Professional Documents
Culture Documents
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File() Open().
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OpenBabel-a
CML, xyz, PBD .
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ethanol.cml
Ball and Stick .
Draw ool Navigate ool.
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. Adjust Hydrogens
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( ). Adjust Hydrogens
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F99
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UFF
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Manipulate Tool
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'Edit->Und' ( Ctrl+Z).
File-> Save as... .
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CM
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1.
2.
2.1.
2.2. SMARTS
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2.4.
2.5.
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Display Types
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Selection Tool Selections Extensions.
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https://www.youtube.com/watch?
feature=player_embedded&v=Y_buZIJ2dz8
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Ctrl+A
Ctrl+Shift+A
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1: / Select.
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(.
Stick).O
(. Simple Wireframe).
SMARTS
[SMARTS] .
SMARTS
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[SMILES] [SMARTS]:
SMILES Opis
C(=O)selektujte sve karboksilne kiseline, estre,...
N selektujte sve alifatine atome azota
N selektujte sve aromatine atome azota
n1ccccc1 selektujte sve atome u piridinskom prstenu
[SMARTS] .
SMARTS-
SMILES:
SMARTS Opis
a1aaaa1 selektujte sve aromatine atome u estolanom
prstenu
A selektujte sve alifatine atome
[O,N][#6]
selektujte ONandNC fragmente(O&N alifatini,
C (moe biti alifatian ili aromatian)
SMILES SMARTS
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[SMILES - A Simplified Chemical Language] [SMARTS - A Language for
Describing Molecular Patterns]
Select by Element...
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2: .
(. "VAL", "TYR", ...). VAL TYR
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, 1DRF.pdb
FOL..
1DRF.pdb:
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HET
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HETNAM
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FORMUL
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ATOM
0.00
ATOM
0.00
ATOM
0.00
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FOL
A 187
32
FOL
4
1508
1509
1510
FOL
C19 H19 N7 O6
N1FOL A 187
N
C2FOL A 187
C
NA2FOL A 187
N
26.779
12.325
-3.996
1.00
27.684
12.453
-5.033
1.00
27.113
12.270
-6.218
1.00
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Select>AddNamedSelection....
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Settings>Toolbars>ProjectTree.
Settings>ConfigureAvogadro... ( 5).
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UserSelections, Molecule, Atoms.
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NavigateTool
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Build >Remove Hydrogens
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Settings
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Stick settings
Stick
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settings residue name
atoms label .
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OK. , Objects Stick settings
display only selected primitives. ,
6 :
: SMILES
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SMILES-
SMILES-
-- --
SMILES,
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. SMILES manual .
SMILES .
, SMILES-
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. SMILES
Wikipedia, PubChem ChemSpider.
SMILES B, C, N, O, P, S, F, Cl,
Br, I. , ,
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C
CC
CCC
CCO or OCC
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Br
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CC(O)C or CC(C)O or OCC(C)C
2,2- CC(Br)(Br)C or BrC(C)(Br)C
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C=C
1- C=CCC
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2-C/C=C/C
2-C/C=C\C
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C#C
C#CC
HCNC#N
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SMILES
SMARTS
Build .
(Peptide Builder).
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Open Babel
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MMFF94(s):
UFF:
Chemical:
(, , ...)
OpenBabelwiki
1 s
1.1 UFF
1.2 MMFF94(s)
1.2.1
1.2.2
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MMFF94(s)
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>>>importAvogadro
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>>>help(Avogadro)
Help on module Avogadro:
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DATA
molecule = <Avogadro.Molecule object at 0x2128130>
molecules = <Avogadro.MoleculeList object at 0x20a33d0>
>>> help (Avogadro.Molecule)
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2 2 DATA. ,
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>>>Avogadro.molecule.clear()
(, ) ( ).
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>>>newMol = Avogadro.Molecule()
# error
Traceback (most recent call last):
File "<string>", line 1, in <module>
RuntimeError: This class cannot be instantiated from Python
>>>newMol = Avogadro.molecules.addMolecule()
# works
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Align.
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Align
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Tool Settings,
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(0, 0, 0).
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"Align Settings" .
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#1 a #2 x-.
Cartesian Editor
Align.
#1 , #11
X. 7.806()
#1 #11.
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7.806 0.0 0.0" .
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