASR
+LSRPTLSSLLQTSEGASAVAVSNIPYSKTITERALVSALDEDDMQDSSDWLLAVRETGRS
+CSSFSATDLVELARETGWRVELSWARQYSQKGALDAVFHRHPVSAGSGRVMFQFPVETED
+RPHISRTNRPLQRLQKKRTETHVHEQLRALLPRYMVPTRIVALDKLPVNANGKVDRQQLA
+RTAQVLPASKAPSACVAPRNELEMTLCEEFSQVLGVEVGITDNFFHLGGHSLMATKFAAR
+ISRRLNAIVSVKNVFDHPVPMDLAATIQEGSKLHTPIPRTAYSGPVEQSFAQGRLWFLDQ
+FNPSSIGYVMPFAARLHGQLQIEALTAALFALEQRHEILRTTLDAHDGVGMQIVHAEHPQ
+QLRIIDVSAKASSSYAQTLRDEQASPFDLSKEPGWRVSLLQLSEIDYVLSIVMHHTIYDG
+WSLDVLRRELSQFYAAAIRGREPLSTIEPLPIQYRDFSVWQKQEDQVAEHRRQLHYWIEQ
+LDGSSPAEFLNDKPRPTLLSGKAGVVEIAVKGTVYQRLLEFCRLHQVTSFMVLLAAFRAT
+HYRLTGTEDATVGTPIANRNRPELENMIGLFVNTQCIRLKIEDNDTLEELVQHVRATITA
+SISNQDVPFEQVVSALLPGSRDTSRNPLVQLTFAVHSQRNLADIQLENVETNAMPICPST
+RFDAEFHLFQEENMLSGRVLFSDDLFEQKTMQGMVDVFQEVLSRGLEQPQIPLATLPLTH
+GLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAVKDSSAQLTYSELDRQSDEL
+AGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKANLAYLPLDVNVPATRLESILSAVGG
+RKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNEAPVVQPSATSLAYVIFTSG
+STGKPKGVMVEHRGVVRLVKQSNVVYHLPSTSRVAHLSNLAFDASAWEIYAALLNGGTLI
+CIDYFTIIDARALGVIFAQQSINATMLSPLLLKQFLSDAPFVLRSLHALYLGGDRLQGRD
+AIQACRVGCAFVINAYGPTENSVISTTYTLVKGNADFPNGVPIGRAVSNSGAYVMDPQQQ
+LVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSVNGQLVRAYRTGDRVRCRPCDGQIE
+FFGRMDRQVKIRGHRIELAEVEHAVLGLEDVQDAAVLIAQTAENEELVGFFTLRQTQAVQ
+SNGAAGVVPEHSDSELAQSCSCTQTERRVRNRLQSCLPRYMVPSRMVLLDRLPVNPNGKV
+DRQELTRRAQDLPISESSPVHVKPRTELERSLCEEFADVIGLEVGVTDNFFDLGGHSLMA
+MKLAARISRRSNAHISVKDIFDHPLIADLAMKIREGSDLHTPIPHRMYVGPIQLSFAQGR
+LWFLDQLNLGASWYVMPLAMRLQGSLQLDALETALFAIEQRHETLRMTFAEQDGVAVQVV
+HAAHYKHIKMIDKPLRQKIDVLKMLEEERTTPFELSREPGWRVALLRLGDDDHVLSIVMH
+HIISDGWSVDVLRHELGQFYSAALRGQDPLSQISPLPIQYRDFALWQRQDEQVAEHQRQL
+EHWTEQLADSSPAELLSDHPRPSILSGQAGAIPVNVQGSLYQALRAFCRAHQVTSFVVLL
+TAFRIAHYRLTGAEDATIGTPIANRNRPELENMIGFFVNTQCMRIVIGSDDTFEGLVQQV
+RSITAAAHENQDVPFERIVSALLPGSRDTSRNPLVQLMFAVHSQRNLGQISLEGLQGELL
+GVAATTRFDVEFHLFQDDDKLSGNVLFATELFEQKTMQGMVDVFQEVLSRGLEQPQIPLA
+TLPLTHGLEELRTMGLLDVEKTDYPRESSVVDVFREQAAACSEAIAVKDSSAQLTYSELD
+RQSDELAGWLRQQRLPAESLVAVLAPRSCQTIVAFLGILKANLAYLPLDVNVPATRLESI
+LSAVGGRKLVLLGADVADPGLRLADVELVRIGDTLGRCVPGAPGDNEAPVVQPSATSLAY
+VIFTSGSTGKPKGVMVEHRGVVRLVKQSNVVYHLPSTSRVAHLSNLAFDASAWEIYAALL
+NGGTLICIDYFTTLDCSALGAKFIKEKIVATMIPPALLKQCLAIFPTALSELVLLFAAGD
+RFSSGDAVEVQRHTKGAVCNAYGPTENTILSTIYEVKQNENFPNGVPIGRAVSNSGAYVM
+DPQQQLVPLGVMGELVVTGDGLARGYTDPSLDADRFVQVSVNGQLVRAYRTGDRVRCRPC
+DGQIEFFGRMDRQVKIRGHRIELAEVEHAVLGLEDVQDAAVIAFDNVDSEEPEMVGFVTI
+TEDNPVREDETSGQVEDWANHFEISTYTDIAAIDQGSIGSDFVGWTSMYDGSEIDKAEMQ
+EWLADTMASMLDGQAPGNVLEIGTGTGMVLFNLGDGLQSYVGLEPSRSAAAFVNQTIKSL
+PTLAGNAEVHIGTATDVARLDGLRPDLVVVNSVVQYFPSPEYLMEVVEALARLPGVERIF
+FGDVRSYAINRDFLAARALHELGDRATKHEIRRKMLEMEEREEELLVDPAFFTMLTSSLP
+GLIQHVEILPKLMRATNELSAYRYTAVVHVCRAGQEPRSVHTIDDDAWVNLGASRLSRPT
+LSSLLQTSEGASAVAVSNIPYSKTITERALVSALDEDDMQDSSDWLLAVRETGRSCSSFS
+ATDLVELARETGWRVELSWARQYSQKGALDAVFHRHPVSAGSGRVMFQFPVETEDRPHIS
+RTNRPLQRLQKKRTETHVHEQLRALLPRYMVPTRIVALDKLPVNANGKVDRQQLARTAQV
+LPASKAPSACVAPRNELEMTLCEEFSQVLGVEVGITDNFFHLGGHSLMATKLAARISRQL
+NIQVSVRDIFDYPVIVDLTDRLRLHHTRILTHDHGQHGQPDLKPFTLLPTNNPQEFLQHH
+ILPQLVPDHAKILDVYPVTRIQRRFLHHPKRGLPRFPSMVFFDFPPGSDPHKLRLACMAL
+VQRFDILRTIFLSVSGQFFQVVLDGYGIVIPVIEVDEELDDATRKLHDSDIQQPLRLGKP
+LIRIAVLKRQHSRVRAVLRLSHALYDGLSFEHIIQSLHALYLDITLSAPPKFGLYVQHMI
+QSRAEGYAFWRSVLKGSSMTILERSSTLQSRQPHLGRFLSAEKIIKAPLHANKSGITQAT
+VFAAANALMLANLTGTNDVVFARIVSGRQSLPKNFQHVVGPCTNDVPVRVRMEPGVGPKA
+LLRQVQDQYVHSFPFETLGFDEIKENCTDWPERITNFGCSTTYQNFDIFPKSQIDHQQIQ
+MASLASEYQNRETWDEAPLYDLNVTGVPQPDGRHIKIYVGVDGQLCDESTLDCILSDICE
+GVVSLTDALQELPAASITE"
+
+  checkEquals(hydrophobicity(seq_B6SF67), -0.078, tolerance = 0.005)
+}