diff --git a/Projects/SDView/SDView.py b/Projects/SDView/SDView.py index 8a59af615..577b102c9 100644 --- a/Projects/SDView/SDView.py +++ b/Projects/SDView/SDView.py @@ -22,16 +22,16 @@ _usage=""" """ _welcomeMessage="This is SDView version %s"%(_version) import sys,os,copy -from pyRDKit.RDLogger import logger +from rdkit.RDLogger import logger logger = logger() -from pyRDKit import Chem -from pyRDKit.Chem import AllChem -from pyRDKit.Chem.ChemUtils.AlignDepict import AlignDepict +from rdkit import Chem +from rdkit.Chem import AllChem +from rdkit.Chem.ChemUtils.AlignDepict import AlignDepict from qt import * -from pyRDKit.qtGui import qtUtils -from pyRDKit.qtGui.GuiLib.MolTable import MolTable -from pyRDKit.qtGui.GuiLib.MolCanvas import MolCanvasView -from pyRDKit.qtGui.GuiBase import GuiBase +from rdkit.qtGui import qtUtils +from rdkit.qtGui.GuiLib.MolTable import MolTable +from rdkit.qtGui.GuiLib.MolCanvas import MolCanvasView +from rdkit.qtGui.GuiBase import GuiBase class SDViewTable(MolTable): def __init__(self,*args,**kwargs): @@ -85,14 +85,14 @@ class SDViewGui(GuiBase): def RunGui(suppl,redraw=False,do3D=False,showOnly=None,numberAtoms=False, alignCore=None,alignPatt=None,keepHs=False,matchConf=False): - from pyRDKit.qtGui import Gui + from rdkit.qtGui import Gui app,win = Gui.Launcher(SDViewGui,None,includeLogo=False) widg = win.centralWidget() widg.molCanvas.includeAtomNumbers=numberAtoms processFunc=None if do3D: - from pyRDKit.Chem.PyMol import MolViewer + from rdkit.Chem.PyMol import MolViewer try: pymol = MolViewer() except: @@ -160,7 +160,7 @@ def RunGui(suppl,redraw=False,do3D=False,showOnly=None,numberAtoms=False, # --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- # set up the option parser from optparse import OptionParser -import os,RDConfig +import os parser=OptionParser(_usage,version='%prog '+_version) parser.add_option('--do3D','--3D','--3d','--do3d',default=False,action='store_true', help='display the molecules in 3D using PyMol') @@ -219,7 +219,7 @@ if __name__=='__main__': options.redraw=True if not options.smiles: - from pyRDKit.Chem.FastSDMolSupplier import FastSDMolSupplier + from rdkit.Chem.FastSDMolSupplier import FastSDMolSupplier if args[0] != "-": suppl = FastSDMolSupplier(args[0],removeHs=options.removeHs) else: diff --git a/rdkit/Chem/Draw/spingCanvas.py b/rdkit/Chem/Draw/spingCanvas.py index f22fcfbae..ba3f09977 100644 --- a/rdkit/Chem/Draw/spingCanvas.py +++ b/rdkit/Chem/Draw/spingCanvas.py @@ -4,7 +4,7 @@ # # @@ All Rights Reserved @@ # -from sping import pid +from rdkit.sping import pid import math faceMap={'sans':'helvetica'} diff --git a/rdkit/ML/Cluster/Butina.py b/rdkit/ML/Cluster/Butina.py index bb6370474..ea1f5bddb 100755 --- a/rdkit/ML/Cluster/Butina.py +++ b/rdkit/ML/Cluster/Butina.py @@ -11,13 +11,18 @@ import numpy from rdkit import RDLogger logger=RDLogger.logger() -def ClusterData(data,nPts,distThresh,isDistData=False): +def EuclideanDist(pi,pj): + dv = array(pi)- array(pj) + return numpy.sqrt(dv*dv) + + +def ClusterData(data,nPts,distThresh,isDistData=False,distFunc=EuclideanDist): """ clusters the data points passed in and returns the list of clusters **Arguments** - - data: a list of lists (or array, or whatever) with the input - data (see discussion of _isDistData_ argument for the exception) + - data: a list of items with the input data + (see discussion of _isDistData_ argument for the exception) - nPts: the number of points to be used @@ -32,6 +37,9 @@ def ClusterData(data,nPts,distThresh,isDistData=False): for i in range(nPts): for j in range(i): dists.append( distfunc(i,j) ) + + - distFunc: a function to calculate distances between points. + Receives 2 points as arguments, should return a float **Returns** @@ -43,7 +51,6 @@ def ClusterData(data,nPts,distThresh,isDistData=False): The first element for each cluster is its centroid. """ - data = numpy.array(data) if isDistData and len(data)>(nPts*(nPts-1)/2): logger.warning("Distance matrix is too long") nbrLists = [None]*nPts @@ -53,12 +60,10 @@ def ClusterData(data,nPts,distThresh,isDistData=False): for i in range(nPts): for j in range(i): if not isDistData: - dv = data[i]-data[j] - dij = numpy.sqrt(dv*dv) + dij = distFunc(data[i],data[j]) else: dij = data[dmIdx] dmIdx+=1 - #print i,j,dij if dij<=distThresh: nbrLists[i].append(j) nbrLists[j].append(i) diff --git a/rdkit/ML/Descriptors/MoleculeDescriptors.py b/rdkit/ML/Descriptors/MoleculeDescriptors.py index 69e29b5d5..f7d257cb5 100755 --- a/rdkit/ML/Descriptors/MoleculeDescriptors.py +++ b/rdkit/ML/Descriptors/MoleculeDescriptors.py @@ -32,9 +32,23 @@ class MolecularDescriptorCalculator(Descriptors.DescriptorCalculator): a list of strings which are keys into _AvailDescriptors.descDict_ """ - self.simpleList = simpleList[:] - self.descriptorNames = self.simpleList[:] + self.simpleList = tuple(simpleList) + self.descriptorNames = tuple(self.simpleList) self.compoundList = None + self._findVersions() + + def _findVersions(self): + """ returns a tuple of the versions of the descriptor calculators + + """ + self.descriptorVersions=[] + for nm in self.simpleList: + vers='N/A' + if AvailDescriptors.descDict.has_key(nm): + fn = AvailDescriptors.descDict[nm] + if hasattr(fn,'version'): + vers = fn.version + self.descriptorVersions.append(vers) def SaveState(self,fileName): """ Writes this calculator off to a file so that it can be easily loaded later @@ -78,7 +92,7 @@ class MolecularDescriptorCalculator(Descriptors.DescriptorCalculator): """ returns a tuple of the names of the descriptors this calculator generates """ - return tuple(self.descriptorNames) + return self.descriptorNames def GetDescriptorSummaries(self): """ returns a tuple of summaries for the descriptors this calculator generates @@ -109,13 +123,5 @@ class MolecularDescriptorCalculator(Descriptors.DescriptorCalculator): """ returns a tuple of the versions of the descriptor calculators """ - res = [] - for nm in self.simpleList: - fn = AvailDescriptors.descDict.get(nm,lambda x:777) - if hasattr(fn,'version'): - vers = fn.version - else: - vers="N/A" - res.append(vers) - return tuple(res) + return tuple(self.descriptorVersions) diff --git a/rdkit/ML/Descriptors/UnitTestMolDescriptors.py b/rdkit/ML/Descriptors/UnitTestMolDescriptors.py index 0ebc41430..449f63c85 100755 --- a/rdkit/ML/Descriptors/UnitTestMolDescriptors.py +++ b/rdkit/ML/Descriptors/UnitTestMolDescriptors.py @@ -14,6 +14,7 @@ from rdkit import Chem class TestCase(unittest.TestCase): def setUp(self): self.descs = ['MolLogP','Chi1v'] + self.vers= ('1.1.0','1.0.0') self.calc = MoleculeDescriptors.MolecularDescriptorCalculator(self.descs) self.testD = [ ('CCOC', (0.6527, 1.40403)), @@ -21,14 +22,14 @@ class TestCase(unittest.TestCase): ('CCC(=O)O',(0.481, 1.48839))] def testGetNames(self): - assert self.calc.GetDescriptorNames()==tuple(self.descs),'bad descriptor names: %s'%(self.calc.GetDescriptorNames()) + self.failUnlessEqual(self.calc.GetDescriptorNames(),tuple(self.descs)) def _testVals(self,calc,testD): for smi,vals in testD: mol = Chem.MolFromSmiles(smi) ans = numpy.array(vals) res = numpy.array(calc.CalcDescriptors(mol)) - assert max(abs(res-ans))<1e-4,'bad descriptor values for SMILES %s (%s)'%(smi,str(res)) + self.failUnless(max(abs(res-ans))<1e-4,'bad descriptor values for SMILES %s (%s)'%(smi,str(res))) def testCalcVals(self): self._testVals(self.calc,self.testD) @@ -48,7 +49,8 @@ class TestCase(unittest.TestCase): assert ok,'problems reading saved file %s'%(fName) - assert calc.GetDescriptorNames()==tuple(self.descs),'bad descriptor names' + self.failUnlessEqual(calc.GetDescriptorNames(),tuple(self.descs)) + self.failUnlessEqual(calc.GetDescriptorVersions(),tuple(self.vers)) self._testVals(calc,self.testD) diff --git a/rdkit/ML/Descriptors/test_data/molcalc.dsc b/rdkit/ML/Descriptors/test_data/molcalc.dsc index b2d64acae..3234618e2 100755 --- a/rdkit/ML/Descriptors/test_data/molcalc.dsc +++ b/rdkit/ML/Descriptors/test_data/molcalc.dsc @@ -4,16 +4,21 @@ p1 (dp2 S'simpleList' p3 -(lp4 -S'MolLogP' +(S'MolLogP' +p4 +S'Chi1v' p5 -aS'Chi1v' -p6 -asS'descriptorNames' +tp6 +sS'descriptorVersions' p7 (lp8 -g5 -ag6 -asS'compoundList' +S'1.1.0' p9 -Nsb. \ No newline at end of file +aS'1.0.0' +p10 +asS'descriptorNames' +p11 +g6 +sS'compoundList' +p12 +Nsb. diff --git a/rdkit/qtGui/DbConnDialog.py b/rdkit/qtGui/DbConnDialog.py index 6abcd61ae..66691f5d6 100755 --- a/rdkit/qtGui/DbConnDialog.py +++ b/rdkit/qtGui/DbConnDialog.py @@ -5,10 +5,10 @@ """ dialog for establishing db connections """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * -from pyRDKit.qtGui.DbConnWidgetImpl import insertConnWidget -from pyRDKit.qtGui.DbDialog import DbDialog +from rdkit.qtGui.DbConnWidgetImpl import insertConnWidget +from rdkit.qtGui.DbDialog import DbDialog class DbConnDialog(DbDialog): diff --git a/rdkit/qtGui/DbConnWidgetImpl.py b/rdkit/qtGui/DbConnWidgetImpl.py index 5cd6f76ed..30c56775a 100755 --- a/rdkit/qtGui/DbConnWidgetImpl.py +++ b/rdkit/qtGui/DbConnWidgetImpl.py @@ -5,12 +5,12 @@ """ implementation bits for DbConnWidgets """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * -from pyRDKit.qtGui.forms.DbConnWidget import DbConnWidget as _Form -from pyRDKit.qtGui import DbWidget +from rdkit.qtGui.forms.DbConnWidget import DbConnWidget as _Form +from rdkit.qtGui import DbWidget import os,os.path -from pyRDKit.Dbase import DbConnection +from rdkit.Dbase import DbConnection def insertConnWidget(parent,*args,**kwargs): diff --git a/rdkit/qtGui/DbDialog.py b/rdkit/qtGui/DbDialog.py index f5467a583..e68b764a9 100755 --- a/rdkit/qtGui/DbDialog.py +++ b/rdkit/qtGui/DbDialog.py @@ -5,7 +5,7 @@ """ contains simple dialog box for holding db widgets """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * class DbDialog(QDialog): diff --git a/rdkit/qtGui/DbQueryDialog.py b/rdkit/qtGui/DbQueryDialog.py index 59a89a83b..ac2c9e94e 100755 --- a/rdkit/qtGui/DbQueryDialog.py +++ b/rdkit/qtGui/DbQueryDialog.py @@ -6,10 +6,10 @@ """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * -from pyRDKit.qtGui.DbQueryWidgetImpl import insertQueryWidget -from pyRDKit.qtGui.DbDialog import DbDialog +from rdkit.qtGui.DbQueryWidgetImpl import insertQueryWidget +from rdkit.qtGui.DbDialog import DbDialog class DbQueryDialog(DbDialog): """ dialog for establishing db connections diff --git a/rdkit/qtGui/DbQueryWidgetImpl.py b/rdkit/qtGui/DbQueryWidgetImpl.py index ee9ac53ed..d66dd955d 100755 --- a/rdkit/qtGui/DbQueryWidgetImpl.py +++ b/rdkit/qtGui/DbQueryWidgetImpl.py @@ -5,13 +5,13 @@ """ implementation bits for DbQueryWidgets """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * -from pyRDKit.qtGui.forms.DbQueryWidget import DbQueryWidget as _Form -from pyRDKit.qtGui.forms.ListSelectorDialog import ListSelectorDialog -from pyRDKit.qtGui import DbWidget +from rdkit.qtGui.forms.DbQueryWidget import DbQueryWidget as _Form +from rdkit.qtGui.forms.ListSelectorDialog import ListSelectorDialog +from rdkit.qtGui import DbWidget import os,os.path -from pyRDKit.Dbase import DbConnection +from rdkit.Dbase import DbConnection def insertQueryWidget(parent,*args,**kwargs): @@ -112,7 +112,7 @@ class DbQueryWidget(DbWidget.DbWidgetMixin,_Form): if __name__ == '__main__': # build the app and widget import os - from pyRDKit.qtGui import Gui + from rdkit.qtGui import Gui app,widg = Gui.Launcher(DbQueryWidget,None) app.exec_loop() diff --git a/rdkit/qtGui/DbWidget.py b/rdkit/qtGui/DbWidget.py index 8c291cfdb..0db225f90 100755 --- a/rdkit/qtGui/DbWidget.py +++ b/rdkit/qtGui/DbWidget.py @@ -5,11 +5,11 @@ """ contains a mixin class for the various Database widgets """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * import os,os.path -from pyRDKit.Dbase import DbConnection -from pyRDKit.qtGui.qtUtils import logger +from rdkit.Dbase import DbConnection +from rdkit.qtGui.qtUtils import logger def insertDbWidget(parent,klass,*args,**kwargs): """ constructs a widget and inserts it into a parent widget @@ -162,7 +162,7 @@ class DbWidgetMixin: def getDbName(self): if not RDConfig.usePgSQL: return None - from pyRDKit.Dbase import DbInfo + from rdkit.Dbase import DbInfo names = QStringList.fromStrList(DbInfo.GetDbNames()) res,ok = QInputDialog.getItem('Select Database','Select Database',names,0,False) diff --git a/rdkit/qtGui/Gui.py b/rdkit/qtGui/Gui.py index 9e402f686..cbda5c5f2 100755 --- a/rdkit/qtGui/Gui.py +++ b/rdkit/qtGui/Gui.py @@ -6,10 +6,10 @@ """ Mixin GUI launcher code """ import qt import os.path -from pyRDKit import qtGui -from pyRDKit.qtGui import qtUtils +from rdkit import qtGui +from rdkit.qtGui import qtUtils -from pyRDKit import RDConfig +from rdkit import RDConfig lookHere = [os.path.join(RDConfig.RDCodeDir,'qtGui/VisProg'), os.path.join(RDConfig.RDCodeDir,'qtGui/MixIns'), '.'] @@ -18,7 +18,7 @@ def StandardGui(args,**kwargs): """ launches a standard mixin GUI """ - from pyRDKit.mixins import Loader + from rdkit.mixins import Loader loadOrder = [] loadedMixIns=Loader.LoadMixIns(args,loadOrder, lookHere) diff --git a/rdkit/qtGui/GuiBase.py b/rdkit/qtGui/GuiBase.py index 5e30602cc..1f4525290 100755 --- a/rdkit/qtGui/GuiBase.py +++ b/rdkit/qtGui/GuiBase.py @@ -6,14 +6,14 @@ """ base class for the main window in the qt MixinGui """ -from pyRDKit import RDConfig +from rdkit import RDConfig import qt -from pyRDKit.qtGui import GuiShell,GuiTextViewer +from rdkit.qtGui import GuiShell,GuiTextViewer try: - from pyRDKit.qtGui import rpcClient + from rdkit.qtGui import rpcClient except: rpcClient=None -from pyRDKit.qtGui import qtUtils +from rdkit.qtGui import qtUtils class GuiBase(qt.QMainWindow): """ Base class for the qt MixinGui diff --git a/rdkit/qtGui/GuiLib/MolCanvas.py b/rdkit/qtGui/GuiLib/MolCanvas.py index bf3f010c1..6e351f8bb 100644 --- a/rdkit/qtGui/GuiLib/MolCanvas.py +++ b/rdkit/qtGui/GuiLib/MolCanvas.py @@ -3,20 +3,20 @@ # Copyright (C) 2005-2006 Rational Discovery LLC # All Rights Reserved # -import RDConfig +from rdkit import RDConfig from qt import * from qtcanvas import * -from qtGui.PiddleWindowImpl import PiddleCanvasView -from Chem.Draw import MolDrawing +from rdkit.qtGui.PiddleWindowImpl import PiddleCanvasView +from rdkit.Chem.Draw import MolDrawing MolDrawing.registerCanvas('sping') import cPickle,os,copy,types -import Chem -from Chem import rdDepictor +from rdkit import Chem +from rdkit.Chem import rdDepictor -from Logger import Logger -from sping.Qt.pidQt import QtCanvas as Canvas -from sping.Qt import pidQt +from rdkit.Logger import Logger +from rdkit.sping.Qt.pidQt import QtCanvas as Canvas +from rdkit.sping.Qt import pidQt import traceback class PickModes: @@ -247,7 +247,7 @@ class MolCanvasView(PiddleCanvasView): if __name__ == '__main__': import sys,getopt - from qtGui import Gui + from rdkit.qtGui import Gui app,widg = Gui.Launcher(MolCanvasView,None,interactive=True) diff --git a/rdkit/qtGui/GuiLib/MolTable.py b/rdkit/qtGui/GuiLib/MolTable.py index 252a29437..830f9b1ee 100755 --- a/rdkit/qtGui/GuiLib/MolTable.py +++ b/rdkit/qtGui/GuiLib/MolTable.py @@ -6,21 +6,21 @@ """ defines classes required for using molecules in QTables """ -import RDConfig -import Chem -from Chem import AllChem -from Chem import rdDepictor +from rdkit import RDConfig +from rdkit import Chem +from rdkit.Chem import AllChem +from rdkit.Chem import rdDepictor from qt import * from qttable import * -from utils.PilTools import PilImgToQPixmap -from qtGui import GuiTable,qtUtils +from rdkit.utils.PilTools import PilImgToQPixmap +from rdkit.qtGui import GuiTable,qtUtils import copy tryChemdraw=False hasCDX=0 if tryChemdraw: try: - from utils import chemdraw + from rdkit.utils import chemdraw except ImportError: hasCDX=0 else: @@ -31,7 +31,7 @@ if tryChemdraw: else: hasCDX=1 try: - from utils import chemdraw_qax + from rdkit.utils import chemdraw_qax except ImportError: hasCDX_ax=0 else: @@ -41,7 +41,7 @@ if tryChemdraw: hasCDX_ax=0 else: hasCDX_ax=1 -from utils import PilTools +from rdkit.utils import PilTools import StringIO,types drawInChemdraw=1 @@ -164,8 +164,8 @@ class MolTableItem(QTableItem): if not where.isVisible(): where.show() def toImage(self,fName=None,size=(100,100),fontSize=12,lineWidth=.5): - from Chem.Draw.MolDrawing import MolDrawing - from sping.ReportLab.pidReportLab import RLCanvas as Canvas + from rdkit.Chem.Draw.MolDrawing import MolDrawing + from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas canv = Canvas(size) d = MolDrawing(canvas=canv) d.atomLabelFontSize=fontSize @@ -277,7 +277,7 @@ class MolTable(GuiTable.GuiTable): def contentsToPDF(self,fName=None,skipCols=None,replaceMolName=0,sketchWidth=1.5): - from Reports import PDFReport, ReportUtils + from rdkit.Reports import PDFReport, ReportUtils from cStringIO import StringIO import os @@ -742,54 +742,3 @@ class MolTable(GuiTable.GuiTable): if itms: popup.exec_loop(pos) - - -def test1(): - import os - # start out by grabbing some data: - from Dbase.DbConnection import DbConnect - from Chem.Suppliers.DbMolSupplier import RandomAccessDbMolSupplier - from Chem.Suppliers.DbMolSupplier import ForwardDbMolSupplier - dbName = os.path.join(RDConfig.RDCodeDir,'qtGui','GuiLib','demoData','data.gdb') - conn = DbConnect(dbName,'some_mols_dupes') - data = conn.GetData() - if 1: - mols = RandomAccessDbMolSupplier(data) - else: - mols = ForwardDbMolSupplier(data) - - - # build the app and widget - from qtGui import Gui - app,widg = Gui.Launcher(MolTable,None) - - # and load up those molecules: - widg.loadFromMolSupplier(mols,includeCheckboxes=0) - - w = Chem.SmilesWriter('foob.txt',delimiter='\t',nameHeader="Mol_ID") - widg.exportToMolWriter(w) - - app.exec_loop() - widg.destroy(1) - -def test2(): - import os - # start out by grabbing some data: - from VLib.NodeLib import DbMolSupply - dbName = os.path.join(RDConfig.RDCodeDir,'qtGui','GuiLib','demoData','data.gdb') - node = DbMolSupply.GetNode(dbName,'some_mols_dupes') - - # build the app and widget - from qtGui import Gui - app,widg = Gui.Launcher(MolTable,None) - - # and load up those molecules: - widg.loadFromVLib(node,includeCheckboxes=0) - - app.exec_loop() - widg.destroy(1) - -if __name__ == '__main__': - #test1() - test2() - diff --git a/rdkit/qtGui/GuiShell.py b/rdkit/qtGui/GuiShell.py index 5443f725d..8ace2e404 100755 --- a/rdkit/qtGui/GuiShell.py +++ b/rdkit/qtGui/GuiShell.py @@ -8,7 +8,7 @@ import sys from qt import * -from pyRDKit.qtGui.forms.pyshell import PyShell as _Form +from rdkit.qtGui.forms.pyshell import PyShell as _Form from code import InteractiveInterpreter class PyShell(_Form,InteractiveInterpreter): diff --git a/rdkit/qtGui/GuiTable.py b/rdkit/qtGui/GuiTable.py index 7b2c33f5f..9167745c6 100755 --- a/rdkit/qtGui/GuiTable.py +++ b/rdkit/qtGui/GuiTable.py @@ -6,16 +6,16 @@ """ defines classes to make QTables more useful for us """ -from pyRDKit import RDConfig +from rdkit import RDConfig from qt import * from qttable import * -from pyRDKit.qtGui.DbConnDialog import DbConnDialog -from pyRDKit.qtGui.qtUtils import logger +from rdkit.qtGui.DbConnDialog import DbConnDialog +from rdkit.qtGui.qtUtils import logger try: from cStringIO import StringIO except ImportError: from StringIO import StringIO -from pyRDKit.Dbase import DbUtils +from rdkit.Dbase import DbUtils import types diff --git a/rdkit/qtGui/GuiTextViewer.py b/rdkit/qtGui/GuiTextViewer.py index 28de32e37..45cac63ed 100755 --- a/rdkit/qtGui/GuiTextViewer.py +++ b/rdkit/qtGui/GuiTextViewer.py @@ -8,8 +8,8 @@ """ import sys from qt import * -from pyRDKit.qtGui.forms.TextViewer import TextViewer as _Form -from pyRDKit.qtGui.qtUtils import warning,error +from rdkit.qtGui.forms.TextViewer import TextViewer as _Form +from rdkit.qtGui.qtUtils import warning,error class GuiTextViewer(_Form): """ a class for displaying rich text diff --git a/rdkit/qtGui/PiddleWindowImpl.py b/rdkit/qtGui/PiddleWindowImpl.py index c3bbb26da..94d17ff1d 100755 --- a/rdkit/qtGui/PiddleWindowImpl.py +++ b/rdkit/qtGui/PiddleWindowImpl.py @@ -9,15 +9,15 @@ this class handles interaction """ -from pyRDKit import RDConfig +from rdkit import RDConfig import qt import qtcanvas -from pyRDKit.qtGui.forms.PiddleWindow import PiddleWindow as _Form -from pyRDKit.qtGui import qtUtils -from pyRDKit.sping.Qt.pidQt import QtCanvas as Canvas +from rdkit.qtGui.forms.PiddleWindow import PiddleWindow as _Form +from rdkit.qtGui import qtUtils +from rdkit.sping.Qt.pidQt import QtCanvas as Canvas import os.path -from pyRDKit.Logger import Logger +from rdkit.Logger import Logger class PiddleCanvasView(qtcanvas.QCanvasView): """ The actual canvas view which is displayed to the user @@ -299,7 +299,7 @@ class PiddleWindow(_Form): def resizeEvent(self,evt): pass if __name__ == '__main__': - from pyRDKit.qtGui import Gui + from rdkit.qtGui import Gui app,widg = Gui.Launcher(PiddleWindow,None) widg.resize(640,480) diff --git a/rdkit/qtGui/qtUtils.py b/rdkit/qtGui/qtUtils.py index b21c524a9..78c2d8beb 100755 --- a/rdkit/qtGui/qtUtils.py +++ b/rdkit/qtGui/qtUtils.py @@ -3,10 +3,10 @@ # Copyright (C) 2002-2005 Greg Landrum and Rational Discovery LLC # All Rights Reserved # -from pyRDKit import RDConfig +from rdkit import RDConfig import qt import os.path -from pyRDKit.sping.utils import availableCanvases +from rdkit.sping.utils import availableCanvases import sys logoImageData=[ @@ -49,7 +49,7 @@ if 0: logger.addHandler(hdlr) logger.setLevel(logging.DEBUG) else: - import pyRDKit.RDLogger as logging + import rdkit.RDLogger as logging def _initLogger(): global logger logger = logging.logger() diff --git a/rdkit/sping/Qt/pidQt.py b/rdkit/sping/Qt/pidQt.py index 628d3a284..c5f00c8e8 100755 --- a/rdkit/sping/Qt/pidQt.py +++ b/rdkit/sping/Qt/pidQt.py @@ -34,7 +34,7 @@ Greg Landrum (Landrum@RationalDiscovery.com) 29 Octover, 2002 """ -from sping import pid +from rdkit.sping import pid import string, os, types from qt import * from qtcanvas import * diff --git a/rdkit/sping/pid.py b/rdkit/sping/pid.py index ed60b1068..ff04db051 100755 --- a/rdkit/sping/pid.py +++ b/rdkit/sping/pid.py @@ -100,7 +100,7 @@ __version_min_number__ = "0" # should match "12" __version__ = __version_maj_number__ + "." + __version_min_number__ # c.f. "1.0.12" from types import StringType, IntType, InstanceType -from sping.colors import * +from rdkit.sping.colors import * inch = 72 # 1 PIDDLE drawing unit == 1/72 imperial inch cm = inch/2.54 # more sensible measurement unit