Приложение не запускается: объект Engine не определено хотя везде задано ,

НИКОГДА НЕ ИЗМЕНЯЙТЕ код, сгенерированный Qt Designer, НИКОГДА.
Создайте другой класс, который наследуется от соответствующего виджета, и используйте созданный класс для его заполнения.

Я не проверял логику вашего приложения, но пару ошибок исправил.

import sys
from datetime import datetime
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtWidgets import QFileDialog, QMessageBox, QApplication, \
    QLineEdit, QMainWindow


class MyWindow(object):
    def setupUi(self, MainWindow):
        MainWindow.setObjectName("MainWindow")
        MainWindow.setEnabled(True)
        MainWindow.resize(800, 608)
        MainWindow.setStyleSheet("background-color:#22222e")
        self.centralwidget = QtWidgets.QWidget(MainWindow)
        self.centralwidget.setObjectName("centralwidget")
        self.lineEdit = QtWidgets.QLineEdit(self.centralwidget)
        self.lineEdit.setGeometry(QtCore.QRect(220, 80, 301, 61))
        self.lineEdit.setStyleSheet("background-color: #22222e;\n"
                                    "border: 2px solid #6B8E23;\n"
                                    "border-radius: 30;\n"
                                    "color: white")
        self.lineEdit.setObjectName("lineEdit")
        self.pushButton = QtWidgets.QPushButton(self.centralwidget)
        self.pushButton.setGeometry(QtCore.QRect(550, 80, 151, 61))
        self.pushButton.setStyleSheet("QPushButton {\n"
                                      "    color: white;\n"
                                      "    background-color:#6B8E23;\n"
                                      "    border-radius: 30;    \n"
                                      "}\n"
                                      "\n"
                                      "QPushButton:pressed {\n"
                                      "background-color: #90EE90\n"
                                      "}")
        self.pushButton.setObjectName("pushButton")
        self.comboBox = QtWidgets.QComboBox(self.centralwidget)
        self.comboBox.setGeometry(QtCore.QRect(220, 210, 311, 31))
        self.comboBox.setStyleSheet("background-color: #22222e;\n"
                                    "border: 2px solid #6B8E23;\n"
                                    "border-radius: 30;\n"
                                    "color: white")
        self.comboBox.setObjectName("comboBox")
        self.comboBox.addItem("")
        self.comboBox.addItem("")
        self.lineEdit_2 = QtWidgets.QLineEdit(self.centralwidget)
        self.lineEdit_2.setGeometry(QtCore.QRect(220, 300, 301, 61))
        self.lineEdit_2.setStyleSheet("background-color: #22222e;\n"
                                      "border: 2px solid #6B8E23;\n"
                                      "border-radius: 30;\n"
                                      "color: white")
        self.lineEdit_2.setObjectName("lineEdit_2")
        self.lineEdit_3 = QtWidgets.QLineEdit(self.centralwidget)
        self.lineEdit_3.setGeometry(QtCore.QRect(220, 420, 311, 61))
        self.lineEdit_3.setStyleSheet("background-color: #22222e;\n"
                                      "border: 2px solid #6B8E23;\n"
                                      "border-radius: 30;\n"
                                      "color: white")
        self.lineEdit_3.setObjectName("lineEdit_3")
        self.pushButton_2 = QtWidgets.QPushButton(self.centralwidget)
        self.pushButton_2.setGeometry(QtCore.QRect(300, 500, 151, 61))
        self.pushButton_2.setStyleSheet("QPushButton {\n"
                                        "    color: white;\n"
                                        "    background-color:#6B8E23;\n"
                                        "    border-radius: 30;    \n"
                                        "}\n"
                                        "\n"
                                        "QPushButton:pressed {\n"
                                        "background-color: #90EE90\n"
                                        "}")
        self.pushButton_2.setObjectName("pushButton_2")
        self.label_3 = QtWidgets.QLabel(self.centralwidget)
        self.label_3.setGeometry(QtCore.QRect(270, 50, 261, 20))
        font = QtGui.QFont()
        font.setPointSize(12)
        font.setBold(True)
        font.setWeight(75)
        self.label_3.setFont(font)
        self.label_3.setStyleSheet("QLabel {\n"
                                   "    color: white;\n"
                                   "    border-radius: 30;\n"
                                   "\n"
                                   "}")
        self.label_3.setObjectName("label_3")
        self.label_4 = QtWidgets.QLabel(self.centralwidget)
        self.label_4.setGeometry(QtCore.QRect(240, 180, 261, 20))
        font = QtGui.QFont()
        font.setPointSize(12)
        font.setBold(True)
        font.setWeight(75)
        self.label_4.setFont(font)
        self.label_4.setStyleSheet("QLabel {\n"
                                   "    color: white;\n"
                                   "    border-radius: 30;\n"
                                   "\n"
                                   "}")
        self.label_4.setObjectName("label_4")
        self.label_5 = QtWidgets.QLabel(self.centralwidget)
        self.label_5.setGeometry(QtCore.QRect(230, 270, 261, 20))
        font = QtGui.QFont()
        font.setPointSize(12)
        font.setBold(True)
        font.setWeight(75)
        self.label_5.setFont(font)
        self.label_5.setStyleSheet("QLabel {\n"
                                   "    color: white;\n"
                                   "    border-radius: 30;\n"
                                   "\n"
                                   "}")
        self.label_5.setObjectName("label_5")
        self.label_6 = QtWidgets.QLabel(self.centralwidget)
        self.label_6.setGeometry(QtCore.QRect(250, 390, 261, 20))
        font = QtGui.QFont()
        font.setPointSize(12)
        font.setBold(True)
        font.setWeight(75)
        self.label_6.setFont(font)
        self.label_6.setStyleSheet("QLabel {\n"
                                   "    color: white;\n"
                                   "    border-radius: 30;\n"
                                   "\n"
                                   "}")
        self.label_6.setObjectName("label_6")
        MainWindow.setCentralWidget(self.centralwidget)
        self.menubar = QtWidgets.QMenuBar(MainWindow)
        self.menubar.setGeometry(QtCore.QRect(0, 0, 800, 21))
        self.menubar.setObjectName("menubar")
        MainWindow.setMenuBar(self.menubar)
        self.statusbar = QtWidgets.QStatusBar(MainWindow)
        self.statusbar.setObjectName("statusbar")
        MainWindow.setStatusBar(self.statusbar)

        self.retranslateUi(MainWindow)
        QtCore.QMetaObject.connectSlotsByName(MainWindow)

    def retranslateUi(self, MainWindow):
        _translate = QtCore.QCoreApplication.translate
        MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
        self.pushButton.setText(_translate("MainWindow", "Выбрать файл"))
        self.comboBox.setItemText(0, _translate("MainWindow", "Зашифровать"))
        self.comboBox.setItemText(1, _translate("MainWindow", "Расшифровать"))
        self.lineEdit_3.setText(_translate("MainWindow", "ваывавы"))
        self.pushButton_2.setText(_translate("MainWindow", "Запустить"))
        self.label_3.setText(_translate("MainWindow", "Введите имя файла"))
        self.label_4.setText(_translate("MainWindow", "            Выберите тип"))
        self.label_5.setText(_translate("MainWindow", "      Введите ключ от 1 до 90"))
        self.label_6.setText(_translate("MainWindow", "            Куда вывести"))
        
        
class Engine(QMainWindow, MyWindow):
    def __init__(self) -> None:
        super().__init__()
        
        self.setupUi(self)

        self.pushButton.clicked.connect(self.openFileNameDialog)
        
        '''   # ???# ???# ???# ???# ???# ???# ???# ???# ???# ???# ???# ???
        MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
        self.pushButton.setText(_translate("MainWindow", "Выбрать файл"))
        self.comboBox.setItemText(0, _translate("MainWindow", "Зашифровать"))
        self.comboBox.setItemText(1, _translate("MainWindow", "Расшифровать"))
        self.lineEdit_3.setText(_translate("MainWindow", "ваывавы"))
        self.pushButton_2.setText(_translate("MainWindow", "Запустить"))
        self.label_3.setText(_translate("MainWindow", "Введите имя файла"))
        self.label_4.setText(_translate("MainWindow", "            Выберите тип"))
        self.label_5.setText(_translate("MainWindow", "      Введите ключ от 1 до 90"))
        self.label_6.setText(_translate("MainWindow", "            Куда вывести"))

        def __init__(self, parent=None):
            super(MyWindow, self).__init__(parent)
        self.lineedit = QLineEdit(self)
        self.lineEdit_2 = QLineEdit()
        self.lineEdit_3 = QLineEdit()
        '''
        
    def openFileNameDialog(self):
        options = QFileDialog.Options()
        options |= QFileDialog.DontUseNativeDialog
# ???        global filelist
        fileName, _ = QFileDialog.getOpenFileName(
            self, 
            "Select Text file", 
            "", 
            "Text Files (*.txt)", 
            options=options
        )
        if not fileName:
            fileName = None
        print(fileName)
#       self.lineedit.setText(fileName)
#            lineEdit
        self.lineEdit.setText(fileName)                              # +++ lineEdit

    def ciphering(self):
        self.filename = self.lineedit.text()
        self.optfilename = self.lineedit_2.text()
        self.process = self.combo.currentText()
        self.key = self.lineedit_3.text()

        assert isinstance(self.key, object)
        password_key = int(self.key)
        store = ''
        Letters = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz' \
                  '!@#$%&*(){}[]<>/\|";:\n-=+.,?0123456789'
        now = datetime.now()
        print(now)

        option_1 = self.process
        if option_1 == 'Зашифровать':
            print('Ok Sir!..You Selected({0})'.format(option_1))
            file = self.filename
            if password_key == 0:
                QMessageBox.critical(self, "Incorrect Encryption Key Entered",
                                     "Please enter Encryption key in range of 1 - 90.")
            else:
                print("password key: ", password_key)
                if file.endswith('.txt'):
                    try:
                        file = open(file, 'r').read()
                        print('Congratualtions output file saved.')
                    except:
                        print('Filename Error: Please! Enter File name in txt form/Enter correct address of file.')
                    for i in file:
                        if i in Letters:
                            number = Letters.find(i)
                            try:
                                number = number + int(password_key)
                            except:
                                print('Key Error: You Enter a Incorrect key.')
                                break
                            if number >= len(Letters):
                                number = number - len(Letters)
                            elif number < 0:
                                number = number + len(Letters)
                            store = store + Letters[number]
                        else:
                            store = store + i
                        save_file = open('{}.txt'.format(self.optfilename), 'w')
                        save_file.write(store)
                        save_file.close()
                    QMessageBox.about(self, "аптаптаптаптап.",
                                      "птататптатпа {} апттпатаппт.".format(self.process))
                else:
                    QMessageBox.critical(self, "тпата", "тпаттата.")

        elif option_1 == 'Расшифровать':
            print(' аптапаптпа({0})'.format(option_1))

            file = self.filename
            if password_key == 0:
                QMessageBox.critical(self, "апркепр.")
            else:
                if file.endswith('.txt'):
                    try:
                        file = open(file, 'r').read()
                        print('успешно сохранено.')
                    except:
                        print('Ошибка файла: пж.')
                        
                    for i in file:
                        if i in Letters:
                            number = Letters.find(i)
                            try:
                                number = number - int(password_key)
                            except:
                                print('Ошибка ключа: Ваш ключ не верный .')
                                break
                            if number >= len(Letters):
                                number = number - len(Letters)
                            elif number < 0:
                                number = number + len(Letters)
                            store = store + Letters[number]
                        else:
                            store = store + i
                        save_file = open('{}.txt'.format(self.optfilename), 'w')
                        save_file.write(store)
                        save_file.close()
                    QMessageBox.about(self, "Процесс завершился.",
                                      "поздравляю {} успешно.".format(self.process))
                else:
                    QMessageBox.critical(self, "Ошибка файла", "Введите txt форму .")


if __name__ == "__main__":
    App = QApplication(sys.argv)
    window = Engine()
    window.show()
    sys.exit(App.exec())