Looking at https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/atomic_data.cpp , the sixth column has the masses to the third decimal place. Using these, 7*1.008+3*12.011+14.007+2*15.999 = 89.094
So, just a matter of where one rounds. Given the uncertainties in http://iupac.org/publications/pac/78/11/2051/ , I would argue that you are concerned with precision at a level beyond what is currently accepted. -- David Hall On Thursday, December 12, 2013 at 5:13 PM, Dimitri Maziuk wrote: > Hi, > > what exactly does > > rdkit.Chem.rdMolDescriptors._CalcMolWt( mol ) > > do? : > > #!/usr/bin/python -u > import sys > import rdkit > import rdkit.Chem.rdMolDescriptors > > PYBEL_PATH = "/share/linux/openbabel-2.3.2/lib" > sys.path.append( PYBEL_PATH ) > import pybel > > H = { "std" : 1.00794 } > C = { "std" : 12.0107 } > N = { "std" : 14.0067 } > O = { "std" : 15.9994 } > > sdf = "CID_5950.sdf" > > mol = rdkit.Chem.SupplierFromFilename( sdf ).next() > rdkit.Chem.AddHs( mol ) > rdwt = rdkit.Chem.rdMolDescriptors._CalcMolWt( mol ) > > obmol = pybel.readfile( "sdf", sdf ).next() > obmol.addh() > obwt = obmol.molwt > > mywt = 0.0 > for a in obmol.atoms : > if a.OBAtom.IsHydrogen() : mywt += H["std"] > if a.OBAtom.IsCarbon() : mywt += C["std"] > if a.OBAtom.IsNitrogen() : mywt += N["std"] > if a.OBAtom.IsOxygen() : mywt += O["std"] > > print > print "ALA", rdkit.Chem.rdMolDescriptors.CalcMolFormula( mol ) > print "**********************" > print "me", mywt > print "ob", obwt > print "rd", rdwt > ######################### > > The output: > > ALA C3H7NO2 > ********************** > me 89.09318 > ob 89.09318 > rd 89.094 > > (without pretty-printing it's > me 89.093180000000032 > ob 89.093180000000032 > rd 89.093999999999994) > > What am I missing? > > TIA > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > (mailto:[email protected]) > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
