* _
C2184 Uvod do programování v Pythonu
Lekce 4 - samostatné úkoly
V hodině je nutné zvládnout 2 samostatné úkoly a zbývající je možné dodělat jako domácí úkol. Ke každé úloze je k dispozici šablona ve studijních materiálech.
A) Caesarova šifra
• napište funkci decodeO, která podle zadaného klíče (celého čísla) provede posun znaků abecedy
BONUS:
• modifikujte skript, aby byl schopný dekódovat i řetězec encoded_text_2
B) Vlastní komparer pro funkci sort()
• v dokumentaci k Pythonu pohledejte očekávané návratové funkce vlastního kompareru
• dopište kód kompareru, aby porovnával absolutní hodnoty čísel
BONUS:
• otestujte i pro absolutní čísla a v případě nutnosti modifikujte, aby se porovnávala pouze reálná část čísla
C) Zpracování CSV (Comma-separated values)
• zjistěte jaký je použit oddělovač sloupečků v přiložené proměnné
• spočítejte průměr, medián a rozptyl pro sloupečky pKa a qH
BONUS:
• spočítejte korelaci mezi sloupečky pKa a qH
D) Molekula ve formátu MOL
• napište funkci, která načte informace o molekule - pro každý atom vytvoří tuple s informacemi např. ( ; D; , 0.4700, 2.5688, 0 .0006) a ty uloží do listu
l('0', 0.4700, 2.5688, 0.0006),   ('0', -3.1271, -0.4436, -0.0003),   ...]
a vrátí jako návratovou hodnotu
• formát molekuly je MDL Molfile1
• spočítejte vzdálenost mezi atomy 3 a 8 (číslováno od 1), vazebný úhel mezi atomy 8, 7 a 9 a torzní úhel mezi 5, 9, 7 a 8
BONUS:
• spočítejte celkovou vazebnou délku (součet všech vazeb zapsaných v souboru)
Poznámka: Zkontrolované úkoly NEnahravejte do odevzdávarny, do odevzdávarny nahrajte pouze úkoly, které nestihnete během hodiny udělat.
podrobněji http: //c4. cabrillo. edu/404/ctf ile .pdf
1
Chapter 2: The Connection Table [CTAB] (V2000)
A connection table (Ctab) contains information describing the structural relationships and properties of a collection of atoms. The atoms may be wholly or partially connected by bonds. Such collections may, for example, describe molecules, molecular fragments, substructures, substituent groups, polymers, alloys, formulations, mixtures, and unconnected atoms. The connection table is fundamental to all of Elsevier MDL's file formats.
The following figure shows the connection table of a simple molecule (alanine) with the various data blocks identified. The connection table corresponds to the following alanine molecule. The atom numbers on the structure correspond to atom numbers in the Ctab. An atom number is assigned according to the order of the atom in the Atom Block.
Figure 3     Connection table organization illustrated using alanine
L-Alanine
Chial
1 0
0.5342 -0.3000
2.0817 -0.3695 -1.8037
0.4244
0 0
3 v2000
1 13
0.0000 c
0.0000 c
0.0000 c
0.0000 n
0.0000 0
0.0000 0
Blocks not used in this Ctab: Atom List, Stext
Counts Line
Atom Block
Bond Block
Properties Block
Connection Table (Ctab)
The format for a Ctab block is:
Counts line:	Important specifications here relate to the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.
Atom block:	Specifies the atomic symbol and any mass difference, charge, stereochemistry, and associated hydrogens for each atom.
Bond block:	Specifies the two atoms connected by the bond, the bond type, and any bond stereochemistry and topology (chain or ring properties) for each bond.
Atom list block:	Identifies the atom (number) of the list and the atoms in the list.
Stext (structural text descriptor) block:	Used by MDL ISIS/Desktop programs.
Properties block:	Provides for future expandability of Ctab features, while maintaining compatibility with earlier Ctab configurations.
CTFile Formats
The detailed format for each block outlined above follows:
Note: A blank numerical entry on any line should be read as "0" (zero). Spaces are significant and correspond to one or more of the following:
• Absence of an entry
• Empty character positions within an entry
• Spaces between entries; single unless specifically noted otherwise
The FORTRAN fcam atforcooidxiate irinrm atbn ii theV 2000 CTfDe fcam atis topically f10.4.
The Counts Line
aaabbbl 11 f f feces s sxxxrrrppp i i iminmwww
Where:		
aaa	= number of atoms (current max 255)*	[Generic]
bbb	= number of bonds (current max 255)*	[Generic]
III	= number of atom lists (max 30)*	[Query]
fff	= (obsolete)	
ccc	= chiral flag: 0=not chiral, 1=chiral	[Generic]
sss	= number of stext entries	[MDL
ISIS/Desktop]
xxx = (obsolete)
rrr = (obsolete)
ppp = (obsolete)
III = (obsolete)
mmm        = number of lines of additional properties, [Generic] including the m   end line. No longer supported, the default is set to 999.
* These limits apply to MACCS-II, REACCS, and the MDL ISIS/Host Reaction Gateway, but not to the MDL ISIS/Host Molecule Gateway or MDL ISIS/Desktop.
For example, the counts line in the Ctab shown in the previous figure shows six atoms, five bonds, the CHIRAL flag on, and three lines in the properties block:
6    5    0    0    10 3 v2000
The Atom Block
The Atom Block is made up of atom lines, one line per atom with the following format: xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvwHHHrrriiimmmnnneee
whets thevaliesate described ii the follow ±ig table:
12
Chapter 2: The Connection Table [CTAB] (V2000)
Figure 4     Meaning of values in the atom block
Field	Meaning	Values	Notes
xy z	atom coordinates		[Generic]
aaa	atom symbol	entry in periodic table or L for atom list, A, Q, * for unspecified atom, and LP for lone pair, or R# for Rgroup label	[Generic, Query, 3D, Rgroup]
del	mass difference	-3,-2, -1,0,1,2,3,4 (0 if value beyond these limits)	[Generic] Difference from mass in periodic table. Wider range of values allowed by m   iso line, below. Retained for compatibility with older Ctabs,m   iso takes precedence.
ccc	charge	0 = uncharged or value other than these, 1 =+3, 2 = +2,3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 = -3	[Generic] Wider range of values in m  CHGandM rad lines below. Retained for compatibility with older Ctabs, m   CHGandM   rad lines take precedence.
sss	atom stereo parity	0 = not stereo, 1 = odd, 2 = even, 3 = either or unmarked stereo center	[Generic] Ignored when read.
hhh	hydrogen count +1	1 =H0,2 = H1,3 = H2,4 = H3, 5 = H4	[Query] HO means no H atoms allowed unless explicitly drawn. Hn means atom must have n or more H's in excess of explicit H's.
bbb	stereo care box	0 = ignore stereo configuration of this double bond atom, 1 = stereo configuration of double bond atom must match	[Query] Double bond stereochemistry is considered during SSS only if both ends of the bond are marked with stereo care boxes.
wv	valence	0 = no marking (default) (1 to 14) = (1 to 14) 15 = zero valence	[Generic] Shows number of bonds to this atom, including bonds to implied H's.
HHH	HO designator	0 = not specified, 1 = no H atoms allowed	[MDL ISIS/Desktop] Redundant with hydrogen count information. May be unsupported in future releases of Elsevier MDL software.
rrr	Not used		
iii	Not used		
mmm	atom-atom mapping number	1 - number of atoms	[Reaction]
nnn	inversion/retention flag	0 = property not applied 1 = configuration is inverted, 2 = configuration is retained,	[Reaction]
eee	exact change flag	0 = property not applied, 1 = change on atom must be exactly as shown	[Reaction, Query]
13
CTFile Formats
w irhC tab version v 2000, the dd andccc fields have been superseded by the m iso,m chg, and m rad lines in the properties block, described below . For com patibihty, aUreieases sinceM ACCS-H2.0,REACCS 81,andM dl EE 1.0:
• Write appropriate values m both places if the values are m the old range.
• Use the atom block fields if there are no M ISO, M CHG, or M RAD lines in the properties block.
Support for these atom block fields may be removed in future releases of Elsevier MDL software.
The Bond Block
The Bond Block is made up of bond lines, one line per bond, with the following format:
111222tttsssxxxrrrccc
where the values are described in the following table:
Figure 5     Meaning of values in the bond block
Field	Meaning	Values	Notes
111	first atom number	1 - number of atoms	[Generic]
222	second atom number	1 - number of atoms	[Generic]
ttt	bond type	1 = Single, 2 = Double, 3 = Triple, 4 = Aromatic, 5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any	[Query] Values 4 through 8 are for SSS queries only.
sss	bond stereo	Single bonds: 0 = not stereo, 1 = Up, 4 = Either, 6 = Down, Double bonds: 0 = Use x-, y-, z-coords from atom block to determine cis or trans, 3 = Cis or trans (either) double bond	[Generic] The wedge (pointed) end of the stereo bond is at the first atom (Field 111 above)
XXX	not used		
rrr	bond topology	0 = Either, 1 = Ring, 2 = Chain	[Query] SSS queries only.
ccc	reacting center status	0 = unmarked, 1 = a center, -1 = not a center, Additional: 2 = no change, 4 = bond made/broken, 8 = bond order changes 12 = 4+8 (both made/broken and changes); 5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) are also possible	[Reaction, Query]
The Atom List Block [Query]
Note: Newer programs use the M   ALS item in the properties block in place of the atom list block. The atom list block is retained for compatibility, but information in an M   ALS item supersedes atom list block information.
Made up of atom list lines, one line per list, with the following format: aaa kSSSSn 111 222  333  444 555
14