@@ -1,12 +1,16 @@

+2012-10-26  Steffen Neumann  <sneumann@ipb-halle.de>

+

+	* src/disop.cpp (decomposeIsotopes): Add support for element count filtering

+

 2012-04-21  Steffen Neumann  <sneumann@ipb-halle.de>

 	* R/elements.R (initializeCharges): Fixed electron mass

 2012-03-28  Steffen Neumann  <sneumann@ipb-halle.de>

 	* Added citations in package and documentation

-	

-2012-03-26  Steffen Neumann  <sneumann@ipb-halle.de>	

-	* src/disop.cpp: fixed missing UNPROTECT(), avoids warning 

+

+2012-03-26  Steffen Neumann  <sneumann@ipb-halle.de>

+	* src/disop.cpp: fixed missing UNPROTECT(), avoids warning

 	and possibly memory corruprtion and crashes

 2012-03-11  Steffen Neumann  <sneumann@ipb-halle.de>

@@ -21,9 +25,9 @@

 2012-02-23  Steffen Neumann  <sneumann@ipb-halle.de>

 	* Moved from the ancient embedded Rcpp to RcppClassic,

   	  thanks to the work of Dirk Eddelbuettel who did the porting

-	

+

 2010-11-04  Steffen Neumann  <sneumann@ipb-halle.de>

-	* Corrected bug that leads to wrong monoisotopic masses for molecules 

+	* Corrected bug that leads to wrong monoisotopic masses for molecules

 	  containing elements where the most abundant isotope is not the first one,

 	  discovered by Ralf Tautenhahn

@@ -51,10 +55,10 @@

 	can be useful for getMolecule("H3O+", elements=c(initializeCHNOPS(),initializeCharges()))

 	* R/Rdisop.R: fixed important bug which always initialised the

 	full PSE when supplying a special elements list

-	

+

 2008-04-23  sneumann  <sneumann@ipb-halle.de>

-	* R/elements.R: fixed some masses/abundances, 

+	* R/elements.R: fixed some masses/abundances,

 	                added more elements

 2008-02-15  sneumann  <sneumann@kons.ipb-sub.ipb-halle.de>

@@ -83,7 +87,7 @@

 2007-10-14  Steffen Neumann  <sneumann@ipb-halle.de>

-	* man: fixed some manpages 

+	* man: fixed some manpages

 2007-07-26  sneumann  <sneumann@ipb-halle.de>

@@ -101,7 +105,7 @@

 2007-07-03  sneumann  <sneumann@ipb-halle.de>

-	* src/disop.cpp: Clear error Message before running 

+	* src/disop.cpp: Clear error Message before running

 2007-06-14  sneumann  <sneumann@ipb-halle.de>

@@ -115,7 +119,7 @@

 2007-06-05  sneumann  <sneumann@ipb-halle.de>

 	* src/disop.cpp: Fixed stack imbalance for empty decompositions

-	* src/disop.cpp: improved Error Handling 

+	* src/disop.cpp: improved Error Handling

 2007-05-25  sneumann  <sneumann@ipb-halle.de>

@@ -125,7 +129,7 @@

 2007-05-15  Steffen Neumann  <sneumann@ipb-halle.de>

-	* Added addMolecule and subMolecule 

+	* Added addMolecule and subMolecule

 	to do arithmetics with adducts / fragments

 2007-05-04  Steffen Neumann  <sneumann@ipb-halle.de>

@@ -134,7 +138,7 @@

 2007-04-30  Steffen Neumann  <sneumann@ipb-halle.de>

-	* R/zzz.R: removed unnecesary library.dynam() 

+	* R/zzz.R: removed unnecesary library.dynam()

 	which also caused problems on systems without libR.so

 	* src/ims/*: moved imslib sources into src/ subfolder

 	instead of using unchanged libims.a

@@ -1,7 +1,7 @@

 Package: Rdisop

 Title: Decomposition of Isotopic Patterns

-Version: 1.19.0

-Date: 2012-04-21

+Version: 1.19.1

+Date: 2012-10-26

 Author: Anton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de> 

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>

 Description: Identification of metabolites using high precision mass

@@ -130,13 +130,16 @@ subMolecules <- function(formula1, formula2,

 decomposeMass <- function(mass, ppm=2.0, mzabs=0.0001,

-                          elements=NULL, filter=NULL, z=0, maxisotopes=10) {

+                          elements=NULL, filter=NULL, z=0, maxisotopes=10,

+                          minElements="C0", maxElements="C999999") {

     decomposeIsotopes(c(mass), c(1), ppm=ppm, mzabs=mzabs,

-                      elements=elements, filter=filter, z=z, maxisotopes=maxisotopes)

+                      elements=elements, filter=filter, z=z, maxisotopes=maxisotopes,

+                      minElements=minElements, maxElements=maxElements)

 }

 decomposeIsotopes <- function(masses, intensities, ppm=2.0, mzabs=0.0001,

-                              elements=NULL, filter=NULL, z=0, maxisotopes=10)

+                              elements=NULL, filter=NULL, z=0, maxisotopes=10,

+                              minElements="C0", maxElements="C999999")

 {

     # Use limited limited CHNOPS unless stated otherwise

     if (!is.list(elements) || length(elements)==0 ) {

@@ -174,6 +177,7 @@ decomposeIsotopes <- function(masses, intensities, ppm=2.0, mzabs=0.0001,

     molecules <- .Call("decomposeIsotopes",

                        masses, intensities, ppm, elements, element_order, z,

                        maxisotopes,

+                       minElements, maxElements,

                        PACKAGE="Rdisop")

     molecules

new file mode 100644

@@ -0,0 +1,15 @@

+test.empty <- function() {

+   checkEquals(length(decomposeMass(12)$formula), 1)

+}

+

+test.exact <- function() {

+   checkEquals(length(decomposeMass(12, minElements="C", maxElements="C")$formula), 1)

+}

+

+test.remove <- function() {

+  checkEquals(length(decomposeMass(12, minElements="C2", maxElements="C4")$formula), 0)

+}

+

+## Martin: Add more unit tests

+

+# decomposeMass(1.00785, minElements="C0", maxElements="C99999")

@@ -8,9 +8,10 @@

   obtained e.g.\ by FTICR or TOF mass spectrometers 

 }

 \usage{

-decomposeMass(mass, ppm=2.0, mzabs=0.0001, elements=NULL, filter=NULL, z=0, maxisotopes = 10)

+decomposeMass(mass, ppm=2.0, mzabs=0.0001, elements=NULL, filter=NULL,

+z=0, maxisotopes = 10, minElements="C0", maxElements="C999999")

 decomposeIsotopes(masses, intensities, ppm=2.0, mzabs=0.0001,

-elements=NULL, filter=NULL,  z=0, maxisotopes = 10)

+elements=NULL, filter=NULL,  z=0, maxisotopes = 10, minElements="C0", maxElements="C999999")

 isotopeScore(molecule, masses, intensities, elements = NULL, filter = NULL, z = 0)

 }

 \arguments{

@@ -24,6 +25,8 @@ isotopeScore(molecule, masses, intensities, elements = NULL, filter = NULL, z =

   \item{maxisotopes}{maximum number of isotopes shown in the resulting

     molecules}

   \item{elements}{list of allowed chemical elements, defaults to CHNOPS}

+  \item{minElements, maxElements}{Molecular formulas, which contain

+    lower and upper boundaries of allowed formula respectively}

   \item{filter}{NYI, will be a selection of DU, DBE and Nitrogen rules}

   \item{molecule}{a molecule as obtained from getMolecule() or

     decomposeMass / decomposeIsotopes}

@@ -79,7 +79,6 @@ float getDBE(const ComposedElement& molecule, int z) {

 // }}}

-

 char getParity(const ComposedElement& molecule, int charge=0) {

   // {{{ 

@@ -95,7 +94,7 @@ char getParity(const ComposedElement& molecule, int charge=0) {

 // }}}

 bool isValidMyNitrogenRule(const ComposedElement& molecule, int z) {

-  // {{{ 

+  // {{{

   bool massodd =  static_cast<int>(molecule.getNominalMass()) % 2 == 1 ? true : false;

   bool masseven = !massodd;

@@ -117,6 +116,30 @@ bool isValidMyNitrogenRule(const ComposedElement& molecule, int z) {

 }

 // }}}

+bool isWithinElementRange(const ComposedElement& molecule, const ComposedElement& minElements, const ComposedElement& maxElements) {

+// {{{

+

+  for (ComposedElement::container::const_iterator it = molecule.getElements().begin(); 

+       it != molecule.getElements().end(); ++it) {

+    

+    int mincount = static_cast<int>(minElements.getElementAbundance((it->first).getName()));

+    int maxcount = static_cast<int>(maxElements.getElementAbundance((it->first).getName()));

+

+    int count = static_cast<int>(molecule.getElementAbundance((it->first).getName()));

+      

+      if (count < mincount) {

+	return false;

+      }

+

+      // TODO: Fails e.g. for "C2N0" 

+      if (maxcount>0 && count > maxcount) {

+	return false;

+      }

+  }

+

+  return true;

+}

+// }}}

 //

 // Decomposition of Mass / Isotope Pattern

@@ -124,7 +147,8 @@ bool isValidMyNitrogenRule(const ComposedElement& molecule, int z) {

 RcppExport SEXP decomposeIsotopes(SEXP v_masses, SEXP v_abundances, SEXP s_error, 

 				  SEXP l_alphabet, SEXP v_element_order, 

-				  SEXP z, SEXP i_maxisotopes) {

+				  SEXP z, SEXP i_maxisotopes,

+				  SEXP s_minElements, SEXP s_maxElements) {

 // {{{ 

     typedef DistributionProbabilityScorer scorer_type;

@@ -229,15 +253,29 @@ RcppExport SEXP decomposeIsotopes(SEXP v_masses, SEXP v_abundances, SEXP s_error

 	// - chemical filter is applied

 	// - isotopic pattern is calculated

 	// - isotopic pattern is matched against input spectrum

+

+	// Initialize minimum/maximum element count "molecules"

+	ComposedElement minElements(CHAR(Rf_asChar(s_minElements)), alphabet);

+	ComposedElement maxElements(CHAR(Rf_asChar(s_maxElements)), alphabet);

+

 	for (decompositions_t::iterator decomps_it = decompositions.begin(); 

 		decomps_it != decompositions.end(); ++decomps_it) {

 		// creates a candidate molecule out of elemental composition and a set of elements

 		ComposedElement candidate_molecule(*decomps_it, alphabet);

+

+		// Check minimum/maximum element counts

+		if (!isWithinElementRange(candidate_molecule, minElements, maxElements)) {

+			continue;

+		} 

+

+

 		// checks on chemical filter

 // 		if (!isValidMyNitrogenRule(candidate_molecule, z)) {

 // 			continue;

 // 		} 

+

+

 		// updates molecules isotope distribution (since its not calculated upon creation: 

 		// it would be time consuming before applying chemical filter)

 		candidate_molecule.updateIsotopeDistribution();

@@ -383,7 +421,7 @@ RcppExport SEXP calculateScore(SEXP v_predictMasses, SEXP v_predictAbundances, S

 RcppExport SEXP getMolecule(SEXP s_formula, SEXP l_alphabet, 

 			    SEXP v_element_order, SEXP z, SEXP i_maxisotopes) {

-  // {{{ 

+// {{{ 

   SEXP  rl=R_NilValue; // Use this when there is nothing to be returned.

@@ -819,7 +857,7 @@ extern "C" {

       {"getMolecule", (void* (*)())&getMolecule, 4},

       {"addMolecules", (void* (*)())&addMolecules, 4},

       {"subMolecules", (void* (*)())&subMolecules, 4},

-      {"decomposeIsotopes", (void* (*)())&decomposeIsotopes, 7},

+      {"decomposeIsotopes", (void* (*)())&decomposeIsotopes, 9},

       {"calculateScore", (void* (*)())&calculateScore, 7},

       {NULL, NULL, 0}

     };