Commit fb24a3b6 authored by eric pellegrini's avatar eric pellegrini Committed by Remi Perenon
Browse files

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

parent f5e41796
...@@ -46,7 +46,7 @@ EXTENSIONS = [Extension('distance_histogram', ...@@ -46,7 +46,7 @@ EXTENSIONS = [Extension('distance_histogram',
sources = glob.glob(os.path.join(QHULL_DIR, 'src','*.c')) + ['qhull.pyx'], sources = glob.glob(os.path.join(QHULL_DIR, 'src','*.c')) + ['qhull.pyx'],
define_macros = [('qh_QHpointer','1')]), define_macros = [('qh_QHpointer','1')]),
Extension('mdanse_xtc', Extension('mdanse_xtc',
include_dirs=['./xtc/include/','./xtc/'], include_dirs=[numpy.get_include(),'./xtc/include/','./xtc/'],
sources=['./xtc/src/xdrfile.c', sources=['./xtc/src/xdrfile.c',
'./xtc/src/xdr_seek.c', './xtc/src/xdr_seek.c',
'./xtc/src/xdrfile_xtc.c', './xtc/src/xdrfile_xtc.c',
......
This diff is collapsed.
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
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
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
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
...@@ -2,4 +2,4 @@ name = 'bromine' ...@@ -2,4 +2,4 @@ name = 'bromine'
symbol = 'Br' symbol = 'Br'
mass = 79.904 mass = [(78.9183, 50.69), (80.9163, 49.31)]
...@@ -2,4 +2,4 @@ name = 'carbon' ...@@ -2,4 +2,4 @@ name = 'carbon'
symbol = 'C' symbol = 'C'
mass = 12.0107 mass = [(12, 98.90), (13.003354826, 1.10)]
...@@ -2,4 +2,9 @@ name = 'calcium' ...@@ -2,4 +2,9 @@ name = 'calcium'
symbol = 'Ca' 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)]
...@@ -2,4 +2,4 @@ name = 'CH' ...@@ -2,4 +2,4 @@ name = 'CH'
symbol = 'C' symbol = 'C'
mass = 13.0190128796 mass = 12.0110369031 + 1.00797597651
...@@ -2,4 +2,4 @@ name = 'CH2' ...@@ -2,4 +2,4 @@ name = 'CH2'
symbol = 'C' symbol = 'C'
mass = 14.0269888561 mass = 12.0110369031 + 2*1.00797597651
...@@ -2,4 +2,4 @@ name = 'CH3' ...@@ -2,4 +2,4 @@ name = 'CH3'
symbol = 'C' symbol = 'C'
mass = 15.0349648326 mass = 12.0110369031 + 3*1.00797597651
...@@ -2,4 +2,4 @@ name = 'chlorine' ...@@ -2,4 +2,4 @@ name = 'chlorine'
symbol = 'Cl' symbol = 'Cl'
mass = 35.453 mass = [(34.968852721, 75.77), (36.96590262, 24.23)]
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
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
...@@ -2,4 +2,5 @@ name = 'iron' ...@@ -2,4 +2,5 @@ name = 'iron'
symbol = 'Fe' symbol = 'Fe'
mass = 55.845 mass = [(53.9396127, 5.845), (55.9349393, 91.754),
(56.9353958, 2.119), (57.9332773, 0.282)]
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
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
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
...@@ -2,4 +2,4 @@ name = 'hydrogen' ...@@ -2,4 +2,4 @@ name = 'hydrogen'
symbol = 'H' symbol = 'H'
mass = 1.0079 mass = [(1.007825035, 99.985), (2.014101779, 0.015)]
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