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chemistry.py
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chemistry.py
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# chemistry.py: The Chemistry module for CSG
#
# Copyright (C) 2020-2021 Jithin Renji, Kannan MD, Pranav Pujar
#
# This file is part of CSG.
#
# CSG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# CSG is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with CSG. If not, see <https://www.gnu.org/licenses/>.
#
class PeriodicTable:
"""
Contains elements elements which can form compounds according to the
VSEPR theory.
"""
def __init__(self):
self.__groups = {
1: {
'H': 1, 'Li': 3, 'Na': 11, 'K': 19,
'Rb': 37, 'Cs': 55, 'Fr': 87
},
2: {
'Be': 4, 'Mg': 12, 'Ca': 20, 'Sr': 38, 'Ba': 56, 'Ra': 88
},
13: {
'B': 5, 'Al': 13, 'Ga': 31, 'In': 49, 'Ti': 81
},
14: {
'C': 6, 'Si': 14, 'Ge': 32, 'Sn': 50, 'Pb': 82
},
15: {
'N': 7, 'P': 15, 'As': 33, 'Sb': 51, 'Bi': 83
},
16: {
'O': 8, 'S': 16, 'Se': 34, 'Te': 52, 'Po': 84
},
17: {
'F': 9, 'Cl': 17, 'Br': 35, 'I': 53, 'At': 85
},
18: {
'He': 2, 'Ne': 10, 'Ar': 18, 'Kr': 36, 'Xe': 54, 'Rn': 86
}
}
self.__group_valencies = {
1: 1,
2: 2,
13: 3,
14: 4,
15: 3,
16: 2,
17: 1,
18: 0
}
self.__group_valence_electrons = {
1: 1,
2: 2,
13: 3,
14: 4,
15: 5,
16: 6,
17: 7,
18: 8
}
self.__atomic_numbers = {
'H': 1,
'He': 2,
'Li': 3,
'Be': 4,
'B': 5,
'C': 6,
'N': 7,
'O': 8,
'F': 9,
'Ne': 10,
'Na': 11,
'Mg': 12,
'Al': 13,
'Si': 14,
'P': 15,
'S': 16,
'Cl': 17,
'Ar': 18,
'K': 19,
'Ca': 20,
'Br': 35,
'I': 53,
'Xe': 54
}
self.__atomic_colors = [
(135, 206, 235), (217, 255, 255), (204, 128, 255), (194, 255, 0),
(255, 181, 181), (144, 144, 144), (48, 80, 248), (255, 13, 13),
(144, 224, 80), (179, 227, 245), (171, 92, 242), (138, 255, 0),
(191, 166, 166), (240, 200, 160), (255, 128, 0), (255, 255, 48),
(31, 240, 31), (128, 209, 227), (143, 64, 212), (61, 225, 0),
(230, 230, 230), (191, 194, 199), (166, 166, 171), (138, 153, 199),
(156, 122, 199), (224, 102, 51), (240, 144, 160), (80, 208, 80),
(200, 128, 51), (125, 128, 176), (194, 143, 143), (102, 143, 143),
(189, 128, 227), (225, 161, 0), (166, 41, 41), (92, 184, 209),
(112, 46, 176), (0, 255, 0), (148, 255, 255), (148, 224, 224),
(115, 194, 201), (84, 181, 181), (59, 158, 158), (36, 143, 143),
(10, 125, 140), (0, 105, 133), (192, 192, 192), (255, 217, 143),
(166, 117, 115), (102, 128, 128), (158, 99, 181), (212, 122, 0),
(148, 0, 148), (66, 158, 176), (87, 23, 143), (0, 201, 0),
(112, 212, 255)
]
def check(self, element: str) -> bool:
"""
Check if an element is present in the periodic table (as defined
above).
Args:
element: the element which should be checked
"""
for i in self.__groups:
if element in self.__groups[i]:
return True
return False
def get_valency(self, element: str) -> int:
"""
Get an element's valency.
Args:
element: the element whose valency should be returned
"""
for n_grp in self.__groups:
if element in self.__groups[n_grp]:
return self.__group_valencies[n_grp]
def get_nvalence_electrons(self, element: str) -> int:
"""
Get number of valence electrons in an element.
Args:
element: the element whose number of valence electrons should be
returned.
"""
if element == 'He':
return 2
for n_grp in self.__groups:
if element in self.__groups[n_grp]:
return self.__group_valence_electrons[n_grp]
def get_group_elements(self, num: int) -> list:
"""
Get elements in a given group number.
Args:
num: group number
"""
return list(self.__groups[num].keys())
def get_markersize(self, element: str) -> int:
"""
Get an element's marker size for rendering purposes.
Args:
element: the element whose marker size should be returned
"""
return self.__atomic_numbers[element] + 4
def get_markercolor(self, element: str) -> list:
"""
Get an element's marker color for rendering purposes.
Args:
element: the element whose marker color should be returned.
"""
atomic_number = self.__atomic_numbers[element]
temp = list(self.__atomic_colors[atomic_number - 1])
color_list = []
for rgb in temp:
color_list.append(rgb / 255)
return color_list
class Stats:
def __init__(self, ca_dict: dict, nca_dict: dict):
"""
Constructor.
Args:
ca_dict: dictionary of the form {"central atom": subscript}.
Rationale: allows for expansion to compounds with more
than one central atom.
nca_dict: dictionary of the form {"non central atom": subscript}
"""
pt = PeriodicTable()
self.c_atom_dict = ca_dict
self.c_atom = list(ca_dict.keys())[0]
self.c_atom_sub = list(ca_dict.values())[0]
self.c_atom_val = 0
self.c_atom_nval_e = 0
for c_atom in ca_dict:
self.c_atom_val = pt.get_valency(c_atom)
self.c_atom_nval_e = pt.get_nvalence_electrons(c_atom)
break
self.nc_atom_dict = nca_dict
self.nc_atom = list(nca_dict.keys())[0]
self.nc_atom_sub = list(nca_dict.values())[0]
self.nc_atom_val = 0
self.nc_atom_nval_e = 0
for nc_atom in nca_dict:
self.nc_atom_val = pt.get_valency(nc_atom)
self.nc_atom_nval_e = pt.get_nvalence_electrons(nc_atom)
self.print_statsnc_atom_nval_e = pt.get_nvalence_electrons(nc_atom)
break
# This exists for debugging purposes
def print_stats(self) -> None:
"""Print compound stats."""
print("=== CENTRAL ATOM ===")
print("\tAtom:\t\t\t\t", self.c_atom)
print("\tValency:\t\t\t", self.c_atom_val)
print("\tNo. of valence electrons:\t", self.c_atom_nval_e)
print()
print("=== NON-CENTRAL ATOM(S) ===")
print("\tAtom\t\t\t\t", self.nc_atom)
print("\tValency:\t\t\t", self.nc_atom_val)
print("\tNo. of valence electrons:\t", self.nc_atom_nval_e)
pt = PeriodicTable()