Geometriniu savybiu aptikimas atviroje mau molekuliu duomenu - - PowerPoint PPT Presentation

Geometriniu ˛ savybiu ˛ aptikimas atviroje mažu ˛ molekuliu ˛ duomenu ˛ baz˙ eje COD

Andrius Merkys, Antanas Vaitkus, Mykolas Okuliˇ c-Kazarinas ir Saulius Gražulis Vilnius, 2016

Vilniaus universiteto Biotechnologijos institutas

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Strukt¯ urin˙ es mažu ˛ molekuliu ˛ duomenu ˛ baz˙ es

Crystallography Open Database (COD) Cambridge Structural Database (CSD) Inorganic Crystal Structure Database (ICSD) 350 000 i ˛rašu ˛ 800 000 i ˛rašu ˛ 180 000 i ˛rašu ˛ atvira prenumeruojama prenumeruojama 2016 m. vasario m˙

• en. duomenys

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Vandenilio talpa kristaluose

in silico tyrimas COD duomenu ˛ baz˙ eje

COD 8100961

Breternitz ir Gregory (2015)

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Ar grafenas tik vienas toks?

Dvimaˇ ciu ˛ alotropu ˛ paieška COD ir ICSD duomenu ˛ baz˙ ese Bi2 C8 Gd In La Nd Pr Sm

COD 9010988

Bi4 Br C60 C60 Ga2 Hg I P2 P42 Sb4 Sn Te2 As2 As4 Ba C16 C2 C8 P4

COD (15 vnt.) ICSD (19 vnt.) Mounet et al. (rengiama)

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Molekuliu ˛ geometrin˙ es savyb˙ es

1.20 1.25 1.30 1.35 1.40 1.45 1.50 1.55 5 10 15 bond length Frequency 50 100 150 200 250 300 350 5 10 15 20 25 30 dihedral angle Frequency 120 125 130 135 140 2 4 6 8 angle size Frequency

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Kristalo simetrijos atstatymas

Pavyzdys: grafito sluoksnis, COD 1011060

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Tarpatominiu ˛ jungˇ ciu ˛ paieška

Pavyzdys: grafito sluoksnis, COD 1011060

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Simetriškai ekvivalenˇ ciu ˛ stebiniu ˛ atmetimas

Pavyzdys: benzeno molekul˙ e, COD COD 2100348

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Stebiniu ˛ imˇ ciu ˛ aprašymas

1.30 1.35 1.40 1.45 1.50 50 100 150 bond length Frequency

N N

1.20 1.25 1.30 1.35 1.40 1.45 1.50 1.55 5 10 15 bond length Frequency

         

C2i−1 H C2i H

          n

1.30 1.35 1.40 1.45 1.50 20 40 60 80 100 bond length Frequency

N N N N

1.30 1.35 1.40 1.45 1.50 20 40 60 80 bond length Frequency

H3C C CH3 CH3 C

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COD geometrijos naršykl˙ e http://www.crystallography.net/geometry

• rder by class name (ascending)
• rder by observation count (descending)

To search for bond models, please enter one to two COD atom class names separated by ';'. Examples: C(CC)2;C(CC)2 c(cCH)2(H);c(cCH)2(H) To search for angle models, please enter three COD atom class names separated by ';'. To search for dihedral angle models, please enter four COD atom class names separated by ';'. Percent sign (%) can be used as a wildcard.

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Paieška: poliino anglis-anglis jungties ilgis

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Dõminanˇ ciu ˛ deskriptoriu ˛ pasirinkimas

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Poliinu ˛ jungtys COD duomenu ˛ baz˙ eje

• rder by class name (ascending)
• rder by observation count (descending)

Distribution of C(CC)2 - C(CC)2 bonds

Breaks: Min: Max: Histogram width: Warning: models for this class are scheduled for recalculation, out-of-date models are presented here for reference only. Distribution Peaks BIC Log-likelihood cauchy 3

• 2983.63250734474 1521.29969433851

cauchy 4

• 2972.23756189253 1526.65851186221

cauchy 5

• 2954.17602788954 1528.68403511053

cauchy 6

• 2945.47851368168 1535.3915682564

cauchy 7

• 2931.49848709219 1539.45784521146

cauchy 8

• 2931.13696008285 1550.3333719566

cauchy 9

• 2911.97656549846 1551.80946491421

cauchy 10

• 2903.18311848377 1558.46903165667

cauchy 2

• 2306.60210414815 1171.72820249042

gaussian 4

• 2174.55991783404 1127.81968983297

gaussian 5

• 2164.18853401055 1133.69028817103

gaussian 2

• 1955.22813260451 996.041216718596

gaussian 3

• 1947.4479559367 1003.2074186345

gaussian 1

• 1773.73018669565 894.235953514359

cauchy 1

• 1556.82925243875 785.785486385914

gaussian 6 NaN NaN gaussian 7 NaN NaN gaussian 8 NaN NaN gaussian 9 NaN NaN gaussian 10 NaN NaN Show individual mixture components

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Poliinu ˛ jungtys COD duomenu ˛ baz˙ eje

• rder by class name (ascending)
• rder by observation count (descending)

Distribution of C(CC)2 - C(CC)2 bonds

Breaks: Min: Max: Histogram width: Warning: models for this class are scheduled for recalculation, out-of-date models are presented here for reference only. Distribution Peaks BIC Log-likelihood cauchy 3

• 2983.63250734474 1521.29969433851

cauchy 4

• 2972.23756189253 1526.65851186221

cauchy 5

• 2954.17602788954 1528.68403511053

cauchy 6

• 2945.47851368168 1535.3915682564

cauchy 7

• 2931.49848709219 1539.45784521146

cauchy 8

• 2931.13696008285 1550.3333719566

cauchy 9

• 2911.97656549846 1551.80946491421

cauchy 10

• 2903.18311848377 1558.46903165667

cauchy 2

• 2306.60210414815 1171.72820249042

gaussian 4

• 2174.55991783404 1127.81968983297

gaussian 5

• 2164.18853401055 1133.69028817103

gaussian 2

• 1955.22813260451 996.041216718596

gaussian 3

• 1947.4479559367 1003.2074186345

gaussian 1

• 1773.73018669565 894.235953514359

cauchy 1

• 1556.82925243875 785.785486385914

gaussian 6 NaN NaN gaussian 7 NaN NaN gaussian 8 NaN NaN gaussian 9 NaN NaN gaussian 10 NaN NaN Show individual mixture components

• C2i−1

C2i

• n

[

C

]m

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Tolimesni planai

◮ Atvira prieiga prie duomenu

˛ MySQL protokolu

◮ Periodiškas duomenu

˛ baz˙ es atnaujinimas

◮ Strukt¯

uru ˛-išskirˇ ciu ˛ pašalinimas iš imties

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Pad˙ ekos

VU Biotechnologijos institutas Virginijus Šikšnys (skyriaus ved˙ ejas) Saulius Gražulis Antanas Vaitkus Mykolas Okuliˇ c-Kazarinas COD Advisory Board Daniel Chateigner Robert T. Downs Werner Kaminsky Armel Le Bail Luca Lutterotti Peter Moeck Peter Murray-Rust Miguel Quirós

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Aˇ ci¯ u už d˙ emesi ˛!

http://en.wikipedia.org/wiki/Topaz http://www.crystallography.net/2207377.html A path to freedom: GNU → Linux → Ubuntu → MySQL → R → L

AT

E X→ TikZ → Beamer