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PyDP4_GUI.py
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PyDP4_GUI.py
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#!/usr/bin/env python
from PyQt5 import QtWidgets, QtCore, QtGui
import os
import shutil
import PyDP4
import queue
import sys
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
from rdkit.Chem import AllChem as Chem
from rdkit.Chem.Draw import rdMolDraw2D
import pickle
from matplotlib import cm
from pathlib import Path
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.resize(self.table_widget.Tab1.Overall_widget.sizeHint())
#self.resize(self.table_widget.sizeHint())
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()
# Initialize tab screen
self.tabs = QtWidgets.QTabWidget()
self.tab1 = QtWidgets.QWidget()
self.Tab1 = CalculationTab()
self.tabs.addTab(self.Tab1, "Calculation")
self.tab1.layout = QtWidgets.QVBoxLayout()
# 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.tab6 = QtWidgets.QWidget()
self.tabs.addTab(self.tab5, "Conformers")
#only add proton/carbon plot tabs if the raw data is there
NMR_list = [str(self.Tab1.NMR_list.item(i).text()) for i in range(self.Tab1.NMR_list.count())]
if 'Proton' in NMR_list or 'Proton.dx' in NMR_list or 'proton' in NMR_list or 'proton.dx' in NMR_list:
self.tabs.addTab(self.tab2, "Proton Plot")
self.Tab2 = ProtonPlotTab()
self.tab2.layout = QtWidgets.QVBoxLayout(self)
self.tab2.layout.addWidget(self.Tab2)
self.tab2.setLayout(self.tab2.layout)
if 'Carbon' in NMR_list or 'Carbon.dx' in NMR_list or 'carbon' in NMR_list or 'carbon.dx' in NMR_list:
self.tabs.addTab(self.tab3, "Carbon Plot")
self.Tab3 = CarbonPlotTab()
self.tab3.layout = QtWidgets.QVBoxLayout(self)
self.tab3.layout.addWidget(self.Tab3)
self.tab3.setLayout(self.tab3.layout)
self.Tab5 = ConformerTab()
self.tab5.layout = QtWidgets.QVBoxLayout(self)
self.tab5.layout.addWidget(self.Tab5)
self.tab5.setLayout(self.tab5.layout)
self.Tab6 = DP5Tab()
if 's' in ui.table_widget.Tab1.settings.Workflow:
self.tabs.addTab(self.tab6, "DP5")
self.tab6.layout = QtWidgets.QVBoxLayout(self)
self.tab6.layout.addWidget(self.Tab6)
self.tab6.setLayout(self.tab6.layout)
self.Tab4 = StatsTab()
if 's' in ui.table_widget.Tab1.settings.Workflow and len(ui.table_widget.Tab1.settings.InputFiles) > 1:
self.tabs.addTab(self.tab4, "DP4")
self.tab4.layout = QtWidgets.QVBoxLayout(self)
self.tab4.layout.addWidget(self.Tab4)
self.tab4.setLayout(self.tab4.layout)
self.layouttabs.addWidget(self.tabs)
self.setLayout(self.layouttabs)
ui.update()
class DP5Tab(QtWidgets.QWidget):
def __init__(self):
super(DP5Tab, self).__init__()
# main horizontal widget
self.main_layout = QtWidgets.QHBoxLayout()
self.setLayout(self.main_layout)
self.Isomers = ui.table_widget.Tab1.worker.Isomers
self.DP5data = ui.table_widget.Tab1.worker.DP5Data
self.DP4data = ui.table_widget.Tab1.worker.DP4Data
self.Isomer_DP5_table = QtWidgets.QTableWidget(self)
self.Isomer_DP5_table.setColumnCount(3)
self.Isomer_DP5_table.setHorizontalHeaderLabels(["Isomer", "DP5", "DP4"])
self.Isomer_DP5_table.setRowCount(len(self.DP5data.DP5scaledprobs))
c = 0
for scaled_DP5, DP4 in zip(self.DP5data.DP5scaledprobs, self.DP4data.DP4probs):
self.Isomer_DP5_table.setItem(c, 0, QtWidgets.QTableWidgetItem(str(c + 1)))
self.Isomer_DP5_table.setItem(c, 1, QtWidgets.QTableWidgetItem(str(round(scaled_DP5, 2))))
self.Isomer_DP5_table.setItem(c, 2, QtWidgets.QTableWidgetItem(str(round(DP4 , 3))))
c += 1
self.Isomer_DP5_table.selectRow(0)
# add error table
self.DP5_table = QtWidgets.QTableWidget(self)
self.DP5_table.setColumnCount(4)
self.DP5_table.setHorizontalHeaderLabels(
["Atom Label", "Atomic Probability", "Scaled error (ppm)", "Unscaled error (ppm)"])
self.DP5_table.setColumnWidth(0, 70)
self.DP5_table.setColumnWidth(1, 70)
self.DP5_table.setColumnWidth(2, 70)
self.DP5_table.setColumnWidth(3, 70)
#########
# add isomer canvas
self.table_widget = QtWidgets.QWidget(self)
self.image = QSvgWidget()
self.image.setMinimumWidth(self.image.height())
# organise layouts
self.table_layout = QtWidgets.QVBoxLayout()
self.table_layout.addWidget(self.Isomer_DP5_table)
self.table_layout.addWidget(self.DP5_table)
#self.image_layout.addWidget(self.image)
self.table_widget.setLayout(self.table_layout)
self.main_layout.addWidget(self.table_widget)
self.main_layout.addWidget(self.image)
# connections
self.Isomer_DP5_table.currentCellChanged.connect(self.Mol_drawer)
self.Isomer_DP5_table.currentCellChanged.connect(self.populatetable)
self.DP5_table.currentCellChanged.connect(self.Mol_drawer)
def populatetable(self):
isomerindex = self.Isomer_DP5_table.currentRow()
# which isomer is selected
self.DP5_table.setRowCount(0)
self.labels, self.shifts, self.exps, self.scaleds = self.DP5data.Clabels[isomerindex], \
self.DP5data.Cshifts[isomerindex], \
self.DP5data.Cexp[isomerindex], \
self.DP5data.Cscaled[isomerindex], \
self.scaled_probs = self.DP5data.BScaledAtomProbs[isomerindex]
self.DP5_table.setRowCount(len(self.labels))
# set info in rows and columns
c = 0
for label, shift, exp, scaled_shift, scaled_prob in zip(self.labels, self.shifts, self.exps,
self.scaleds,
self.scaled_probs):
self.DP5_table.setItem(c, 0, QtWidgets.QTableWidgetItem(label))
self.DP5_table.setItem(c, 1, QtWidgets.QTableWidgetItem(str(round(scaled_prob, 2))))
self.DP5_table.setItem(c, 2, QtWidgets.QTableWidgetItem(str(round(abs(scaled_shift - exp), 2))))
self.DP5_table.setItem(c, 3, QtWidgets.QTableWidgetItem(str(round(abs(shift - exp), 2))))
c += 1
self.DP5_table.selectRow(0)
# self.plot()
def Isomer_number(self):
Isomer_list = []
for c, i in enumerate(self.Isomers):
Isomer_list.append("Isomer " + str(c + 1))
return Isomer_list
def Mol_drawer(self):
isomerindex = self.Isomer_DP5_table.currentRow()
highlight = {}
inds = []
for label in self.DP5data.Clabels[isomerindex]:
inds.append(int(label.split("C")[1]) - 1)
for i, s in zip(inds, self.DP5data.BScaledAtomProbs[isomerindex]):
highlight[i] = cm.RdYlGn(s)
# pick selected atom
if self.DP5_table.item(self.DP5_table.currentRow(), 0):
error_ind = int(self.DP5_table.currentRow())
atom_ind = inds[error_ind]
highlight[atom_ind] = cm.viridis( self.DP5data.BScaledAtomProbs[isomerindex][error_ind])
#m = Chem.MolFromMolFile(str(ui.table_widget.Tab1.worker.settings.InputFiles[0]).split('.sdf')[0] + '.sdf', removeHs=False)
m = Chem.MolFromMolFile(str(ui.table_widget.Tab1.worker.settings.InputFilesPaths[isomerindex]).split('.sdf')[0] + '.sdf',removeHs=False)
Chem.Compute2DCoords(m)
drawer = rdMolDraw2D.MolDraw2DSVG(self.image.width(), self.image.height())
drawer.DrawMolecule(m, highlightAtoms=inds, highlightAtomColors=highlight, highlightBonds=False)
# ,addStereoAnnotation = True,addAtomIndices = True
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:', '')
svg_bytes = bytearray(svg, encoding='utf-8')
self.image.renderer().load(svg_bytes)
ui.update()
class StatsTab(QtWidgets.QWidget):
def __init__(self):
super(StatsTab, self).__init__()
#main horizontal widget
self.main_layout = QtWidgets.QHBoxLayout()
self.setLayout(self.main_layout)
self.Isomers = ui.table_widget.Tab1.worker.Isomers
self.dp4data = ui.table_widget.Tab1.worker.DP4Data
# add isomer selection
self.IsomerSelect = QtWidgets.QComboBox(self)
self.IsomerSelect.addItems(self.Isomer_number())
# add isomer canvas
self.image = QSvgWidget()
#make vertical isomer layout
self.isomer_layout = QtWidgets.QVBoxLayout()
self.isomer_layout.addWidget(self.IsomerSelect)
self.isomer_layout.addWidget(self.image)
self.isomer_widget = QtWidgets.QWidget(self)
self.isomer_widget.setLayout(self.isomer_layout)
# make error table
# populate table based on the Isomer selected
self.Hplot = plotstats('H')
#check if there is a DP4 result for this atomt type:
if not np.isnan(ui.table_widget.Tab1.worker.DP4Data.HDP4probs).any() :
self.IsomerSelect.currentIndexChanged.connect(self.Hplot.populatetable)
self.IsomerSelect.currentIndexChanged.connect(self.RenderImage)
self.Hplot.errortable.itemSelectionChanged.connect(self.RenderImage)
self.Cplot = plotstats('C')
if not np.isnan(ui.table_widget.Tab1.worker.DP4Data.CDP4probs).any() :
self.IsomerSelect.currentIndexChanged.connect(self.Cplot.populatetable)
self.IsomerSelect.currentIndexChanged.connect(self.RenderImage)
self.Cplot.errortable.itemSelectionChanged.connect(self.RenderImage)
#make error table layout
self.error_layout = QtWidgets.QVBoxLayout()
self.error_layout.addWidget(self.Cplot.errortable)
self.error_layout.addWidget(self.Hplot.errortable)
self.error_widget = QtWidgets.QWidget(self)
self.error_widget.setLayout(self.error_layout)
#make plot layout
self.plot_layout = QtWidgets.QVBoxLayout()
self.plot_layout.addWidget(self.Cplot.statscanvas)
self.plot_layout.addWidget(self.Hplot.statscanvas)
self.plot_widget = QtWidgets.QWidget(self)
self.plot_widget.setLayout(self.plot_layout)
# add these widgets to main horizontal layout
self.isomer_widget.setMinimumWidth(400)
self.error_widget.setFixedWidth(400)
self.main_layout.addWidget(self.isomer_widget)
self.main_layout.addWidget(self.error_widget)
self.main_layout.addWidget(self.plot_widget)
def Isomer_number(self):
Isomer_list = []
for c, i in enumerate(self.Isomers):
Isomer_list.append("Isomer " + str(c + 1))
return Isomer_list
def RenderImage(self):
'''colors = [(0.12, 0.47, 0.71), (1.0, 0.5, 0.05), (0.17, 0.63, 0.17), (0.84, 0.15, 0.16), (0.58, 0.4, 0.74),
(0.55, 0.34, 0.29), (0.89, 0.47, 0.76), (0.5, 0.5, 0.5), (0.74, 0.74, 0.13), (0.09, 0.75, 0.81)]'''
isomerindex = self.IsomerSelect.currentIndex()
atom = []
highlight = {}
if self.Cplot.errortable.item(self.Cplot.errortable.currentRow(), 0):
C_atom = int(self.Cplot.errortable.item(self.Cplot.errortable.currentRow(), 0).text().split("C")[1])
atom.append(C_atom - 1 )
highlight[C_atom - 1] = (0.12, 0.47, 0.71)
if self.Hplot.errortable.item(self.Hplot.errortable.currentRow(), 0):
H_atom = int(self.Hplot.errortable.item(self.Hplot.errortable.currentRow(), 0).text().split("H")[1])
atom.append(H_atom - 1)
highlight[H_atom - 1] = (0.84, 0.15, 0.16)
m = Chem.MolFromMolFile(str(ui.table_widget.Tab1.worker.settings.InputFilesPaths[isomerindex]).split('.sdf')[0] + '.sdf',removeHs=False)
Chem.Compute2DCoords(m)
drawer = rdMolDraw2D.MolDraw2DSVG(self.image.width(), self.image.height())
drawer.DrawMolecule(m, highlightAtoms=atom, highlightAtomColors=highlight,highlightBonds = False)
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:', '')
svg_bytes = bytearray(svg, encoding='utf-8')
self.image.renderer().load(svg_bytes)
#self.image.setGeometry(QtCore.QRect(0, 50, 500, 500))
ui.update()
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.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))
p_color = 3
elif self.atom == 'C':
m = abs(max([item for sublist in self.dp4data.Cerrors for item in sublist], key=abs))
p_color = 0
# plot all errors at low transparency
for e in self.errors:
self.statsfig.plot([e, e], [0, self.multipdf([float(e)])], color='C'+ str(p_color), alpha=0.25)
self.statsfig.plot(e, self.multipdf([float(e)]), 'o', color='C'+ str(p_color), alpha=0.25)
x = np.linspace(- 2 * m, 2 * m, 1000)
self.statsfig.plot(x, self.multipdf(x),color = "C1")
self.statsfig.plot([error, error], [0, self.multipdf([float(error)])], color='C'+ str(p_color), alpha=1)
self.statsfig.plot(error, self.multipdf([float(error)]), 'o', color='C'+ str(p_color), alpha= 1)
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 closest 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):
self.log_file = ''
super(CalculationTab, self).__init__()
self.cwd = Path(os.getcwd())
self.Overall_verticallayout =QtWidgets.QVBoxLayout(self)
self.Overall_widget = QtWidgets.QWidget(self)
self.title = QtWidgets.QLabel(self)
self.title.setText("DP5 GUI")
self.title.setObjectName("Title")
self.Overall_verticallayout.addWidget(self.title)
########### input
self.input_widget = QtWidgets.QWidget(self)
self.input_layout = QtWidgets.QHBoxLayout(self)
self.structure_widget = QtWidgets.QWidget(self)
self.structure_layout = QtWidgets.QVBoxLayout(self)
self.Add_structure = QtWidgets.QPushButton(self)
self.Add_structure.setObjectName("Add_structure")
self.Add_structure.setText("Add structure")
self.remove_structure = QtWidgets.QPushButton(self)
self.remove_structure.setObjectName("remove_structure")
self.remove_structure.setText("Remove selected")
self.structure_layout.addWidget(self.Add_structure)
self.structure_layout.addWidget(self.remove_structure)
self.structure_widget.setLayout(self.structure_layout)
self.input_layout.addWidget(self.structure_widget)
self.Structure_list = QtWidgets.QListWidget(self)
self.Structure_list.setMaximumHeight(self.Add_structure.sizeHint().height() * 2)
self.Structure_list.setObjectName("Structure_list")
self.input_layout.addWidget(self.Structure_list)
self.NMR_widget = QtWidgets.QWidget(self)
self.NMR_layout = QtWidgets.QVBoxLayout(self)
self.Add_NMR = QtWidgets.QPushButton(self)
self.Add_NMR.setObjectName("Add_NMR")
self.Add_NMR.setText("Add raw NMR")
self.Add_NMR_desc = QtWidgets.QPushButton(self)
self.Add_NMR_desc.setObjectName("Add_NMR")
self.Add_NMR_desc.setText("Add NMR desc")
self.remove_NMR = QtWidgets.QPushButton(self)
self.remove_NMR.setObjectName("remove_NMR")
self.remove_NMR.setText("Remove selected")
self.NMR_layout.addWidget(self.Add_NMR)
self.NMR_layout.addWidget(self.Add_NMR_desc)
self.NMR_layout.addWidget(self.remove_NMR)
self.NMR_widget.setLayout(self.NMR_layout)
self.input_layout.addWidget(self.NMR_widget)
self.NMR_list = QtWidgets.QListWidget(self)
self.NMR_list.setObjectName("NMR_list")
self.NMR_list.setMaximumHeight(self.Add_structure.sizeHint().height() * 3)
self.input_layout.addWidget(self.NMR_list)
self.Output_add = QtWidgets.QPushButton(self)
self.Output_add.setObjectName("Out add")
self.Output_add.setText("Output Folder")
self.input_layout.addWidget(self.Output_add)
self.Output_list = QtWidgets.QListWidget(self)
self.Output_list.setObjectName("Out list")
self.Output_list.setMaximumHeight(self.Add_structure.sizeHint().height() * 2)
self.input_layout.addWidget(self.Output_list)
self.input_widget.setLayout(self.input_layout)
self.Overall_verticallayout.addWidget(self.input_widget)
############ workflow
self.workflow_layout = QtWidgets.QGridLayout(self)
self.workflow_widget = QtWidgets.QWidget(self)
self.workflow_title = QtWidgets.QLabel(self)
self.workflow_title.setObjectName("workflow_title")
self.workflow_title.setText("Workflow")
self.workflow_layout.addWidget(self.workflow_title, 0, 0)
self.CleanUp_yn = QtWidgets.QCheckBox(self)
self.CleanUp_yn.setObjectName("CleanUp_yn")
self.CleanUp_yn.setText("Clean\n"
"Structures")
self.workflow_layout.addWidget(self.CleanUp_yn,1,0)
self.Gen_diastereomers_yn = QtWidgets.QCheckBox(self)
self.Gen_diastereomers_yn.setObjectName("Gen_diastereomers_yn")
self.Gen_diastereomers_yn.setText("Generate\n"
"Diastereomers")
self.workflow_layout.addWidget(self.Gen_diastereomers_yn,1,1)
self.Solvent_yn = QtWidgets.QCheckBox(self)
self.Solvent_yn.setObjectName("Solvent_yn")
self.Solvent_yn.setText("Solvent")
self.workflow_layout.addWidget(self.Solvent_yn,1,2)
self.solvent_drop = QtWidgets.QComboBox(self)
self.solvent_drop.setObjectName("solvent_drop")
solvents = ['chloroform', 'dimethylsulfoxide', 'benzene', 'methanol', 'pyridine', 'acetone']
self.solvent_drop.addItems(solvents)
self.workflow_layout.addWidget(self.solvent_drop,2,2)
self.MM_yn = QtWidgets.QCheckBox(self)
self.MM_yn.setObjectName("MM_yn")
self.MM_yn.setText("Molecular\nMechanics")
self.workflow_layout.addWidget(self.MM_yn,1,3)
self.MM_drop = QtWidgets.QComboBox(self)
self.MM_drop.setObjectName("MM_drop")
MM = ["MacroModel","Tinker"]
self.MM_drop.addItems(MM)
self.workflow_layout.addWidget(self.MM_drop,2,3)
self.MM_advanced = QtWidgets.QPushButton(self)
self.MM_advanced.setText("Advanced Settings")
self.workflow_layout.addWidget(self.MM_advanced,3,3)
self.DFT_yn = QtWidgets.QCheckBox(self)
self.DFT_yn.setObjectName("DFT_yn")
self.DFT_yn.setText("DFT\nCalculations")
self.workflow_layout.addWidget(self.DFT_yn, 1, 4)
self.DFT_drop = QtWidgets.QComboBox(self)
self.DFT_drop.setObjectName("DFT_drop")
DFT = ["Gaussian", "NWChem"]
self.DFT_drop.addItems(DFT)
self.workflow_layout.addWidget(self.DFT_drop, 2, 4)
self.DFT_advanced = QtWidgets.QPushButton(self)
self.DFT_advanced.setText("Advanced Settings")
self.workflow_layout.addWidget(self.DFT_advanced,3,4)
self.Assignment_yn = QtWidgets.QCheckBox(self)
self.Assignment_yn.setObjectName("Assignment_yn")
self.Assignment_yn.setText("NMR\nAssignment")
self.workflow_layout.addWidget(self.Assignment_yn, 1, 5)
self.DP5_stat_yn = QtWidgets.QCheckBox(self)
self.DP5_stat_yn.setObjectName("DP5_stat_yn")
self.DP5_stat_yn.setText("DP5 Statistics")
self.workflow_layout.addWidget(self.DP5_stat_yn, 1, 6)
self.DP4_stat_yn = QtWidgets.QCheckBox(self)
self.DP4_stat_yn.setObjectName("DP4_stat_yn")
self.DP4_stat_yn.setText("DP4 Statistics")
self.workflow_layout.addWidget(self.DP4_stat_yn, 1, 7)
self.Add_stats_model = QtWidgets.QPushButton(self)
self.Add_stats_model.setObjectName("Add_stats_model")
self.Add_stats_model.setText("Add stats model")
self.workflow_layout.addWidget(self.Add_stats_model, 2, 7)
self.Stats_list = QtWidgets.QListWidget(self)
self.Stats_list.setMaximumHeight(self.Add_structure.sizeHint().height())
self.Stats_list.setObjectName("Stats_list")
self.workflow_layout.addWidget(self.Stats_list, 3, 7)
self.workflow_widget.setLayout(self.workflow_layout)
self.Overall_verticallayout.addWidget(self.workflow_widget)
############ calc
self.Gobutton = QtWidgets.QPushButton(self)
self.Gobutton.setObjectName("Gobutton")
self.Gobutton.setText("Calculate")
self.Overall_verticallayout.addWidget(self.Gobutton)
self.Output_box = QtWidgets.QTextEdit(self)
self.Output_box.setObjectName("Output_box")
self.Overall_verticallayout.addWidget(self.Output_box)
self.Overall_widget.setLayout(self.Overall_verticallayout)
#################################################################################################buttons methods
# adding structures to the gui
self.NMR_paths = []
self.Structure_paths = []
self.Output_folder = Path.cwd()
self.Add_structure.clicked.connect(self.addstructure)
self.remove_structure.clicked.connect(self.removestructure)
self.Add_NMR.clicked.connect(self.addNMR)
self.Add_NMR_desc.clicked.connect(self.remove_all_NMR)
self.Add_NMR_desc.clicked.connect(self.addNMRdesc)
self.remove_NMR.clicked.connect(self.removeNMR)
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_drop.setEnabled(False)
self.MM_advanced.setEnabled(False)
self.MM_yn.stateChanged.connect(self.MMtoggle)
self.DFT_drop.setEnabled(False)
self.DFT_advanced.setEnabled(False)
self.DFT_yn.stateChanged.connect(self.DFTtoggle)
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.DP4toggle)
self.DP5_stat_yn.stateChanged.connect(self.DP5toggle)
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)
self.DFT_settings = DFT_advanced_settings()
self.DFT_advanced.clicked.connect(self.DFT_pop)
self.MM_settings = MM_advanced_settings()
self.MM_advanced.clicked.connect(self.MM_pop)
def DFT_pop(self):
self.DFT_settings.show()
def MM_pop(self):
self.MM_settings.show()
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.clear()
self.Output_list.addItem(filename)
self.Output_folder = Path(filename)
def get_current_values(self):
import PyDP4
import datetime
import getpass
self.settings = PyDP4.Settings()
self.settings.GUIRunning = True
now = datetime.datetime.now()
self.settings.StartTime = now.strftime('%d%b%H%M')
self.settings.user = getpass.getuser()
self.settings.DarwinScrDir.replace('/u/', self.settings.user)
# Read config file and fill in settings in from that
self.settings = PyDP4.ReadConfig(self.settings)
# add output folder
self.settings.OutputFolder = self.Output_folder
self.log_file = open(self.Output_folder / "DP4_log.log", "w+")
self.settings.InputFilesPaths = self.Structure_paths
# copy structures to output folder
for f in self.Structure_paths:
if not Path(self.Output_folder / f).exists():
shutil.copyfile(f, self.settings.OutputFolder / f)
# add structures
Smiles = []
Smarts = []
InChIs = []
for index in range(self.Structure_list.count()):
list_text = self.Structure_list.item(index).text()
if list_text != '':
# check if file is text or sdf
if list_text.endswith('.sdf'):
self.settings.InputFiles.append(list_text[:-4])
# else its a text file - work out if it contains smiles smarts or inchis
elif (list_text.endswith('Smiles')) or (list_text.endswith('smiles')):
Smiles.append(list_text)
elif (list_text.endswith('Smarts')) or (list_text.endswith('smarts')):
Smarts.append(list_text)