Added MMTK database entries and harmonized when needed the mass values with the MDANSE ones

Extensions/setup.py

@@ -46,7 +46,7 @@ EXTENSIONS = [Extension('distance_histogram',
                         sources =  glob.glob(os.path.join(QHULL_DIR, 'src','*.c')) + ['qhull.pyx'],
                         define_macros = [('qh_QHpointer','1')]),
               Extension('mdanse_xtc',
-                        include_dirs=['./xtc/include/','./xtc/'],
+                        include_dirs=[numpy.get_include(),'./xtc/include/','./xtc/'],
                         sources=['./xtc/src/xdrfile.c',
                                  './xtc/src/xdr_seek.c',
                                  './xtc/src/xdrfile_xtc.c',

MDANSE/Data/Atoms/alanine

+name = 'alanine_calpha'
+symbol = 'C'
+mass = 71.079018
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 17.965276*fm
+b_incoherent = 129.181000*fm
+b_coherent_deut = 21.805667*fm
+b_incoherent_deut = 23.206000*fm

MDANSE/Data/Atoms/arginine

+name = 'arginine_calpha'
+symbol = 'C'
+mass = 157.196106
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 28.753600*fm
+b_incoherent = 338.495000*fm
+b_coherent_deut = 34.984040*fm
+b_incoherent_deut = 62.960000*fm

MDANSE/Data/Atoms/asparagine

+name = 'asparagine_calpha'
+symbol = 'C'
+mass = 114.104059
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 22.385936*fm
+b_incoherent = 156.924000*fm
+b_coherent_deut = 26.161294*fm
+b_incoherent_deut = 29.754000*fm

MDANSE/Data/Atoms/aspartic_acid

+name = 'aspartic_acid_calpha'
+symbol = 'C'
+mass = 114.080689
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 20.502390*fm
+b_incoherent = 104.249000*fm
+b_coherent_deut = 23.292419*fm
+b_incoherent_deut = 19.469000*fm

MDANSE/Data/Atoms/br

@@ -2,4 +2,4 @@ name = 'bromine'
 
 symbol = 'Br'
 
-mass = 79.904
+mass = [(78.9183, 50.69), (80.9163, 49.31)]

MDANSE/Data/Atoms/c

@@ -2,4 +2,4 @@ name = 'carbon'
 
 symbol = 'C'
 
-mass = 12.0107
+mass = [(12, 98.90), (13.003354826, 1.10)]

MDANSE/Data/Atoms/ca

@@ -2,4 +2,9 @@ name = 'calcium'
 
 symbol = 'Ca'
 
-mass = 40.078
+mass = [(39.9625906, 96.941),
+        (41.9586176,  0.647),
+        (42.9587662,  0.135),
+        (43.9554806,  2.086),
+        (45.953689,   0.004),
+        (47.952533,   0.187)]

MDANSE/Data/Atoms/ch

@@ -2,4 +2,4 @@ name = 'CH'
 
 symbol = 'C'
 
-mass = 13.0190128796
+mass = 12.0110369031 + 1.00797597651

MDANSE/Data/Atoms/ch2

@@ -2,4 +2,4 @@ name = 'CH2'
 
 symbol = 'C'
 
-mass = 14.0269888561
+mass = 12.0110369031 + 2*1.00797597651

MDANSE/Data/Atoms/ch3

@@ -2,4 +2,4 @@ name = 'CH3'
 
 symbol = 'C'
 
-mass = 15.0349648326
+mass = 12.0110369031 + 3*1.00797597651

MDANSE/Data/Atoms/cl

@@ -2,4 +2,4 @@ name = 'chlorine'
 
 symbol = 'Cl'
 
-mass = 35.453
+mass = [(34.968852721, 75.77), (36.96590262, 24.23)]

MDANSE/Data/Atoms/cysteine

+name = 'cysteine_calpha'
+symbol = 'C'
+mass = 103.143407
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 18.189463*fm
+b_incoherent = 129.369000*fm
+b_coherent_deut = 21.990737*fm
+b_incoherent_deut = 23.394000*fm

MDANSE/Data/Atoms/cystine_ss

+name = 'cystine_calpha'
+symbol = 'C'
+mass = 102.135431
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 17.800603*fm
+b_incoherent = 104.152000*fm
+b_coherent_deut = 20.953526*fm
+b_incoherent_deut = 19.372000*fm

MDANSE/Data/Atoms/fe

@@ -2,4 +2,5 @@ name = 'iron'
 
 symbol = 'Fe'
 
-mass = 55.845
+mass = [(53.9396127, 5.845), (55.9349393, 91.754),
+	    (56.9353958, 2.119), (57.9332773, 0.282)]

MDANSE/Data/Atoms/glutamic_acid

+name = 'glutamic_acid_calpha'
+symbol = 'C'
+mass = 128.107678
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 22.193109*fm
+b_incoherent = 154.968000*fm
+b_coherent_deut = 25.996485*fm
+b_incoherent_deut = 27.798000*fm

MDANSE/Data/Atoms/glutamine

+name = 'glutamine_calpha'
+symbol = 'C'
+mass = 128.131048
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 23.944023*fm
+b_incoherent = 207.643000*fm
+b_coherent_deut = 28.595345*fm
+b_incoherent_deut = 38.083000*fm

MDANSE/Data/Atoms/glycine

+name = 'glycine_calpha'
+symbol = 'C'
+mass = 57.052030
+color = 'black'
+vdW_radius = 0.17
+
+b_coherent = 15.829247*fm
+b_incoherent = 78.462000*fm
+b_coherent_deut = 18.498829*fm
+b_incoherent_deut = 14.877000*fm

MDANSE/Data/Atoms/h

@@ -2,4 +2,4 @@ name = 'hydrogen'
 
 symbol = 'H'
 
-mass = 1.0079
+mass = [(1.007825035, 99.985), (2.014101779, 0.015)]