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simpleNMR.py
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simpleNMR.py
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import sys
import os
import pathlib
import json
import webbrowser
import math
import PyQt5
from PyQt5 import QtCore
from PyQt5 import QtWidgets
from PyQt5.QtCore import QUrl
from PyQt5.QtCore import pyqtSlot
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import QWidget
from PyQt5.QtWidgets import QMainWindow
from PyQt5.QtWidgets import QApplication
from PyQt5.QtWidgets import QFileDialog
from PyQt5.QtWidgets import QMessageBox
from PyQt5.QtWidgets import QVBoxLayout
from PyQt5.QtWidgets import QHBoxLayout
from PyQt5.QtWidgets import QLineEdit
from PyQt5.QtWidgets import QPushButton
from PyQt5.QtWidgets import QSplitter
from PyQt5.QtWidgets import QMenu
from PyQt5.QtWidgets import QSpinBox
from PyQt5.QtWidgets import QLabel
from PyQt5.QtWidgets import QAction
from qtutils import warning_dialog
from functools import partial
from matplotlib.backends.backend_qt5agg import (
FigureCanvasQTAgg,
NavigationToolbar2QT as NavigationToolbar,
)
from rdkit import Chem
# from rdkit.Chem import AllChem
from rdkit.Chem import Draw
# import networkx as nx
# import nx_pylab
import numpy as np
import pandas as pd
from inspect import currentframe, getframeinfo
pd.options.mode.chained_assignment = "raise"
from PIL import Image
import platform
import nmrProblem
# from test_excel_simplenmr import TestExcelSimpleNMR
from qt5_tabs_001 import EditDataFrameDialog
from moleculePlot import MatplotlibMoleculePlot
from spectraPlot import MatplotlibH1C13Plot
from xy3_dialog import XY3dialog
from about_dialog import Aboutdialog
import problemtohtml
import java
import exampleProblems
from smiles_dialog import SmilesDialog
import simpleNMRutils
import mnovautils
import problemToD3html
PLOTLINECOLORS = ("blue", "orange", "green", "red", "purple")
SCATTERFACECOLORS = ("blue", "orange", "green", "red", "purple")
SCATTEREDGECOLORS = ("blue", "orange", "green", "red", "purple")
PLOTLINECOLORS = ['#377eb8', '#ff7f00', '#4daf4a',
'#f781bf', '#a65628', '#984ea3',
'#999999', '#e41a1c', '#dede00']
SCATTERFACECOLORS = ['#377eb8', '#ff7f00', '#4daf4a',
'#f781bf', '#a65628', '#984ea3',
'#999999', '#e41a1c', '#dede00']
SCATTEREDGECOLORS = ['#377eb8', '#ff7f00', '#4daf4a',
'#f781bf', '#a65628', '#984ea3',
'#999999', '#e41a1c', '#dede00']
YELLOW = (1.0, 1.0, 0.0, 1.0)
RED = (1.0, 0.0, 0.0, 1.0)
WHITE = (1.0, 1.0, 1.0, 1.0)
CB_color_cycle = ['#377eb8', '#ff7f00', '#4daf4a',
'#f781bf', '#a65628', '#984ea3',
'#999999', '#e41a1c', '#dede00']
# Test if we can run JAVA
# global JAVA_AVAILABLE
# global JAVA_COMMAND
# JAVA_AVAILABLE = False
# JAVA_COMMAND = "Undefined"
# Test what system we are running on
# global WINDOWS_OS
# global LINUX_OS
# global MAC_OS
# WINDOWS_OS = False
# LINUX_OS = False
# MAC_OS = False
# global XYDIM
# XYDIM = 800
# # set current working directory to the directory of this file
os.chdir(os.path.dirname(os.path.realpath(__file__)))
class MoleculePlotCanvas(FigureCanvasQTAgg):
def __init__(self, fig, parent=None):
super(MoleculePlotCanvas, self).__init__(fig)
class MainWidget(QMainWindow):
def __init__(self, nmrproblem, parent=None):
self.nmrproblem = nmrproblem
self.hmbc_edge_colors = nmrproblem.hmbc_edge_colors
self.old_node = ""
self.new_node = ""
self.selection = None
super().__init__(parent)
self.setGeometry(100, 100, 1200, 900)
self.setWindowTitle(self.nmrproblem.problemDirectory)
self._createActions()
self._createMenuBar()
# self._createToolBars()
# Uncomment the call to ._createContextMenu() below to create a context
# menu using menu policies. To test this out, you also need to
# comment .contextMenuEvent() and uncomment ._createContextMenu()
# self._createContextMenu()
self._connectActions()
self._createStatusBar()
self.centralWidget = QWidget()
# self.centralWidget.setAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.setCentralWidget(self.centralWidget)
if self.nmrproblem.data_complete:
print("line 142")
print("nmrproblem.c13")
print(nmrproblem.c13)
print("nmrproblem.h1")
print(self.nmrproblem.h1)
print("nmrproblem.hsqc")
print(self.nmrproblem.hsqc)
nmrproblem.save_dataframes_in_nmrproblem_to_json()
self.initiate_windows(self.nmrproblem)
def initiate_windows(self, nmrproblem):
del self.centralWidget
self.centralWidget = QWidget()
# self.centralWidget.setAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.setCentralWidget(self.centralWidget)
self.nmrproblem = nmrproblem
jsmewidget = QWidget()
moleculewidget = QWidget()
spectrawidget = QWidget()
self.moleculePlot = MatplotlibMoleculePlot(self.nmrproblem)
self.spectraPlot = MatplotlibH1C13Plot(self.nmrproblem)
self.spectraCanvas = MoleculePlotCanvas(self.spectraPlot)
self.spectraCanvas.setGeometry(0, 0, 600, 1100)
self.moleculeCanvas = MoleculePlotCanvas(self.moleculePlot)
self.moleculeCanvas.setGeometry(0, 0, 300, 300)
self.moltoolbar = NavigationToolbar(self.moleculeCanvas, self)
self.spctoolbar = NavigationToolbar(self.spectraCanvas, self)
# self.webEngineView = QWebEngineView()
# self.loadPage()
# self.smilesInput = QLineEdit()
# self.button = QPushButton("Display Smiles Molecule", self)
self.sync_button = QPushButton("Synchronize with MesReNova", self)
self.sync_button.clicked.connect(self.on_sync_click)
# connect button to function on_click
# self.button.clicked.connect(self.on_click)
splitter1 = QSplitter(Qt.Vertical)
splitter2 = QSplitter(Qt.Horizontal)
hbox = QHBoxLayout()
molvbox = QVBoxLayout()
jsmevbox = QVBoxLayout()
spcvbox = QVBoxLayout()
spcvbox.addWidget(self.spctoolbar)
spcvbox.addWidget(self.spectraCanvas)
spectrawidget.setLayout(spcvbox)
molvbox.addWidget(self.moltoolbar)
molvbox.addWidget(self.moleculeCanvas)
moleculewidget.setLayout(molvbox)
jsmevbox.addWidget(self.sync_button)
# jsmevbox.addWidget(self.smilesInput)
# jsmevbox.addWidget(self.button)
jsmewidget.setLayout(jsmevbox)
splitter1.addWidget(moleculewidget)
splitter1.addWidget(jsmewidget)
splitter2.addWidget(splitter1)
splitter2.addWidget(spectrawidget)
hbox.addWidget(splitter2)
# hbox.addLayout(molvbox)
self.centralWidget.setLayout(hbox)
splitter2.setSizes([600, 600])
self.centralWidget.show()
# add callbacks to the moleculeCanvas
self.node_pick_ind = None
self.node_hover_ind = None
self.node_picked = False
self.highlighted_peak_lbl = None
self.old_lbl = None
self.moleculePlot.canvas.mpl_connect(
"button_release_event",
lambda event: self.button_release_molecule(
event, specplot=self.spectraPlot, molplot=self.moleculePlot
),
)
self.moleculePlot.canvas.mpl_connect(
"motion_notify_event",
lambda event: self.motion_notify_callback(
event, specplot=self.spectraPlot, molplot=self.moleculePlot
),
)
self.moleculePlot.canvas.mpl_connect(
"pick_event",
lambda event: self.pick_molecule(
event,
event_name="pick_event",
specplot=self.spectraPlot,
molplot=self.moleculePlot,
),
)
self.spectraPlot.canvas.mpl_connect(
"motion_notify_event",
lambda event: self.hover_over_specplot(
event, specplot=self.spectraPlot, molplot=self.moleculePlot
),
)
self.setWindowTitle(self.nmrproblem.problemDirectory)
self.wcLabel.setText(
f"Molecule: {self.nmrproblem.moleculeAtomsStr} DBE: {int(self.nmrproblem.dbe)}"
)
# self.spectraPlot.canvas.draw_idle()
# self.moleculePlot.canvas.draw_idle()
def hover_over_specplot(self, event, specplot, molplot):
# just return if toolbar is active
if (self.moltoolbar.mode != "") or (self.spctoolbar.mode != ""):
return
in_plot = []
in_plot_label = []
in_plot_index = []
pos = None
self.mol_nodes = molplot.mol_nodes
for k, v in specplot.peak_overlays_dict.items():
# in_c13plots, c13plots_index = v["highlight"].contains(event)
in_c13plots, c13plots_index = v.contains(event)
in_plot.append(in_c13plots)
in_plot_label.append(k)
in_plot_index.append(c13plots_index)
if any(in_plot):
lbl = in_plot_label[in_plot.index(True)]
# if lbl != self.highlighted_peak_lbl:
# highlight new peak
specplot.peak_overlays_dict[lbl].set_visible(True)
specplot.peak_overlays_dict[lbl].set_color(RED)
specplot.peak_overlays_dict[lbl].set_linewidth(1.2)
# annotate new peak
if "H" in lbl:
# set the annotation to the peak
atom_index = int(lbl[1:])
ppm = self.nmrproblem.h1.loc[atom_index, "ppm"]
integral = float(self.nmrproblem.h1.loc[atom_index, "integral"])
jcoupling = self.nmrproblem.h1.loc[atom_index, "jCouplingClass"]
jcouplingvals = self.nmrproblem.h1.loc[atom_index, "jCouplingVals"]
jcouplingvals = simpleNMRutils.stringify_vals(jcouplingvals)
annot_text = f"{lbl}: {ppm:.2f} ppm\nInt:{integral:.1f}\nJ: {jcoupling}: {jcouplingvals} Hz"
specplot.annot_H1.xy = (event.xdata, event.ydata)
specplot.annot_H1.set_text(annot_text)
specplot.annot_H1.set_visible(True)
elif "C" in lbl:
# set the annotation to the peak
atom_index = int(lbl[1:])
ppm = self.nmrproblem.c13.loc[atom_index, "ppm"]
annot_text = f"{lbl}: {ppm:.1f} ppm"
x = event.xdata
y = event.ydata
specplot.annot_C13.set_text(annot_text)
specplot.annot_C13.xy = (x, y)
specplot.annot_C13.set_visible(True)
self.highlighted_peak_lbl = lbl
if "H" in lbl:
try:
clbl = self.nmrproblem.hsqc[self.nmrproblem.hsqc.f2H_i == lbl][
"f1C_i"
].values[0]
except IndexError:
print(f"no HSQC peak found for this H1 peak {lbl}")
clbl = ""
else:
clbl = lbl
if "C" not in clbl:
specplot.canvas.draw_idle()
return
self.node_hover_lbl = clbl
# update molplot highlights
self.update_molplot_highlights(molplot, specplot, clbl)
# uddate specplot canvas
specplot.canvas.draw_idle()
# uddate title in molplot
c13_ind = int(clbl[1:])
ppm_val = self.nmrproblem.c13.loc[c13_ind]["ppm"]
attached_protons = self.nmrproblem.c13.loc[c13_ind]["attached_protons"]
title_str = (
f"{clbl}: {ppm_val:.1f} ppm, attached protons: {attached_protons}"
)
self.moleculePlot.ax.set_title(title_str)
else:
# unhilight old peak
if self.highlighted_peak_lbl is not None:
self.mol_nodes.set_fc(self.mol_nodes.scatter_facecolors_rgba)
self.mol_nodes.set_ec(self.mol_nodes.scatter_edgecolors_rgba)
self.moleculePlot.hide_hmbc_graph_networks()
specplot.reset_peak_overlays_eeh()
specplot.hide_annotation(specplot.annot_C13)
specplot.hide_annotation(specplot.annot_H1)
# unhighlight distributions
specplot.reset_distributions_eeh()
# uddate specplot canvas
specplot.canvas.draw_idle()
molplot.canvas.draw_idle()
def update_molplot_highlights(self, molplot, specplot, lbl):
molplot.mol_nodes.node_highlighted = True
ind = int(lbl[1:]) - 1
scatter_facecolors_highlight = molplot.mol_nodes.get_facecolors()
scatter_edgecolors_highlight = molplot.mol_nodes.get_edgecolors()
scatter_facecolors_highlight[ind] = WHITE
scatter_edgecolors_highlight[ind] = RED
molplot.mol_nodes.set_fc(scatter_facecolors_highlight)
if lbl in self.nmrproblem.hmbc_graphs.keys():
# self.hide_hmbc_graph_networks()
self.moleculePlot.draw_hmbc_graph_network(lbl)
# higlight C13 hmbc peaks
specplot.highlight_hmbc_C13_peaks(lbl)
# self.redraw_axes()
# highlight H1 hmbc peaks
specplot.highlight_H1_HMBC_peaks(lbl)
# highlight C13 peak in graph x1
specplot.highlight_C13_peak(lbl)
# higlight H1 peaks in graph x1
specplot.highlight_H1_peaks_from_highlighted_carbon_atom(lbl)
# self.c13_plots[lbl]['highlight'].set_visible(True)
# annotate C13 peak in graph x1
specplot.display_annotation_C13_from_molplot(lbl, specplot.annot_C13)
# annotate H1 peaks in graph x1
specplot.display_annotation_H1_from_molplot(
lbl, specplot.annot_H1, self.nmrproblem
)
# annotate distributions
hpks = self.nmrproblem.hsqc[self.nmrproblem.hsqc.f1C_i == lbl]["f2H_i"].values
cpks = [lbl]
self.display_distributions(cpks, hpks, specplot)
molplot.canvas.draw_idle()
specplot.canvas.draw_idle()
def display_distributions(self, C_pks, H_pks, specplot):
# add highlighted distributions
colors = ["b", "g", "r", "c", "m", "y", "k"]
# used to dsplay legends of highlighted distributions
plinesH = []
plabelsH = []
plinesC = []
plabelsC = []
ppmH = []
ppmC = []
# set visible
# circle through colors
# create proton distribution legends
for pk in H_pks:
numplots = len(specplot.h1c13distlist[0][pk]) - 1
for i, aa in enumerate(specplot.h1c13distlist[0][pk]):
ppmH.append(self.nmrproblem.udic[0]["info"].loc[pk, "ppm"])
# sel.extras.append(self.cursor.add_highlight(aa))
aa.set_visible(True)
aa.set_linewidth(0.75)
aa.set_color(colors[i % 7])
# do not add legend info if plot is just single line showing where peak pos is
if i < numplots:
plabelsH.append(aa.get_label())
plinesH.append(aa)
# create carbon distribution legends
for pk in C_pks:
numplots = len(specplot.h1c13distlist[1][pk]) - 1
for i, aa in enumerate(specplot.h1c13distlist[1][pk]):
ppmC.append(self.nmrproblem.udic[1]["info"].loc[pk, "ppm"])
# sel.extras.append(self.cursor.add_highlight(aa))
aa.set_visible(True)
aa.set_linewidth(0.75)
aa.set_color(colors[i % 7])
if i < numplots:
plabelsC.append(aa.get_label())
plinesC.append(aa)
# adjust x-axis width H1 and C13 of distribution plots
# and add legend information
if len(ppmH) > 0:
# calculate average position of peaks which will be used to adjust the x axis ppm range
ppmmmH = np.mean(ppmH)
specplot.h1dist_ax.set_xlim(ppmmmH + 2, ppmmmH - 2)
specplot.h1dist_ax.legend(plinesH, plabelsH)
if len(ppmC) > 0:
ppmmmC = np.mean(ppmC)
specplot.c13dist_ax.set_xlim(ppmmmC + 50, ppmmmC - 50)
specplot.c13dist_ax.legend(plinesC, plabelsC)
def button_release_molecule(self, event, molplot, specplot):
if (self.moltoolbar.mode != "") or (self.spctoolbar.mode != ""):
return
self.mol_nodes.set_fc(self.mol_nodes.scatter_facecolors_rgba)
self.mol_nodes.set_ec(self.mol_nodes.scatter_edgecolors_rgba)
self.moleculePlot.hide_hmbc_graph_networks()
specplot.reset_peak_overlays_eeh()
specplot.hide_annotation(specplot.annot_C13)
specplot.hide_annotation(specplot.annot_H1)
# unhighlight distributions
specplot.reset_distributions_eeh()
molplot.canvas.draw_idle()
specplot.canvas.draw_idle()
self.node_pick_ind = None
self.node_hover_ind = None
self.node_picked = False
self.node_moved = False
def motion_notify_callback(self, event, specplot, molplot):
if (self.moltoolbar.mode != "") or (self.spctoolbar.mode != ""):
return
self.hover_over_molecule(
event, event_name="motion_notify_event", molplot=molplot, specplot=specplot
)
if not hasattr(self, "label_id"):
# print("not hasattr(self, 'label_id')")
return
# else:
# print("self.label_id: ", self.label_id)
in_node, _ = self.mol_nodes.contains(event)
if (not in_node) and (event.button != 1):
self.mol_nodes.node_highlighted = False
self.mol_nodes.set_fc(self.mol_nodes.scatter_facecolors_rgba)
self.mol_nodes.set_ec(self.mol_nodes.scatter_edgecolors_rgba)
self.moleculePlot.hide_hmbc_graph_networks()
specplot.reset_peak_overlays_eeh()
specplot.hide_annotation(specplot.annot_C13)
specplot.hide_annotation(specplot.annot_H1)
# unhighlight distributions
specplot.reset_distributions_eeh()
molplot.canvas.draw_idle()
specplot.canvas.draw_idle()
return
if event.button != 1:
# print("event.button != 1, return")
return
self.node_moved = True
x, y = event.xdata, event.ydata
# if x or y is None: return mouse beyond plotting area
if x is None:
return
if y is None:
return
self.hmbc_graph_plots = self.moleculePlot.hmbc_graph_plots
self.mol_nodes = self.moleculePlot.mol_nodes
self.mol_edges = self.moleculePlot.mol_edges
self.mol_labels = self.moleculePlot.mol_labels
self.mol_ind = self.node_pick_ind
# move nodes, edges and labels associated with hmbc network for each carbon atom
for n in self.nmrproblem.nx_graph_molecule.nodes:
if n in self.hmbc_graph_plots:
hmbc_nodes = self.hmbc_graph_plots[n]["hmbc_nodes"]
hmbc_edges = self.hmbc_graph_plots[n]["hmbc_edges"]
hmbc_labels = self.hmbc_graph_plots[n]["hmbc_labels"]
hmbc_vertices_moved = self.hmbc_graph_plots[n]["hmbc_vertices_moved"]
if self.label_id in hmbc_labels.keys():
self.hmbc_ind = [list(hmbc_labels.keys()).index(self.label_id)]
# readjust coords of nodes in hmbc network
xy = np.asarray(hmbc_nodes.get_offsets())
xy[self.hmbc_ind[0]] = np.array([x, y])
hmbc_nodes.set_offsets(xy)
# readjust coords of labels in hmbc network
hmbc_labels[self.label_id].set_x(x)
hmbc_labels[self.label_id].set_y(y)
if not isinstance(hmbc_edges, list):
verts = []
for i, e in enumerate(hmbc_edges.get_paths()):
v = []
for j, c in enumerate(e.vertices):
if hmbc_vertices_moved[i][j] == True:
v.append([x, y])
else:
v.append(c)
verts.append(v)
# readjust coords of edges in hmbc network
hmbc_edges.set_verts(verts)
# move nodes, edges and labels associated with molecule
xy = np.asarray(self.mol_nodes.get_offsets())
xy[self.mol_ind] = np.array([x, y])
# readjust coords of nodes in molecule network
self.mol_nodes.set_offsets(xy)
# readjust coords of labels in molecule network
self.mol_labels[self.label_id].set_x(x)
self.mol_labels[self.label_id].set_y(y)
verts = []
if not isinstance(self.mol_edges, list):
for i, e in enumerate(self.mol_edges.get_paths()):
v = []
for j, c in enumerate(e.vertices):
if self.moleculePlot.mol_vertices_moved[i][j] == True:
v.append([x, y])
else:
v.append(c)
verts.append(v)
# readjust coords of edges in molecule network
self.mol_edges.set_verts(verts)
self.moleculePlot.ax.figure.canvas.draw_idle()
self.moved_node = self.mol_ind
self.moved_x = x
self.moved_y = y
def hover_over_molecule(self, event, event_name, molplot, specplot):
self.mol_nodes = molplot.mol_nodes
self.mol_labels = molplot.mol_labels
in_node, node_index = self.mol_nodes.contains(event)
if self.node_picked:
self.mol_nodes.node_highlighted = False
return
if in_node:
self.mol_nodes.node_highlighted = True
ind = node_index["ind"][0]
lbl = f"{self.mol_nodes.my_labels[ind]}"
x, y = self.mol_nodes.get_offsets()[ind]
self.node_hover_ind = ind
self.node_hover_lbl = lbl
self.node_hover_x = x
self.node_hover_y = y
if lbl != self.old_lbl:
self.old_lbl = lbl
self.mol_nodes.node_highlighted = False
self.mol_nodes.set_fc(self.mol_nodes.scatter_facecolors_rgba)
self.mol_nodes.set_ec(self.mol_nodes.scatter_edgecolors_rgba)
self.moleculePlot.hide_hmbc_graph_networks()
specplot.reset_peak_overlays_eeh()
specplot.hide_annotation(specplot.annot_C13)
specplot.hide_annotation(specplot.annot_H1)
# unhighlight distributions
specplot.reset_distributions_eeh()
molplot.canvas.draw_idle()
specplot.canvas.draw_idle()
c13_ind = int(lbl[1:])
ppm_val = self.nmrproblem.c13.loc[c13_ind]["ppm"]
attached_protons = self.nmrproblem.c13.loc[c13_ind]["attached_protons"]
title_str = (
f"{lbl}: {ppm_val:.1f} ppm, attached protons: {attached_protons}"
)
self.moleculePlot.ax.set_title(title_str)
scatter_facecolors_highlight = self.mol_nodes.get_facecolors()
scatter_edgecolors_highlight = self.mol_nodes.get_edgecolors()
scatter_facecolors_highlight[ind] = WHITE
scatter_edgecolors_highlight[ind] = RED
self.mol_nodes.set_fc(scatter_facecolors_highlight)
if lbl in self.nmrproblem.hmbc_graphs.keys():
# self.hide_hmbc_graph_networks()
self.moleculePlot.draw_hmbc_graph_network(lbl)
# higlight C13 hmbc peaks
specplot.highlight_hmbc_C13_peaks(lbl)
# self.redraw_axes()
# highlight H1 hmbc peaks
specplot.highlight_H1_HMBC_peaks(lbl)
# highlight C13 peak in graph x1
specplot.highlight_C13_peak(lbl)
# higlight H1 peaks in graph x1
specplot.highlight_H1_peaks_from_highlighted_carbon_atom(lbl)
# self.c13_plots[lbl]['highlight'].set_visible(True)
# annotate C13 peak in graph x1
specplot.display_annotation_C13_from_molplot(lbl, specplot.annot_C13)
# annotate H1 peaks in graph x1
specplot.display_annotation_H1_from_molplot(
lbl, specplot.annot_H1, self.nmrproblem
)
# annotate distributions
hpks = self.nmrproblem.hsqc[self.nmrproblem.hsqc.f1C_i == lbl][
"f2H_i"
].values
cpks = [lbl]
self.display_distributions(cpks, hpks, specplot)
molplot.canvas.draw_idle()
specplot.canvas.draw_idle()
else:
# if self.mol_nodes.node_highlighted:
self.mol_nodes.node_highlighted = False
self.mol_nodes.set_fc(self.mol_nodes.scatter_facecolors_rgba)
self.mol_nodes.set_ec(self.mol_nodes.scatter_edgecolors_rgba)
self.moleculePlot.hide_hmbc_graph_networks()
specplot.reset_peak_overlays_eeh()
specplot.hide_annotation(specplot.annot_C13)
specplot.hide_annotation(specplot.annot_H1)
# unhighlight distributions
specplot.reset_distributions_eeh()
molplot.canvas.draw_idle()
specplot.canvas.draw_idle()
def pick_molecule(self, event, event_name, specplot, molplot):
global JAVA_AVAILABLE
in_node, node_index = self.moleculePlot.mol_nodes.contains(event.mouseevent)
print("in_node: ", in_node)
print("node_index: ", node_index)
print("event_name: ", event_name)
print("event.mouseevent: ", event.mouseevent)
print(dir(event))
if in_node:
self.node_picked = True
# self.mol_ind = event.ind
# self.node_pick_ind = event.ind
self.node_pick_ind = node_index["ind"][0]
ptcoords = np.ma.compressed(
self.moleculePlot.mol_nodes.get_offsets()[self.node_pick_ind]
)
# find label id
self.label_id = list(self.moleculePlot.mol_labels.keys())[self.node_pick_ind]
print("self.label_id: ", self.label_id, self.node_pick_ind, f"C{self.node_pick_ind+1}")
# hide all highlights before dragging node
if self.mol_nodes.node_highlighted:
self.mol_nodes.set_fc(self.mol_nodes.scatter_facecolors_rgba)
self.mol_nodes.set_ec(self.mol_nodes.scatter_edgecolors_rgba)
self.moleculePlot.hide_hmbc_graph_networks()
specplot.reset_peak_overlays_eeh()
specplot.hide_annotation(specplot.annot_C13)
specplot.hide_annotation(specplot.annot_H1)
# unhighlight distributions
specplot.reset_distributions_eeh()
specplot.canvas.draw_idle()
molplot.canvas.draw_idle()
# for each carbon atom in moleule check to see if it is in
# the associated hmbc network then set the vertices_moved flag
# to true if the picked node is in the network
# update edges, nodes and labels
# update them even if they are not visible so that keep in sync
# with the moved display
for n in self.nmrproblem.nx_graph_molecule.nodes:
hmbc_nodes = self.moleculePlot.hmbc_graph_plots[n]["hmbc_nodes"]
hmbc_edges = self.moleculePlot.hmbc_graph_plots[n]["hmbc_edges"]
hmbc_labels = self.moleculePlot.hmbc_graph_plots[n]["hmbc_labels"]
hmbc_vertices_moved = self.moleculePlot.hmbc_graph_plots[n][
"hmbc_vertices_moved"
]
# check if picked node is in hmbc network and then
# if the picked coords match of the edges match set them to True
# so that the values of the edges will be moved during the motion notify
# event
if self.label_id in hmbc_labels.keys():
self.hmbc_ind = [list(hmbc_labels.keys()).index(self.label_id)]
if not isinstance(hmbc_edges, list):
for i, e in enumerate(hmbc_edges.get_paths()):
for j, c in enumerate(e.vertices):
if c[0] == ptcoords[0] and c[1] == ptcoords[1]:
hmbc_vertices_moved[i][j] = True
else:
hmbc_vertices_moved[i][j] = False
else:
# if the hmbc fragment does not contain the picked node
# set all the moved_vertices to False
if not isinstance(hmbc_edges, list):
for i, e in enumerate(hmbc_edges.get_paths()):
for j, c in enumerate(e.vertices):
hmbc_vertices_moved[i][j] = False
self.hmbc_ind = None
# do the same for the molecule network
if self.label_id in self.moleculePlot.mol_labels.keys():
if not isinstance(self.moleculePlot.mol_edges, list):
for i, e in enumerate(self.moleculePlot.mol_edges.get_paths()):
for j, c in enumerate(e.vertices):
if c[0] == ptcoords[0] and c[1] == ptcoords[1]:
self.moleculePlot.mol_vertices_moved[i][j] = True
else:
self.moleculePlot.mol_vertices_moved[i][j] = False
else:
if not isinstance(self.moleculePlot.mol_edges, list):
for i, e in enumerate(self.moleculePlot.mol_edges.get_paths()):
for j, c in enumerate(e.vertices):
self.moleculePlot.mol_vertices_moved[i][j] = False
def _createMenuBar(self):
menuBar = self.menuBar()
# File menu
fileMenu = QMenu("&File", self)
menuBar.addMenu(fileMenu)
# fileMenu.addAction(self.newAction)
fileMenu.addAction(self.newFromMresNovaAction)
# fileMenu.addAction(self.newFromTopspinAction)
fileMenu.addAction(self.openAction)
# Open Recent submenu
# self.openRecentMenu = fileMenu.addMenu("Open Recent")
fileMenu.addAction(self.saveAction)
# Separator
fileMenu.addSeparator()
fileMenu.addAction(self.exitAction)
# # exampleProblems menu
# exampleProblemsMenu = menuBar.addMenu("&Example Problems")
examples_menu = menuBar.addMenu("Examples")
self.initExampleMenu(examples_menu)
# for action in self.exampleProblemsActions:
# exampleProblemsMenu.addAction(action)
# Edit menu
# editMenu = menuBar.addMenu("&Edit")
# editMenu.addAction(self.copyAction)
# editMenu.addAction(self.pasteAction)
# editMenu.addAction(self.cutAction)
# Separator
# editMenu.addSeparator()
# Find and Replace submenu
# findMenu = editMenu.addMenu("Find and Replace")
# findMenu.addAction("Find...")
# findMenu.addAction("Replace...")
# Help menu
# helpMenu = menuBar.addMenu(QIcon(":help-content.svg"), "&Help")
helpMenu = menuBar.addMenu("&Help")
helpMenu.addAction(self.helpContentAction)
helpMenu.addAction(self.aboutAction)
def initExampleMenu(self, menu):
self.exampleProblems = exampleProblems.exampleproblems_names
for actionName in self.exampleProblems:
qa = QAction(actionName, self)
menu.addAction(qa)
qa.triggered.connect(self.exampleProblem_selected)
def exampleProblem_selected(self):
action = self.sender()
exampleproblem_name = action.text()
self.excel_path, self.tmpdir = exampleProblems.create_tmp_excel_file(
exampleproblem_name, exampleProblems.exampleproblems_df[exampleproblem_name]
)
data_info = nmrProblem.parse_argv(
my_argv=[
"simplepy",
self.tmpdir.name,
]
)
xy3_dlg = XY3dialog(
java_available=java.JAVA_AVAILABLE,
sheets_missing=nmrProblem.get_missing_sheets(data_info["excel_fn"], True),
)
if xy3_dlg.exec():
xy3_calc_method, expts_available = xy3_dlg.get_method()
# add "molecule" to expts_available
expts_available.append("molecule")
self.nmrproblem = nmrProblem.NMRproblem(
data_info,
java_available=java.JAVA_AVAILABLE,
xy3_calc_method=xy3_calc_method,
java_command=java.JAVA_COMMAND,
expts_available=expts_available,
)
if self.nmrproblem.data_complete:
print("line 918")
print("nmrproblem.c13")
print(self.nmrproblem.c13)
print("nmrproblem.h1")
print(self.nmrproblem.h1)
print("nmrproblem.hsqc")
print(self.nmrproblem.hsqc)
self.nmrproblem.initiate_df_data_complete()
self.initiate_windows(self.nmrproblem)
else:
print("xy3_dlg.exec() failed")
def _createToolBars(self):
# File toolbar
fileToolBar = self.addToolBar("File")
fileToolBar.setMovable(False)
# fileToolBar.addAction(self.newAction)
fileToolBar.addAction(self.newFromMresNovaAction)
# fileToolBar.addAction(self.newFromTopspinAction)
fileToolBar.addAction(self.openAction)
fileToolBar.addAction(self.saveAction)
# Edit toolbar
# editToolBar = QToolBar("Edit", self)
# self.addToolBar(editToolBar)
# editToolBar.addAction(self.copyAction)
# editToolBar.addAction(self.pasteAction)
# editToolBar.addAction(self.cutAction)
# Widgets
self.fontSizeSpinBox = QSpinBox()
self.fontSizeSpinBox.setFocusPolicy(Qt.NoFocus)
# editToolBar.addWidget(self.fontSizeSpinBox)
def _createStatusBar(self):
self.statusbar = self.statusBar()
# Temporary message
self.statusbar.showMessage("Ready", 3000)
# Permanent widget
self.wcLabel = QLabel(
f"Molecule: {self.nmrproblem.moleculeAtomsStr} DBE: {int(self.nmrproblem.dbe)}"
)
self.statusbar.addPermanentWidget(self.wcLabel)
def _createActions(self):
# File actions
self.newAction = QAction(self)
self.newAction.setText("&New")
self.newFromMresNovaAction = QAction(self)
self.newFromMresNovaAction.setText("New from MNova")
# self.newFromTopspinAction = QAction(self)
# self.newFromTopspinAction.setText("New from Topspin")
# self.newAction.setIcon(QIcon(":file-new.svg"))
# self.openAction = QAction(QIcon(":file-open.svg"), "&Open...", self)
# self.saveAction = QAction(QIcon(":file-save.svg"), "&Save", self)
self.openAction = QAction("&Open...", self)
self.saveAction = QAction("&Save", self)
self.exitAction = QAction("&Exit", self)
# String-based key sequences
# self.newAction.setShortcut("Ctrl+N")