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Edison rda #10

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4f5d26d
distance matrix V1: Andy
AndyDanian Nov 17, 2020
018f271
add atoms label: first col and row: Dist-Mat
AndyDanian Nov 24, 2020
7a37be6
aprovecho simetria Matriz R, adiciono indice label
AndyDanian Nov 24, 2020
779a4f8
sin indice
AndyDanian Nov 24, 2020
94f62da
New distance matrix script and RDA based on filter DataFrames
e-florez Dec 1, 2020
8bd3ed4
getting column and row index individually, trying :(
e-florez Dec 2, 2020
45a2ffe
from Df to np array, to check is filtering is more efficient
e-florez Dec 14, 2020
cfe1ab1
Numpy array to look up distances and get index
e-florez Jan 20, 2021
311e35a
function to choose atoms (pairing) in a region defined by rmin, rmax
e-florez Jan 29, 2021
6e80410
gruopping atoms index
e-florez Feb 8, 2021
72582fb
function to get index for atoms to compute distance, angle or dihedral
e-florez Feb 10, 2021
3af0fe2
dictionary with atoms index according to input list
e-florez Feb 10, 2021
9e33c4d
starting a function to get histograms for bond distance, angle and di…
e-florez Feb 10, 2021
d4cd033
starting function to make RDA
e-florez Feb 10, 2021
225865e
function to get histograms for distance, angle, and dihedral is DONE …
e-florez Feb 11, 2021
6d67afd
starting Stern-Limbach atom transfer analysis
e-florez Feb 21, 2021
4bf6594
fixing RDA indixes duplicates
e-florez Feb 23, 2021
061c081
Stern-Limbach atom transfer analysis is working
e-florez Feb 24, 2021
5def9ca
Stern-Limbach analysis is DONE. We need to thing about how to choose …
e-florez Feb 24, 2021
1ef79d3
function to plot a Stern-Limbach analysis
e-florez Feb 24, 2021
bc35ccc
Done. We should think about UX and how to desing a good integration.
e-florez Feb 25, 2021
f5ca438
Merge pull request #8 from e-florez/Matriz_R_Andy
cesar-ibarguen Mar 2, 2021
7ad3d39
Improving the function to choose index for atoms (file: atoms_index_l…
e-florez Mar 5, 2021
c5fe877
adding ice Ih unit cell coordinates .CIF
e-florez Mar 14, 2021
c8b7234
Improving distance matrix nested loop
e-florez Mar 16, 2021
99c28db
Merge branch 'edison_rda' of github.com:e-florez/radial_distribution …
e-florez Mar 23, 2022
3fc1a79
ploting RDA
e-florez Mar 23, 2022
bb6b72d
improving notebooks for Hg(H2O) paper
e-florez Sep 15, 2022
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3 changes: 3 additions & 0 deletions .idea/.gitignore
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6 changes: 6 additions & 0 deletions .idea/inspectionProfiles/profiles_settings.xml
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8 changes: 8 additions & 0 deletions .idea/modules.xml
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10 changes: 10 additions & 0 deletions .idea/radial_distribution.iml
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6 changes: 6 additions & 0 deletions .idea/vcs.xml
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9 changes: 7 additions & 2 deletions .vscode/settings.json
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114 changes: 114 additions & 0 deletions 0zd.xyz
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112
Chemical Component 0ZD, taken from http://ligand-expo.rcsb.org/reports/0/0ZD/index.html
O62 -16.202 18.781 -35.336 O 1 O62
C60 -16.663 19.920 -35.553 C 2 C60
O61 -16.903 20.277 -36.716 O 3 O61
C56 -16.953 20.857 -34.410 C 4 C56
C57 -18.450 20.786 -34.033 C 5 C57
C59 -18.804 21.710 -32.879 C 6 C59
C58 -19.029 19.391 -33.818 C 7 C58
N40 -15.967 20.685 -33.315 N 8 N40
S41 -14.862 21.721 -33.178 S 9 S41
O43 -15.375 23.018 -33.550 O 10 O43
C45 -13.666 21.295 -34.178 C 11 C45
C5A -13.608 21.787 -35.489 C 12 C5A
C49 -12.580 21.412 -36.358 C 13 C49
C48 -11.556 20.555 -35.938 C 14 C48
C50 -10.438 20.173 -36.850 C 15 C50
C55 -9.924 18.877 -36.889 C 16 C55
C54 -8.871 18.564 -37.754 C 17 C54
C53 -8.316 19.542 -38.575 C 18 C53
C52 -8.806 20.842 -38.528 C 19 C52
C51 -9.865 21.147 -37.670 C 20 C51
C47 -11.595 20.071 -34.623 C 21 C47
C46 -12.639 20.435 -33.755 C 22 C46
O42 -14.303 21.712 -31.839 O 23 O42
C39 -15.913 19.409 -32.579 C 24 C39
C38 -16.273 19.461 -31.104 C 25 C38
N37 -16.036 18.123 -30.578 N 26 N37
C35 -16.798 17.063 -30.835 C 27 C35
O36 -17.843 17.161 -31.482 O 28 O36
C33 -16.400 15.716 -30.280 C 29 C33
C32 -17.287 14.645 -30.364 C 30 C32
C31 -16.928 13.402 -29.843 C 31 C31
C30 -15.687 13.222 -29.239 C 32 C30
C34 -15.155 15.529 -29.668 C 33 C34
C29 -14.789 14.283 -29.148 C 34 C29
C27 -13.449 14.069 -28.495 C 35 C27
O28 -13.253 13.028 -27.868 O 36 O28
N26 -12.488 14.993 -28.605 N 37 N26
C25 -11.210 14.876 -27.900 C 38 C25
C24 -11.412 15.375 -26.475 C 39 C24
N16 -10.222 15.420 -25.603 N 40 N16
C17 -10.014 14.395 -24.551 C 41 C17
C21 -11.099 14.469 -23.506 C 42 C21
O23 -10.828 14.180 -22.324 O 43 O23
O22 -12.261 14.798 -23.804 O 44 O22
C18 -9.827 12.933 -24.999 C 45 C18
C20 -8.739 12.773 -26.054 C 46 C20
C19 -11.107 12.190 -25.375 C 47 C19
S13 -9.378 16.690 -25.588 S 48 S13
O14 -8.025 16.425 -25.183 O 49 O14
O15 -9.451 17.315 -26.887 O 50 O15
C10 -10.049 17.691 -24.490 C 51 C10
C9 -9.657 17.722 -23.139 C 52 C9
C8 -10.253 18.590 -22.217 C 53 C8
C11 -11.067 18.572 -24.877 C 54 C11
C12 -11.666 19.442 -23.963 C 55 C12
C7 -11.271 19.457 -22.619 C 56 C7
C1 -11.886 20.424 -21.661 C 57 C1
C6 -13.250 20.714 -21.686 C 58 C6
C5 -13.791 21.636 -20.787 C 59 C5
C4 -12.965 22.295 -19.879 C 60 C4
C3 -11.601 22.028 -19.863 C 61 C3
C2 -11.066 21.100 -20.749 C 62 C2
H1 -16.095 18.320 -36.160 H 63 H1
H2 -16.797 21.872 -34.805 H 64 H2
H3 -18.985 21.191 -34.905 H 65 H3
H4 -19.877 21.620 -32.653 H 66 H4
H5 -18.217 21.430 -31.992 H 67 H5
H6 -18.574 22.749 -33.157 H 68 H6
H7 -20.094 19.472 -33.556 H 69 H7
H8 -18.922 18.803 -34.742 H 70 H8
H9 -18.488 18.891 -33.001 H 71 H9
H10 -14.372 22.468 -35.834 H 72 H10
H11 -12.575 21.789 -37.370 H 73 H11
H12 -10.341 18.113 -36.249 H 74 H12
H13 -8.485 17.556 -37.786 H 75 H13
H14 -7.508 19.291 -39.246 H 76 H14
H15 -8.371 21.610 -39.150 H 77 H15
H16 -10.248 22.156 -37.640 H 78 H16
H17 -10.815 19.411 -34.273 H 79 H17
H18 -12.652 20.047 -32.747 H 80 H18
H19 -16.609 18.711 -33.068 H 81 H19
H20 -14.887 19.020 -32.659 H 82 H20
H21 -15.639 20.193 -30.583 H 83 H21
H22 -17.330 19.737 -30.979 H 84 H22
H23 -15.244 17.992 -29.981 H 85 H23
H24 -18.251 14.777 -30.832 H 86 H24
H25 -17.618 12.573 -29.909 H 87 H25
H26 -15.419 12.255 -28.839 H 88 H26
H27 -14.467 16.359 -29.596 H 89 H27
H28 -12.648 15.790 -29.188 H 90 H28
H29 -10.887 13.825 -27.885 H 91 H29
H30 -10.448 15.487 -28.405 H 92 H30
H31 -11.817 16.396 -26.536 H 93 H31
H32 -12.150 14.716 -25.995 H 94 H32
H33 -9.081 14.668 -24.037 H 95 H33
H34 -11.610 14.261 -21.790 H 96 H34
H35 -9.444 12.411 -24.110 H 97 H35
H36 -7.840 13.323 -25.740 H 98 H36
H37 -8.494 11.707 -26.170 H 99 H37
H38 -9.098 13.173 -27.014 H 100 H38
H39 -11.860 12.334 -24.587 H 101 H39
H40 -11.493 12.583 -26.327 H 102 H40
H41 -10.890 11.117 -25.483 H 103 H41
H42 -8.874 17.057 -22.804 H 104 H42
H43 -9.924 18.589 -21.188 H 105 H43
H44 -11.396 18.579 -25.906 H 106 H44
H45 -12.444 20.112 -24.297 H 107 H45
H46 -13.891 20.223 -22.404 H 108 H46
H47 -14.852 21.838 -20.796 H 109 H47
H48 -13.384 23.012 -19.189 H 110 H48
H49 -10.958 22.541 -19.163 H 111 H49
H50 -10.005 20.898 -20.734 H 112 H50
Binary file removed 2020-10-14-Note-11-34.pdf
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39 changes: 39 additions & 0 deletions ada_C-C-C.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
# angle [Degrees] occurrence (total=50)
0.000000 0
5.135135 0
10.270270 0
15.405405 0
20.540541 0
25.675676 0
30.810811 0
35.945946 0
41.081081 0
46.216216 0
51.351351 0
56.486486 0
61.621622 0
66.756757 0
71.891892 0
77.027027 0
82.162162 0
87.297297 0
92.432432 0
97.567568 0
102.702703 0
107.837838 0
112.972973 4
118.108108 5
123.243243 41
128.378378 0
133.513514 0
138.648649 0
143.783784 0
148.918919 0
154.054054 0
159.189189 0
164.324324 0
169.459459 0
174.594595 0
179.729730 0
184.864865 0
190.000000 0
39 changes: 39 additions & 0 deletions ada_C1-C2-C3.dat
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# angle [Degrees] occurrence (total=1)
0.000000 0
5.135135 0
10.270270 0
15.405405 0
20.540541 0
25.675676 0
30.810811 0
35.945946 0
41.081081 0
46.216216 0
51.351351 0
56.486486 0
61.621622 0
66.756757 0
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87.297297 0
92.432432 0
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102.702703 0
107.837838 0
112.972973 0
118.108108 0
123.243243 1
128.378378 0
133.513514 0
138.648649 0
143.783784 0
148.918919 0
154.054054 0
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164.324324 0
169.459459 0
174.594595 0
179.729730 0
184.864865 0
190.000000 0
39 changes: 39 additions & 0 deletions ada_C5-C4-C3.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
# angle [Degrees] occurrence (total=1)
0.000000 0
5.135135 0
10.270270 0
15.405405 0
20.540541 0
25.675676 0
30.810811 0
35.945946 0
41.081081 0
46.216216 0
51.351351 0
56.486486 0
61.621622 0
66.756757 0
71.891892 0
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82.162162 0
87.297297 0
92.432432 0
97.567568 0
102.702703 0
107.837838 0
112.972973 0
118.108108 0
123.243243 1
128.378378 0
133.513514 0
138.648649 0
143.783784 0
148.918919 0
154.054054 0
159.189189 0
164.324324 0
169.459459 0
174.594595 0
179.729730 0
184.864865 0
190.000000 0
39 changes: 39 additions & 0 deletions ada_H-O-H.dat
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# angle [Degrees] occurrence (total=27)
0.000000 0
5.135135 0
10.270270 0
15.405405 6
20.540541 0
25.675676 0
30.810811 2
35.945946 0
41.081081 0
46.216216 0
51.351351 0
56.486486 0
61.621622 0
66.756757 0
71.891892 0
77.027027 0
82.162162 0
87.297297 0
92.432432 0
97.567568 0
102.702703 0
107.837838 0
112.972973 8
118.108108 2
123.243243 8
128.378378 0
133.513514 1
138.648649 0
143.783784 0
148.918919 0
154.054054 0
159.189189 0
164.324324 0
169.459459 0
174.594595 0
179.729730 0
184.864865 0
190.000000 0
39 changes: 39 additions & 0 deletions ada_Hg-O-H.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
# angle [Degrees] occurrence (total=6)
0.000000 0
5.135135 0
10.270270 0
15.405405 0
20.540541 0
25.675676 0
30.810811 0
35.945946 0
41.081081 0
46.216216 0
51.351351 0
56.486486 0
61.621622 0
66.756757 0
71.891892 0
77.027027 0
82.162162 0
87.297297 0
92.432432 0
97.567568 0
102.702703 0
107.837838 0
112.972973 1
118.108108 2
123.243243 1
128.378378 2
133.513514 0
138.648649 0
143.783784 0
148.918919 0
154.054054 0
159.189189 0
164.324324 0
169.459459 0
174.594595 0
179.729730 0
184.864865 0
190.000000 0
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