src.chemistry Namespace Reference

Functions
def	LookupByMass (mass)
def	BondStrengthByLength (A, B, length, artol=0.33, bias=0.0)

Variables
	BondEnergies = defaultdict(lambda:defaultdict(dict))
list	Radii
	Covalent radii from Cordero et al. More...
	PeriodicTable
list	Elements
list	BondChars = ['-','=','3']
string	data_from_web
	line = line.expandtabs()
	BE = float(line.split()[1])
float	L = float(line.split()[2]) * 0.01
	atoms = re.split('[-=3]', line.split()[0])
	A = atoms[0]
	B = atoms[1]
list	bo = BondChars.index(re.findall('[-=3]', line.split()[0])[0]) + 1

Function Documentation

BondStrengthByLength()

def src.chemistry.BondStrengthByLength	(		A,
			B,
			length,
			artol = 0.33,
			bias = 0.0
	)

Definition at line 169 of file chemistry.py.

LookupByMass()

def src.chemistry.LookupByMass

(

mass

)

Definition at line 160 of file chemistry.py.

Variable Documentation

A

src.chemistry.A = atoms[0]

Definition at line 154 of file chemistry.py.

atoms

src.chemistry.atoms = re.split('[-=3]', line.split()[0])

Definition at line 153 of file chemistry.py.

B

src.chemistry.B = atoms[1]

Definition at line 155 of file chemistry.py.

BE

src.chemistry.BE = float(line.split()[1])

Definition at line 151 of file chemistry.py.

bo

list src.chemistry.bo = BondChars.index(re.findall('[-=3]', line.split()[0])[0]) + 1

Definition at line 156 of file chemistry.py.

BondChars

list src.chemistry.BondChars = ['-','=','3']

Definition at line 51 of file chemistry.py.

BondEnergies

src.chemistry.BondEnergies = defaultdict(lambda:defaultdict(dict))

Definition at line 8 of file chemistry.py.

data_from_web

string src.chemistry.data_from_web

Definition at line 56 of file chemistry.py.

Elements

list src.chemistry.Elements

Initial value:

=  ["None",'H','He',
            'Li','Be','B','C','N','O','F','Ne',
            'Na','Mg','Al','Si','P','S','Cl','Ar',
            'K','Ca','Sc','Ti','V','Cr','Mn','Fe','Co','Ni','Cu','Zn','Ga','Ge','As','Se','Br','Kr',
            'Rb','Sr','Y','Zr','Nb','Mo','Tc','Ru','Rh','Pd','Ag','Cd','In','Sn','Sb','Te','I','Xe',
            'Cs','Ba','La','Ce','Pr','Nd','Pm','Sm','Eu','Gd','Tb','Dy','Ho','Er','Tm','Yb',
            'Lu','Hf','Ta','W','Re','Os','Ir','Pt','Au','Hg','Tl','Pb','Bi','Po','At','Rn',
            'Fr','Ra','Ac','Th','Pa','U','Np','Pu','Am','Cm','Bk','Cf','Es','Fm','Md','No','Lr','Rf','Db','Sg','Bh','Hs','Mt']

Definition at line 42 of file chemistry.py.

L

float src.chemistry.L = float(line.split()[2]) * 0.01

Definition at line 152 of file chemistry.py.

line

src.chemistry.line = line.expandtabs()

Definition at line 150 of file chemistry.py.

PeriodicTable

src.chemistry.PeriodicTable

Initial value:

=  OrderedDict([('H',1.0079),('He',4.0026),
                             ('Li',6.941),('Be',9.0122),('B',10.811),('C',12.0107),('N',14.0067),('O',15.9994),('F',18.9984),('Ne',20.1797),
                             ('Na',22.9897),('Mg',24.305),('Al',26.9815),('Si',28.0855),('P',30.9738),('S',32.065),('Cl',35.453),('Ar',39.948),
                             ('K',39.0983),('Ca',40.078),('Sc',44.9559),('Ti',47.867),('V',50.9415),('Cr',51.9961),('Mn',54.938),('Fe',55.845),('Co',58.9332),
                             ('Ni',58.6934),('Cu',63.546),('Zn',65.39),('Ga',69.723),('Ge',72.64),('As',74.9216),('Se',78.96),('Br',79.904),('Kr',83.8),
                             ('Rb',85.4678),('Sr',87.62),('Y',88.9059),('Zr',91.224),('Nb',92.9064),('Mo',95.94),('Tc',98),('Ru',101.07),('Rh',102.9055),
                             ('Pd',106.42),('Ag',107.8682),('Cd',112.411),('In',114.818),('Sn',118.71),('Sb',121.76),('Te',127.6),('I',126.9045),('Xe',131.293),
                             ('Cs',132.9055),('Ba',137.327),('La',138.9055),('Ce',140.116),('Pr',140.9077),('Nd',144.24),('Pm',145),('Sm',150.36),
                             ('Eu',151.964),('Gd',157.25),('Tb',158.9253),('Dy',162.5),('Ho',164.9303),('Er',167.259),('Tm',168.9342),('Yb',173.04),
                             ('Lu',174.967),('Hf',178.49),('Ta',180.9479),('W',183.84),('Re',186.207),('Os',190.23),('Ir',192.217),('Pt',195.078),
                             ('Au',196.9665),('Hg',200.59),('Tl',204.3833),('Pb',207.2),('Bi',208.9804),('Po',209),('At',210),('Rn',222),
                             ('Fr',223),('Ra',226),('Ac',227),('Th',232.0381),('Pa',231.0359),('U',238.0289),('Np',237),('Pu',244),
                             ('Am',243),('Cm',247),('Bk',247),('Cf',251),('Es',252),('Fm',257),('Md',258),('No',259),
                             ('Lr',262),('Rf',261),('Db',262),('Sg',266),('Bh',264),('Hs',277),('Mt',268)])

Definition at line 27 of file chemistry.py.

Radii

list src.chemistry.Radii

Initial value:

=  [0.31, 0.28, # H and He
         1.28, 0.96, 0.84, 0.76, 0.71, 0.66, 0.57, 0.58, # First row elements
         0.0, 1.41, 1.21, 1.11, 1.07, 1.05, 1.02, 1.06, # Second row elements
         2.03, 1.76, 1.70, 1.60, 1.53, 1.39, 1.61, 1.52, 1.50, 
         1.24, 1.32, 1.22, 1.22, 1.20, 1.19, 1.20, 1.20, 1.16, # Third row elements, K through Kr
         2.20, 1.95, 1.90, 1.75, 1.64, 1.54, 1.47, 1.46, 1.42, 
         1.39, 1.45, 1.44, 1.42, 1.39, 1.39, 1.38, 1.39, 1.40, # Fourth row elements, Rb through Xe
         2.44, 2.15, 2.07, 2.04, 2.03, 2.01, 1.99, 1.98, 
         1.98, 1.96, 1.94, 1.92, 1.92, 1.89, 1.90, 1.87, # Fifth row elements, s and f blocks
         1.87, 1.75, 1.70, 1.62, 1.51, 1.44, 1.41, 1.36, 
         1.36, 1.32, 1.45, 1.46, 1.48, 1.40, 1.50, 1.50, # Fifth row elements, d and p blocks
         2.60, 2.21, 2.15, 2.06, 2.00, 1.96, 1.90, 1.87, 1.80, 1.69]

Covalent radii from Cordero et al.

'Covalent radii revisited' Dalton Transactions 2008, 2832-2838. Sodium replaced 1.66 -> 1.0. I think ionic radii are more appropriate.

Definition at line 12 of file chemistry.py.