#!/usr/bin/python3
# -*- coding: utf-8 -*-
'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2025, Juan José Gómez Romera <jjgomera@gmail.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Module with the openbabel functionality, optional module for
graphics representation of chemical compound from its smile code
* :func:`imageFromSmile`: Generate image file with expanded formulae
* :class:`ConfBabel`: Openbabel image generation configuration options
'''
import os
import tempfile
from configparser import ConfigParser
from tools.qt import QtCore, QtGui, QtWidgets
try:
from openbabel.pybel import readstring
except ImportError:
pass
from UI.widgets import ColorSelector
[docs]
def imageFromSmile(smile, fname, conf):
"""Generate image file with the compound chemical structure
Parameters
----------
smile : str
Smile code for compound
fname : str
Filename to save the image
conf : configparser.ConfigParser
Configuration parameters
"""
# Get dict parameters for exported image configuration
# Parameters available from openbabel documentation
# https://openbabel.org/docs/current/FileFormats/PNG_2D_depiction.html
# - p <num>: px Image size, default 300
# - w <pixels>: image width (or from image size)
# - h <pixels>: image height (or from image size)
# - c <num>: number of columns in table
# - r <num>: number of rows in table
# - N <num>:max number objects to be output
# + u: no element-specific atom coloring
# - U: can define alternate color to internally-specified
# + b: background color
# + C: Do not draw terminal C (and H) explicitly
# + a: draw all carbon atoms
# - d: do not display molecule name
# - m: do not add margins to the image
# + s: use asymmetric double bonds
# + t: use thicker lines
# - A: display aliases, if present
# - O <format ID>: Format of embedded text. For example, molfile or smi.
# If there is no parameter, input format is used.
# - y <additional chunk ID>: Write to a chunk with specified ID
opt = {}
opt["m"] = None
opt["B"] = conf.get("Openbabel", 'BondColor')
alpha = conf.getboolean("Openbabel", "BackColorTransparent")
if alpha:
opt["b"] = "none"
else:
opt["b"] = conf.get("Openbabel", 'BackgroundColor')
if not conf.getboolean("Openbabel", 'AtomsColor'):
opt["u"] = None
if conf.getboolean("Openbabel", 'AtomsAll'):
opt["a"] = None
elif conf.getboolean("Openbabel", 'AtomsNone'):
opt["C"] = None
if conf.getboolean("Openbabel", 'TighBond'):
opt["t"] = None
if conf.getboolean("Openbabel", 'AsymetricDouble'):
opt["s"] = None
opt["x"] = None
mol = readstring("smi", smile)
mol.write("_png2", filename=fname, overwrite=True, opt=opt)
[docs]
class ConfBabel(QtWidgets.QDialog):
"""Openbabel image generation configuration options"""
[docs]
def __init__(self, config=None, parent=None):
super().__init__(parent)
layout = QtWidgets.QGridLayout(self)
layout.addWidget(QtWidgets.QLabel(self.tr("Bond color:")), 1, 1)
self.BondColor = ColorSelector()
self.BondColor.valueChanged.connect(self.updateImage)
layout.addWidget(self.BondColor, 1, 2)
layout.addWidget(QtWidgets.QLabel(self.tr("Background color:")), 2, 1)
self.BackColor = ColorSelector()
self.BackColor.valueChanged.connect(self.updateImage)
layout.addWidget(self.BackColor, 2, 2)
self.BackColorTransparent = QtWidgets.QCheckBox(
self.tr("Transparent background color"))
self.BackColorTransparent.stateChanged.connect(self.updateImage)
layout.addWidget(self.BackColorTransparent, 3, 1, 1, 2)
layout.addItem(QtWidgets.QSpacerItem(
20, 20, QtWidgets.QSizePolicy.Policy.Fixed,
QtWidgets.QSizePolicy.Policy.Fixed), 4, 1, 1, 2)
group = QtWidgets.QGroupBox(self.tr("Atom details"))
layout.addWidget(group, 5, 1, 1, 2)
lyt = QtWidgets.QVBoxLayout(group)
self.radioAll = QtWidgets.QRadioButton(self.tr("Show all atoms"))
self.radioAll.clicked.connect(self.updateImage)
lyt.addWidget(self.radioAll)
self.radioEnd = QtWidgets.QRadioButton(
self.tr("Show only terminal atoms"))
self.radioEnd.clicked.connect(self.updateImage)
lyt.addWidget(self.radioEnd)
self.radioNone = QtWidgets.QRadioButton(self.tr("Do not show atoms"))
self.radioNone.clicked.connect(self.updateImage)
lyt.addWidget(self.radioNone)
layout.addItem(QtWidgets.QSpacerItem(
20, 20, QtWidgets.QSizePolicy.Policy.Fixed,
QtWidgets.QSizePolicy.Policy.Fixed), 6, 1, 1, 2)
self.checkColor = QtWidgets.QCheckBox(self.tr("Heteroatom in color"))
self.checkColor.stateChanged.connect(self.updateImage)
layout.addWidget(self.checkColor, 7, 1, 1, 2)
self.checkTighBond = QtWidgets.QCheckBox(self.tr("Thicker bond lines"))
self.checkTighBond.stateChanged.connect(self.updateImage)
layout.addWidget(self.checkTighBond, 8, 1, 1, 2)
self.checkAsym = QtWidgets.QCheckBox(self.tr("Asymetric double bond"))
self.checkAsym.stateChanged.connect(self.updateImage)
layout.addWidget(self.checkAsym, 9, 1, 1, 2)
if os.environ["openbabel"] == "False":
self.example = QtWidgets.QLabel(
self.tr("Openbabel library don´t found"))
self.example.setStyleSheet("color: red")
else:
self.example = QtWidgets.QLabel()
layout.addWidget(self.example, 13, 1, 1, 2,
QtCore.Qt.AlignmentFlag.AlignCenter)
layout.addItem(QtWidgets.QSpacerItem(
10, 0, QtWidgets.QSizePolicy.Policy.Expanding,
QtWidgets.QSizePolicy.Policy.Expanding), 14, 1, 1, 4)
if config and config.has_section("Openbabel"):
self.BondColor.setColor(config.get("Openbabel", 'BondColor'))
self.BackColorTransparent.setChecked(
config.getboolean("Openbabel", 'BackColorTransparent'))
self.BackColor.setColor(
config.get("Openbabel", 'BackgroundColor'))
self.checkColor.setChecked(
config.getboolean("Openbabel", 'AtomsColor'))
self.radioAll.setChecked(
config.getboolean("Openbabel", 'AtomsAll'))
self.radioEnd.setChecked(
config.getboolean("Openbabel", 'AtomsEnd'))
self.radioNone.setChecked(
config.getboolean("Openbabel", 'AtomsNone'))
self.checkTighBond.setChecked(
config.getboolean("Openbabel", 'TighBond'))
self.checkAsym.setChecked(
config.getboolean("Openbabel", 'AsymetricDouble'))
self.updateImage(config)
[docs]
def updateImage(self, config=None):
"""Update image shown when changing some of the parameters"""
if os.environ["openbabel"] == "False":
return
if not isinstance(config, ConfigParser):
config = ConfigParser()
config = self.value(config)
with tempfile.NamedTemporaryFile("w", suffix=".png") as imageFile:
smile = "C=CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
imageFromSmile(smile, imageFile.name, config)
self.example.setPixmap(QtGui.QPixmap(imageFile.name))
[docs]
def value(self, config):
"""Update ConfigParser instance with the config"""
if not config.has_section("Openbabel"):
config.add_section("Openbabel")
config.set("Openbabel", "BondColor", self.BondColor.color.name())
config.set("Openbabel", "BackgroundColor",
self.BackColor.color.name(QtGui.QColor.NameFormat.HexRgb))
config.set("Openbabel", "BackColorTransparent",
str(self.BackColorTransparent.isChecked()))
config.set("Openbabel", "AtomsColor", str(self.checkColor.isChecked()))
config.set("Openbabel", "AtomsAll", str(self.radioAll.isChecked()))
config.set("Openbabel", "AtomsEnd", str(self.radioEnd.isChecked()))
config.set("Openbabel", "AtomsNone", str(self.radioNone.isChecked()))
config.set("Openbabel", "TighBond",
str(self.checkTighBond.isChecked()))
config.set("Openbabel", "AsymetricDouble",
str(self.checkAsym.isChecked()))
return config
