molSimplify 1.7.4__py3-none-any.whl

molSimplify/Classes/mGUI.py

@@ -0,0 +1,2493 @@
+# @file mGUI.py
+#  Contains main GUI class and routines.
+#
+#  Written by Tim Ioannidis for HJK Group
+#
+#  Modified by JP Janet
+#
+#  Dpt of Chemical Engineering, MIT
+
+from PyQt5.QtCore import Qt, QSize
+from PyQt5.QtWidgets import (QWidget, QGridLayout, QStackedLayout, QAction,
+                             QFileDialog, QMessageBox, QPushButton,
+                             QDesktopWidget)
+from PyQt5.QtGui import QPalette, QFont, QIcon
+from molSimplify.Classes.mWidgets import (mQMainWindow, mQPixmap, mQLabel,
+                                          mQLineEdit, mQLineEditL, mQTextEdit,
+                                          mQCheckBox, mQComboBox, mQSpinBox,
+                                          mQPushButton, mQSlider, mQDialogWarn,
+                                          mSvgWidget, relresize, center)
+from molSimplify.Classes.globalvars import globalvars, mybash
+from molSimplify.Scripts.generator import startgen
+from molSimplify.Scripts.grabguivars import (grabguivars, grabguivarsqch,
+                                             grabguivarstc, grabguivarsgam,
+                                             grabguivarsjob, grabguivarsP,
+                                             grabdbguivars, loadfrominputfile,
+                                             loadfrominputtc, loadfrominputgam,
+                                             loadfrominputqch, writeinputc,
+                                             loadfrominputjob)
+from molSimplify.Scripts.io import (readdict, getgeoms, getcores, getmcores,
+                                    getbcores, getlicores, getslicores,
+                                    getligs, getbinds, getligroups,
+                                    lig_load, copy_to_custom_path)
+from molSimplify.Scripts.addtodb import (addtoldb, addtocdb, addtobdb,
+                                         removefromDB)
+import sys
+import os
+import shutil
+import unicodedata
+import glob
+import tempfile
+import re
+from importlib_resources import files as resource_files
+import xml.etree.ElementTree as ET
+
+try:
+    from openbabel import openbabel  # version 3 style import
+except ImportError:
+    import openbabel  # fallback to version 2
+
+# Main GUI class
+
+
+class mGUI():
+    getgeoms()
+
+    def __init__(self, app):
+        # build gui
+        self.app = app
+        self.initGUI(app)
+        cwd = os.getcwd()
+        globs = globalvars()  # global variables
+        globs.rundir = os.path.join(cwd, 'Runs')
+        if not os.path.exists(globs.rundir):
+            print((globs.rundir))
+            os.makedirs(globs.rundir)
+    # builds the gui
+
+    def initGUI(self, app):
+        '''
+        ######################
+        ### build main GUI ###
+        ######################
+        '''
+        # ## check for configuration file ###
+        cwd = os.getcwd()
+        globs = globalvars()  # global variables
+        globs.rundir = os.path.join(cwd, 'Runs')
+        if not os.path.exists(globs.rundir):
+            os.makedirs(globs.rundir)
+        # overX = True if 'localhost' in os.environ['DISPLAY'].lower() else False # detect running over X
+#        configfile = False if not glob.glob(homedir+'/.molSimplify') else True
+#        if not configfile:
+#            self.wwindow = mQMainWindow()
+#            self.wwindow.resize(0.5,0.5)
+#            QMessageBox.information(self.wwindow, 'Setup', 'It looks like the '
+#                                    'configuration file "~/.molSimplify" does '
+#                                    'not exist!Please follow the next steps to '
+#                                    'configure the file.')
+#            QMessageBox.information(self.wwindow, 'Installation directory',
+#                                    "Please select the top installation "
+#                                    "directory for the program.")
+#            instdir = QFileDialog.getExistingDirectory(self.wwindow, "Select Directory")
+#            f = open(homedir+'/.molSimplify','w')
+#            if len(instdir) > 1:
+#                f.write("INSTALLDIR="+instdir+'\n')
+        # ## end set-up configuration file ###
+        # main window widget
+        self.wmwindow = mQMainWindow()
+        self.wmwindow.show()
+        self.wmain = QWidget()
+        self.wmwindow.setWindowTitle("molSimplify")
+        self.wmwindow.setMinimumSize(1000, 700)
+        # set background color
+        p = QPalette()
+        p.setColor(QPalette.Background, Qt.white)
+        self.wmwindow.setPalette(p)
+        # ## main grid layout ###
+        self.grid = QGridLayout()
+        # ## stacked layouts ###
+        self.sgrid = QStackedLayout()
+        self.sgrid.setStackingMode(1)
+        self.sgrid.addWidget(self.wmain)
+        # set manually size of rows/columns
+        self.grid.setRowMinimumHeight(0, 15)
+        self.grid.setRowMinimumHeight(2, 90)
+        self.grid.setRowMinimumHeight(3, 15)
+        self.grid.setRowMinimumHeight(4, 50)
+        ####################################
+        # ## create menubar and callbacks ###
+        menubar = self.wmwindow.menuBar()
+        menu0 = menubar.addMenu('&File')
+        menu1 = menubar.addMenu('&Load')
+        menu2 = menubar.addMenu('&Help')
+        exitAction = QAction('&Exit', self.wmwindow)
+        exitAction.setShortcut('Ctrl+Q')
+        exitAction.setStatusTip('Exit application')
+        exitAction.triggered.connect(self.qexit)
+        menu0.addAction(exitAction)
+        saveAction = QAction('&Save As..', self.wmwindow)
+        saveAction.setShortcut('Ctrl+S')
+        saveAction.setStatusTip('Save current input settings')
+        saveAction.triggered.connect(self.qsaveinput)
+        menu0.addAction(saveAction)
+        loadAction = QAction('&Load', self.wmwindow)
+        loadAction.setShortcut('Ctrl+O')
+        loadAction.setStatusTip('Load input file')
+        loadAction.triggered.connect(self.qloadinput)
+        menu1.addAction(loadAction)
+        helpAction = QAction('&About', self.wmwindow)
+        helpAction.setShortcut('Ctrl+H')
+        helpAction.setStatusTip('Show program information')
+        helpAction.triggered.connect(self.qshowhelp)
+        menu2.addAction(helpAction)
+        # ## place title top ###
+        f = resource_files("molSimplify").joinpath("icons/logo.png")
+        clogo = mQPixmap(f)
+        self.grid.addWidget(clogo, 2, 8, 1, 10)
+        self.txtdev = mQLabel('Developed by Kulik group @ MIT', '', 'c', 16)
+        self.grid.addWidget(self.txtdev, 19, 8, 2, 10)
+        # ##################################################
+        # ##################################################
+        # ######### STRUCTURE GENERATION INPUTS ############
+        # ##################################################
+        # ##################################################
+        # ## title ###
+        self.txtgpar = mQLabel('Structure specification', '', 'c', 20)
+        self.grid.addWidget(self.txtgpar, 4, 0, 2, 14)
+        # ## core structure specification ###
+        ctip = 'Core of structure'
+        self.rtcore = mQLabel('Core:', ctip, 'C', 12)
+        f = QFont("Helvetica", 14, 75)
+        self.rtcore.setFont(f)
+        self.grid.addWidget(self.rtcore, 7, 2, 1, 1)
+        cores = list(sorted(getmcores()))
+        self.etcore = mQLineEditL('', ctip, 'l', 12, cores)
+        self.grid.addWidget(self.etcore, 7, 3, 1, 3)
+        # ## Connection atoms for core ###
+        ctip = 'Specify connection atoms for core if using SMILES or custom cores (default: 1)'
+        self.rtccat = mQLabel('Core connections:', ctip, 'C', 12)
+        self.rtccat.setWordWrap(True)
+        self.grid.addWidget(self.rtccat, 7, 6, 1, 2)
+        self.etccat = mQLineEdit('', ctip, 'l', 12)
+        self.grid.addWidget(self.etccat, 7, 8, 1, 2)
+        # ## replace option ###
+        ctip = 'Replace ligand at specified connection point'
+        self.replig = mQCheckBox('replace', ctip, 12)
+        self.grid.addWidget(self.replig, 7, 10, 1, 4)
+        # coordination
+        ctip = 'Number of ligands connected to the metal.'
+        self.rcoord = mQLabel('Coordination:', ctip, 'Cr', 12)
+        self.grid.addWidget(self.rcoord, 8, 2, 1, 2)
+        coords, geomnames, geomshorts, geomgroups = getgeoms()
+        qcav = sorted(list(set(coords)))
+        self.dcoord = mQComboBox(qcav, ctip, 12)
+        self.dcoord.setCurrentIndex(5)
+        self.dcoord.currentIndexChanged.connect(self.matchgeomcoord)
+        self.grid.addWidget(self.dcoord, 8, 4, 1, 1)
+        # geometry of coordination
+        self.dcoordg = mQComboBox('', '', 12)
+        self.dcoordg.setCurrentIndex(0)
+        self.matchgeomcoord()
+        self.grid.addWidget(self.dcoordg, 8, 5, 1, 2)
+        # add new coordination
+        ctip = 'Add geometry'
+        self.butaddg = mQPushButton('Add\ngeometry', ctip, 12)
+        self.butaddg.clicked.connect(self.addgeom)
+        self.grid.addWidget(self.butaddg, 8, 7, 1, 2)
+        # add new coordination
+        ctip = 'View geometry with atom labels'
+        self.butvg = mQPushButton('View\ngeometry', ctip, 12)
+        self.butvg.clicked.connect(self.viewgeom)
+        self.grid.addWidget(self.butvg, 8, 9, 1, 2)
+        # ############################################
+        # ################# LIGANDS ##################
+        # ## ligands tables ###
+        ctip0 = 'Ligand(s) to be used'
+        self.rtligh = mQLabel('Ligand', ctip0, 'c', 12)  # ligand header
+        f = QFont("Helvetica", 12, 75)
+        self.rtligh.setFont(f)
+        ctip1 = 'Occurrence of corresponding ligand(s)'
+        self.rtligocch = mQLabel(
+            'Frequency', ctip1, 'c', 12)  # occurrence header
+        ctip2 = 'Connection atom(s) of ligands (default: 1).'
+        # connection atom header
+        self.rtsmicath = mQLabel('Connections', ctip2, 'c', 12)
+        # keep Hs header
+        ctip3 = 'Do not remove hydrogens while connecting ligand to core. default True'
+        self.keepHh = mQLabel('keep\nHs', ctip3, 'c', 12)  # occurrence header
+        ctip4 = 'Custom bond length for M-L in Angstrom'
+        # custom metal ligand bond length header
+        self.MLbondsh = mQLabel('M-L\nbond', ctip4, 'c', 12)
+        ctip5 = 'Custom angles for connection points (polar theta, azimuthal phi) in degrees separated with /. e.g 10/20'
+        # custom angles for distortion header
+        self.canglesh = mQLabel('Angle', ctip5, 'c', 12)
+        ctip6 = 'Name of ligand'
+        # name of ligand header
+        self.nameligh = mQLabel('Name', ctip6, 'c', 12)
+        ctip7 = 'Force ligand order and disable smart reordering'
+        self.ligfloc = mQCheckBox('Force location', ctip7, 12)
+        ctip8 = 'Ligand smart alignment. Aligns first the bulky ligands.'
+        self.ligfalign = mQCheckBox('Smart alignment', ctip8, 12)
+        self.ligfalign.setChecked(True)
+        # add to layout
+        self.grid.setColumnMinimumWidth(0, 150)
+        self.grid.addWidget(self.rtligh, 9, 0, 1, 2)
+        self.grid.addWidget(self.rtligocch, 9, 2, 1, 2)
+        self.grid.addWidget(self.rtsmicath, 9, 4, 1, 2)
+        self.grid.addWidget(self.keepHh, 9, 6, 1, 1)
+        self.grid.addWidget(self.MLbondsh, 9, 7, 1, 2)
+        self.grid.addWidget(self.canglesh, 9, 9, 1, 1)
+        self.grid.addWidget(self.nameligh, 9, 10, 1, 1)
+        self.grid.addWidget(self.ligfalign, 13, 15, 1, 2)
+        self.grid.addWidget(self.ligfloc, 13, 17, 1, 2)
+        # ligands #
+        licores = list(sorted(getlicores()))
+        self.lig = []
+        self.ligocc = []
+        self.ligconn = []
+        self.ligH = []
+        self.ligML = []
+        self.ligan = []
+        self.lignam = []
+        self.ligadd = []
+        for ii in range(0, 8):
+            # ligands #
+            self.lig.append(mQLineEditL('', ctip0, 'l', 12, licores))
+            self.grid.addWidget(self.lig[ii], 10+ii, 0, 1, 2)  # add to layout
+            # occurrences #
+            self.ligocc.append(mQSpinBox(ctip1))
+            self.grid.addWidget(self.ligocc[ii], 10+ii, 2, 1, 2)
+            # connections #
+            self.ligconn.append(mQLineEdit('', ctip2, 'l', 12))
+            self.grid.addWidget(self.ligconn[ii], 10+ii, 4, 1, 2)
+            # keep Hydrogens #
+            self.ligH.append(mQComboBox(['yes', 'no'], ctip3, 12))
+            self.grid.addWidget(self.ligH[ii], 10+ii, 6, 1, 1)
+            # ML bond lengths #
+            self.ligML.append(mQLineEdit('', ctip4, 'l', 12))
+            self.grid.addWidget(self.ligML[ii], 10+ii, 7, 1, 2)
+            # custom angles #
+            self.ligan.append(mQLineEdit('', ctip5, 'l', 12))
+            self.grid.addWidget(self.ligan[ii], 10+ii, 9, 1, 1)
+            # ligand names #
+            self.lignam.append(mQLineEdit('', ctip6, 'l', 12))
+            self.grid.addWidget(self.lignam[ii], 10+ii, 10, 1, 1)
+            # ligand buttons #
+            if ii < 7:
+                ctip = 'Add new ligand.'
+                self.ligadd.append(mQPushButton('+', ctip, 12))
+                self.grid.addWidget(self.ligadd[ii], 10+ii, 13, 1, 1)
+                self.ligadd[ii].setDisabled(True)
+                self.ligadd[ii].hide()
+            if ii > 0:
+                self.lig[ii].setDisabled(True)  # disable
+                self.ligocc[ii].setDisabled(True)
+                self.ligconn[ii].setDisabled(True)
+                self.ligH[ii].setDisabled(True)
+                self.ligML[ii].setDisabled(True)
+                self.ligan[ii].setDisabled(True)
+                self.lignam[ii].setDisabled(True)
+            self.ligadd[0].setDisabled(False)
+            self.ligadd[0].show()
+        # callbacks
+        self.ligadd[0].clicked.connect(self.addlig0)  # callback
+        self.ligadd[1].clicked.connect(self.addlig1)  # callback
+        self.ligadd[2].clicked.connect(self.addlig2)  # callback
+        self.ligadd[3].clicked.connect(self.addlig3)  # callback
+        self.ligadd[4].clicked.connect(self.addlig4)  # callback
+        self.ligadd[5].clicked.connect(self.addlig5)  # callback
+        self.ligadd[6].clicked.connect(self.addlig6)  # callback
+        #############################################
+        # List molecules  #
+        ctip = 'Generate 2D ligand representation.'
+        self.butList = mQPushButton('List molecules', ctip, 12)
+        self.butList.clicked.connect(self.listmols)
+        self.grid.addWidget(self.butList, 18, 3, 1, 2)
+        # Draw ligand button #
+        ctip = 'Generate 2D ligand representation.'
+        self.butDrl = mQPushButton('Draw ligands', ctip, 12)
+        self.butDrl.clicked.connect(self.drawligs_svg)
+        self.grid.addWidget(self.butDrl, 18, 1, 1, 2)
+        # Local database button #
+        ctip = 'Add core/ligand/binding species to local database.'
+        self.butADB = mQPushButton('Add to local DB', ctip, 12)
+        self.butADB.clicked.connect(self.enableDB)
+        self.grid.addWidget(self.butADB, 18, 5, 1, 3)
+        # #################################################
+        # #################################################
+        # ########## GENERAL PARAMETERS INPUTS ############
+        # #################################################
+        # #################################################
+        self.txtgp = mQLabel('General parameters', '', 'c', 20)
+        self.grid.addWidget(self.txtgp, 4, 13, 2, 8)
+        # random generation
+        ctip = 'Enable random generation.'
+        self.randomchk = mQCheckBox('Random generation', ctip, 12)
+        self.randomchk.stateChanged.connect(self.enablerandom)
+        self.grid.addWidget(self.randomchk, 7, 15, 1, 2)
+        # charge calculation
+        ctip = 'Calculate charge based on ox state and ligands'
+        self.chch = mQCheckBox('Calculate\ncharge', ctip, 12)
+        self.chch.setDisabled(True)
+        self.grid.addWidget(self.chch, 7, 17, 1, 1)
+        # keep Hs
+        ctip = 'Keep hydrogens for random generation.'
+        self.randkHs = mQCheckBox('Keep\nHs', ctip, 12)
+        self.grid.addWidget(self.randkHs, 7, 18, 1, 1)
+        self.randkHs.setDisabled(True)
+        # number of random generated structures
+        ctip = 'Number of structures to be randomly generated.'
+        self.rtrgen = mQLabel('Structures:', ctip, 'Cr', 12)
+        self.etrgen = mQLineEdit('', ctip, 'l', 12)
+        self.grid.addWidget(self.rtrgen, 8, 15, 1, 1)
+        self.grid.addWidget(self.etrgen, 8, 16, 1, 1)
+        self.rtrgen.setDisabled(True)
+        self.etrgen.setDisabled(True)
+        # number of different ligands to use
+        ctip = 'For random generation: total number of different ligands including specified ones.'
+        self.rtlignum = mQLabel('Different\nligands:', ctip, 'Cr', 12)
+        qcav = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
+        self.etlignum = mQComboBox(qcav, ctip, 12)
+        self.grid.addWidget(self.rtlignum, 8, 17, 1, 1)
+        self.grid.addWidget(self.etlignum, 8, 18, 1, 1)
+        self.rtlignum.setDisabled(True)
+        self.etlignum.setDisabled(True)
+        # group of different ligands
+        ctip = 'For random generation: select random ligands from group.'
+        self.rtliggrp = mQLabel('Ligand\ngroup:', ctip, 'Cr', 12)
+        cwd = os.getcwd()
+        globs = globalvars()
+        globs.rundir = os.path.join(cwd, 'Runs')
+        if globs.custom_path:
+            f = globs.custom_path + "/Ligands/ligands.dict"
+        else:
+            f = str(resource_files("molSimplify").joinpath("Ligands/ligands.dict"))
+        qcav0 = getligroups(readdict(f))
+        qcav = [_f for _f in qcav0.split(' ') if _f]
+        self.etliggrp = mQComboBox(qcav, ctip, 12)
+        self.grid.addWidget(self.rtliggrp, 9, 15, 1, 1)
+        self.grid.addWidget(self.etliggrp, 9, 16, 1, 1)
+        self.rtliggrp.setDisabled(True)
+        self.etliggrp.setDisabled(True)
+        # ligand category
+        ctip = 'For random generation: select random ligands from category.\nOptions are all'
+        ctip += '"build" for building complexes, "functionalize" for functionalizing'
+        self.rtligctg = mQLabel('Ligand\ncategory:', ctip, 'Cr', 12)
+        qcav = ['all', 'build', 'functionalize']
+        self.etligctg = mQComboBox(qcav, ctip, 12)
+        self.grid.addWidget(self.rtligctg, 9, 17, 1, 1)
+        self.grid.addWidget(self.etligctg, 9, 18, 1, 1)
+        self.rtligctg.setDisabled(True)
+        self.etligctg.setDisabled(True)
+        # oxidation state
+        ctip = 'Metal Oxidation state'
+        self.roxstate = mQLabel('Ox State:', ctip, 'Cr', 12)
+        qcav = ['0', 'I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII']
+        self.doxs = mQComboBox(qcav, ctip, 12)
+        self.doxs.setCurrentIndex(0)
+        self.grid.addWidget(self.roxstate, 10, 15, 1, 1)
+        self.grid.addWidget(self.doxs, 10, 16, 1, 1)
+        # spin state
+        ctip = 'System spin multiplicity'
+        self.rspstate = mQLabel('Spin:', ctip, 'Cr', 12)
+        qcav = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
+        self.dspin = mQComboBox(qcav, ctip, 12)
+        self.dspin.setCurrentIndex(0)
+        self.grid.addWidget(self.rspstate, 10, 17, 1, 1)
+        self.grid.addWidget(self.dspin, 10, 18, 1, 1)
+        # force field optimization
+        ctip = 'Perform Force Field optimization'
+        self.chkFF = mQCheckBox('FF optimize', ctip, 12)
+        self.chkFF.stateChanged.connect(self.enableffinput)
+        self.grid.addWidget(self.chkFF, 11, 15, 1, 1)
+        # generate all
+        ctip = 'Generate structure with and without optimization.'
+        self.chkgenall = mQCheckBox('Generate\nall', ctip, 12)
+        self.chkgenall.stateChanged.connect(self.disableffinput)
+        self.grid.addWidget(self.chkgenall, 12, 15, 1, 1)
+        # perform optimization
+        ctip = 'Select Force Field'
+        qcav = ['MMFF94', 'UFF', 'gchemical', 'GAFF']
+        self.dff = mQComboBox(qcav, ctip, 12)
+        self.dff.setCurrentIndex(0)
+        self.dff.setDisabled(True)
+        self.grid.addWidget(self.dff, 11, 16, 1, 1)
+        # optimize before or after
+        ctip = 'Optimize before or after building the structure'
+        qcav = ['Before', 'After', 'Before & After']
+        self.dffba = mQComboBox(qcav, ctip, 12)
+        self.dffba.setDisabled(True)
+        self.dffba.setCurrentIndex(2)
+        self.grid.addWidget(self.dffba, 11, 17, 1, 2)
+        # create distortion slider
+        ctip = 'Percent random distortion from default coordination geometry.'
+        self.distper = mQLabel('Distort:0%', ctip, 'Cr', 12)
+        self.sdist = mQSlider(ctip)
+        self.sdist.valueChanged.connect(self.sliderChanged)
+        self.grid.addWidget(self.distper, 12, 17, 1, 1)
+        self.grid.addWidget(self.sdist, 12, 18, 1, 1)
+        # jobs dir #
+        ctip = 'Top directory for job folders.'
+        self.rtrdir = mQLabel('Jobs dir:', ctip, 'Cr', 12)
+        self.grid.addWidget(self.rtrdir, 14, 15, 1, 1)
+        self.etrdir = mQLineEdit(globs.rundir, ctip, 'l', 12)
+        self.grid.addWidget(self.etrdir, 14, 16, 1, 2)
+        # button for browsing rundir
+        ctip = 'Browse running directory.'
+        self.butpbrdir = mQPushButton('Browse..', ctip, 12)
+        self.butpbrdir.clicked.connect(self.dirload)
+        self.grid.addWidget(self.butpbrdir, 14, 18, 1, 1)
+        # suffix
+        ctip = 'Suffix for job directories.'
+        self.rtsuff = mQLabel('Suffix:', ctip, 'Cr', 12)
+        self.etsuff = mQLineEdit('', ctip, 'l', 12)
+        self.grid.addWidget(self.rtsuff, 15, 15, 1, 1)
+        self.grid.addWidget(self.etsuff, 15, 16, 1, 2)
+        # structure generation
+        ctip = 'Generate structures'
+        self.butGen = mQPushButton('Generate', ctip, 18)
+        self.butGen.clicked.connect(self.runGUI)
+        self.grid.addWidget(self.butGen, 17, 15, 2, 2)
+        # post-processing setup
+        ctip = 'Setup post-processing'
+        self.butPost = mQPushButton('Post-process', ctip, 16)
+        self.butPost.clicked.connect(self.setupp)
+        self.grid.addWidget(self.butPost, 17, 17, 2, 2)
+        # Search DB button #
+        ctip = 'Search for ligands in chemical databases.'
+        self.searchDB = mQPushButton('Search DB', ctip, 16)
+        self.searchDB.clicked.connect(self.searchDBW)
+        self.grid.addWidget(self.searchDB, 17, 20, 2, 2)
+        # ##################################################
+        # ##################################################
+        # ########## ADDITIONAL MOLECULE INPUTS ############
+        # ##################################################
+        # ##################################################
+        # generate edit texts for additional molecule
+        self.txtamol = mQLabel('Additional molecule', '', 'c', 20)
+        self.txtamol.setDisabled(True)
+        self.grid.addWidget(self.txtamol, 4, 19, 2, 5)
+        # additional molecule
+        ctip = 'Place additional molecule'
+        self.chkM = mQCheckBox('Extra molecule', ctip, 12)
+        self.chkM.stateChanged.connect(self.enableemol)
+        self.grid.addWidget(self.chkM, 7, 20, 1, 3)
+        # name of binding species
+        ctip = 'Binding species'
+        self.rtbind = mQLabel('Molecule:', ctip, 'Cr', 12)
+        bicores = list(sorted(getbcores()))
+        self.etbind = mQLineEditL('', ctip, 'l', 12, bicores)
+        self.rtbind.setDisabled(True)
+        self.etbind.setDisabled(True)
+        self.grid.addWidget(self.rtbind, 8, 20, 1, 1)
+        self.grid.addWidget(self.etbind, 8, 21, 1, 2)
+        # name of binding molecule from SMILES
+        ctip = 'Name of binding molecule using SMILES'
+        self.rtbsmi = mQLabel('Name:', ctip, 'Cr', 12)
+        self.etbsmi = mQLineEdit('', ctip, 'l', 12)
+        self.rtbsmi.setDisabled(True)
+        self.etbsmi.setDisabled(True)
+        self.grid.addWidget(self.rtbsmi, 9, 20, 1, 1)
+        self.grid.addWidget(self.etbsmi, 9, 21, 1, 2)
+        # separate in xyz file
+        ctip = 'Separate molecules in xyz or input file with ------'
+        self.chsep = mQCheckBox('separate', ctip, 12)
+        self.chsep.setDisabled(True)
+        self.grid.addWidget(self.chsep, 9, 23, 1, 2)
+        # number of binding conformations to generate
+        ctip = 'Number of different conformations to be generated'
+        self.rtnbind = mQLabel('Conformations:', ctip, 'Cr', 12)
+        self.etnbind = mQLineEdit('', ctip, 'l', 12)
+        self.rtnbind.setDisabled(True)
+        self.etnbind.setDisabled(True)
+        self.grid.addWidget(self.rtnbind, 10, 20, 1, 1)
+        self.grid.addWidget(self.etnbind, 10, 21, 1, 1)
+        # charge of binding species
+        ctip = 'Charge of binding species'
+        self.rtchbind = mQLabel('Charge:', ctip, 'Cr', 12)
+        self.etchbind = mQLineEdit('', ctip, 'l', 12)
+        self.rtchbind.setDisabled(True)
+        self.etchbind.setDisabled(True)
+        self.grid.addWidget(self.rtchbind, 10, 22, 1, 1)
+        self.grid.addWidget(self.etchbind, 10, 23, 1, 1)
+        # min/max distance
+        ctip = 'Specify placing minimum/maximum distance (in A)'
+        self.rtplace = mQLabel('Distance:', ctip, 'Cr', 12)
+        ctip = 'Minimum distance between the two molecules. 0 corresponds the marginally non-overlapping configuration'
+        self.etplacemin = mQLineEdit('', ctip, 'l', 12)
+        ctip = 'Maximum distance between the two molecules. 0 corresponds the marginally non-overlapping configuration'
+        self.etplacemax = mQLineEdit('', ctip, 'l', 12)
+        self.rtplace.setDisabled(True)
+        self.etplacemin.setDisabled(True)
+        self.etplacemax.setDisabled(True)
+        self.grid.addWidget(self.rtplace, 11, 20, 1, 1)
+        self.grid.addWidget(self.etplacemin, 11, 21, 1, 1)
+        self.grid.addWidget(self.etplacemax, 11, 22, 1, 1)
+        # mask for atom/center of mass reference
+        ctip = ('Reference atoms in extra molecules to be used for placement '
+                '(e.g. 1,2 or 1-6 or COM or Fe) Default COM (center mass)')
+        # self.rtmaskbind = mQLabel('Reference:',ctip,'r',14)
+        self.etmaskbind = mQLineEdit('COM', ctip, 'l', 12)
+        # self.rtmaskbind.setDisabled(True)
+        self.etmaskbind.setDisabled(True)
+        # self.grid.addWidget(self.rtmaskbind,11,23,1,1)
+        self.grid.addWidget(self.etmaskbind, 11, 23, 1, 1)
+        # angle/orientation
+        ctip = 'Specify placement type or angle. Angle overwrites placement.'
+        self.rtplacea = mQLabel('Angle:', ctip, 'Cr', 12)
+        ctip = 'Azimouthal angle phi from 0 to 180'
+        self.etplacephi = mQLineEdit('', ctip, 'l', 12)
+        ctip = 'Polar angle theta from 0 to 360'
+        self.etplacetheta = mQLineEdit('', ctip, 'l', 12)
+        self.rtplacea.setDisabled(True)
+        self.etplacephi.setDisabled(True)
+        self.etplacetheta.setDisabled(True)
+        self.grid.addWidget(self.rtplacea, 12, 20, 1, 1)
+        self.grid.addWidget(self.etplacephi, 12, 21, 1, 1)
+        self.grid.addWidget(self.etplacetheta, 12, 22, 1, 1)
+        # placement of extr molecule
+        ctip = 'Orientation for placing additional molecule'
+        qcav = ['', 'axial', 'equatorial']
+        self.dmolp = mQComboBox(qcav, ctip, 12)
+        self.dmolp.setDisabled(True)
+        self.dmolp.currentIndexChanged.connect(self.checkaxial)
+        self.grid.addWidget(self.dmolp, 12, 23, 1, 1)
+        # input file generation
+        ctip = 'Generate input files'
+        self.chkI = mQCheckBox('Input files', ctip, 12)
+        self.chkI.stateChanged.connect(self.enableqeinput)
+        self.grid.addWidget(self.chkI, 13, 20, 1, 2)
+        # jobscript generation
+        ctip = 'Generate jobscripts'
+        self.chkJ = mQCheckBox('Jobscripts', ctip, 12)
+        self.chkJ.stateChanged.connect(self.enablejinput)
+        self.grid.addWidget(self.chkJ, 13, 22, 1, 2)
+        # input for QC calculation
+        ctip = 'Enter input for Quantum Chemistry calculations'
+        self.butQc = mQPushButton('Enter QC input', ctip, 12)
+        self.butQc.setDisabled(True)
+        self.butQc.clicked.connect(self.qcinput)
+        ctip = 'Select QC code'
+        qcav = ['TeraChem', 'GAMESS', 'QChem']
+        self.qcode = mQComboBox(qcav, ctip, 12)
+        self.qcode.setDisabled(True)
+        self.grid.addWidget(self.butQc, 14, 20, 1, 2)
+        self.grid.addWidget(self.qcode, 15, 20, 1, 2)
+        # input for jobscripts
+        ctip = 'Enter input for jobscript files'
+        self.butJob = mQPushButton('Enter job input', ctip, 12)
+        self.butJob.setDisabled(True)
+        self.butJob.clicked.connect(self.jobenable)
+        ctip = 'Select job scheduler'
+        qcav = ['SGE', 'SLURM']
+        self.scheduler = mQComboBox(qcav, ctip, 12)
+        self.scheduler.setDisabled(True)
+        self.grid.addWidget(self.butJob, 14, 22, 1, 2)
+        self.grid.addWidget(self.scheduler, 15, 22, 1, 2)
+        # quit button
+        ctip = 'Quit program'
+        self.butQ = mQPushButton('Quit', ctip, 14)
+        self.butQ.clicked.connect(self.qexit)
+        self.grid.addWidget(self.butQ, 17, 23, 1, 1)
+        # ###############################################
+        # ###############################################
+        # ###############################################
+        # #########################
+        # ## information window ###
+        # #########################
+        self.iWind = QWidget()
+        self.iWind.setWindowTitle('Running')
+        self.iWtxt = mQTextEdit('Program started..', 'l', 14)
+        self.iWtxt.setParent(self.iWind)
+        self.sgrid.addWidget(self.iWind)
+        # ######################################
+        # ## create terachem-qc input window ###
+        # ######################################
+        self.qctWindow = QWidget()  # TC QC window
+        self.qctgrid = QGridLayout()
+        self.qctWindow.setWindowTitle('Terachem Input')
+        self.sgrid.addWidget(self.qctWindow)  # add to stacked grid
+        self.qctWindow.setPalette(p)  # set background color
+        self.qctWindow.setLayout(self.qctgrid)  # set layout
+
+        f = resource_files("molSimplify").joinpath("icons/petachem.png")
+        c0 = mQPixmap(f)
+        self.qctgrid.addWidget(c0, 0, 2, 1, 1)
+        # top text
+        self.txtqc = mQLabel('   TeraChem Input', '', 'C', 18)
+        self.qctgrid.addWidget(self.txtqc, 0, 3, 1, 2)
+        # text for specifying charge
+        ctip = 'Charge of the system, default: 0'
+        self.rtqctch = mQLabel('Charge:', ctip, 'r', 14)
+        self.etqctch = mQLineEdit('0', ctip, 'l', 14)
+        self.qctgrid.addWidget(self.rtqctch, 1, 1, 1, 1)
+        self.qctgrid.addWidget(self.etqctch, 1, 2, 1, 1)
+        # text for specifying spin state
+        ctip = 'Spin multiplicity of the system, default: 1'
+        self.rtqctspin = mQLabel('Spin:', ctip, 'r', 14)
+        self.etqctspin = mQLineEdit('1', ctip, 'l', 14)
+        self.qctgrid.addWidget(self.rtqctspin, 1, 3, 1, 1)
+        self.qctgrid.addWidget(self.etqctspin, 1, 4, 1, 1)
+        # drop menu for selecting type of calculation
+        qcav = ['energy', 'minimize', 'gradient', 'ts']
+        ctip = 'Specify calculation type, default: minimize'
+        self.rtqctcalc = mQLabel('Calculation:', ctip, 'r', 14)
+        self.qctcalc = mQComboBox(qcav, ctip, 14)
+        self.qctgrid.addWidget(self.rtqctcalc, 2, 1, 1, 1)
+        self.qctgrid.addWidget(self.qctcalc, 2, 2, 1, 1)
+        # text for specifying electronic structure method
+        ctip = 'Select electronic structure method, default: ub3lyp'
+        self.rtqctmethod = mQLabel('Method:', ctip, 'r', 14)
+        self.etqctmethod = mQLineEdit('ub3lyp', ctip, 'l', 14)
+        self.qctgrid.addWidget(self.rtqctmethod, 2, 3, 1, 1)
+        self.qctgrid.addWidget(self.etqctmethod, 2, 4, 1, 1)
+        # text for specifying basis set
+        ctip = 'Select basis set, default: lacvp_s'
+        self.rtqctbasis = mQLabel('Basis:', ctip, 'r', 14)
+        self.etqctbasis = mQLineEdit('lacvps_ecp', ctip, 'l', 14)
+        self.qctgrid.addWidget(self.rtqctbasis, 3, 1, 1, 1)
+        self.qctgrid.addWidget(self.etqctbasis, 3, 2, 1, 1)
+        # drop menu for selecting dispersion
+        qcav = ['yes', 'no', 'd2', 'd3']
+        ctip = 'Select dispersion correction'
+        self.rtcdisp = mQLabel('Dispersion:', ctip, 'r', 14)
+        self.qctsel = mQComboBox(qcav, ctip, 14)
+        self.qctgrid.addWidget(self.rtcdisp, 3, 3, 1, 1)
+        self.qctgrid.addWidget(self.qctsel, 3, 4, 1, 1)
+        self.qctsel.setCurrentIndex(1)
+        # editor for additional input
+        ctip = 'Specify additional input here'
+        self.rtqctadd = mQLabel('Additional input:', ctip, 'Cr', 14)
+        self.qceditor = mQTextEdit('', 'l', 14)
+        self.qctgrid.addWidget(self.rtqctadd, 4, 2, 1, 1)
+        self.qctgrid.addWidget(self.qceditor, 4, 3, 1, 2)
+        # button for addition
+        ctip = 'make default'
+        self.butqctlf = mQPushButton('Make default', ctip, 14)
+        self.butqctlf.clicked.connect(self.qctdef)
+        self.qctgrid.addWidget(self.butqctlf, 5, 1, 2, 1)
+        # button for addition
+        ctip = 'Submit input for Quantum Chemistry'
+        self.butqctSub = mQPushButton('Submit', ctip, 14)
+        self.butqctSub.clicked.connect(self.qretmain)
+        self.qctgrid.addWidget(self.butqctSub, 5, 2, 2, 1)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butqctRet = mQPushButton('Return', ctip, 14)
+        self.butqctRet.clicked.connect(self.qretmain)
+        self.qctgrid.addWidget(self.butqctRet, 5, 4, 2, 1)
+        # load defaults if existing
+        if glob.glob(str(globs.custom_path)+'/Data/.tcdefinput.inp'):
+            loadfrominputtc(self, str(globs.custom_path) +
+                            '/Data/.tcdefinput.inp')
+        # ####################################
+        # ## create gamess-qc input window ###
+        # ######################################
+        self.qcgWindow = QWidget()  # TC QC window
+        self.qcggrid = QGridLayout()
+        self.qcgWindow.setWindowTitle('GAMESS Input')
+        self.sgrid.addWidget(self.qcgWindow)  # add to stacked grid
+        self.qcgWindow.setPalette(p)  # set background color
+        self.qcgWindow.setLayout(self.qcggrid)  # set layout
+        # top text
+        self.txtqcg = mQLabel('GAMESS Input', '', 'c', 18)
+        self.qcggrid.addWidget(self.txtqcg, 0, 0, 1, 4)
+        # text for specifying charge
+        ctip = 'Charge of the system, default: 0'
+        self.rtqcgch = mQLabel('Charge:', ctip, 'r', 14)
+        self.etqcgch = mQLineEdit('0', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcgch, 1, 0, 1, 1)
+        self.qcggrid.addWidget(self.etqcgch, 1, 1, 1, 1)
+        # text for specifying spin state
+        ctip = 'Spin multiplicity of the system, default: 1'
+        self.rtqcgspin = mQLabel('Spin:', ctip, 'r', 14)
+        self.etqcgspin = mQLineEdit('1', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcgspin, 1, 2, 1, 1)
+        self.qcggrid.addWidget(self.etqcgspin, 1, 3, 1, 1)
+        # drop menu for selecting type of calculation
+        qcav = ['energy', 'minimize', 'ts']
+        ctip = 'Specify calculation type, default: minimize'
+        self.rtqcgcalc = mQLabel('Calculation:', ctip, 'r', 14)
+        self.qcgcalc = mQComboBox(qcav, ctip, 14)
+        self.qcggrid.addWidget(self.rtqcgcalc, 2, 0, 1, 1)
+        self.qcggrid.addWidget(self.qcgcalc, 2, 1, 1, 1)
+        # text for specifying electronic structure method
+        ctip = 'Select electronic structure method, default: ub3lyp'
+        self.rtqcgmethod = mQLabel('Method:', ctip, 'r', 14)
+        self.etqcgmethod = mQLineEdit('ub3lyp', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcgmethod, 2, 2, 1, 1)
+        self.qcggrid.addWidget(self.etqcgmethod, 2, 3, 1, 1)
+        # text for specifying basis set
+        ctip = 'Select GBASIS input, default: 6'
+        self.rtqcgbasis = mQLabel('GBASIS:', ctip, 'r', 14)
+        self.etqcgbasis = mQLineEdit('6', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcgbasis, 3, 0, 1, 1)
+        self.qcggrid.addWidget(self.etqcgbasis, 3, 1, 1, 1)
+        # text for specifying basis set
+        ctip = 'Select NGAUSS input, default: N31'
+        self.rtqcngauss = mQLabel('NGAUSS:', ctip, 'r', 14)
+        self.etqcngauss = mQLineEdit('N31', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcngauss, 3, 2, 1, 1)
+        self.qcggrid.addWidget(self.etqcngauss, 3, 3, 1, 1)
+        # text for specifying polarization functions
+        ctip = 'Select NPFUNC input, default: 0'
+        self.rtqcnpfunc = mQLabel('NPFUNC:', ctip, 'r', 14)
+        self.etqcnpfunc = mQLineEdit('', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcnpfunc, 4, 0, 1, 1)
+        self.qcggrid.addWidget(self.etqcnpfunc, 4, 1, 1, 1)
+        # text for specifying polarization functions
+        ctip = 'Select NDFUNC input, default: 0'
+        self.rtqcndfunc = mQLabel('NDFUNC:', ctip, 'r', 14)
+        self.etqcndfunc = mQLineEdit('', ctip, 'l', 14)
+        self.qcggrid.addWidget(self.rtqcndfunc, 4, 2, 1, 1)
+        self.qcggrid.addWidget(self.etqcndfunc, 4, 3, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional input for block SYS here'
+        self.rtqcgadd1 = mQLabel('SYS input:', ctip, 'Cr', 14)
+        self.qcgedsys = mQTextEdit('', 'l', 12)
+        self.qcggrid.addWidget(self.rtqcgadd1, 5, 0, 1, 1)
+        self.qcggrid.addWidget(self.qcgedsys, 5, 1, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional input for block CTRL here'
+        self.rtqcgadd1 = mQLabel('CTRL input:', ctip, 'Cr', 14)
+        self.qcgedctrl = mQTextEdit('', 'l', 12)
+        self.qcggrid.addWidget(self.rtqcgadd1, 5, 2, 1, 1)
+        self.qcggrid.addWidget(self.qcgedctrl, 5, 3, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional input for block SCF here'
+        self.rtqcgadd3 = mQLabel('SCF input:', ctip, 'Cr', 14)
+        self.qcgedscf = mQTextEdit('', 'l', 12)
+        self.qcggrid.addWidget(self.rtqcgadd3, 6, 0, 1, 1)
+        self.qcggrid.addWidget(self.qcgedscf, 6, 1, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional input for block STAT here'
+        self.rtqcgadd4 = mQLabel('STAT input:', ctip, 'Cr', 14)
+        self.qcgedstat = mQTextEdit('', 'l', 12)
+        self.qcggrid.addWidget(self.rtqcgadd4, 6, 2, 1, 1)
+        self.qcggrid.addWidget(self.qcgedstat, 6, 3, 1, 1)
+        # button for addition
+        ctip = 'make default'
+        self.butqcglf = mQPushButton('Make default', ctip, 14)
+        self.butqcglf.clicked.connect(self.qcgdef)
+        self.qcggrid.addWidget(self.butqcglf, 7, 0, 1, 1)
+        # button for addition
+        ctip = 'Submit input for Quantum Chemistry'
+        self.butqcgSub = mQPushButton('Submit', ctip, 14)
+        self.butqcgSub.clicked.connect(self.qretmain)
+        self.qcggrid.addWidget(self.butqcgSub, 7, 1, 1, 2)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butqcgRet = mQPushButton('Return', ctip, 14)
+        self.butqcgRet.clicked.connect(self.qretmain)
+        self.qcggrid.addWidget(self.butqcgRet, 7, 3, 1, 1)
+        self.qcggrid.setRowMinimumHeight(7, 30)
+        # load defaults if existing
+        if glob.glob(str(globs.custom_path)+'/Data/.gamdefinput.inp'):
+            loadfrominputgam(self, str(globs.custom_path))
+        # ######################################
+        # ### create Qchem-qc input window #####
+        # ######################################
+        self.qcQWindow = QWidget()  # TC QC window
+        self.qcQgrid = QGridLayout()
+        self.qcQWindow.setWindowTitle('QChem Input')
+        self.sgrid.addWidget(self.qcQWindow)  # add to stacked grid
+        self.qcQWindow.setPalette(p)  # set background color
+        self.qcQWindow.setLayout(self.qcQgrid)  # set layout
+        # top text
+        self.txtQqc = mQLabel('QChem Input', '', 'c', 18)
+        self.qcQgrid.addWidget(self.txtQqc, 0, 0, 1, 5)
+        # text for specifying charge
+        ctip = 'Charge of the system, default: 0'
+        self.rtqcQch = mQLabel('Charge:', ctip, 'r', 14)
+        self.etqcQch = mQLineEdit('0', ctip, 'l', 14)
+        self.qcQgrid.addWidget(self.rtqcQch, 1, 0, 1, 1)
+        self.qcQgrid.addWidget(self.etqcQch, 1, 1, 1, 1)
+        # text for specifying spin state
+        ctip = 'Spin multiplicity of the system, default: 1'
+        self.rtqcQspin = mQLabel('Spin:', ctip, 'r', 14)
+        self.etqcQspin = mQLineEdit('1', ctip, 'l', 14)
+        self.qcQgrid.addWidget(self.rtqcQspin, 1, 2, 1, 1)
+        self.qcQgrid.addWidget(self.etqcQspin, 1, 3, 1, 1)
+        # additional molecule
+        ctip = 'Unrestricted calculation?'
+        self.chQun = mQCheckBox('Unrestricted', ctip, 14)
+        self.chQun.setChecked(True)
+        self.qcQgrid.addWidget(self.chQun, 1, 4, 1, 1)
+        # drop menu for selecting type of calculation
+        qcav = ['energy', 'minimize', 'ts']
+        ctip = 'Specify calculation type, default: minimize'
+        self.rtqcQcalc = mQLabel('Calculation:', ctip, 'r', 14)
+        self.qcQcalc = mQComboBox(qcav, ctip, 14)
+        self.qcQgrid.addWidget(self.rtqcQcalc, 2, 0, 1, 1)
+        self.qcQgrid.addWidget(self.qcQcalc, 2, 1, 1, 1)
+        # text for specifying basis set
+        ctip = 'Select basis set, default: lanl2dz'
+        self.rtqcQbasis = mQLabel('Basis:', ctip, 'r', 14)
+        self.etqcQbasis = mQLineEdit('lanl2dz', ctip, 'l', 14)
+        self.qcQgrid.addWidget(self.rtqcQbasis, 2, 2, 1, 1)
+        self.qcQgrid.addWidget(self.etqcQbasis, 2, 3, 1, 1)
+        # text for specifying exchange
+        ctip = 'Select exchange, default: b3lyp'
+        self.rtqcQex = mQLabel('Exchange:', ctip, 'r', 14)
+        self.etqcQex = mQLineEdit('b3lyp', ctip, 'l', 14)
+        self.qcQgrid.addWidget(self.rtqcQex, 3, 0, 1, 1)
+        self.qcQgrid.addWidget(self.etqcQex, 3, 1, 1, 1)
+        # text for specifying electronic structure method
+        ctip = 'Select correlation, default: none'
+        self.rtqcQcor = mQLabel('Correlation:', ctip, 'r', 14)
+        self.etqcQcor = mQLineEdit('none', ctip, 'l', 14)
+        self.qcQgrid.addWidget(self.rtqcQcor, 3, 2, 1, 1)
+        self.qcQgrid.addWidget(self.etqcQcor, 3, 3, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional input here'
+        self.rtqcQadd = mQLabel('Additional input:', ctip, 'Cr', 14)
+        self.qcQeditor = mQTextEdit('', 'l', 12)
+        self.qcQgrid.addWidget(self.rtqcQadd, 4, 1, 1, 1)
+        self.qcQgrid.addWidget(self.qcQeditor, 4, 2, 1, 2)
+        # button for addition
+        ctip = 'make default'
+        self.butqcQlf = mQPushButton('Make default', ctip, 14)
+        self.butqcQlf.clicked.connect(self.qcqdef)
+        self.qcQgrid.addWidget(self.butqcQlf, 5, 0, 1, 1)
+        # button for addition
+        ctip = 'Submit input for Quantum Chemistry'
+        self.butqcQSub = mQPushButton('Submit', ctip, 14)
+        self.butqcQSub.clicked.connect(self.qretmain)
+        self.qcQgrid.addWidget(self.butqcQSub, 5, 2, 1, 2)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butqcQRet = mQPushButton('Return', ctip, 14)
+        self.butqcQRet.clicked.connect(self.qretmain)
+        self.qcQgrid.addWidget(self.butqcQRet, 5, 4, 1, 1)
+        # load defaults if existing
+        if glob.glob(str(globs.custom_path)+'/Data/.qchdefinput.inp'):
+            loadfrominputqch(self, str(globs.custom_path) +
+                             '/Data/.qchdefinput.inp')
+        # ####################################
+        # ## create jobscript input window ###
+        # ####################################
+        self.jWindow = QWidget()  # jobscript window
+        self.jgrid = QGridLayout()
+        self.jWindow.setWindowTitle('Jobscript parameters')
+        self.sgrid.addWidget(self.jWindow)  # add to stacked grid
+        self.jWindow.setPalette(p)  # set background color
+        self.jWindow.setLayout(self.jgrid)  # set layout
+        f1 = resource_files("molSimplify").joinpath("icons/sge.png")
+        f2 = resource_files("molSimplify").joinpath("icons/slurm.png")
+        c1 = mQPixmap(f1)
+        c2 = mQPixmap(f2)
+        self.jgrid.addWidget(c1, 1, 2, 1, 1)
+        self.jgrid.addWidget(c2, 1, 4, 1, 1)
+        # top text
+        self.txtj = mQLabel('Jobscript Input', '', 'r', 18)
+        self.jgrid.addWidget(self.txtj, 0, 2, 1, 2)
+        # text for main job identifier
+        ctip = 'Job main identifier, e.g. feII'
+        self.rtjname = mQLabel('Job name:', ctip, 'r', 14)
+        self.etjname = mQLineEdit('myjob', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjname, 2, 1, 1, 1)
+        self.jgrid.addWidget(self.etjname, 2, 2, 1, 1)
+        # text for specifying spin state
+        ctip = 'Queue to use, e.g. gpus'
+        self.rtjqueue = mQLabel('Queue:', ctip, 'r', 14)
+        self.etjqueue = mQLineEdit('', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjqueue, 2, 3, 1, 1)
+        self.jgrid.addWidget(self.etjqueue, 2, 4, 1, 1)
+        # text for specifying wall time
+        ctip = 'Wall time request, e.g. 48'
+        self.rtjwallt = mQLabel('Wall time:', ctip, 'r', 14)
+        self.etjwallt = mQLineEdit('48h', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjwallt, 3, 1, 1, 1)
+        self.jgrid.addWidget(self.etjwallt, 3, 2, 1, 1)
+        # text for specifying memory
+        ctip = 'Memory request, e.g. 10G'
+        self.rtjmem = mQLabel('Memory:', ctip, 'r', 14)
+        self.etjmem = mQLineEdit('10G', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjmem, 3, 3, 1, 1)
+        self.jgrid.addWidget(self.etjmem, 3, 4, 1, 1)
+        # text for specifying charge
+        ctip = 'Number of CPUs requested, default: 0'
+        self.rtjcpus = mQLabel('CPUs:', ctip, 'r', 14)
+        self.etjcpus = mQLineEdit('', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjcpus, 4, 1, 1, 1)
+        self.jgrid.addWidget(self.etjcpus, 4, 2, 1, 1)
+        # text for specifying spin state
+        ctip = 'Number of GPUs requested, default: 0'
+        self.rtjgpus = mQLabel('GPUs:', ctip, 'r', 14)
+        self.etjgpus = mQLineEdit('', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjgpus, 4, 3, 1, 1)
+        self.jgrid.addWidget(self.etjgpus, 4, 4, 1, 1)
+        # text for modules to be loaded
+        ctip = 'Modules to be loaded, e.g. terachem, openmpi'
+        self.rtjmod = mQLabel('Modules:', ctip, 'r', 14)
+        self.etjmod = mQLineEdit('', ctip, 'l', 14)
+        self.jgrid.addWidget(self.rtjmod, 5, 1, 1, 1)
+        self.jgrid.addWidget(self.etjmod, 5, 2, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional input for initial options, e.g. -j y'
+        self.rtjadd1 = mQLabel('Options:', ctip, 'r', 14)
+        self.etjopt = mQTextEdit('', 'l', 12)
+        self.jgrid.addWidget(self.rtjadd1, 6, 1, 1, 1)
+        self.jgrid.addWidget(self.etjopt, 6, 2, 1, 1)
+        # editor for additional input
+        ctip = 'Specify additional commands, e.g. mkdir $WORKDIR/test'
+        self.rtjadd2 = mQLabel('Commands:', ctip, 'Cr', 14)
+        self.jcomm = mQTextEdit('', 'l', 12)
+        self.jgrid.addWidget(self.rtjadd2, 6, 3, 1, 1)
+        self.jgrid.addWidget(self.jcomm, 6, 4, 1, 1)
+        # button for addition
+        ctip = 'make default'
+        self.butqcJlf = mQPushButton('Make default', ctip, 14)
+        self.butqcJlf.clicked.connect(self.jobdef)
+        self.jgrid.addWidget(self.butqcJlf, 7, 1, 1, 1)
+        # button for addition
+        ctip = 'Submit input for Quantum Chemistry'
+        self.butqcgSub = mQPushButton('Submit', ctip, 14)
+        self.butqcgSub.clicked.connect(self.qretmain)
+        self.jgrid.addWidget(self.butqcgSub, 7, 2, 1, 2)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butqcgRet = mQPushButton('Return', ctip, 14)
+        self.butqcgRet.clicked.connect(self.qretmain)
+        self.jgrid.addWidget(self.butqcgRet, 7, 4, 1, 1)
+        # load defaults if existing
+        if glob.glob(str(globs.custom_path)+'/Data/.jobdefinput.inp'):
+            loadfrominputjob(self, str(globs.custom_path)+'/Data/.jobdefinput.inp')
+        # #########################################
+        # ## create local DB interaction window ###
+        # #########################################
+        self.DBWindow = QWidget()  # DB Window
+        self.DBlgrid = QGridLayout()
+        self.sgrid.addWidget(self.DBWindow)
+        self.DBWindow.setPalette(p)
+        self.DBWindow.setLayout(self.DBlgrid)
+        self.DBWindow.setWindowTitle('Insert/remove to/from Database')
+        # top text
+        self.txtdb = mQLabel('Database Update', '', 'c', 18)
+        self.DBlgrid.addWidget(self.txtdb, 0, 0, 1, 4)
+        # drop menu for selecting type
+        ctip = 'Select what type of molecule you want to add/remove to/from the database'
+        self.rtDBsel = mQLabel('Select type:', '', 'r', 14)
+        qcav = ['core', 'ligand', 'binding']
+        self.DBsel = mQComboBox(qcav, ctip, 14)
+        self.DBsel.setCurrentIndex(1)
+        self.DBlgrid.addWidget(self.rtDBsel, 1, 1, 1, 1)
+        self.DBlgrid.addWidget(self.DBsel, 1, 2, 1, 1)
+        # text for selecting type
+        ctip = 'Type SMILES string for molecule'
+        self.rtDBsmi = mQLabel('SMILES or file:', '', 'r', 14)
+        self.etDBsmi = mQLineEdit('', ctip, 'l', 14)
+        self.DBlgrid.addWidget(self.rtDBsmi, 2, 1, 1, 1)
+        self.DBlgrid.addWidget(self.etDBsmi, 2, 2, 1, 1)
+        # text for specifying name
+        ctip = 'Type name for molecule'
+        self.rtDBname = mQLabel('Name:', '', 'r', 14)
+        self.etDBname = mQLineEdit('', ctip, 'l', 14)
+        self.DBlgrid.addWidget(self.rtDBname, 3, 1, 1, 1)
+        self.DBlgrid.addWidget(self.etDBname, 3, 2, 1, 1)
+        # text for specifying category
+        ctip = 'Type groups for ligand'
+        self.rtDBgrps = mQLabel('Groups:', '', 'r', 14)
+        self.etDBgrps = mQLineEdit('', ctip, 'l', 14)
+        self.DBlgrid.addWidget(self.rtDBgrps, 4, 1, 1, 1)
+        self.DBlgrid.addWidget(self.etDBgrps, 4, 2, 1, 1)
+        # text for specifying groups
+        ctip = 'Type category for ligand. It can be used for building complexes("build")\n'
+        ctip += 'functionalizing existing cores("functionalize") or both.'
+        self.rtDBctg = mQLabel('Category:', '', 'r', 14)
+        self.etDBctg = mQComboBox(['all', 'build', 'functionalize'], ctip, 14)
+        self.DBlgrid.addWidget(self.rtDBctg, 5, 1, 1, 1)
+        self.DBlgrid.addWidget(self.etDBctg, 5, 2, 1, 1)
+        # checkboxes for FF optimization
+        ctip = 'Force-field optimize in isolation'
+        self.lFFb = mQCheckBox('FF before', ctip, 14)
+        self.DBlgrid.addWidget(self.lFFb, 6, 1, 1, 1)
+        self.lFFb.setChecked(True)
+        # checkboxes for FF optimization
+        ctip = 'Force-field optimize in molecule'
+        self.lFFa = mQCheckBox('FF after', ctip, 14)
+        self.DBlgrid.addWidget(self.lFFa, 6, 2, 1, 1)
+        self.lFFa.setChecked(True)
+        # drop menu for denticity
+        ctip = 'Type denticity for SMILES molecule'
+        self.rtDBsmident = mQLabel('Denticity:', '', 'r', 14)
+        qcav = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
+        self.DBdent = mQComboBox(qcav, ctip, 14)
+        self.DBdent.setCurrentIndex(0)
+        self.DBlgrid.addWidget(self.rtDBsmident, 7, 1, 1, 1)
+        self.DBlgrid.addWidget(self.DBdent, 7, 2, 1, 1)
+        self.DBsel.currentIndexChanged.connect(
+            self.dbchange)  # error if not here
+        # text for typing input connection atoms
+        ctip = 'Type indices for connection atoms, default: 1'
+        self.rtDBsmicat = mQLabel('Catoms:', ctip, 'r', 14)
+        self.etDBsmicat = mQLineEdit('', ctip, 'l', 14)
+        self.DBlgrid.addWidget(self.rtDBsmicat, 8, 1, 1, 1)
+        self.DBlgrid.addWidget(self.etDBsmicat, 8, 2, 1, 1)
+        # button for addition
+        ctip = 'Load molecule from file'
+        self.butDBAlf = mQPushButton('Load file..', ctip, 14)
+        self.butDBAlf.clicked.connect(self.qDBload)
+        self.DBlgrid.addWidget(self.butDBAlf, 9, 0, 1, 1)
+        # button for addition
+        ctip = 'Add new molecule to database'
+        self.butDBAub = mQPushButton('Add', ctip, 14)
+        self.butDBAub.clicked.connect(self.qaddDB)
+        self.DBlgrid.addWidget(self.butDBAub, 9, 1, 1, 1)
+        # button for removal
+        ctip = 'Remove molecule from database'
+        self.butDBDub = mQPushButton('Remove', ctip, 14)
+        self.butDBDub.clicked.connect(self.qdelDB)
+        self.DBlgrid.addWidget(self.butDBDub, 9, 2, 1, 1)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butDBRet = mQPushButton('Return', ctip, 14)
+        self.butDBRet.clicked.connect(self.qretmain)
+        self.DBlgrid.addWidget(self.butDBRet, 9, 3, 1, 1)
+        # ############################################
+        # ## create chemical DB interaction window ###
+        # ############################################
+        self.cDBWindow = QWidget()  # DB Window
+        self.cDBgrid = QGridLayout()
+        self.sgrid.addWidget(self.cDBWindow)
+        self.cDBWindow.setPalette(p)
+        self.cDBWindow.setLayout(self.cDBgrid)
+        self.cDBWindow.setWindowTitle('Chemical Database Search')
+        ctip = 'Specify screening options or similarity search.'
+        # top text
+        self.txtcdb = mQLabel('Database Search', ctip, 'c', 18)
+        self.cDBgrid.addWidget(self.txtcdb, 0, 0, 1, 9)
+        # text for reference
+        self.rtcDBref = mQLabel('Similarity search', '', 'c', 18)
+        self.cDBgrid.addWidget(self.rtcDBref, 1, 0, 1, 3)
+        # text for selecting type
+        ctip = 'Type SMILES string or molecule name for reference molecule in similarity search'
+        self.rtcDBsmi = mQLabel('SMILES:', ctip, 'r', 14)
+        self.etcDBsmi = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.rtcDBsmi, 2, 0, 1, 1)
+        self.cDBgrid.addWidget(self.etcDBsmi, 2, 1, 1, 2)
+        # button for loading from file
+        ctip = 'Load reference molecule from file'
+        self.rtcDBAlf = mQLabel('From file:', ctip, 'r', 14)
+        self.butcDBAlf = mQPushButton('Load..', ctip, 14)
+        self.butcDBAlf.clicked.connect(self.qcDBload)
+        self.cDBgrid.addWidget(self.rtcDBAlf, 3, 0, 1, 1)
+        self.cDBgrid.addWidget(self.butcDBAlf, 3, 1, 1, 2)
+        # connection atoms for smarts/smiles
+        ctip = 'Specify the connection atoms in SMARTS/SMILES. Default: 1'
+        self.rtcDBcatoms = mQLabel('Conn atoms:', ctip, 'r', 14)
+        self.etcDBcatoms = mQLineEdit('1', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.rtcDBcatoms, 4, 0, 1, 1)
+        self.cDBgrid.addWidget(self.etcDBcatoms, 4, 1, 1, 1)
+        # how many molecules to return
+        ctip = 'Specify the number of results you want.'
+        self.rtcDBres = mQLabel('Results:', ctip, 'r', 14)
+        self.etcDBnres = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.rtcDBres, 5, 0, 1, 1)
+        self.cDBgrid.addWidget(self.etcDBnres, 5, 1, 1, 1)
+        # text for output file
+        ctip = 'Please type in output file'
+        self.rtcDBsoutf = mQLabel('Output file:', ctip, 'r', 14)
+        self.etcDBoutf = mQLineEdit('simres', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.rtcDBsoutf, 6, 0, 1, 1)
+        self.cDBgrid.addWidget(self.etcDBoutf, 6, 1, 1, 1)
+        # drop menu for output file
+        qcav = ['.smi']  # ,'.mol','.sdf']
+        self.cDBdent = mQComboBox(qcav, ctip, 14)
+        self.cDBgrid.addWidget(self.cDBdent, 6, 2, 1, 1)
+        # text for screening options
+        self.rtcDBsc = mQLabel('Screening options', ctip, 'c', 18)
+        self.cDBgrid.addWidget(self.rtcDBsc, 1, 6, 1, 4)
+        # text for selecting database
+        self.rtcDBsel = mQLabel('Select database:', ctip, 'c', 14)
+        self.cDBgrid.addWidget(self.rtcDBsel, 2, 5, 1, 2)
+        # get existing databases
+        ctip = 'Select the database you want to use. Please note that fastsearch indexes DBs allow for much faster screening.'
+        dbdir = globs.chemdbdir
+        dbs0 = glob.glob(dbdir+"/*.sdf")
+        dbs1 = [d.rsplit('/', 1)[-1] for d in dbs0]
+        dbs = [d.split('.', 1)[0] for d in dbs1]
+        self.cDBsel = mQComboBox(dbs, ctip, 14)
+        self.cDBgrid.addWidget(self.cDBsel, 2, 7, 1, 2)
+        # text for SMARTS pattern
+        ctip = 'Type SMARTS pattern for matching'
+        self.rtcDBsmarts = mQLabel('SMARTS:', ctip, 'r', 14)
+        self.etcDBsmarts = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.rtcDBsmarts, 3, 5, 1, 2)
+        self.cDBgrid.addWidget(self.etcDBsmarts, 3, 7, 1, 2)
+        ctip = 'Select molecular fingerprint'
+        # text for selecting fingerprint
+        self.rtcDBsf = mQLabel('Select Fingerprint:', ctip, 'r', 14)
+        self.cDBgrid.addWidget(self.rtcDBsf, 4, 5, 1, 2)
+        # select fingerprint
+        opts = ['FP2', 'FP3', 'FP4', 'MACCS']
+        self.cDBsf = mQComboBox(opts, ctip, 14)
+        self.cDBgrid.addWidget(self.cDBsf, 4, 7, 1, 2)
+        # get options for screening
+        ctip = 'Specify minimum and maximum values for filters.'
+        self.rtcDBmin = mQLabel('min', ctip, 'c', 14)
+        self.rtcDBmax = mQLabel('max', ctip, 'c', 14)
+        self.cDBgrid.addWidget(self.rtcDBmin, 6, 7, 1, 1)
+        self.cDBgrid.addWidget(self.rtcDBmax, 6, 8, 1, 1)
+        ctip = 'Total number of atoms.'
+        self.rtcDBat0 = mQLabel('atoms:', ctip, 'r', 14)
+        self.cDBgrid.addWidget(self.rtcDBat0, 7, 5, 1, 2)
+        ctip = 'Minimum number of atoms.'
+        self.etcDBsatoms0 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsatoms0, 7, 7, 1, 1)
+        ctip = 'Maximum number of atoms.'
+        self.etcDBsatoms1 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsatoms1, 7, 8, 1, 1)
+        ctip = 'Total number of bonds.'
+        self.rtcDBb0 = mQLabel('bonds:', ctip, 'r', 14)
+        self.cDBgrid.addWidget(self.rtcDBb0, 8, 5, 1, 2)
+        ctip = 'Minimum number of total bonds.'
+        self.etcDBsbonds0 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsbonds0, 8, 7, 1, 1)
+        ctip = 'Maximum number of total bonds.'
+        self.etcDBsbonds1 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsbonds1, 8, 8, 1, 1)
+        ctip = 'Total number of aromatic.'
+        self.rtcDBba0 = mQLabel('aromatic bonds:', ctip, 'r', 14)
+        self.cDBgrid.addWidget(self.rtcDBba0, 9, 5, 1, 2)
+        ctip = 'Minimum number of aromatic bonds.'
+        self.etcDBsabonds0 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsabonds0, 9, 7, 1, 1)
+        ctip = 'Maximum number of aromatic bonds.'
+        self.etcDBsabonds1 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsabonds1, 9, 8, 1, 1)
+        ctip = 'Total number of single bonds.'
+        self.rtcDBs0 = mQLabel('single bonds:', ctip, 'r', 14)
+        self.cDBgrid.addWidget(self.rtcDBs0, 10, 5, 1, 2)
+        ctip = 'Minimum number of single bonds.'
+        self.etcDBsbondss0 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsbondss0, 10, 7, 1, 1)
+        ctip = 'Maximum number of single bonds.'
+        self.etcDBsbondss1 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBsbondss1, 10, 8, 1, 1)
+        ctip = 'Molecular weight.'
+        self.rtcDBbtmw0 = mQLabel('MW:', ctip, '', 14)
+        self.cDBgrid.addWidget(self.rtcDBbtmw0, 11, 5, 1, 2)
+        ctip = 'Minimum molecular weight.'
+        self.etcDBmw0 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBmw0, 11, 7, 1, 1)
+        ctip = 'Maximum molecular weight.'
+        self.etcDBmw1 = mQLineEdit('', ctip, 'l', 14)
+        self.cDBgrid.addWidget(self.etcDBmw1, 11, 8, 1, 1)
+        # aspirin icon
+        f = resource_files("molSimplify").joinpath("icons/chemdb.png")
+        c = mQPixmap(f)
+        relresize(c, c, 0.4)
+        self.cDBgrid.addWidget(c, 7, 0, 4, 2)
+        # button for addition
+        ctip = 'Search database:'
+        self.butcDBAub = mQPushButton('Search', ctip, 14)
+        self.butcDBAub.clicked.connect(self.qaddcDB)
+        self.cDBgrid.addWidget(self.butcDBAub, 11, 0, 1, 2)
+        # button for addition
+        ctip = 'Draw results'
+        self.butcDBd0 = mQPushButton('Draw', ctip, 14)
+        self.butcDBd0.clicked.connect(self.drawres)
+        self.cDBgrid.addWidget(self.butcDBd0, 9, 2, 1, 1)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butcDBRet = mQPushButton('Return', ctip, 14)
+        self.butcDBRet.clicked.connect(self.qretmain)
+        self.cDBgrid.addWidget(self.butcDBRet, 11, 2, 1, 1)
+        # ##########################
+        # ## post-process window ###
+        # ##########################
+        self.pWindow = QWidget()  # Post Window
+        self.pgrid = QGridLayout()
+        self.sgrid.addWidget(self.pWindow)
+        self.pWindow.setPalette(p)
+        self.pWindow.setLayout(self.pgrid)
+        self.pWindow.setWindowTitle('Post-processing')
+        self.pgrid.setRowMinimumHeight(0, 50)
+        self.pgrid.setRowMinimumHeight(2, 30)
+        # top text
+        self.txtp = mQLabel('Post-processing setup', '', 'c', 18)
+        self.pgrid.addWidget(self.txtp, 0, 0, 1, 4)
+        # input for jobscripts
+        ctip = 'Select top jobs directory'
+        self.butpd = mQPushButton('Select directory', ctip, 16)
+        self.butpd.clicked.connect(self.pdload)
+        self.pgrid.addWidget(self.butpd, 1, 0, 1, 1)
+        self.etpdir = mQLineEdit(globs.rundir, ctip, 'l', 16)
+        self.pgrid.addWidget(self.etpdir, 1, 1, 1, 1)
+        # select qc code
+        ctip = 'Select QC code'
+        qcav = ['TeraChem', 'GAMESS']
+        self.rpcode = mQLabel('QC code:', '', 'c', 16)
+        self.pgrid.addWidget(self.rpcode, 1, 2, 1, 1)
+        self.pqcode = mQComboBox(qcav, ctip, 14)
+        self.pgrid.addWidget(self.pqcode, 1, 3, 1, 1)
+        # general summary
+        ctip = 'Generate results summary'
+        self.psum = mQCheckBox('Summary', ctip, 16)
+        self.pgrid.addWidget(self.psum, 3, 1, 1, 1)
+        # metal charges
+        ctip = 'Calculate metal charge'
+        self.pch = mQCheckBox('Charge', ctip, 16)
+        self.pgrid.addWidget(self.pch, 3, 2, 1, 1)
+        # wavefunction properties
+        ctip = 'Generate average properties of the wavefunction'
+        self.pwfnav = mQCheckBox('Wavefunction', ctip, 16)
+        self.pgrid.addWidget(self.pwfnav, 4, 1, 1, 1)
+        # cube files
+        ctip = 'Generate cubefiles'
+        self.pcub = mQCheckBox('Cubes', ctip, 16)
+        self.pgrid.addWidget(self.pcub, 4, 2, 1, 1)
+        # molecular orbital information
+        ctip = 'Molecular Orbital information'
+        self.porbs = mQCheckBox('MO', ctip, 16)
+        self.pgrid.addWidget(self.porbs, 5, 1, 1, 1)
+        # NBO analysis
+        ctip = 'NBO analysis'
+        self.pnbo = mQCheckBox('NBO', ctip, 16)
+        self.pgrid.addWidget(self.pnbo, 5, 2, 1, 1)
+        # d-orbital information
+        # ctip = 'd-orbital information'
+        # self.pdorbs = mCheck(self.pWindow,0.55,0.525,0.2,0.1,'d-orbitals',ctip,16)
+        # delocalization indices
+        ctip = 'Localization and delocalization indices'
+        self.pdeloc = mQCheckBox('Deloc', ctip, 16)
+        self.pgrid.addWidget(self.pdeloc, 6, 1, 1, 1)
+        # button for addition
+        ctip = 'Run post-processing'
+        self.butpR = mQPushButton('Run', ctip, 16)
+        self.pgrid.addWidget(self.butpR, 7, 1, 1, 2)
+        self.butpR.clicked.connect(self.postprocGUI)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butpret = mQPushButton('Return', ctip, 16)
+        self.butpret.clicked.connect(self.qretmain)
+        self.pgrid.addWidget(self.butpret, 7, 3, 1, 2)
+        # c1p = mPic(self.pWindow,globs.installdir+'/icons/wft1.png',0.04,0.7,0.2)
+        f = resource_files("molSimplify").joinpath("icons/wft3.png")
+        c3p = mQPixmap(f)
+        self.pgrid.addWidget(c3p, 3, 0, 4, 1)
+        # c2p = mPic(self.pWindow,globs.installdir+'/icons/wft2.png',0.04,0.035,0.2)
+        # #################################
+        # ## create add geometry window ###
+        # #################################
+        self.geWindow = QWidget()  # Geometry window
+        self.gegrid = QGridLayout()
+        self.sgrid.addWidget(self.geWindow)
+        self.geWindow.setPalette(p)
+        self.geWindow.setLayout(self.gegrid)
+        self.geWindow.setWindowTitle('Add new geometry')
+        # top text
+        self.txtg = mQLabel('New geometry', '', 'c', 18)
+        self.gegrid.addWidget(self.txtg, 0, 0, 1, 4)
+        # text for specifying name
+        ctip = 'Type name of geometry'
+        self.rtgname = mQLabel('Name:', '', 'r', 14)
+        self.etgname = mQLineEdit('', ctip, 'l', 14)
+        self.gegrid.addWidget(self.rtgname, 1, 0, 1, 1)
+        self.gegrid.addWidget(self.etgname, 1, 1, 1, 1)
+        # text for specifying short name
+        ctip = 'Type short identifier of geometry (2-4 letters)'
+        self.rtgshort = mQLabel('Short identifier:', '', 'r', 14)
+        self.etgshort = mQLineEdit('', ctip, 'l', 14)
+        self.gegrid.addWidget(self.rtgshort, 2, 0, 1, 1)
+        self.gegrid.addWidget(self.etgshort, 2, 1, 1, 1)
+        # xyz file
+        ctip = 'Load xyz file with geometry.'
+        self.rtgf = mQLabel('Filename:', '', 'r', 14)
+        self.etgf = mQLineEdit('', ctip, 'l', 14)
+        self.gegrid.addWidget(self.rtgf, 3, 0, 1, 1)
+        self.gegrid.addWidget(self.etgf, 3, 1, 1, 1)
+        # png file
+        ctip = 'Load png file with chemdraw for geometry.'
+        self.rtgfc = mQLabel('Chemdraw file:', '', 'r', 14)
+        self.etgfc = mQLineEdit('', ctip, 'l', 14)
+        self.gegrid.addWidget(self.rtgfc, 4, 0, 1, 1)
+        self.gegrid.addWidget(self.etgfc, 4, 1, 1, 1)
+        # load file
+        self.butge = mQPushButton('Load geometry file..', ctip, 14)
+        self.butge.clicked.connect(self.qgeomload)
+        self.gegrid.addWidget(self.butge, 5, 0, 1, 1)
+        # load file
+        self.butge2 = mQPushButton('Load Chemdraw file..', ctip, 14)
+        self.butge2.clicked.connect(self.qgeomload2)
+        self.gegrid.addWidget(self.butge2, 5, 1, 1, 1)
+        # button for addition
+        ctip = 'Add new geometry to database'
+        self.butgAub = mQPushButton('Add', ctip, 14)
+        self.butgAub.clicked.connect(self.qaddg)
+        self.gegrid.addWidget(self.butgAub, 6, 0, 1, 1)
+        # button for removal
+        ctip = 'Remove geometry from database'
+        self.butgDub = mQPushButton('Remove', ctip, 14)
+        self.butgDub.clicked.connect(self.qdelg)
+        self.gegrid.addWidget(self.butgDub, 6, 1, 1, 1)
+        # button for return
+        ctip = 'Return to main menu'
+        self.butgRet = mQPushButton('Return', ctip, 14)
+        self.butgRet.clicked.connect(self.qretmain)
+        self.gegrid.addWidget(self.butgRet, 7, 1, 1, 1)
+        # ###############################
+        # ## create ligands 2D window ###
+        # ###############################
+        self.lwindow = QWidget()
+        self.lwindow.setPalette(p)
+        self.lgrid = QGridLayout()
+        self.lwindow.setLayout(self.lgrid)
+        # self.sgrid.addWidget(self.lwindow)
+        self.lwindow.setWindowTitle('Ligands 2D')
+        self.c1p = QWidget()
+        # ###################
+        # ###################
+        # ###################
+        # ## Run main GUI ###
+        # ###################
+        # ###################
+        # ###################
+        self.wmain.setLayout(self.grid)
+        self.wmwindow.setCentralWidget(self.wmain)
+        self.sgrid.setCurrentWidget(self.wmain)
+        self.wmain.showMaximized()
+        self.wmwindow.showMaximized()
+        # resize other windows
+        relresize(self.iWind, self.wmwindow, 0.7)
+        relresize(self.iWtxt, self.iWind, 1.0)
+
+    def update_ligands_binds(self):
+        # this function updates the list
+        # of ligand and binding species
+        ctip0 = 'Ligand(s) to be used'
+        self.rtligh = mQLabel('Ligand', ctip0, 'c', 12)  # ligand header
+        f = QFont("Helvetica", 12, 75)
+        self.rtligh.setFont(f)
+        # add to layout
+        self.grid.addWidget(self.rtligh, 9, 0, 1, 2)
+        # ligands #
+        licores = list(sorted(getlicores()))
+        self.lig = []
+        self.ligocc = []
+        self.ligconn = []
+        self.ligH = []
+        self.ligML = []
+        self.ligan = []
+        self.lignam = []
+        self.ligadd = []
+        for ii in range(0, 8):
+            # ligands #
+            self.lig.append(mQLineEditL('', ctip0, 'l', 12, licores))
+            self.grid.addWidget(self.lig[ii], 10+ii, 0, 1, 2)  # add to layout
+            # ligand buttons #
+        #############################################
+
+        '''
+        #############################
+        ### Callbacks for buttons ###
+        #############################
+        '''
+        # ##################################
+        # ##### Add new ligands input ######
+        # ##################################
+
+    def addlig0(self):
+        idx = 0
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def addlig1(self):
+        idx = 1
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def addlig2(self):
+        idx = 2
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def addlig3(self):
+        idx = 3
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def addlig4(self):
+        idx = 4
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def addlig5(self):
+        idx = 5
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def addlig6(self):
+        idx = 6
+        txt0 = self.lig[idx].currentText().replace(' ', '')
+        if len(txt0) == 0:
+            mQDialogWarn('No ligand specified',
+                         'Please specify a ligand before adding another one.')
+        else:
+            self.ligadd[idx].setDisabled(True)
+            self.ligadd[idx].hide()
+            self.ligadd[idx+1].setDisabled(False)
+            self.ligadd[idx+1].show()
+            self.lig[idx+1].setDisabled(False)
+            self.ligocc[idx+1].setDisabled(False)
+            self.ligconn[idx+1].setDisabled(False)
+            self.ligH[idx+1].setDisabled(False)
+            self.ligML[idx+1].setDisabled(False)
+            self.ligan[idx+1].setDisabled(False)
+            self.lignam[idx+1].setDisabled(False)
+
+    def checkaxial(self):
+        if self.dmolp.currentIndex() > 0:
+            self.etplacephi.setText('')
+            self.etplacephi.setDisabled(True)
+            self.etplacetheta.setText('')
+            self.etplacetheta.setDisabled(True)
+        else:
+            self.etplacephi.setDisabled(False)
+            self.etplacetheta.setDisabled(False)
+        # #############################
+        # ## Local Database window ####
+        # #############################
+        # load molecule from file
+
+    def qDBload(self):
+        name = QFileDialog.getOpenFileName(
+            self.DBWindow, 'Open File', '.', "Molecule files *.xyz, *.mol (*.xyz *.mol)")
+        if name[0] != '':
+            self.etDBsmi.setText(os.path.relpath(name[0]))
+        # enable add to database interface
+
+    def enableDB(self):
+        self.DBWindow.setWindowModality(2)
+        self.DBWindow.show()
+        self.sgrid.setCurrentWidget(self.DBWindow)
+        # callback for addition button, adds to database
+
+    def qaddDB(self):
+        coption = self.DBsel.currentText()
+        smimol = self.etDBsmi.text()
+        sminame = self.etDBname.text()
+        smident = self.DBdent.currentText()
+        smicat = self.etDBsmicat.text()
+        smigrps = self.etDBgrps.text()
+        smictg = self.etDBctg.currentText()
+        globs = globalvars()
+        if not globs.custom_path:  # this will be false unless set
+            choice = QMessageBox.question(self.cDBWindow, 'Custom path needed',
+                                          'In order to add to the database, you'
+                                          ' need to select a local path for '
+                                          'molSimplify to store data files. '
+                                          'Would you like to configure it now?',
+                                          QMessageBox.Yes, QMessageBox.No)
+            if choice == QMessageBox.Yes:
+                QMessageBox.information(
+                    self.cDBWindow, 'Custom path needed',
+                    "Please select a local, user-writable location.")
+                new_path = QFileDialog.getExistingDirectory(
+                    self.cDBWindow, 'Select a writable directory.')
+                if len(new_path) > 0:
+                    globs.add_custom_path(new_path)
+                    globs.custom_path = new_path
+                    copy_to_custom_path()  # this function lives in scripts/io.py
+        # instdir = globs.installdir
+        if self.lFFb.getState() and self.lFFa.getState():
+            ffopt = 'BA'
+        elif self.lFFb.getState() and not self.lFFa.getState():
+            ffopt = 'B'
+        elif not self.lFFb.getState() and self.lFFa.getState():
+            ffopt = 'A'
+        else:
+            ffopt = 'N'
+        if smictg == 'all':
+            smictg = 'build functionalize'
+        if smimol == '' or sminame == '':
+            _ = QMessageBox.warning(
+                self.DBWindow, 'Error', 'Please specify molecule and name!')
+        else:
+            # add to database
+            emsg = ''
+            if 'ligand' in coption:
+                emsg = addtoldb(smimol, sminame, smident,
+                                smicat, smigrps, smictg, ffopt)
+            elif 'core' in coption:
+                emsg = addtocdb(smimol, sminame, smicat)
+            elif 'bind' in coption:
+                emsg = addtobdb(smimol, sminame)
+            if emsg:
+                _ = QMessageBox.warning(self.DBWindow, 'Error', emsg)
+            else:
+                _ = QMessageBox.information(
+                    self.DBWindow, 'Add', 'Successfully added to the database!')
+        self.update_ligands_binds()
+        # callback for removal button, removes from db
+
+    def qdelDB(self):
+        globs = globalvars()
+        if not globs.custom_path:  # this will be false unless set
+            choice = QMessageBox.question(self.cDBWindow, 'Custom path needed',
+                                          'In order to add to the database, you'
+                                          ' need to select a local path for '
+                                          'molSimplify to store data files. '
+                                          'Would you like to configure it now?',
+                                          QMessageBox.Yes, QMessageBox.No)
+            if choice == QMessageBox.Yes:
+                QMessageBox.information(
+                    self.cDBWindow, 'Custom path needed',
+                    "Please select a local, user-writable location.")
+                new_path = QFileDialog.getExistingDirectory(
+                    self.cDBWindow, 'Select a writable directory.')
+                if len(new_path) > 0:
+                    globs.add_custom_path(new_path)
+                    copy_to_custom_path()  # this function lives in scripts/io.py
+
+        coption = self.DBsel.currentIndex()
+        sminame = self.etDBname.text()
+        if sminame == '':
+            _ = QMessageBox.warning(
+                self.DBWindow, 'Error', 'Please specify name!')
+        else:
+            # remove from database
+            emsg = removefromDB(sminame, int(coption))
+            if emsg:
+                _ = QMessageBox.warning(self.DBWindow, 'Error', emsg)
+            else:
+                _ = QMessageBox.information(
+                    self.DBWindow, 'Remove', 'Removed from the database!')
+        # db type change
+
+    def dbchange(self):
+        ci = self.DBsel.currentIndex()
+        if ci == 1:
+            self.rtDBsmident.setDisabled(False)
+            self.DBdent.setDisabled(False)
+            self.rtDBsmicat.setDisabled(False)
+            self.etDBsmicat.setDisabled(False)
+            self.etDBgrps.setDisabled(False)
+            self.etDBgrps.setDisabled(False)
+            self.lFFb.setDisabled(False)
+            self.lFFa.setDisabled(False)
+        elif ci == 0:
+            self.rtDBsmident.setDisabled(True)
+            self.DBdent.setDisabled(True)
+            self.rtDBsmicat.setDisabled(False)
+            self.etDBsmicat.setDisabled(False)
+            self.etDBgrps.setDisabled(True)
+            self.etDBgrps.setDisabled(True)
+            self.lFFb.setDisabled(True)
+            self.lFFa.setDisabled(True)
+        else:
+            self.rtDBsmident.setDisabled(True)
+            self.DBdent.setDisabled(True)
+            self.rtDBsmicat.setDisabled(True)
+            self.etDBsmicat.setDisabled(True)
+            self.etDBgrps.setDisabled(True)
+            self.etDBgrps.setDisabled(True)
+            self.lFFb.setDisabled(True)
+            self.lFFa.setDisabled(True)
+        # perform post-processing
+
+    def postprocGUI(self):
+        rdir = self.etpdir.text()
+        if rdir[-1] == '/':
+            rdir = rdir[:-1]
+        defaultparams = ['main.py', '-i', rdir+'/postproc.inp']
+        grabguivarsP(self)
+        self.pWindow.close()
+        self.sgrid.setCurrentWidget(self.iWind)
+        emsg = startgen(defaultparams, True, self)
+        if not emsg:
+            QMessageBox.information(
+                self.pWindow, 'DONE', 'Your results are ready..')
+        # ############################
+        # ### Add geometry window ####
+        # ############################
+        # load molecule from file
+
+    def qgeomload(self):
+        name = QFileDialog.getOpenFileName(
+            self.DBWindow, 'Open File', '.', "Molecule files *.xyz (*.xyz)")
+        if name[0] != '':
+            self.etgf.setText(os.path.relpath(name[0]))
+        # load png from file
+
+    def qgeomload2(self):
+        name = QFileDialog.getOpenFileName(
+            self.DBWindow, 'Open File', '.', "Geometry image files *.png (*.png)")
+        if name[0] != '':
+            self.etgfc.setText(os.path.relpath(name[0]))
+        # enable add new geometry
+
+    def addgeom(self):
+        self.geWindow.setWindowModality(2)
+        self.geWindow.show()
+        # callback for addition button, adds to database
+
+    def qaddg(self):
+        globs = globalvars()
+        if not globs.custom_path:  # this will be false unless set
+            choice = QMessageBox.question(self.cDBWindow, 'Custom path needed',
+                                          'In order to add to the database, you'
+                                          ' need to select a local path for '
+                                          'molSimplify to store data files. '
+                                          'Would you like to configure it now?',
+                                          QMessageBox.Yes, QMessageBox.No)
+            if choice == QMessageBox.Yes:
+                QMessageBox.information(
+                    self.cDBWindow, 'Custom path needed', "Please select a local, user-writable location.")
+                new_path = QFileDialog.getExistingDirectory(
+                    self.cDBWindow, 'Select a writable directory.')
+                if len(new_path) > 0:
+                    globs.add_custom_path(new_path)
+                    copy_to_custom_path()  # this funciton lives in scripts/io.py
+        gname = self.etgname.text().lower()
+        gname = gname.replace(' ', '_')
+        gfile = self.etgf.text()
+        if gname == '' or gfile == '':
+            _ = QMessageBox.warning(
+                self.geWindow, 'Error', 'Please specify name and xyz file!')
+        elif not glob.glob(gfile):
+            _ = QMessageBox.warning(
+                self.geWindow, 'Error', 'XYZ file '+gfile+' does not exist!')
+        else:
+            globs = globalvars()
+            if globs.custom_path:
+                f = globs.custom_path + "/Data/coordinations.dict"
+            else:
+                f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict"))
+            with open(f, 'r') as fl:
+                s = fl.read().splitlines()
+            if gname.lower() in s:
+                _ = QMessageBox.warning(
+                    self.geWindow, 'Add', 'Coordination '+gname+' already exists.')
+            return
+
+            gshort = self.etgshort.text()
+            cfile = self.etgfc.text()
+            # get geometry from xyz file
+            with open(gfile, 'r') as f:
+                snew = f.read().splitlines()
+            dent = int(snew[0])-1
+            xyzl = ''
+            for ii in range(0, dent+1):
+                li = [_f for _f in re.split(' |\t', snew[2+ii]) if _f]
+                xyzl += li[1]+' '+li[2]+' '+li[3]+'\n'
+            # write new entry in coordinations.dict
+            s.append(str(dent)+': '+gname+' '+gshort)
+            ssort = [_f for _f in list(sorted(s[1:])) if _f]
+            globs = globalvars()
+            if globs.custom_path:
+                f = globs.custom_path + "/Data/coordinations.dict"
+            else:
+                print('Error, please set custom file path')
+                QMessageBox.warning(
+                    self.wmain, 'Error, please set custom file path (dd to database)')
+            with open(f, 'w') as fl:
+                fl.write(s[0]+'\n')
+                for ss in ssort:
+                    fl.write(ss+'\n')
+            # write new backbone file
+            if globs.custom_path:
+                f = globs.custom_path + "/Data/"
+            else:
+                print('Error, please set custom file path')
+                QMessageBox.warning(
+                    self.wmain, 'Error, please set custom file path (dd to database)')
+            with open(f+gshort+'.dat', 'w') as fl:
+                fl.write(xyzl)
+            # write png file
+            if glob.glob(cfile):
+                f = str(resource_files("molSimplify").joinpath("icons/geoms/"))
+                shutil.copy2(cfile, f+gshort+'.png')
+            choice = QMessageBox.information(
+                self.geWindow, 'Add', 'Successfully added to the database!')
+        self.matchgeomcoord()
+
+        # callback for removal button, removes from db
+    def qdelg(self):
+        globs = globalvars()
+        if not globs.custom_path:  # this will be false unless set
+            choice = QMessageBox.question(self.cDBWindow, 'Custom path needed',
+                                          'In order to add to the database, you'
+                                          ' need to select a local path for '
+                                          'molSimplify to store data files. '
+                                          'Would you like to configure it now?',
+                                          QMessageBox.Yes, QMessageBox.No)
+            if choice == QMessageBox.Yes:
+                QMessageBox.information(
+                    self.cDBWindow, 'Custom path needed', "Please select a local, user-writable location.")
+                new_path = QFileDialog.getExistingDirectory(
+                    self.cDBWindow, 'Select a writable directory.')
+                if len(new_path) > 0:
+                    globs.add_custom_path(new_path)
+                    copy_to_custom_path()  # this funciton lives in scripts/io.py
+
+        globs = globalvars()
+        gname = self.etgname.text().lower()
+        gname = gname.replace(' ', '_')
+        gshort = self.etgshort.text()
+        if gname == '' and gshort == '':
+            _ = QMessageBox.warning(
+                self.geWindow, 'Error', 'Please specify geometry name!')
+        else:
+            if globs.custom_path:
+                f = globs.custom_path + "/Data/coordinations.dict"
+            else:
+                f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict"))
+            with open(f, 'r') as fl:
+                s = fl.read()
+            if gname.lower() not in s and gshort.lower() not in s:
+                _ = QMessageBox.warning(
+                    self.geWindow, 'Remove', 'Coordination '+gname+' does not exist.')
+                return
+            # remove entry from coordinations.dict
+            snew = ''
+            srem = ''
+            for ss in s.splitlines():
+                sl = [_f for _f in ss.split(' ') if _f]
+                if gname.lower() != sl[1] and gshort.lower() != sl[2]:
+                    snew += ss+'\n'
+                else:
+                    srem = [_f for _f in ss.split(' ')[-1] if _f]
+            if globs.custom_path:
+                f = globs.custom_path + "/Data/coordinations.dict"
+            else:
+                f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict"))
+            with open(f, 'w') as fl:
+                fl.write(snew)
+            # remove file
+            if glob.glob(str(globs.custom_path)+'/Data/'+srem+'.dat'):
+                os.remove(str(globs.custom_path)+'/Data/'+srem+'.dat')
+            _ = QMessageBox.information(
+                self.geWindow, 'Remove', 'Successfully removed from the database!')
+        self.matchgeomcoord()
+    # ############################
+    # ## Chem Database window ####
+    # ############################
+    # load molecule from file
+
+    def qcDBload(self):
+        name = QFileDialog.getOpenFileName(
+            self.DBWindow, 'Open File', '.', "Molecule files *.xyz, *.mol *.sdf *.smi (*.xyz *.mol *.sdf *.smi)")
+        if name[0] != '':
+            self.etcDBsmi.setText(os.path.relpath(name[0]))
+    # enable add to database interface
+
+    def searchDBW(self):
+        globs = globalvars()
+        self.cDBWindow.setWindowModality(2)
+        self.cDBWindow.show()
+        writef = False
+        # instdir = globs.installdir
+        mwfn = globs.multiwfn
+        cdbdir = globs.chemdbdir
+        if not os.path.isdir(globs.chemdbdir):
+            choice = QMessageBox.question(self.cDBWindow, 'Database setup',
+                                          'It looks like the Chemical Database'
+                                          ' directory is not configured or '
+                                          'does not exist. Would you like '
+                                          'to configure it now?',
+                                          QMessageBox.Yes, QMessageBox.No)
+            if choice == QMessageBox.Yes:
+                QMessageBox.information(
+                    self.cDBWindow, 'Chem DB', "Please select the directory containing chemical databases.")
+                cdbdir = QFileDialog.getExistingDirectory(
+                    self.cDBWindow, 'Select the directory containing chemical databases.')
+                if len(cdbdir) > 0:
+                    writef = True
+        if writef:
+            with open(globs.homedir+'/.molSimplify', 'w') as f:
+                #  f.write("INSTALLDIR="+instdir+'\n')
+                f.write("CHEMDBDIR="+cdbdir+'\n')
+                if len(mwfn) > 1:
+                    f.write("MULTIWFN="+mwfn[0]+'\n')
+            # get existing databases
+            globsnew = globalvars()
+            dbdir = globsnew.chemdbdir
+            dbs0 = glob.glob(dbdir+"/*.sdf")
+            dbs1 = [d.rsplit('/', 1)[-1] for d in dbs0]
+            dbs = [d.split('.', 1)[0] for d in dbs1]
+            for d in dbs:
+                self.cDBsel.addItem(d)
+        # callback for database search
+
+    def qaddcDB(self):
+        """Collects all the info and passes it to molSimplify."""
+        rdir = self.etrdir.text()
+        if rdir[-1] == '/':
+            rdir = rdir[:-1]
+        # create running dir if not existing
+        if not os.path.isdir(rdir):
+            os.mkdir(rdir)
+        grabdbguivars(self)
+        defaultparams = ['main.py', '-i', rdir+'/dbinput.inp']
+        emsg = startgen(defaultparams, True, self)
+        if not emsg:
+            QMessageBox.information(
+                self.cDBWindow, 'DONE', 'Search is done..')
+        self.sgrid.setCurrentWidget(self.cDBWindow)
+        # db type change
+
+    def cdbchange(self):
+        ci = self.DBsel.currentIndex()
+        if (ci == 1):
+            self.rtDBsmident.setDisabled(False)
+            self.DBdent.setDisabled(False)
+            self.rtDBsmicat.setDisabled(False)
+            self.etDBsmicat.setDisabled(False)
+        else:
+            self.rtDBsmident.setDisabled(True)
+            self.DBdent.setDisabled(True)
+            self.rtDBsmicat.setDisabled(True)
+            self.etDBsmicat.setDisabled(True)
+        # ###################
+        # ## Main window ####
+        # ###################
+        # run generation
+
+    def runGUI(self):
+        # collects all the info and passes it to molSimplify #
+        rdir = self.etrdir.text()
+        if rdir[-1] == '/':
+            rdir = rdir[:-1]
+        # create running dir if not existing
+        if not os.path.isdir(rdir):
+            try:
+                os.mkdir(rdir)
+            except FileExistsError:
+                emsg = 'Directory '+rdir+' could not be created. Check your input.\n'
+                QMessageBox.critical(self.wmain, 'Problem', emsg)
+                return
+        # check for extra molecule
+        if self.chkM.getState() and self.etbind.currentText() == '':
+            emsg = ('You checked the extra molecule box but specified\n'
+                    'no extra molecule. No extra molecule will be generated.\n')
+            QMessageBox.warning(self.wmain, 'Warning', emsg)
+        # get parameters
+        grabguivars(self)
+        defaultparams = ['main.py', '-i', rdir+'/geninput.inp']
+        self.iWind.hide()
+        self.sgrid.setCurrentWidget(self.iWind)
+        self.iWind.show()
+        msgBox = QMessageBox()
+        if self.randomchk.getState():
+            msgBox.setText(
+                "Random generation initiated. This process might take some time.")
+            msgBox.setIcon(1)
+            msgBox.setInformativeText('Please be patient. OK?')
+            msgBox.setWindowTitle('Running..')
+            msgBox.exec_()
+        # do the generation
+        emsg = startgen(defaultparams, True, self)
+        if not emsg:
+            QMessageBox.information(
+                self.wmain, 'Done', 'Structure generation terminated successfully!')
+        else:
+            QMessageBox.warning(self.wmain, 'Problem', emsg)
+        # list molecules
+
+    def listmols(self):
+        coreslist = getcores()
+        liglist = getligs()
+        bindlist = getbinds()
+        msg = 'Available cores in the database:\n'+coreslist
+        msg += '\n\nAvailable ligands in the database:\n'+liglist
+        msg += '\n\nAvailable extra molecules in the database:\n'+bindlist+'\n'
+        QMessageBox.information(self.wmain, 'List of molecules', msg)
+        # draw ligands
+
+    def drawligs_svg(self):
+        """Draw the ligands entered into the GUI as SVGs in a pop-up window"""
+        # collects all the info and passes it to molSimplify #
+        args = grabguivars(self)
+        # processes ligand arguments
+        if len(args['-lig']) < 1:
+            mQDialogWarn('Warning', 'No ligands are specified.')
+            return False
+        else:
+            rows = self.lgrid.rowCount()
+            # Clear existing widgets in layout
+            if rows > 1:
+                for i in reversed(list(range(self.lgrid.count()))):
+                    self.lgrid.itemAt(i).widget().setParent(None)
+
+            args['-lig'] = args['-lig'].replace(' ', '')
+            lls = args['-lig'].split(',')
+            liglist = []
+            # check if multiple ligands in .smi file
+            for li in lls:
+                if '.smi' in li:
+                    with open(li, 'r') as f:
+                        smis = [_f for _f in f.read().splitlines() if _f]
+                    liglist += smis
+                else:
+                    liglist.append(li)
+            # Get known ligand dictionaries
+            licores = getlicores()
+            simpleligs = getslicores()
+            ligs = []
+            for li in liglist:
+                # check in simple dictionary
+                if li in list(simpleligs.keys()):
+                    li = simpleligs[li][0]
+                if isinstance(li, str):
+                    ll = unicodedata.normalize(
+                        'NFKD', li).encode('ascii', 'ignore')
+                else:
+                    ll = li
+                # load ligands as molecules
+                lig, emsg = lig_load(ll, licores)
+                if emsg:
+                    mQDialogWarn('Error', emsg)
+                else:
+                    ligs.append(lig.OBMol)
+            if len(ligs) == 0:
+                return
+            else:
+                for i, pmol in enumerate(ligs):
+                    # use openbabel to convert to labeled SVG
+                    obConversion = openbabel.OBConversion()
+                    obConversion.SetOutFormat("svg")
+                    obConversion.AddOption("i", obConversion.OUTOPTIONS, "")
+                    # return the svg with atom labels as a string
+                    svgstr = obConversion.WriteString(pmol)
+                    # unpacked nested svg as in pybel._repr_svg_
+                    namespace = "http://www.w3.org/2000/svg"
+                    ET.register_namespace("", namespace)
+                    tree = ET.fromstring(svgstr)
+                    svg = tree.find(
+                        "{{{ns}}}g/{{{ns}}}svg".format(ns=namespace))
+                    newsvg = ET.tostring(svg).decode("utf-8")
+                    # write unpacked svg to temp file
+                    filedes, filename = tempfile.mkstemp()
+                    with open(filename, "w") as svg_file:
+                        svg_file.write(newsvg)
+                    # Read the temp file into an SvgWidget
+                    self.svgwidget = mSvgWidget(filename)
+                    # Add the svg to the window
+                    self.lgrid.addWidget(self.svgwidget, 0, i)
+                    # Cleanup temp files
+                    os.close(filedes)
+                    os.remove(filename)
+                # Build close button
+                self.lwindow.setWindowTitle('Ligands 2D')
+                self.lwclose = QPushButton('Close')
+                self.lwclose.clicked.connect(self.qcloseligs)
+                # Add close button to window
+                self.lgrid.addWidget(self.lwclose, 1, 0)
+                self.lwindow.show()
+
+    def viewgeom(self):
+        # get geometry
+        geom = self.dcoordg.currentText()
+        gfname = str(resource_files("molSimplify").joinpath(f"icons/geoms/{geom}.png"))
+        if glob.glob(gfname):
+            rows = self.lgrid.rowCount()
+            # Clear existing widgets in layout
+            if rows > 1:
+                for i in reversed(list(range(self.lgrid.count()))):
+                    self.lgrid.itemAt(i).widget().setParent(None)
+            self.c1p = mQPixmap(gfname)
+            self.lgrid.addWidget(self.c1p, 0, 0)
+            # button for closing window
+            ctip = 'Close current window'
+            self.lwclose = mQPushButton('Close', ctip, 14)
+            self.lwclose.clicked.connect(self.qcloseligs)
+            self.lgrid.addWidget(self.lwclose, 1, 0)
+            self.lwindow.setWindowTitle('Geometry:'+self.dcoordg.currentText())
+            self.lwindow.show()
+            center(self.lwindow)
+        else:
+            mQDialogWarn('Warning', 'No file '+gfname+' exists..')
+    # draw results from db search
+
+    def drawres(self):
+        # collects all the info and passes it to molSimplify #
+        rdir = self.etrdir.text()
+        if rdir[-1] == '/':
+            rdir = rdir[:-1]
+        # creat running dir if not existing
+        if not os.path.isdir(rdir):
+            os.mkdir(rdir)
+        outf = rdir+'/'+self.etcDBoutf.text()
+        outf = outf.replace(' ', '')+'.smi'
+        if not glob.glob(outf):
+            mQDialogWarn('Warning', 'No database results file in '+rdir)
+            return False
+        else:
+            lls = [outf]
+            liglist = []
+            # check if multiple ligands in .smi file
+            for li in lls:
+                if '.smi' in li:
+                    with open(li, 'r') as f:
+                        smis = [_f for _f in f.read().splitlines() if _f]
+                    liglist += smis
+                else:
+                    liglist.append(li)
+            licores = getlicores()
+            ligs = []
+            for li in liglist:
+                if isinstance(li, str):
+                    ll = unicodedata.normalize(
+                        'NFKD', li).encode('ascii', 'ignore')
+                else:
+                    ll = li
+
+                lig, emsg = lig_load(ll, licores)
+                if not emsg:
+                    ligs.append(lig.OBMol)
+            if len(ligs) == 0:
+                return
+            else:
+                for i, pmol in enumerate(ligs):
+                    # use openbabel to convert to labeled SVG
+                    obConversion = openbabel.OBConversion()
+                    obConversion.SetOutFormat("svg")
+                    obConversion.AddOption("i", obConversion.OUTOPTIONS, "")
+                    # return the svg with atom labels as a string
+                    svgstr = obConversion.WriteString(pmol)
+                    # unpacked nested svg as in pybel._repr_svg_
+                    namespace = "http://www.w3.org/2000/svg"
+                    ET.register_namespace("", namespace)
+                    tree = ET.fromstring(svgstr)
+                    svg = tree.find(
+                        "{{{ns}}}g/{{{ns}}}svg".format(ns=namespace))
+                    newsvg = ET.tostring(svg).decode("utf-8")
+                    # write unpacked svg to temp file
+                    filedes, filename = tempfile.mkstemp()
+                    with open(filename, "w") as svg_file:
+                        svg_file.write(newsvg)
+                    # Read the temp file into an SvgWidget
+                    self.svgwidget = mSvgWidget(filename)
+                    # Add the svg to the window
+                    self.lgrid.addWidget(self.svgwidget, 0, i)
+                    # Cleanup temp files
+                    os.close(filedes)
+                    os.remove(filename)
+                # Build close button
+                self.lwindow.setWindowTitle('Ligands 2D')
+                self.lwclose = QPushButton('Close')
+                self.lwclose.clicked.connect(self.qcloseligs)
+                # Add close button to window
+                self.lgrid.addWidget(self.lwclose, 1, 0)
+                self.lwindow.show()
+    # enable random input
+
+    def enablerandom(self):
+        if self.randomchk.isChecked():
+            self.rtrgen.setDisabled(False)
+            self.etrgen.setDisabled(False)
+            self.rtlignum.setDisabled(False)
+            self.etlignum.setDisabled(False)
+            self.rtliggrp.setDisabled(False)
+            self.etliggrp.setDisabled(False)
+            self.rtligctg.setDisabled(False)
+            self.etligctg.setDisabled(False)
+            self.randkHs.setDisabled(False)
+            if len(self.etrgen.text()) == 0:
+                self.etrgen.setText('1')
+        else:
+            self.rtrgen.setDisabled(True)
+            self.etrgen.setDisabled(True)
+            self.rtlignum.setDisabled(True)
+            self.etlignum.setDisabled(True)
+            self.rtliggrp.setDisabled(True)
+            self.etliggrp.setDisabled(True)
+            self.rtligctg.setDisabled(True)
+            self.etligctg.setDisabled(True)
+            self.randkHs.setDisabled(True)
+    # generate all enable FF input
+
+    def disableffinput(self):
+        if self.chkgenall.isChecked():
+            self.dff.setDisabled(True)
+            self.dffba.setDisabled(True)
+            self.chkFF.state = True
+            self.chkFF.setDisabled(True)
+        else:
+            self.dff.setDisabled(False)
+            self.dffba.setDisabled(False)
+            self.chkFF.setDisabled(False)
+            self.enableffinput()
+    # enable FF input
+
+    def enableffinput(self):
+        if self.chkFF.isChecked():
+            self.chkFF.state = False
+            self.dff.setDisabled(False)
+            self.dffba.setDisabled(False)
+        else:
+            self.dff.setDisabled(True)
+            self.dffba.setDisabled(True)
+            self.chkFF.state = True
+    # load file for editing
+
+    def qloadinput(self):
+        name = QFileDialog.getOpenFileName(self.wmain, 'Open File')[0]
+        if name != '':
+            loadfrominputfile(self, name)
+    # load directory
+
+    def dirload(self):
+        name = QFileDialog.getExistingDirectory(self.wmain, 'Select Directory')
+        if len(name) > 0 and name[0] != '':
+            self.etrdir.setText(name)
+    # save as input file
+
+    def qsaveinput(self, gui):
+        name = QFileDialog.getSaveFileName(
+            self.wmain, 'Save as..', '.', "Input files * (*)")[0]
+        if name != '':
+            varsg = grabguivars(self)
+            writeinputc(varsg, name)
+    # show help menu
+
+    def qshowhelp(self):
+        globs = globalvars()
+        QMessageBox.information(self.wmain, 'About', globs.about)
+
+    def getscreensize(self):
+        screenShape = QDesktopWidget().screenGeometry()
+        width = int(screenShape.width())
+        height = int(screenShape.height())
+        return [width, height]
+    # slider changed value
+
+    def sliderChanged(self, val):
+        self.distper.setText('Distort:'+str(val)+'%')
+    # match index with coordination
+
+    def matchgeomcoord(self):
+        # get current index
+        dc = self.dcoord.currentIndex()
+        coords, geomnames, geomshorts, geomgroups = getgeoms()
+        qcav = geomgroups
+        ctip = geomnames
+        # empty the box
+        for i in range(0, self.dcoordg.count()):
+            self.dcoordg.removeItem(0)
+        qc = qcav[dc]
+        # add to box
+        for i, t in enumerate(qc):
+            # File f is never actually used? RM 2022/02/17
+            f = str(resource_files("molSimplify").joinpath(f"icons/geoms/{t}.png"))  # noqa F841
+            self.dcoordg.addItem(QIcon(t), t)
+        self.dcoordg.setIconSize(QSize(60, 60))
+        # set default geometry
+        self.dcoordg.setCurrentIndex(0)
+        # get global index
+        elem = [i for i, s in enumerate(
+            geomshorts) if s in self.dcoordg.currentText()]
+        ct = ''
+        for ii in range(elem[0], elem[0]+len(geomgroups[dc])):
+            ct += ctip[ii]+', '
+        ct = ct[:-2]
+        # set correct tooltip
+        self.dcoordg.setToolTip(ct)
+    # enable extra molecule input
+
+    def enableemol(self):
+        if self.chkM.isChecked():
+            self.chkM.state = False
+            self.txtamol.setDisabled(False)
+            self.rtbind.setDisabled(False)
+            self.etbind.setDisabled(False)
+            self.rtbsmi.setDisabled(False)
+            self.etbsmi.setDisabled(False)
+            self.rtnbind.setDisabled(False)
+            self.etnbind.setDisabled(False)
+            if self.etnbind.text() == '':
+                self.etnbind.setText('1')
+            self.rtplace.setDisabled(False)
+            self.etplacemin.setDisabled(False)
+            self.etplacemax.setDisabled(False)
+            self.dmolp.setDisabled(False)
+            self.rtchbind.setDisabled(False)
+            self.etchbind.setDisabled(False)
+            self.rtplacea.setDisabled(False)
+            self.etplacephi.setDisabled(False)
+            self.etplacetheta.setDisabled(False)
+            # self.rtmaskbind.setDisabled(False)
+            self.etmaskbind.setDisabled(False)
+            self.chsep.setDisabled(False)
+        else:
+            self.txtamol.setDisabled(True)
+            self.rtbind.setDisabled(True)
+            self.etbind.setDisabled(True)
+            self.rtbsmi.setDisabled(True)
+            self.etbsmi.setDisabled(True)
+            self.rtnbind.setDisabled(True)
+            self.etnbind.setDisabled(True)
+            self.rtplace.setDisabled(True)
+            self.etplacemin.setDisabled(True)
+            self.etplacemax.setDisabled(True)
+            self.dmolp.setDisabled(True)
+            self.chkM.state = True
+            self.rtchbind.setDisabled(True)
+            self.etchbind.setDisabled(True)
+            self.rtplacea.setDisabled(True)
+            self.etplacephi.setDisabled(True)
+            self.etplacetheta.setDisabled(True)
+            # self.rtmaskbind.setDisabled(True)
+            self.etmaskbind.setDisabled(True)
+            self.chsep.setDisabled(True)
+    # ####################
+    # ### QEt/g input ####
+    # ####################
+    # callback for QE input
+
+    def qcinput(self):
+        if self.chch.getState():
+            self.etqcgch.setDisabled(True)
+            self.etqctch.setDisabled(True)
+            self.etqcQch.setDisabled(True)
+        if self.qcode.currentIndex() == 0:  # generate terachem input
+            self.qctWindow.setWindowModality(2)
+            self.qctWindow.show()
+        elif self.qcode.currentIndex() == 1:  # generate GAMESS input
+            self.qcgWindow.setWindowModality(2)
+            self.qcgWindow.show()
+        elif self.qcode.currentIndex() == 2:  # generate Qchem input
+            self.qcQWindow.setWindowModality(2)
+            self.qcQWindow.show()
+    # make default button callback
+
+    def jobdef(self):
+        grabguivarsjob(self)
+        QMessageBox.information(
+            self.wmain, 'Done', 'The current settings are the default ones now.')
+
+    def qctdef(self):
+        grabguivarstc(self)
+        QMessageBox.information(
+            self.wmain, 'Done', 'The current settings are the default ones now.')
+
+    def qcgdef(self):
+        grabguivarsgam(self)
+        QMessageBox.information(
+            self.wmain, 'Done', 'The current settings are the default ones now.')
+
+    def qcqdef(self):
+        grabguivarsqch(self)
+        QMessageBox.information(
+            self.wmain, 'Done', 'The current settings are the default ones now.')
+
+    def qcgload(self):
+        name = QFileDialog.getOpenFileName(
+            self.qctWindow, 'Open File', '.', "GAMESS input files")
+        if name[0] != '':
+            with open(name[0], 'r') as f:
+                self.qcgWindow.molf = f.read()
+    # enable QE input
+
+    def enableqeinput(self):
+        if self.chkI.isChecked():
+            self.chkI.state = False
+            self.qcode.setDisabled(False)
+            self.butQc.setDisabled(False)
+            self.chch.setDisabled(False)
+        else:
+            self.qcode.setDisabled(True)
+            self.butQc.setDisabled(True)
+            self.chch.setDisabled(True)
+            self.chkI.state = True
+    # ########################
+    # ### jobscript input ####
+    # ########################
+    # enable Jobscript input
+
+    def enablejinput(self):
+        if self.chkJ.isChecked():
+            self.chkJ.state = False
+            self.scheduler.setDisabled(False)
+            self.butJob.setDisabled(False)
+        else:
+            self.scheduler.setDisabled(True)
+            self.butJob.setDisabled(True)
+            self.chkJ.state = True
+
+    def jobenable(self):
+        self.jWindow.setWindowModality(2)
+        self.jWindow.show()
+    # load file
+
+    def jload(self):
+        name = QFileDialog.getOpenFileName(
+            self.qctWindow, 'Open File', '.', "Jobscript files")
+        if name[0] != '':
+            with open(name[0], 'r') as f:
+                self.jWindow.molf = f.read()
+    # ##############################
+    # ### post-processing input ####
+    # ##############################
+    # enable Post processing input
+
+    def setupp(self):
+        self.pWindow.setWindowModality(2)
+        self.pWindow.show()
+        # check if Multiwfn exists
+        globs = globalvars()
+        cwd = os.getcwd()
+        os.chdir(globs.homedir)
+        inputtxt = '0\n0\n'
+        with open('input1', 'w') as f:
+            f.write(inputtxt)
+        writef = False
+        mwfn = globs.multiwfn
+        cdbdir = globs.chemdbdir
+        if not os.path.isfile(globs.multiwfn[1:-1]):
+            choice = QMessageBox.question(self.pWindow, 'Multiwfn setup',
+                                          'It looks like the Multiwfn '
+                                          'executable is not configured '
+                                          'or does not exist. Would you '
+                                          'like to configure it now?',
+                                          QMessageBox.Yes, QMessageBox.No)
+            if choice == QMessageBox.Yes:
+                QMessageBox.information(
+                    self.pWindow, 'Multiwfn', "Please select the Multiwfn executable.")
+                mwfn = QFileDialog.getOpenFileName(
+                    self.pWindow, 'Select the Multiwfn executable.', '.')
+                if len(mwfn[0]) > 1:
+                    writef = True
+        if writef:
+            with open(globs.homedir+'/.molSimplify', 'w') as f:
+                # f.write("INSTALLDIR="+instdir+'\n')
+                if len(cdbdir) > 0:
+                    f.write("CHEMDBDIR="+cdbdir+'\n')
+                if len(mwfn) > 0:
+                    f.write("MULTIWFN="+mwfn[0]+"\n")
+        newglobs = globalvars()
+        com = newglobs.multiwfn
+        tt = mybash(com + '< input1')
+        os.remove('input1')
+        if 'Multifunctional Wavefunction Analyzer' not in tt:
+            self.pch.setDisabled(True)
+            self.pwfnav.setDisabled(True)
+            self.pcub.setDisabled(True)
+            self.pdeloc.setDisabled(True)
+        os.chdir(cwd)
+    # load directory
+
+    def pdload(self):
+        name = QFileDialog.getExistingDirectory(
+            self.pWindow, 'Select Directory')
+        if len(name) > 0 and name[0] != '':
+            self.etpdir.setText(name)
+    # ##############################
+    # ##### general callbacks ######
+    # ##############################
+    # ## exit application ###
+
+    def qexit(self):
+        choice = QMessageBox.question(self.wmain, 'Exit', 'Are you sure you want to quit?',
+                                      QMessageBox.Yes, QMessageBox.No)
+        if choice == QMessageBox.Yes:
+            sys.exit()
+        else:
+            pass
+    # hide current widget #
+
+    def qhide(self):
+        self.hide()
+    # close ligands window
+
+    def qcloseligs(self):
+        self.lwindow.hide()
+    # return to main window #
+
+    def qretmain(self):
+        # hide all windows
+        self.qctWindow.hide()
+        self.qcgWindow.hide()
+        self.qcQWindow.hide()
+        self.pWindow.hide()
+        self.jWindow.hide()
+        self.DBWindow.hide()
+        self.cDBWindow.hide()
+        self.geWindow.hide()