Skip to content

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

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

parent f5e41796
Expand all Hide whitespace changes
Inline Side-by-side
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)]
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment