On 11/18/2013 01:32 PM, Geoffrey Hutchison wrote: >> make an isotope/mass vector a member of OBElement instead of its "mass >> Atomic mass (in amu)", but that's just me.) > > The problem is that the full isotope table is fairly huge and rarely used. Checking memory use, I see that in my programs, it's usually never even initialized, while the element table obviously is. > > I agree that it's perhaps not as convenient, but that's something to consider in a backwards-incompatible Open Babel 3 effort.
The file itself is 58K, even if you get double that with the overhead, I wouldn't call it huge even by the cellphone standards anymore... (I calculate C13, N15, and C13+N15 mol. weights for each molecule -- I work for NMR people -- so I use those 2 all the time.) In the meantime, here's the patch -- feel free to rename "Prevalent" if you can think of a better word. (All I could think of along the lines of "NaturalAbundance" was too long for my liking.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
--- openbabel-2.3.2.orig/include/openbabel/data.h 2010-10-09 21:05:12.000000000 -0500
+++ openbabel-2.3.2/include/openbabel/data.h 2013-11-14 14:14:35.620535084 -0600
@@ -218,10 +218,18 @@
size_t GetSize() { return _isotopes.size(); }
void ParseLine(const char*);
- //! \return the exact masss of the isotope
+ //! \return the exact mass of the isotope
//! (or by default (i.e. "isotope 0") the most abundant isotope)
double GetExactMass(const unsigned int atomicNum,
const unsigned int isotope = 0);
+
+ //! \return the number of "natural abundance" isotope (aka isotope 0)
+ // or 0 if there's a problem
+ unsigned int GetPrevalentIsotope( const unsigned int ele );
+
+ //! \return true if the isotope is known to exist, false otherwise (on error as well)
+ bool IsValidIsotope( const unsigned int ele, const unsigned int iso );
+
};
// class introduction in data.cpp
--- openbabel-2.3.2.orig/src/data.cpp 2012-10-03 14:08:15.000000000 -0500
+++ openbabel-2.3.2/src/data.cpp 2013-11-14 14:14:48.996570004 -0600
@@ -425,6 +425,40 @@
return 0.0;
}
+ unsigned int OBIsotopeTable::GetPrevalentIsotope( const unsigned int ele )
+ {
+ if (!_init) Init();
+ unsigned int iso = 0;
+
+ if (ele > _isotopes.size()) return iso;
+ if (_isotopes[ele].size() < 1) return iso;
+
+ double mass = _isotopes[ele][0].second;
+ for( std::vector<std::pair <unsigned int, double> >::iterator i = _isotopes[ele].begin(); i != _isotopes[ele].end(); i++ )
+ if( (i->first != 0) && (i->second == mass) ) {
+ iso = i->first;
+ break;
+ }
+ return iso;
+ }
+
+ bool OBIsotopeTable::IsValidIsotope( const unsigned int ele, const unsigned int iso )
+ {
+ if (!_init) Init();
+
+ if( iso == 0 ) return true;
+ if (ele > _isotopes.size()) return false;
+ if (_isotopes[ele].size() < 1) return false;
+
+ bool rc = false;
+ for( std::vector<std::pair <unsigned int, double> >::iterator i = _isotopes[ele].begin(); i != _isotopes[ele].end(); i++ )
+ if( i->first == iso ) {
+ rc = true;
+ break;
+ }
+ return rc;
+ }
+
/** \class OBTypeTable data.h <openbabel/data.h>
\brief Atom Type Translation Table
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