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MDANSE
Commit fb24a3b6 authored by eric pellegrini's avatar eric pellegrini Committed by Remi Perenon
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Added MMTK database entries and harmonized when needed the mass values with the MDANSE ones

parent f5e41796
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Showing with 17469 additions and 13 deletions
Extensions/setup.py
View file @ fb24a3b6
......@@ -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',
......
Extensions/xtc/xtc.c 0 → 100644
View file @ fb24a3b6
This diff is collapsed.
MDANSE/Data/Atoms/alanine 0 → 100644
View file @ fb24a3b6
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 0 → 100644
View file @ fb24a3b6
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 0 → 100644
View file @ fb24a3b6
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 0 → 100644
View file @ fb24a3b6
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
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'bromine'
symbol = 'Br'
mass = 79.904
mass = [(78.9183, 50.69), (80.9163, 49.31)]
MDANSE/Data/Atoms/c
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'carbon'
symbol = 'C'
mass = 12.0107
mass = [(12, 98.90), (13.003354826, 1.10)]
MDANSE/Data/Atoms/ca
View file @ fb24a3b6
......@@ -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
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'CH'
symbol = 'C'
mass = 13.0190128796
mass = 12.0110369031 + 1.00797597651
MDANSE/Data/Atoms/ch2
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'CH2'
symbol = 'C'
mass = 14.0269888561
mass = 12.0110369031 + 2*1.00797597651
MDANSE/Data/Atoms/ch3
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'CH3'
symbol = 'C'
mass = 15.0349648326
mass = 12.0110369031 + 3*1.00797597651
MDANSE/Data/Atoms/cl
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'chlorine'
symbol = 'Cl'
mass = 35.453
mass = [(34.968852721, 75.77), (36.96590262, 24.23)]
MDANSE/Data/Atoms/cysteine 0 → 100644
View file @ fb24a3b6
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 0 → 100644
View file @ fb24a3b6
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
View file @ fb24a3b6
......@@ -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 0 → 100644
View file @ fb24a3b6
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 0 → 100644
View file @ fb24a3b6
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 0 → 100644
View file @ fb24a3b6
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
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'hydrogen'
symbol = 'H'
mass = 1.0079
mass = [(1.007825035, 99.985), (2.014101779, 0.015)]
MDANSE/Data/Atoms/histidine 0 → 100644
View file @ fb24a3b6
name = 'histidine_deltah_calpha'
symbol = 'C'
mass = 137.141527
color = 'black'
vdW_radius = 0.17
b_coherent = 25.618529*fm
b_incoherent = 184.952000*fm
b_coherent_deut = 29.498125*fm
b_incoherent_deut = 36.587000*fm
MDANSE/Data/Atoms/histidine_deltah 0 → 100644
View file @ fb24a3b6
name = 'histidine_deltah_calpha'
symbol = 'C'
mass = 137.141527
color = 'black'
vdW_radius = 0.17
b_coherent = 25.618529*fm
b_incoherent = 184.952000*fm
b_coherent_deut = 29.498125*fm
b_incoherent_deut = 36.587000*fm
MDANSE/Data/Atoms/histidine_epsilonh 0 → 100644
View file @ fb24a3b6
name = 'histidine_epsilonh_calpha'
symbol = 'C'
mass = 137.141527
color = 'black'
vdW_radius = 0.17
b_coherent = 25.618529*fm
b_incoherent = 184.952000*fm
b_coherent_deut = 29.498125*fm
b_incoherent_deut = 36.587000*fm
MDANSE/Data/Atoms/histidine_plus 0 → 100644
View file @ fb24a3b6
name = 'histidine_plus_calpha'
symbol = 'C'
mass = 138.149503
color = 'black'
vdW_radius = 0.17
b_coherent = 25.890232*fm
b_incoherent = 210.169000*fm
b_coherent_deut = 30.243704*fm
b_incoherent_deut = 40.609000*fm
MDANSE/Data/Atoms/isoleucine 0 → 100644
View file @ fb24a3b6
name = 'isoleucine_calpha'
symbol = 'C'
mass = 113.159985
color = 'black'
vdW_radius = 0.17
b_coherent = 23.223035*fm
b_incoherent = 281.338000*fm
b_coherent_deut = 29.585951*fm
b_incoherent_deut = 48.193000*fm
MDANSE/Data/Atoms/leucine 0 → 100644
View file @ fb24a3b6
name = 'leucine_calpha'
symbol = 'C'
mass = 113.159985
color = 'black'
vdW_radius = 0.17
b_coherent = 23.223035*fm
b_incoherent = 281.338000*fm
b_coherent_deut = 29.585951*fm
b_incoherent_deut = 48.193000*fm
MDANSE/Data/Atoms/lysine 0 → 100644
View file @ fb24a3b6
name = 'lysine_calpha'
symbol = 'C'
mass = 129.182660
color = 'black'
vdW_radius = 0.17
b_coherent = 25.569308*fm
b_incoherent = 334.013000*fm
b_coherent_deut = 32.417635*fm
b_incoherent_deut = 58.478000*fm
MDANSE/Data/Atoms/methionine 0 → 100644
View file @ fb24a3b6
name = 'methionine_calpha'
symbol = 'C'
mass = 131.197384
color = 'black'
vdW_radius = 0.17
b_coherent = 21.799740*fm
b_incoherent = 230.807000*fm
b_coherent_deut = 27.388929*fm
b_incoherent_deut = 40.052000*fm
MDANSE/Data/Atoms/nh2 0 → 100644
View file @ fb24a3b6
name = 'NH2'
symbol = 'N'
mass = 16.022675
color = 'blue'
vdW_radius = 0.155000
import numpy
b_coherent = (9.300 + 2*(-3.741))*fm
b_incoherent = numpy.sqrt(2.241**2 + 2*25.217**2)*fm
b_coherent_deut = (9.300 + 2*6.674)*fm
b_incoherent_deut = numpy.sqrt(2.241**2 + 2*4.022**2)*fm
del numpy
MDANSE/Data/Atoms/nh3 0 → 100644
View file @ fb24a3b6
name = 'NH3'
symbol = 'N'
mass = 17.030651
color = 'blue'
vdW_radius = 0.155000
import numpy
b_coherent = (9.300 + 3*(-3.741))*fm
b_incoherent = numpy.sqrt(2.241**2 + 3*25.217**2)*fm
b_coherent_deut = (9.300 + 3*6.674)*fm
b_incoherent_deut = numpy.sqrt(2.241**2 + 3*4.022**2)*fm
del numpy
MDANSE/Data/Atoms/o
View file @ fb24a3b6
......@@ -2,4 +2,4 @@ name = 'oxygen'
symbol = 'O'
mass = 15.9994
mass = [(15.99491463, 99.762), (16.9991312, 0.038), (17.9991603, 0.200)]
MDANSE/Data/Atoms/phenylalanine 0 → 100644
View file @ fb24a3b6
name = 'phenylalanine_calpha'
symbol = 'C'
mass = 147.177144
color = 'black'
vdW_radius = 0.17
b_coherent = 25.375320*fm
b_incoherent = 231.759000*fm
b_coherent_deut = 30.312236*fm
b_incoherent_deut = 41.004000*fm
MDANSE/Data/Atoms/proline 0 → 100644
View file @ fb24a3b6
name = 'proline_calpha'
symbol = 'C'
mass = 97.117044
color = 'black'
vdW_radius = 0.17
b_coherent = 20.955503*fm
b_incoherent = 180.185000*fm
b_coherent_deut = 25.553150*fm
b_incoherent_deut = 31.820000*fm
MDANSE/Data/Atoms/s
View file @ fb24a3b6
......@@ -2,4 +2,5 @@ name = 'sulfur'
symbol = 'S'
mass = 32.065
mass = [(31.97207070, 95.02), (32.97145843, 0.75),
(33.96786665, 4.21), (35.9670806, 0.02)]
MDANSE/Data/Atoms/serine 0 → 100644
View file @ fb24a3b6
name = 'serine_calpha'
symbol = 'C'
mass = 87.078323
color = 'black'
vdW_radius = 0.17
b_coherent = 18.879861*fm
b_incoherent = 129.181000*fm
b_coherent_deut = 22.565131*fm
b_incoherent_deut = 23.206000*fm
MDANSE/Data/Atoms/threonine 0 → 100644
View file @ fb24a3b6
name = 'threonine_calpha'
symbol = 'C'
mass = 101.105312
color = 'black'
vdW_radius = 0.17
b_coherent = 20.703508*fm
b_incoherent = 179.900000*fm
b_coherent_deut = 25.346905*fm
b_incoherent_deut = 31.535000*fm
MDANSE/Data/Atoms/tryptophan 0 → 100644
View file @ fb24a3b6
name = 'tryptophan_calpha'
symbol = 'C'
mass = 186.213917
color = 'black'
vdW_radius = 0.17
b_coherent = 28.857993*fm
b_incoherent = 259.787000*fm
b_coherent_deut = 33.738046*fm
b_incoherent_deut = 47.837000*fm
MDANSE/Data/Atoms/tyrosine 0 → 100644
View file @ fb24a3b6
name = 'tyrosine_calpha'
symbol = 'C'
mass = 163.176449
color = 'black'
vdW_radius = 0.17
b_coherent = 26.030845*fm
b_incoherent = 231.759000*fm
b_coherent_deut = 30.863079*fm
b_incoherent_deut = 41.004000*fm
MDANSE/Data/Atoms/valine 0 → 100644
View file @ fb24a3b6
name = 'valine_calpha'
symbol = 'C'
mass = 99.132996
color = 'black'
vdW_radius = 0.17
b_coherent = 21.613035*fm
b_incoherent = 230.619000*fm
b_coherent_deut = 27.240559*fm
b_incoherent_deut = 39.864000*fm
MDANSE/Data/Atoms/zn
View file @ fb24a3b6
......@@ -2,4 +2,5 @@ name = 'zinc'
symbol = 'Zn'
mass = 65.39
mass = [(63.9291448, 48.6), (65.9260347, 27.9),
(66.9271291, 4.1), (67.9248459, 18.8), (69.925325, 0.6)]
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