def stringToComp(self, original):
sideChains = []
nameArr = original.split('-')
for i in range (len(nameArr)):#sec-butyl to secbutyl or similar and get rid of the di/tri/etc. stuff
nameArr[i] = self.cropNumPrefix(nameArr[i])[1]
if nameArr[i] in self.hyphenatedPrefixes:
nameArr[i] = "(" + nameArr[i] + ")" + nameArr[i+1]
del nameArr[i+1]
if nameArr[-1] in self.suffixes: #the @@@@-5-ol case
name = nameArr.pop()
location = nameArr.pop()
sideChains.append([self.getShape(name), location])
splitMain = self.cropSuffix(nameArr.pop())
secondSplit = self.cropPrefix(splitMain[0])
if secondSplit[0] != '' and nameArr[-1][0].isdigit(): #the 5-methyl@@@@ case
location = nameArr.pop()
secondSplit[0] = self.cropYL(secondSplit[0])
sideChains.append([ self.getShape(secondSplit[0]), location])
splitMain[0] = secondSplit[1]
if splitMain[1] != 'ane' and splitMain[1] != 'an':
sideChains.append([ self.getShape(splitMain[1]), 0])
elif splitMain[1] != 'ane' and len(nameArr) > 0 and nameArr[-1][0].isdigit(): #the 5-@@@@-ol case
if len(nameArr[-1]) > 1: #meaning mutliple sidechains --> need to also remove the di/tri/etc. prefix/suffix thing
splitMain[0] = self.cropNumPrefix(splitMain[0])[1]
location = nameArr.pop()
sideChains.append( self.getShape([splitMain[1], location]))
if (splitMain[0][-1] == 'a'): #hexa --> hex
splitMain[0]= splitMain[0][:-1]
cycloBool = False
if len(splitMain[0]) >5 and splitMain[0][:5] == 'cyclo': #if cyclo, gets rid of the cyclo bit and sets cyclo to be true
cycloBool = True
splitMain[0] = splitMain[0][5:]
mainCompound = None
if splitMain[0] in self.alkaneRoots:
mainCompound = Compound( self.alkaneRoots[splitMain[0]], cycloBool)##here is the main compound
else:
if splitMain[0] in self.sideChainRoots:
mainCompound = Compound(self.sideChainRoots[splitMain[0]], cycloBool)
else:
raise Exception('I do not recognize ", splitMain[0]')
for i in range(0, len(nameArr), 2):
sideChains.append( [self.getShape(nameArr[1]), nameArr[0]])
del nameArr[0] #deletes the chain and its location, which was just added to the sideChains
del nameArr[0]
for i in range(len(sideChains)): #parse the location into an int array
j = 0
locs = []
while j<len(sideChains[i][1]):
if sideChains[i][1][j] == ',':
locs.append(int(sideChains[i][1][:j] ))
sideChains[i][1] = sideChains[i][1][j+1:]
j = 0
j += 1
locs.append(int(sideChains[i][1]))
sideChains[i][1] = locs
mainCompound.addSideChains(sideChains)
return mainCompound
def getCompound(self):
cp1 = Compound()
tok1 = self.lex.getLookAheadToken()
while (tok1.getTokType() == TokenType.ID or tok1.getTokType() == TokenType.IF or tok1.getTokType() is TokenType.PRINT
# should have == instead of is
or tok1.getTokType() == TokenType.FROM):
state1 = self.getStatement()
cp1.addStatement(state1)
tok1 = self.lex.getLookAheadToken()
return cp1
def getCompound(self):
comp= Compound()
s = self.getStatement()
comp.add(s)
tok = self.lex.getLookaheadToken()
while self.isValidStartOfStatement(tok):
s= self.getStatement()
comp.add(s)
tok= self.lex.getLookaheadToken()
return comp
def molecularFormula(self):
empiricalFormula = self.empiricalFormula()
compound = Compound(empiricalFormula)
if self.availableMass == 0:
return "No Mass Inputted"
multiplier = self.availableMass / compound.molarMass()
molecularFormula = {
symbol: round(quantity * multiplier)
for symbol, quantity in empiricalFormula.items()
}
return molecularFormula
def bond(e1, e2):
if not isinstance(e1, Element):
raise TypeError("First item is not an element")
elif not isinstance(e2, Element):
raise TypeError("First item is not an element")
if (e1.dictionary['type'] == 'Non Metal' and e2.dictionary['type'] == 'Non Metal') \
and (abs(e1.dictionary['electronegativity'] - e2.dictionary['electronegativity']) < 2):
return Compound({e1: abs(charge(e2)), e2: abs(charge(e1))}, 'covalent')
elif (e1.dictionary['type'] == 'Metal' and e2.dictionary['type'] == 'Non Metal') \
or (e1.dictionary['type'] == 'Non Metal' and e2.dictionary['type'] == 'Metal'):
return Compound({e1: abs(charge(e2)), e2: abs(charge(e1))}, 'ionic')
elif e1.dictionary['type'] == 'Metal' and e2.dictionary['type'] == 'Metal':
return Compound({e1: abs(charge(e2)), e2: abs(charge(e1))}, 'metallic')
else:
return Compound({e1: abs(charge(e2)), e2: abs(charge(e1))}, None)
async def molarMass(inputs, author, channel):
malformedCompounds = []
validCompounds = []
for item in inputs:
if Compound.isMalformed(item):
malformedCompounds.append(item)
continue
compound = Compound(item) # class used to calculate molar mass
validCompounds.append(compound)
# if there are malformed compounds
if malformedCompounds:
await channel.send(
f"{author} Error: Invalid Compound(s): "
f"{', '.join(malformedCompounds)}. Please try again.")
else:
await channel.send(f"{author} ```Molar Mass(es)\n"
f"{showMolarMass(validCompounds)}```")
def p_compound(self, p):
'''Compound : Id checkIdIsCompoundOrElem
| Id checkIdIsElem Integer
| FormFunc Bond FormFunc
| Id checkIdIsElem Bond FormFunc
| FormFunc Bond Id checkIdIsElem
| Id checkIdIsElem Bond Id checkIdIsElem
| FormFunc'''
# print(p[2])
if self.trace:
print("--Compound: ")
if len(p) > 5:
if p[2] and p[5]:
p[0] = utils.manageTermOperation(self.variables.get(p[1]), p[3],self.variables.get(p[4]))
else:
raise TypeError("Invalid Ids passed as compound")
elif len(p) > 4:
if p[2] == '&':
if p[4]:
p[0] = utils.manageTermOperation(p[1], p[2],self.variables.get(p[3]))
else:
raise TypeError("Invalid Id passed as Element")
else:
if p[4]:
p[0] = utils.manageTermOperation(self.variables.get(p[1]), p[3],p[4])
else:
raise TypeError("Invalid Id passed as Element")
elif len(p) > 3:
if p[2] == '&':
p[0] = utils.manageTermOperation(p[1], p[2], p[3])
else:
p[0] = Compound({self.variables.get(p[1]):p[3]}, "covalent")
elif len(p) > 2:
if p[2]:
if isinstance(self.variables.get(p[1]), Element):
p[0] = Compound({self.variables.get(p[1]):1}, "covalent")
else:
p[0] = self.variables.get(p[1])
else:
raise TypeError("Invalid Id passed as compound")
else:
p[0] = Compound({p[1]:1}, "covalent")
def availableElements(self, reactants, products):
availableElements = []
compounds = reactants + products
for compound in compounds:
compound = Compound(compound)
for part in compound:
if part not in availableElements:
availableElements.append(part)
return availableElements
def _findBalancedEquation(self, unBalancedEquation):
balancedEquation = ""
rawEquation = [[
compound.strip() for compound in re.split(r"\+", side.strip())
] for side in re.split("->|=", unBalancedEquation)]
realSolution = True
reactants = rawEquation[0]
products = rawEquation[1]
print(f"{reactants=}, {products=}")
availableElements = self.availableElements(
reactants, products) # unique elements within the chem eq
print(f"{availableElements=}")
matrixA = []
vectorB = []
# Initialize the matrix and vector
for availableElement in availableElements:
matrixEntry = []
vectorEntry = []
for index in range(len(reactants)):
exists = False
compound = Compound(reactants[index])
for constituentPart in compound:
if availableElement == constituentPart:
exists = True
coefficient = compound[constituentPart]
matrixEntry.append(coefficient)
if not exists:
matrixEntry.append(0)
for index in range(len(products)):
exists = False
compound = Compound(products[index])
constituentParts = compound.keys()
# last entry
if len(products) - 1 == index:
for constituentPart in constituentParts:
if availableElement == constituentPart:
exists = True
coefficient = compound[constituentPart]
vectorEntry.append(coefficient)
if not exists:
vectorEntry.append(0)
else:
for constituentPart in constituentParts:
if availableElement == constituentPart:
exists = True
coefficient = compound[constituentPart]
matrixEntry.append(-coefficient)
# matrixEntry.append(-coefficient)
if not exists:
matrixEntry.append(0)
matrixA.append(matrixEntry)
vectorB.append(vectorEntry)
print(f"{matrixA=}, {vectorB=}")
matrixA = np.array(matrixA)
vectorB = np.array(vectorB)
linearRegression = np.linalg.lstsq(matrixA, vectorB, rcond=None)
solution = linearRegression[0]
residual = linearRegression[
1] # this shows whether there are real solutions or not
# print(f"{solution=}, {residual=}")
# if there are residuals
if residual.size > 0:
# this equation most likely does not exist in real life and probably has no real solution
realSolution = False
if realSolution:
determinantOfA = np.linalg.det(matrixA)
solution *= determinantOfA
gcd = np.gcd.reduce(np.round(solution).astype(int))
solution /= gcd
solution = np.round(solution).astype(int)
print(f"1. {solution=}")
for index, reactant in enumerate(reactants):
coefficient = abs(solution[index])[0]
if index == len(reactants) - 1:
if coefficient == 1:
balancedEquation += f"{reactant} ->"
else:
balancedEquation += f"{coefficient}{reactant} ->"
else:
if coefficient == 1:
balancedEquation += f"{reactant} + "
else:
balancedEquation += f"{coefficient}{reactant} + "
for index, product in enumerate(products):
index += len(reactants)
if index >= len(product) - 1:
coefficient = abs(int(determinantOfA / gcd))
if coefficient == 1:
balancedEquation += f" {product}"
else:
balancedEquation += f" {coefficient}{product}"
else:
coefficient = abs(solution[index])
if coefficient == 1:
balancedEquation += f" {product} + "
else:
balancedEquation += f" {coefficient}{product} + "
else:
balancedEquation = f"No Real Solution for {self.__unBalancedEquation}"
return balancedEquation
scale = 1
# My Mac desktop seems to have a different dot-pitch than what TK is expecting
ppmm = scale * root.winfo_fpixels('1m') * (100 / 70)
cp = CAMParameters()
render_params = RenderParameters(ppmm, cp)
depth = -0.20
c = tk.Canvas(root,
bg="#b87333",
width=cp.board_w * ppmm,
height=cp.board_h * ppmm)
# -----------------------------------------------------------------
# A hard-coded board design for testing. This will come from
# an external file once we are finished.
e = Compound()
"""
# ---- IQ Modulator Project ---------------------------------------
# Top grid
e.add((30, 0), Grid(6, 1))
e.add((15, 10), Dip8(True))
e.add((55, 10), Dip8(True))
e.add((10, 25), Grid(6, 2))
e.add((50, 25), Grid(6, 2))
e.add((35, 45), Dip14(True))
e.add((18, 70), Grid(10, 2))
"""
"""
newList = []
keys = list(lists.keys())
keys.sort(key=get_value)
for i in range(9):
for j in keys:
newList.append(lists[j][i])
self.comps = newList
######################################
######################################
######################################
path = "Tuttle/VaspRuns/ABC4/"
xml = "vasprun.xml"
comp = []
for x, q, u in os.walk(path):
if x.find("runnable") > 0:
c = Vasprun(x + '/' + xml)
comp.append(Compound(c))
mplot = MultiPlot(comp)
mplot.sort()
mplot.plot(color='r')
mplot.change_limits(xlim=(-15, 10), ylim=(0, 20))
mplot.fig.savefig("a3bc6.png")
async def formula(inputs, author, channel):
print(f"{inputs=}")
inputs = re.split(r"(?<=[A-Za-z0-9])\s*?:\s*?(?=[0-9.])", inputs)
print(f"{inputs=}")
rawInputs = []
for input in inputs:
rawInputs += [
entry.strip() for entry in re.split(r",\s*?|;\s*?", input)
]
print(f"{rawInputs=}")
percentDict = {}
totalPercent = 0
epsilon = 0.011
mass = 0
for index in range(len(rawInputs)):
if index % 2 == 0:
element = rawInputs[index]
if "mass" in element:
# this entry contains the mass
element = element.split("=")
mass = float(element[1])
continue
percent = rawInputs[index + 1]
if "%" in percent:
percent = int(percent.replace("%", "")) / 100
totalPercent += percent
elif "." in percent:
percent = float(percent)
totalPercent += percent
else:
await channel.send(
f"{author} The inputs for the command are inputted wrong.")
return
if element not in periodic_table:
await channel.send(
f"{author} One or more of the inputted elements is not inputted correctly."
)
percentDict[rawInputs[index]] = percent
# if the total percent is within an acceptable range
if 1 - epsilon <= totalPercent <= 1 + epsilon:
print(f"{percentDict=}")
# if the user inputted a mass value
if mass > 0:
# give the molecular formula
compoundFormula = Formula(**percentDict, mass=mass)
compound = Compound(compoundFormula.molecularFormula())
await channel.send(f"{author} The molecular formula is: {compound}"
)
else:
# give the empirical formula
compoundFormula = Formula(**percentDict)
compound = Compound(compoundFormula.empiricalFormula())
await channel.send(f"{author} The empirical formula is: {compound}"
)
else:
await channel.send(f"{author} The percentages do not add up to 100%.")
return