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PyDP4_GUI.py
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PyDP4_GUI.py
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from PyQt5 import QtWidgets, QtCore, QtGui
import time
import os
import PyDP4
import queue
import sys
from PyQt5.QtGui import QIcon
from PyQt5.QtCore import pyqtSlot
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure
import numpy as np
from scipy.stats import norm
from PyQt5.QtSvg import QSvgWidget, QSvgRenderer
from rdkit.Chem import AllChem as Chem
from rdkit.Chem import Draw
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
import pickle
class Window(QtWidgets.QMainWindow):
# create signal to start background job
signal_start_PyDP4 = QtCore.pyqtSignal()
# signal_finished_PyDP4 = QtCore.pyqtSignal()
def __init__(self):
super(Window, self).__init__()
self.table_widget = TabWidget(self)
self.setCentralWidget(self.table_widget)
# self.tabs.currentChanged.connect(self.onChange) # changed!
self.show()
# check if DP4outfile is there
class TabWidget(QtWidgets.QWidget):
def __init__(self, parent):
super(QtWidgets.QWidget, self).__init__(parent)
self.layouttabs = QtWidgets.QVBoxLayout(self)
# Initialize tab screen
self.tabs = QtWidgets.QTabWidget()
self.tab1 = QtWidgets.QWidget()
self.Tab1 = CalculationTab()
# Add tabs
self.tabs.addTab(self.tab1, "Calculation")
self.tab1.layout = QtWidgets.QVBoxLayout(self)
self.tab1.layout.addWidget(self.Tab1)
self.tab1.setLayout(self.tab1.layout)
# Add tabs to widget
self.layouttabs.addWidget(self.tabs)
self.setLayout(self.layouttabs)
def addplottabs(self):
self.tab2 = QtWidgets.QWidget()
self.tab3 = QtWidgets.QWidget()
self.tab4 = QtWidgets.QWidget()
self.tab5 = QtWidgets.QWidget()
self.tabs.addTab(self.tab2, "Proton Plot")
self.tabs.addTab(self.tab3, "Carbon Plot")
if 's' in ui.table_widget.Tab1.settings.Workflow:
self.tabs.addTab(self.tab4, "Stats")
self.tab4.layout = QtWidgets.QVBoxLayout(self)
self.tab4.layout.addWidget(self.Tab4)
self.tab4.setLayout(self.tab4.layout)
self.tabs.addTab(self.tab5, "Conformers")
self.Tab2 = ProtonPlotTab()
self.Tab3 = CarbonPlotTab()
self.Tab4 = StatsTab()
self.Tab5 = ConformerTab()
self.tab2.layout = QtWidgets.QVBoxLayout(self)
self.tab2.layout.addWidget(self.Tab2)
self.tab2.setLayout(self.tab2.layout)
self.tab3.layout = QtWidgets.QVBoxLayout(self)
self.tab3.layout.addWidget(self.Tab3)
self.tab3.setLayout(self.tab3.layout)
self.tab5.layout = QtWidgets.QVBoxLayout(self)
self.tab5.layout.addWidget(self.Tab5)
self.tab5.setLayout(self.tab5.layout)
self.layouttabs.addWidget(self.tabs)
self.setLayout(self.layouttabs)
ui.update()
class StatsTab(QtWidgets.QWidget):
def __init__(self):
super(StatsTab, self).__init__()
self.setFixedSize(876, 875)
self.layout = QtWidgets.QGridLayout()
self.setLayout(self.layout)
# add isomer selection
self.IsomerSelect = QtWidgets.QComboBox(self)
self.Isomers = ui.table_widget.Tab1.worker.Isomers
self.dp4data = ui.table_widget.Tab1.worker.DP4Data
self.IsomerSelect.addItems(self.Isomer_number())
# make error table
# populate table based on the Isomer selected
self.Hplot = plotstats('H')
self.IsomerSelect.currentIndexChanged.connect(self.Hplot.populatetable)
self.layout.addWidget(self.Hplot.errortable ,0 ,0)
self.layout.addWidget(self.Hplot.statscanvas ,0 ,1)
self.Cplot = plotstats('C')
self.IsomerSelect.currentIndexChanged.connect(self.Cplot.populatetable)
self.layout.addWidget(self.Cplot.errortable ,2 ,0)
self.layout.addWidget(self.Cplot.statscanvas ,2 ,1)
self.layout.setColumnStretch(0 ,4)
self.layout.setColumnStretch(1, 5)
self.layout.setContentsMargins(0, 50, 0, 0)
def Isomer_number(self):
Isomer_list = []
for c, i in enumerate(self.Isomers):
Isomer_list.append("Isomer " + str(c + 1))
return Isomer_list
class plotstats(QtWidgets.QWidget):
def __init__(self ,Atom):
super(plotstats, self).__init__()
# when a cell is selected signal to plot stats
self.atom = Atom
self.findmeans()
self.dp4data = ui.table_widget.Tab1.worker.DP4Data
self.Isomers = ui.table_widget.Tab1.worker.Isomers
self.errortable = QtWidgets.QTableWidget(self)
# self.errortable.setGeometry(QtCore.QRect(10, 50,400, 400))
self.errortable.setColumnCount(5)
self.errortable.setHorizontalHeaderLabels(["Atom Label" ,"Calc Shift" ,"Scaled" ,"Exp" ,"Error"])
self.errortable.setColumnWidth(0, 70)
self.errortable.setColumnWidth(1, 70)
self.errortable.setColumnWidth(2, 70)
self.errortable.setColumnWidth(3, 70)
self.errortable.setColumnWidth(4, 70)
self.statsfigure = Figure()
self.statscanvas = FigureCanvas(self.statsfigure)
# self.errortable.cellClicked.connect(self.plot)
self.errortable.itemSelectionChanged.connect(self.plot)
self.statscanvas.mpl_connect('button_press_event', self.selectpoint)
def plot(self):
r = int(self.errortable.currentRow())
if r >= 0:
error = float(self.errortable.item(r, 4).text())
# decide which stats params have been used
self.statsfigure.clear()
self.statsfig = self.statsfigure.add_subplot(111)
if self.atom =='H':
m = abs(max([item for sublist in self.dp4data.Herrors for item in sublist] ,key= abs))
elif self.atom =='C':
m = abs(max([item for sublist in self.dp4data.Cerrors for item in sublist], key=abs))
# plot all errors at low transparency
for e in self.errors:
self.statsfig.plot([e, e], [0, self.multipdf([float(e)])], color='C1' ,alpha = 0.5)
self.statsfig.plot(e, self.multipdf([float(e)]), 'o', color='C1' ,alpha = 0.5)
x = np.linspace(- 2* m, 2 * m, 1000)
self.statsfig.plot(x, self.multipdf(x))
self.statsfig.plot([error, error], [0, self.multipdf([float(error)])], color='red', alpha=0.75)
self.statsfig.plot(error, self.multipdf([float(error)]), 'o', color='red', alpha=0.75)
self.statsfig.set_xlim([x[0], x[-1]])
self.statsfig.set_xlabel("error (ppm)")
self.statsfig.set_ylabel("probability density")
self.statscanvas.draw()
def multipdf(self, x):
y = np.zeros(len(x))
if self.atom == 'H':
for mean, std in zip(self.Hmeans, self.Hstdevs):
y += norm.pdf(x, loc=mean, scale=std)
elif self.atom == 'C':
for mean, std in zip(self.Cmeans, self.Cstdevs):
y += norm.pdf(x, loc=mean, scale=std)
return y
def findmeans(self):
if ui.table_widget.Tab1.worker.settings.StatsParamFile == 'none':
self.Hmeans = [0]
self.Hstdevs = [0.18731058105269952]
self.Cmeans = [0]
self.Cstdevs = [2.269372270818724]
else:
self.Cmeans, self.Cstdevs, self.Hmeans, self.Hstdevs = ReadParamFile(
ui.table_widget.Tab1.worker.settings.StatsParamFile, 'g')
def populatetable(self):
# which isomer is selected
self.isomerindex = int(str(ui.table_widget.Tab4.IsomerSelect.currentText())[-1]) - 1
self.errortable.setRowCount(0)
if self.atom == 'H':
self.labels, self.shifts, self.exps, self.scaleds, self.errors = self.dp4data.Hlabels[self.isomerindex], \
self.dp4data.Hshifts[self.isomerindex], \
self.dp4data.Hexp[self.isomerindex], \
self.dp4data.Hscaled[self.isomerindex], \
self.dp4data.Herrors[self.isomerindex]
elif self.atom == 'C':
self.labels, self.shifts, self.exps, self.scaleds, self.errors = self.dp4data.Clabels[self.isomerindex], \
self.dp4data.Cshifts[self.isomerindex], \
self.dp4data.Cexp[self.isomerindex], \
self.dp4data.Cscaled[self.isomerindex], \
self.dp4data.Cerrors[self.isomerindex]
self.errortable.setRowCount(len(self.labels))
# set info in rows and columns
c = 0
for label, shift, exp, scaled, error in zip(self.labels, self.shifts, self.exps, self.scaleds, self.errors):
self.errortable.setItem(c, 0, QtWidgets.QTableWidgetItem(label))
self.errortable.setItem(c, 1, QtWidgets.QTableWidgetItem(str(round(shift, 2))))
self.errortable.setItem(c, 2, QtWidgets.QTableWidgetItem(str(round(scaled, 2))))
self.errortable.setItem(c, 3, QtWidgets.QTableWidgetItem(str(round(exp, 2))))
self.errortable.setItem(c, 4, QtWidgets.QTableWidgetItem(str(round(error, 2))))
c += 1
self.errortable.selectRow(0)
self.plot()
def selectpoint(self, event):
self.xpos = event.xdata
self.ypos = event.ydata
# find the cloest point to the click
coords = self.statsfig.transData.transform((self.xpos, self.ypos))
coordinates = np.array(self.statsfig.transData.transform(list(zip(self.errors, self.multipdf(self.errors)))))
mindis = np.argmin((coordinates[:, 0] - coords[0]) ** 2 + (coordinates[:, 1] - coords[1]) ** 2)
self.errortable.selectRow(mindis)
class CalculationTab(QtWidgets.QWidget):
signal_start_PyDP4 = QtCore.pyqtSignal()
def __init__(self):
super(CalculationTab, self).__init__()
self.setFixedSize(876, 875)
self.label = QtWidgets.QLabel(self)
self.label.setGeometry(QtCore.QRect(10, 10, 121, 16))
self.label.setObjectName("label")
self.label_2 = QtWidgets.QLabel(self)
self.label_2.setGeometry(QtCore.QRect(10, 140, 57, 15))
self.label_2.setObjectName("label_2")
self.solvent_drop = QtWidgets.QComboBox(self)
self.solvent_drop.setGeometry(QtCore.QRect(120, 240, 101, 31))
self.solvent_drop.setObjectName("solvent_drop")
self.DFT_geom_functional_drop = QtWidgets.QComboBox(self)
self.DFT_geom_functional_drop.setGeometry(QtCore.QRect(370, 240, 101, 31))
self.DFT_geom_functional_drop.setObjectName("DFT_geom_functional_drop")
self.DFT_geom_basis_drop = QtWidgets.QComboBox(self)
self.DFT_geom_basis_drop.setGeometry(QtCore.QRect(370, 300, 101, 31))
self.DFT_geom_basis_drop.setObjectName("DFT_geom_basis_drop")
self.label_3 = QtWidgets.QLabel(self)
self.label_3.setGeometry(QtCore.QRect(370, 220, 81, 16))
self.label_3.setObjectName("label_3")
self.label_4 = QtWidgets.QLabel(self)
self.label_4.setGeometry(QtCore.QRect(370, 280, 81, 16))
self.label_4.setObjectName("label_4")
self.Energy_functional_drop = QtWidgets.QComboBox(self)
self.Energy_functional_drop.setGeometry(QtCore.QRect(490, 240, 101, 31))
self.Energy_functional_drop.setObjectName("Energy_functional_drop")
self.label_5 = QtWidgets.QLabel(self)
self.label_5.setGeometry(QtCore.QRect(490, 280, 81, 16))
self.label_5.setObjectName("label_5")
self.Energy_basis_drop = QtWidgets.QComboBox(self)
self.Energy_basis_drop.setGeometry(QtCore.QRect(490, 300, 101, 31))
self.Energy_basis_drop.setObjectName("Energy_basis_drop")
self.label_6 = QtWidgets.QLabel(self)
self.label_6.setGeometry(QtCore.QRect(490, 220, 81, 16))
self.label_6.setObjectName("label_6")
self.label_7 = QtWidgets.QLabel(self)
self.label_7.setGeometry(QtCore.QRect(610, 280, 81, 16))
self.label_7.setObjectName("label_7")
self.NMR_basis_drop = QtWidgets.QComboBox(self)
self.NMR_basis_drop.setGeometry(QtCore.QRect(610, 300, 101, 31))
self.NMR_basis_drop.setObjectName("NMR_basis_drop")
self.label_8 = QtWidgets.QLabel(self)
self.label_8.setGeometry(QtCore.QRect(610, 220, 81, 16))
self.label_8.setObjectName("label_8")
self.NMR_functional_drop = QtWidgets.QComboBox(self)
self.NMR_functional_drop.setGeometry(QtCore.QRect(610, 240, 101, 31))
self.NMR_functional_drop.setObjectName("NMR_functional_drop")
self.label_9 = QtWidgets.QLabel(self)
self.label_9.setGeometry(QtCore.QRect(120, 220, 81, 16))
self.label_9.setObjectName("label_9")
self.Output_box = QtWidgets.QTextEdit(self)
self.Output_box.setGeometry(QtCore.QRect(0, 460, 875, 415))
self.Output_box.setObjectName("Output_box")
self.label_11 = QtWidgets.QLabel(self)
self.label_11.setGeometry(QtCore.QRect(20, 440, 57, 15))
self.label_11.setObjectName("label_11")
self.Stats_list = QtWidgets.QListWidget(self)
self.Stats_list.setGeometry(QtCore.QRect(730, 330, 121, 91))
self.Stats_list.setObjectName("Stats_list")
self.Gobutton = QtWidgets.QPushButton(self)
self.Gobutton.setGeometry(QtCore.QRect(300, 370, 251, 81))
self.Gobutton.setObjectName("Gobutton")
self.Add_stats_model = QtWidgets.QPushButton(self)
self.Add_stats_model.setGeometry(QtCore.QRect(730, 300, 121, 23))
self.Add_stats_model.setObjectName("Add_stats_model")
self.widget = QtWidgets.QWidget(self)
self.widget.setGeometry(QtCore.QRect(10, 40, 841, 91))
self.widget.setObjectName("widget")
self.horizontalLayout_2 = QtWidgets.QHBoxLayout(self.widget)
self.horizontalLayout_2.setContentsMargins(0, 0, 0, 0)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
self.Add_structure = QtWidgets.QPushButton(self.widget)
self.Add_structure.setObjectName("Add_structure")
self.horizontalLayout_2.addWidget(self.Add_structure)
self.Structure_list = QtWidgets.QListWidget(self.widget)
self.Structure_list.setObjectName("Structure_list")
self.horizontalLayout_2.addWidget(self.Structure_list)
self.Add_NMR = QtWidgets.QPushButton(self.widget)
self.Add_NMR.setObjectName("Add_NMR")
self.horizontalLayout_2.addWidget(self.Add_NMR)
self.NMR_list = QtWidgets.QListWidget(self.widget)
self.NMR_list.setObjectName("NMR_list")
self.horizontalLayout_2.addWidget(self.NMR_list)
self.Output_add = QtWidgets.QPushButton(self.widget)
self.Output_add.setObjectName("Out add")
self.horizontalLayout_2.addWidget(self.Output_add)
self.Output_list = QtWidgets.QListWidget(self.widget)
self.Output_list.setObjectName("Out list")
self.horizontalLayout_2.addWidget(self.Output_list)
self.widget1 = QtWidgets.QWidget(self)
self.widget1.setGeometry(QtCore.QRect(10, 160, 710, 51))
self.widget1.setObjectName("widget1")
self.horizontalLayout = QtWidgets.QHBoxLayout(self.widget1)
self.horizontalLayout.setContentsMargins(0, 0, 0, 0)
self.horizontalLayout.setObjectName("horizontalLayout")
self.Gen_diastereomers_yn = QtWidgets.QCheckBox(self.widget1)
self.Gen_diastereomers_yn.setObjectName("Gen_diastereomers_yn")
self.horizontalLayout.addWidget(self.Gen_diastereomers_yn)
self.Solvent_yn = QtWidgets.QCheckBox(self.widget1)
self.Solvent_yn.setObjectName("Solvent_yn")
self.horizontalLayout.addWidget(self.Solvent_yn)
self.MM_yn = QtWidgets.QCheckBox(self.widget1)
self.MM_yn.setObjectName("MM_yn")
self.horizontalLayout.addWidget(self.MM_yn)
self.DFTGeom_yn = QtWidgets.QCheckBox(self.widget1)
self.DFTGeom_yn.setObjectName("DFTGeom_yn")
self.horizontalLayout.addWidget(self.DFTGeom_yn)
self.Energy_yn = QtWidgets.QCheckBox(self.widget1)
self.Energy_yn.setObjectName("Energy_yn")
self.horizontalLayout.addWidget(self.Energy_yn)
self.NMR_calc_yn = QtWidgets.QCheckBox(self.widget1)
self.NMR_calc_yn.setObjectName("NMR_calc_yn")
self.horizontalLayout.addWidget(self.NMR_calc_yn)
self.Assignment_yn = QtWidgets.QCheckBox(self)
self.Assignment_yn.setGeometry(QtCore.QRect(730, 170, 101, 31))
self.Assignment_yn.setObjectName("Assignment_yn")
self.Assignment_yn.setText("NMR\nAssignment")
self.DP4_stat_yn = QtWidgets.QCheckBox(self)
self.DP4_stat_yn.setGeometry(QtCore.QRect(730, 240, 101, 31))
self.DP4_stat_yn.setObjectName("DP4_stat_yn")
#self.horizontalLayout.addWidget(self.DP4_stat_yn)
self.label.setText("PyDP4 GUI")
self.label_2.setText("Workflow")
self.label_3.setText("Functional")
self.label_4.setText("Basis set")
self.label_5.setText("Basis set")
self.label_6.setText("Functional")
self.label_7.setText("Basis set")
self.label_8.setText("Functional")
self.label_9.setText("Solvent")
self.label_11.setText("Output")
self.Gobutton.setText("Calculate")
self.Add_stats_model.setText("Add stats model")
self.Add_structure.setText("Add structure")
self.Add_NMR.setText("Add NMR")
self.Solvent_yn.setText("Solvent")
self.Gen_diastereomers_yn.setText("Generate\n"
"diastereomers")
self.MM_yn.setText("Molecular\n"
"mechanics")
self.DFTGeom_yn.setText("DFT\n"
"Geometry\n"
"optimisation")
self.Energy_yn.setText("Split single\n"
"point energy")
self.NMR_calc_yn.setText("NMR\n"
"calculations")
self.DP4_stat_yn.setText("DP4 Statistics")
self.Output_add.setText("Output Folder")
self.MM_rb = QtWidgets.QRadioButton(self)
self.MM_rb.setGeometry(QtCore.QRect(250, 240, 101, 31))
self.MM_rb.setObjectName("MM_rb")
self.label_12 = QtWidgets.QLabel(self)
self.label_12.setGeometry(QtCore.QRect(270, 240, 101, 31))
self.label_12.setText("MacroModel")
self.Tinker_rb = QtWidgets.QRadioButton(self)
self.Tinker_rb.setGeometry(QtCore.QRect(250, 300, 101, 31))
self.Tinker_rb.setObjectName("Tinker_rb")
self.label_13 = QtWidgets.QLabel(self)
self.label_13.setGeometry(QtCore.QRect(270, 300, 101, 31))
self.label_13.setText("Tinker")
#################################################################################################buttons methods
# adding structures to the gui
self.Add_structure.clicked.connect(self.addstructure)
self.Add_NMR.clicked.connect(self.addNMR)
self.Output_add.clicked.connect(self.addoutputfolder)
# selecting solvent check box
self.solvent_drop.setEnabled(False)
self.Solvent_yn.stateChanged.connect(self.solventtoggle)
self.MM_yn.stateChanged.connect(self.MMtoggle)
self.MM_rb.toggled.connect(self.rb_toggle)
self.Tinker_rb.toggled.connect(self.rb_toggle)
# selecting DFT geometry opt box
self.DFT_geom_functional_drop.setEnabled(False)
self.DFT_geom_basis_drop.setEnabled(False)
self.DFTGeom_yn.stateChanged.connect(self.DFTopttoggle)
# selecting Split Single point box
self.Energy_functional_drop.setEnabled(False)
self.Energy_basis_drop.setEnabled(False)
self.Energy_yn.stateChanged.connect(self.Energytoggle)
# selecting NMR box
self.NMR_functional_drop.setEnabled(False)
self.NMR_basis_drop.setEnabled(False)
self.NMR_calc_yn.stateChanged.connect(self.NMRtoggle)
# add solvents to solvent box
solvents = ['chloroform', 'dimethylsulfoxide', 'benzene', 'methanol', 'pyridine', 'acetone']
self.solvent_drop.addItems(solvents)
# add functionals and basis sets to DFTopt, Energy and NMR
DFTopt_basis = ['6-31g(d)', '6-311g(d)', 'def2svp', 'def2tzvp']
DFTopt_functional = ['B3LYP', 'm062x', 'mPW1PW91']
Energy_basis = ['6-31g(d)', '6-311g(d)', 'def2svp', 'def2tzvp']
Energy_functional = ['m062x', 'mPW1PW91', 'B3LYP']
NMR_basis = ['6-311g(d)', '6-31g(d)', 'def2svp', 'def2tzvp']
NMR_functional = ['mPW1PW91', 'B3LYP', 'M062X']
self.DFT_geom_functional_drop.addItems(DFTopt_functional)
self.DFT_geom_basis_drop.addItems(DFTopt_basis)
self.Energy_functional_drop.addItems(Energy_functional)
self.Energy_basis_drop.addItems(Energy_basis)
self.NMR_basis_drop.addItems(NMR_basis)
self.NMR_functional_drop.addItems(NMR_functional)
self.Assignment_yn.stateChanged.connect(self.Assignment_toggle)
# adding a stats model
self.Add_stats_model.setEnabled(False)
self.DP4_stat_yn.stateChanged.connect(self.Statstoggle)
self.Add_stats_model.clicked.connect(self.addstats)
#####################################################################################running PyDP4 in new thread
# self.Gobutton.clicked.connect(self.Gotoggle)
self.Gobutton.clicked.connect(self.get_current_values)
# make worker object
self.worker = PyDP4WorkerObject()
# make thread
self.thread = QtCore.QThread()
# move the worker object to the ne thread
self.worker.moveToThread(self.thread)
# connect workers finished signal to quit thread
self.worker.finished.connect(self.thread.quit)
# connect workers finished signal to enable go button
self.worker.finished.connect(self.Gotoggle)
self.worker.finished.connect(self.enabletabs)
# connect start background signal to background job slot
self.Gobutton.clicked.connect(self.start_PyDP4)
# start pydp4 give start signal
# go button press disables go button
self.Gobutton.clicked.connect(self.Gotoggle)
# start signal starts pydp4
self.signal_start_PyDP4.connect(self.worker.runPyDP4)
##############################################################################getting current values of boxs etc
###################################################################################
def enabletabs(self):
ui.table_widget.addplottabs()
def addoutputfolder(self):
# filename = QtWidgets.QFileDialog.getOpenFileName()
filename = QtWidgets.QFileDialog.getExistingDirectory()
# self.NMR_list.addItem(str(filename[0].split("/")[-1]))
self.Output_list.addItem(filename)
def get_current_values(self):
import PyDP4
self.settings = PyDP4.Settings()
# add structures
for index in range(self.Structure_list.count()):
if self.Structure_list.item(index).text() != '':
self.settings.InputFiles.append(self.Structure_list.item(index).text())
# add NMR
self.settings.NMRsource = self.NMR_list.item(0).text()
# get workflow information
# solvent
if self.Solvent_yn.isChecked() == 1:
self.settings.Solvent = self.solvent_drop.currentText()
# generate diastereomers
self.settings.Workflow = ''
if self.Gen_diastereomers_yn.isChecked() == 1:
self.settings.Workflow += 'g'
# molecular mechanics
if self.MM_yn.isChecked() == 1:
self.settings.Workflow += 'm'
if self.MM_rb.isChecked() == True:
self.settings.MM = 'm'
else:
self.settings.MM = 't'
# DFT Geometry optimisation
if self.DFTGeom_yn.isChecked() == 1:
self.settings.Workflow += 'o'
self.settings.oBasisSet = self.DFT_geom_basis_drop.currentText()
self.settings.oFunctional = self.DFT_geom_functional_drop.currentText()
# Split single point
if self.Energy_yn.isChecked() == 1:
self.settings.Workflow += 'e'
self.settings.eBasisSet = self.Energy_basis_drop.currentText()
self.settings.eFunctional = self.Energy_functional_drop.currentText()
# NMR
# Split single point
if self.NMR_calc_yn.isChecked() == 1:
self.settings.Workflow += 'n'
self.settings.nBasisSet = self.NMR_basis_drop.currentText()
self.settings.nFunctional = self.NMR_functional_drop.currentText()
if self.DP4_stat_yn.isChecked():
self.settings.Workflow += 's'
if self.Stats_list.item(0) != None:
self.settings.StatsParamFile = self.Stats_list.item(0).text()
self.settings.StatsModel = 'm'
elif self.Assignment_yn.isChecked():
self.settings.Workflow += 'a'
self.settings.ScriptDir = os.path.dirname(os.path.realpath(sys.argv[0]))
def start_PyDP4(self):
# No harm in calling thread.start() after the thread is already started.
# start the thread
self.thread.start()
self.thread.finished.connect(self.Gotoggle)
# send background job start signal
self.signal_start_PyDP4.emit()
self.thread.disconnect()
def addstructure(self):
filename = QtWidgets.QFileDialog.getOpenFileName()
self.Structure_list.addItem(str(filename[0].split("/")[-1]))
def addNMR(self):
# filename = QtWidgets.QFileDialog.getOpenFileName()
filename = QtWidgets.QFileDialog.getExistingDirectory()
# self.NMR_list.addItem(str(filename[0].split("/")[-1]))
self.NMR_list.addItem(str(filename.split("/")[-1]))
def addstats(self):
filename = QtWidgets.QFileDialog.getOpenFileName()
self.Stats_list.addItem(str(filename[0]))
def solventtoggle(self, state):
if state > 0:
self.solvent_drop.setEnabled(True)
self.Gen_diastereomers_yn.setChecked(True)
else:
self.solvent_drop.setEnabled(False)
self.MM_yn.setChecked(False)
def MMtoggle(self, state):
if state > 0:
self.Gen_diastereomers_yn.setChecked(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
if (self.MM_rb.isDown() == False) & (self.Tinker_rb.isDown() == False):
self.MM_rb.toggle()
else:
self.solvent_drop.setEnabled(False)
self.Solvent_yn.setChecked(False)
self.MM_rb.setChecked(False)
self.Tinker_rb.setChecked(False)
def rb_toggle(self,state):
if state > 0:
if state > 0:
self.MM_yn.setChecked(True)
self.Gen_diastereomers_yn.setChecked(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
else:
self.solvent_drop.setEnabled(False)
def Energytoggle(self, state):
if state > 0:
self.Energy_functional_drop.setEnabled(True)
self.Energy_basis_drop.setEnabled(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
self.Gen_diastereomers_yn.setChecked(True)
self.MM_yn.setChecked(True)
else:
self.Energy_functional_drop.setEnabled(False)
self.Energy_basis_drop.setEnabled(False)
def DFTopttoggle(self, state):
if state > 0:
self.DFT_geom_functional_drop.setEnabled(True)
self.DFT_geom_basis_drop.setEnabled(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
self.Gen_diastereomers_yn.setChecked(True)
self.MM_yn.setChecked(True)
else:
self.DFT_geom_functional_drop.setEnabled(False)
self.DFT_geom_basis_drop.setEnabled(False)
def NMRtoggle(self, state):
if state > 0:
self.NMR_functional_drop.setEnabled(True)
self.NMR_basis_drop.setEnabled(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
self.Gen_diastereomers_yn.setChecked(True)
self.MM_yn.setChecked(True)
else:
self.NMR_functional_drop.setEnabled(False)
self.NMR_basis_drop.setEnabled(False)
def Assignment_toggle(self,state):
if state > 0:
self.NMR_calc_yn.setChecked(True)
self.NMR_functional_drop.setEnabled(True)
self.NMR_basis_drop.setEnabled(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
self.Gen_diastereomers_yn.setChecked(True)
self.MM_yn.setChecked(True)
else:
self.DP4_stat_yn.setChecked(False)
self.Add_stats_model.setEnabled(False)
def Statstoggle(self, state):
if state > 0:
self.Add_stats_model.setEnabled(True)
self.NMR_calc_yn.setChecked(True)
self.NMR_functional_drop.setEnabled(True)
self.NMR_basis_drop.setEnabled(True)
self.Solvent_yn.setChecked(True)
self.solvent_drop.setEnabled(True)
self.Gen_diastereomers_yn.setChecked(True)
self.MM_yn.setChecked(True)
self.Assignment_yn.setChecked(True)
else:
self.Add_stats_model.setEnabled(False)
def append_text(self, text):
self.Output_box.moveCursor(QtGui.QTextCursor.End)
self.Output_box.insertPlainText(text)
def Gotoggle(self):
if self.Gobutton.isEnabled() == True:
self.Gobutton.setEnabled(False)
else:
self.Gobutton.setEnabled(True)
class ProtonPlotTab(QtWidgets.QWidget):
def __init__(self):
super(ProtonPlotTab, self).__init__()
# create a figure instance
self.figure = Figure()
# create the canvas widget thats displays figure
self.canvas = FigureCanvas(self.figure)
# make the navigation widget - this takes the canvas widget as the parent
self.toolbar = NavigationToolbar(self.canvas, self)
self.IsomerSelect = QtWidgets.QComboBox(self)
self.IsomerSelect.addItems(self.Isomer_number())
self.IsomerSelect.currentIndexChanged.connect(self.PlotProton)
self.image = QSvgWidget()
self.widget1 = QtWidgets.QWidget(self)
self.widget2 = QtWidgets.QWidget(self)
self.hl1 = QtWidgets.QVBoxLayout(self.widget1)
self.hl2 = QtWidgets.QVBoxLayout(self.widget2)
self.hl1.addWidget(self.toolbar)
self.hl1.addWidget(self.canvas)
self.hl2.addWidget(self.IsomerSelect)
self.hl2.addWidget(self.image)
self.widget1.setGeometry(QtCore.QRect(300, 0, 1200, 875))
# self.IsomerSelect.setGeometry(QtCore.QRect(0,0,100,50))
# self.image.setGeometry(QtCore.QRect(0,50,300,300))
self.widget2.setGeometry(QtCore.QRect(0, 0, 300, 400))
self.canvas.mpl_connect('button_press_event', self.selectpoint)
################################################################################################################
if ui.table_widget.Tab1.settings.OutputFolder == '':
pdir = str(os.getcwd()) + "/Pickles/"
else:
pdir = ui.table_widget.Tab1.settings.OutputFolder + "/Pickles/"
if os.path.isfile(pdir + ui.table_widget.Tab1.settings.InputFiles[0] + "protondata"):
self.protondata = pickle.load(open(pdir + ui.table_widget.Tab1.settings.InputFiles[0] + "protondata", "rb"))
self.xdata = self.protondata["xdata"]