Merge pull request #5 from dosorio/develop

1.0.3

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: Peptides
-Version: 1.0.2
-Date: 2014-11-15
-Title: Calculate indices and theoretical physicochemical properties of peptides and protein sequences
+Version: 1.0.3
+Date: 2014-12-14
+Title: Calculate Indices and Theoretical Properties of Protein Sequences
 Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
 Maintainer: Daniel Osorio <[email protected]>
 URL: https://github.com/dosorio/Peptides/
 Suggests: RUnit
-Description: Calculate physicochemical properties and indices from aminoacid sequences of peptides and proteins. Include also utilities for read and plot GROMACS output files.
+Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot XVG output files from GROMACS molecular dynamics package.
 License: GPL-2

NEWS

@@ -0,0 +1,55 @@
+NEWS
+====
+
+**Peptides v.1.0.3**
+* A membpos function bug has been fixed.
+* The results now are not rounded.
+
+**Peptides v.1.0.2**
+
+* Hydrophobicity function now can compute the GRAVY index with one of the 38 scales includes in Peptides (*new):
+
+  1. **Aboderin:** Aboderin, A. A. (1971). An empirical hydrophobicity scale for α-amino-acids and some of its applications. International Journal of Biochemistry, 2(11), 537-544.
+  2. **AbrahamLeo:** Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987).
+  3. ***Argos:** Argos, P., Rao, J. K., & Hargrave, P. A. (1982). Structural Prediction of Membrane‐Bound Proteins. European Journal of Biochemistry, 128(2‐3), 565-575.
+  4. **BlackMould:** Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991).
+  5. **BullBreese:** Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974).
+  6. ***Casari:** Casari, G., & Sippl, M. J. (1992). Structure-derived hydrophobic potential: hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. Journal of molecular biology, 224(3), 725-732.
+  7. **Chothia:** Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. Journal of molecular biology, 105(1), 1-12.
+  8. ***Cid:** Cid, H., Bunster, M., Canales, M., & Gazitúa, F. (1992). Hydrophobicity and structural classes in proteins. Protein engineering, 5(5), 373-375.
+  9. **Cowan3.4:** Cowan R., Whittaker R.G. Hydrophobicity indices at pH 3.4 determined by HPLC. Peptide Research 3:75-80(1990).
+  10. **Cowan7.5:** Cowan R., Whittaker R.G. Hydrophobicity indices at pH 7.5 determined by HPLC. Peptide Research 3:75-80(1990).
+  11. **Eisenberg:** Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984).
+  12. ***Engelman:** Engelman, D. M., Steitz, T. A., & Goldman, A. (1986). Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annual review of biophysics and biophysical chemistry, 15(1), 321-353.
+  13. ***Fasman:** Fasman, G. D. (Ed.). (1989). Prediction of protein structure and the principles of protein conformation. Springer.
+  14. **Fauchere:** Fauchere J.-L., Pliska V.E. Hydrophobicity scale (pi-r). Eur. J. Med. Chem. 18:369-375(1983).
+  15. ***Goldsack:** Goldsack, D. E., & Chalifoux, R. C. (1973). Contribution of the free energy of mixing of hydrophobic side chains to the stability of the tertiary structure of proteins. Journal of theoretical biology, 39(3), 645-651.
+  16. **Guy:** Guy H.R. Hydrophobicity scale based on free energy of transfer (kcal/mole). Biophys J. 47:61-70(1985).
+  17. **HoppWoods:** Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
+  18. **Janin:** Janin J. Free energy of transfer from inside to outside of a globular protein. Nature 277:491-492(1979).
+  19. ***Jones:** Jones, D. D. (1975). Amino acid properties and side-chain orientation in proteins: a cross correlation approach. Journal of theoretical biology, 50(1), 167-183.
+  20. ***Juretic:** Juretic, D., Lucic, B., Zucic, D., & Trinajstic, N. (1998). Protein transmembrane structure: recognition and prediction by using hydrophobicity scales through preference functions. Theoretical and computational chemistry, 5, 405-445.
+  21. ***Kidera:** Kidera, A., Konishi, Y., Oka, M., Ooi, T., & Scheraga, H. A. (1985). Statistical analysis of the physical properties of the 20 naturally occurring amino acids. Journal of Protein Chemistry, 4(1), 23-55.
+  22. ***Kuhn:** Kuhn, L. A., Swanson, C. A., Pique, M. E., Tainer, J. A., & Getzoff, E. D. (1995). Atomic and residue hydrophilicity in the context of folded protein structures. Proteins: Structure, Function, and Bioinformatics, 23(4), 536-547.
+  23. **KyteDoolittle:** Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982).
+  24. ***Levitt:** Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. Journal of molecular biology, 104(1), 59-107.
+  25. **Manavalan:** Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978).
+  26. **Miyazawa:** Miyazawa S., Jernigen R.L. Hydrophobicity scale (contact energy derived from 3D data). Macromolecules 18:534-552(1985).
+  27. **Parker:** Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986).
+  28. ***Ponnuswamy:** Ponnuswamy, P. K. (1993). Hydrophobic charactesristics of folded proteins. Progress in biophysics and molecular biology, 59(1), 57-103.
+  29. ***Prabhakaran:** Prabhakaran, M. (1990). The distribution of physical, chemical and conformational properties in signal and nascent peptides. Biochem. J, 269, 691-696.
+  30. **Rao:** Rao M.J.K., Argos P. Membrane buried helix parameter. Biochim. Biophys. Acta 869:197-214(1986).
+  31. **Rose:** Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Mean fractional area loss (f) [average area buried/standard state area]. Science 229:834-838(1985)
+  32. **Roseman:** Roseman M.A. Hydrophobicity scale (pi-r). J. Mol. Biol. 200:513-522(1988).
+  33. **Sweet:** Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983).
+  34. **Tanford:** Tanford C. Hydrophobicity scale (Contribution of hydrophobic interactions to the stability of the globular conformation of proteins). J. Am. Chem. Soc. 84:4240-4274(1962).
+  35. **Welling:** Welling G.W., Weijer W.J., Van der Zee R., Welling-Wester S. Antigenicity value X 10. FEBS Lett. 188:215-218(1985).
+  36. **Wilson:** Wilson K.J., Honegger A., Stotzel R.P., Hughes G.J. Hydrophobic constants derived from HPLC peptide retention times. Biochem. J. 199:31-41(1981).
+  37. **Wolfenden:** Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981).
+  38. ***Zimmerman:** Zimmerman, J. M., Eliezer, N., & Simha, R. (1968). The characterization of amino acid sequences in proteins by statistical methods. Journal of theoretical biology, 21(2), 170-201.
+
+
+* The mw function has been fixed to give the same result as ExPASy pI/mw tool.
+* The hmoment function is now vectorized and allow adjust the windows size. (thanks to an anonymous reviewer of RJournal).
+* The pepdata dataset and the variable name are now unified to lowercases.
+* The seqinr package dependency was removed.

R/aindex.R

@@ -14,5 +14,5 @@ aindex<-function(seq){
   # and of Leu/Ile side chains (b = 3.9) to the side chain of alanine. 
 
   # Return the result as percentage rounded to 2 decimals
-  round(sum(c(p["A"],(2.9*p["V"]),3.9*p[c("L","I")]),na.rm=T)*100,2)
+  sum(c(p["A"],(2.9*p["V"]),3.9*p[c("L","I")]),na.rm=T)*100
 }

R/hmoment.R

@@ -2,24 +2,25 @@
 # This function compute the hmoment based on Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). 
 # The hydrophobic moment detects periodicity in protein hydrophobicity. 
 # Proceedings of the National Academy of Sciences of the United States of America, 81(1), 140–4.
+# This function was written by an anonymous reviewer of the RJournal
 
 hmoment<-function(seq,angle=100,window=11){
-  # Load hydrophobicity scale
+  # Loading hydrophobicity scale
   data(H,envir = environment())
+  H<-H
   h<-H[["Eisenberg"]]
-  # Spliting the sequence
+  # Splitting the sequence in amino acids
   aa<-strsplit(toupper(seq),"")[[1]]
   window<-min(length(aa),window)
-  # Setting the sequences
+  # Setting the sequence length
   pep<-embed(aa,window)
-  # Evaluating angles and functions
+  # Applying the hmoment function to each amino acids window
   angle<- angle*(pi/180)*1:window
   vcos<-h[t(pep)]*cos(angle)
   vsin<-h[t(pep)]*sin(angle)
   dim(vcos)<-dim(vsin)<-dim(t(pep))
-  vcos<-colSums(vcos)
-  vsin<-colSums(vsin)
-  # Applying the moment function to each 10 amino acids window
+  vcos<-colSums(vcos,na.rm = TRUE)
+  vsin<-colSums(vsin,na.rm = TRUE)
   # Return the max value
   max(sqrt(vsin*vsin + vcos*vcos)/window)
 }

R/hydrophobicity.R

@@ -6,16 +6,13 @@
 # Journal of Molecular Biology, 157(1), 105–32.
 
 hydrophobicity<-function(seq,scale="KyteDoolittle"){
-  # Setting the hydrophobicity scale
-  M<-c("KyteDoolittle","AbrahamLeo",   "BullBreese",   "Guy",          "Miyazawa",     "Roseman",      "Wolfenden",   
-       "Wilson",       "Cowan3.4",     "Aboderin",     "Sweet",        "Eisenberg",    "HoppWoods",    "Manavalan",   
-       "BlackMould",   "Fauchere",     "Janin",        "Rao",          "Tanford",      "Cowan7.5",     "Chothia",
-       "Rose")
-  scale<-match.arg(scale,M)
   # Loading hydrophobicity scales
   data(H, envir = environment())
   H<-H
+  # Setting the hydrophobicity scale
+  M<-names(H)
+  scale<-match.arg(scale,M)
   # Sum the hydrophobicity of each amino acid and divide them between the sequence length
   # Return the GRAVY value
-  sum(H[[scale]][strsplit(seq,"")[[1]]])/nchar(seq)
+  sum(H[[scale]][strsplit(seq,"")[[1]]],na.rm = TRUE)/nchar(seq)
 }

R/membpos.R

@@ -5,12 +5,8 @@
 
 membpos<-function(seq,angle=100){ 
   # Setting input length
-  aa<-strsplit(toupper(seq),"")[[1]]
-  window<-min(length(aa),11)
-  pep<-character(nchar(seq)-window)
-  for (i in 1: (nchar(seq)-window)){
-    pep[i]<-paste(aa[i:(i+window)],collapse = "")
-  }
+  window<-min(nchar(seq),11)
+  pep<-substring(toupper(seq),(window):nchar(seq),first = 1:((nchar(seq)-window)+1))
   # Compute the hmoment and hydrophobicity for each amino acid window
   data<-as.data.frame(matrix(nrow = length(pep),ncol = 5))
   data[,1]<-pep

README.md

@@ -1,10 +1,10 @@
 Peptides
 ========
-R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. Include also utilities for read and plot GROMACS output files .XVG
+R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. Include also the option to read and plot XVG output files from the GROMACS molecular dynamics package.
 
 Install
 -------
-This package required R version 2.10 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.
+This package required R version 1.2.2 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.
 
 The official release of Peptides is available on CRAN. To install from CRAN, use the following command:
 ```
@@ -38,17 +38,17 @@ Available functions
 |membpos |	Compute theoretically the class of a protein sequence |
 |mw	| Compute the molecular weight of a protein sequence |
 |pI	| Compute the isoelectic point (pI) of a protein sequence |
-|plot.xvg	| Plot time series from GROMACS XVG files | 
+|plot.xvg	| Plot time series from GROMACS XVG files |
 |read.xvg |	Read XVG files from GROMACS molecular dynamics package |
 
 Available datasets
 -------------------
 | Code        | Description |
 |:----------- |:------------|
-|H  | 22 Hydrophobicity values for amino acids form ExPASy "protscale"  |
-|Pepdata | A data frame with physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial)  |
+|H  | 38 Hydrophobicity values for amino acids form various sources |
+|pepdata | A data frame with physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial)  |
 |pKscales | 9 pKa scales for the side chain of charged amino acids from various sources |
 
 Citation
 --------
-D. Osorio, P. Rondón-Villarreal and R. Torres. **Peptides: *Calculate indices and theoretical physicochemical properties of peptides and protein sequences*.**, 2014. URL: http: //CRAN.R-project.org/package=Peptides. R Package Version 1.0.
+D. Osorio, P. Rondón-Villarreal and R. Torres. **Peptides: *Calculate indices and theoretical physicochemical properties of peptides and protein sequences*.**, 2014. URL: http: //CRAN.R-project.org/package=Peptides. R Package Version 1.0.3.

inst/tests/runit.pI.R

@@ -5,8 +5,8 @@ test.pI<- function(){
   # Theoretical pI: 9.88
 
   # CHECK pI VALUE
-  checkEquals(pI("QWGRRCCGWGPGRRYCVRWC","Bje"),9.88)
+  checkEquals(pI("QWGRRCCGWGPGRRYCVRWC","Bjellqvist"),9.88,tolerance = 0.01)
 
   # CHECK OUTPUT CLASS
-  checkTrue(is.numeric(pI("QWGRRCCGWGPGRRYCVRWC","Bje")))
+  checkTrue(is.numeric(pI("QWGRRCCGWGPGRRYCVRWC","Bjellqvist")))
 }

man/AAcomp.Rd

@@ -54,13 +54,13 @@ aacomp("KWKLFKKIGIGKFLHSAKKFX")
 
 ## Output
 #          Number Mole\%
-# Tiny           4 19.05
-# Small          4 19.05
-# Aliphatic      5 23.81
-# Aromatic       5 23.81
-# Non Polar     11 52.38
-# Polar          9 42.86
-# Charged        8 38.10
-# Basic          8 38.10
-# Acidic         0  0.00
+# Tiny           4 19.048
+# Small          4 19.048
+# Aliphatic      5 23.810
+# Aromatic       5 23.810
+# NonPolar      11 52.381
+# Polar          9 42.857
+# Charged        8 38.095
+# Basic          8 38.095
+# Acidic         0  0.000
 }

man/Boman.Rd

@@ -28,5 +28,5 @@ Radzicka, A., & Wolfenden, R. (1988). Comparing the polarities of the amino acid
 # BOMAN INDEX  -1.24  
 
 boman("FLPVLAGLTPSIVPKLVCLLTKKC")
-# [1] -1.24
+# [1] -1.235833
 }

man/MW.Rd

@@ -31,5 +31,5 @@ Chicago
 # Theoretical pI/Mw: 9.88 / 2485.91 
 
 mw("QWGRRCCGWGPGRRYCVRWC")
-# [1] 2485.9
+# [1] 2485.911
 }

man/Peptides-package.Rd

@@ -2,18 +2,18 @@
 \alias{Peptides}
 \docType{package}
 \title{
-Calculate indices and theoretical physicochemical properties of peptides and proteins sequences.
+Calculate Indices and Theoretical Properties of Protein Sequences
 }
 \description{
-Calculate physicochemical properties and indices from amino acid sequences of peptides 
-and proteins. Include also utilities for read and plot GROMACS output files .XVG.
+Calculate physicochemical properties and indices from amino-acid sequences of peptides 
+and proteins. Include also the option to read and plot XVG output files from GROMACS molecular dynamics package.
 }
 \details{
 \tabular{ll}{
 Package: \tab Peptides\cr
 Type: \tab Package\cr
-Version: \tab 1.0.2\cr
-Date: \tab 2014-11-11\cr
+Version: \tab 1.0.3\cr
+Date: \tab 2014-12-12\cr
 License: \tab GPL-2\cr
 }
 }

man/aindex.Rd

@@ -5,14 +5,14 @@
 %%  ~~function to do ... ~~
 }
 \description{
-This function calculates the Ikai (1980) aliphatic index of a protein. The aindex is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins.  
+This function calculates the Ikai (1980) aliphatic index of a protein. The \code{aindex} is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins.  
 } 
 \usage{
 aindex(seq)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
-  \item{seq}{amino acid sequence string in upper case}
+  \item{seq}{amino acid sequence string}
 }
 
 \references{
@@ -22,7 +22,6 @@ Ikai (1980). Thermostability and aliphatic index of globular proteins. Journal o
 \examples{
 # COMPARED TO ExPASy ALIPHATIC INDEX
 # http://web.expasy.org/protparam/
-
 # SEQUENCE: SDKEVDEVDAALSDLEITLE
 # Aliphatic index: 117.00