# $Id$
#
#  Copyright (C) 2008-2011 Greg Landrum
#
#   @@ All Rights Reserved @@
#  This file is part of the RDKit.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the RDKit source tree.
#
from rdkit import Chem
from rdkit import RDConfig
import numpy
import math
import sys
import copy
import pprint
from rdkit.six import cmp

periodicTable=Chem.GetPeriodicTable()

class Font(object):
  face='sans'
  size='12'
  weight='normal'
  name=None
  def __init__(self,face=None,size=None,name=None,weight=None):
    if face: self.face=face
    if size: self.size=size
    if name: self.name=name
    if weight: self.weight=weight

class DrawingOptions(object):
  dotsPerAngstrom= 30
  useFraction= 0.85
  
  atomLabelFontFace= "sans"
  atomLabelFontSize= 12
  atomLabelMinFontSize= 7

  bondLineWidth= 1.2
  dblBondOffset= .25
  dblBondLengthFrac= .8

  defaultColor= (1,0,0)
  selectColor= (1,0,0)
  bgColor = (1,1,1)

  colorBonds= True
  noCarbonSymbols= True
  includeAtomNumbers= False
  atomNumberOffset= 0
  radicalSymbol= u'\u2219'

  dash= (4,4)

  wedgeDashedBonds= True
  showUnknownDoubleBonds= True

  # used to adjust overall scaling for molecules that have been laid out with non-standard
  # bond lengths
  coordScale= 1.0

  elemDict={
    1:(0.55,0.55,0.55),
    7:(0,0,1),
    8:(1,0,0),
    9:(.2,.8,.8),
    15:(1,.5,0),
    16:(.8,.8,0),
    17:(0,.8,0),
    35:(.5,.3,.1),
    53:(.63,.12,.94),
    0:(.5,.5,.5),
    }

class MolDrawing(object):
  atomPs = None
  canvas = None
  canvasSize = None

  def __init__(self,canvas=None, drawingOptions=None):
    self.canvas = canvas
    if canvas:
      self.canvasSize=canvas.size
    self.atomPs = {}
    if drawingOptions is None:
      self.drawingOptions=DrawingOptions()
    else:
      self.drawingOptions=drawingOptions
    self.boundingBoxes = {}

    if self.drawingOptions.bgColor is not None:
      self.canvas.addCanvasPolygon(((0,0),
                                    (canvas.size[0],0),
                                    (canvas.size[0],canvas.size[1]),
                                    (0,canvas.size[1])),
                                   color=self.drawingOptions.bgColor,
                                   fill=True,stroke=False)

    
  def transformPoint(self,pos):
    res = [0,0]
    res[0] = (pos[0] + self.molTrans[0])*self.currDotsPerAngstrom*self.drawingOptions.useFraction + self.drawingTrans[0]
    res[1] = self.canvasSize[1]-((pos[1] + self.molTrans[1])*self.currDotsPerAngstrom*self.drawingOptions.useFraction + \
                                 self.drawingTrans[1])
    return res
  

  def _getBondOffset(self,p1,p2):
    # get the vector between the points:
    dx = p2[0]-p1[0]
    dy = p2[1]-p1[1]

    # figure out the angle and the perpendicular:
    ang = math.atan2(dy,dx)
    perp = ang + math.pi/2.

    # here's the offset for the parallel bond:
    offsetX = math.cos(perp)*self.drawingOptions.dblBondOffset*self.currDotsPerAngstrom
    offsetY = math.sin(perp)*self.drawingOptions.dblBondOffset*self.currDotsPerAngstrom

    return perp,offsetX,offsetY

  def _getOffsetBondPts(self,p1,p2,
                        offsetX,offsetY,
                        lenFrac=None):
    if not lenFrac:
      lenFrac = self.drawingOptions.dblBondLengthFrac
      
    dx = p2[0]-p1[0]
    dy = p2[1]-p1[1]
    # ----
    # now figure out where to start and end it:
    
    # offset the start point:
    fracP1 = p1[0]+offsetX,p1[1]+offsetY

    # now move a portion of the way along the line to the neighbor:
    frac = (1.-lenFrac)/2
    fracP1 = fracP1[0]+dx*frac,\
             fracP1[1]+dy*frac

    fracP2 = fracP1[0]+dx*lenFrac,\
             fracP1[1]+dy*lenFrac
    return fracP1,fracP2

  def _offsetDblBond(self,p1,p2,bond,a1,a2,conf,dir=1,
                     lenFrac=None):
    perp,offsetX,offsetY = self._getBondOffset(p1,p2)
    offsetX = offsetX*dir
    offsetY = offsetY*dir
    
    # if we're a ring bond, we may need to flip over to the other side:
    if bond.IsInRing():
      bondIdx = bond.GetIdx()
      a1Idx = a1.GetIdx()
      a2Idx = a2.GetIdx()
      # find a ring bond from a1 to an atom other than a2:
      for otherBond in a1.GetBonds():
        if otherBond.GetIdx()!=bondIdx and \
           otherBond.IsInRing():
          sharedRing=False
          for ring in self.bondRings:
            if bondIdx in ring and otherBond.GetIdx() in ring:
              sharedRing=True
              break
          if not sharedRing:
            continue
          a3 = otherBond.GetOtherAtom(a1)
          if a3.GetIdx() != a2Idx:
            p3 = self.transformPoint(conf.GetAtomPosition(a3.GetIdx())*self.drawingOptions.coordScale)
            dx2 = p3[0] - p1[0]
            dy2 = p3[1] - p1[1]
            dotP = dx2*offsetX + dy2*offsetY
            if dotP < 0:
              perp += math.pi
              offsetX = math.cos(perp)*self.drawingOptions.dblBondOffset*self.currDotsPerAngstrom
              offsetY = math.sin(perp)*self.drawingOptions.dblBondOffset*self.currDotsPerAngstrom
            
    fracP1,fracP2 = self._getOffsetBondPts(p1,p2,
                                           offsetX,offsetY,
                                           lenFrac=lenFrac)
    return fracP1,fracP2

  def _getBondAttachmentCoordinates(self, p1, p2, labelSize):
    newpos = [None, None]
    if labelSize != None:
      labelSizeOffset = [labelSize[0][0]/2 + (cmp(p2[0], p1[0]) * labelSize[0][2]), labelSize[0][1]/2]
      if p1[1] == p2[1]:
        newpos[0] = p1[0] + cmp(p2[0], p1[0]) * labelSizeOffset[0]
      else:
        if abs(labelSizeOffset[1] * (p2[0] - p1[0]) / (p2[1] - p1[1])) < labelSizeOffset[0]:
          newpos[0] = p1[0] + cmp(p2[0], p1[0]) * abs(labelSizeOffset[1] * (p2[0] - p1[0]) / (p2[1] - p1[1]))
        else:
          newpos[0] = p1[0] + cmp(p2[0], p1[0]) * labelSizeOffset[0]
      if p1[0] == p2[0]:
        newpos[1] = p1[1] + cmp(p2[1], p1[1]) * labelSizeOffset[1]
      else:
        if abs(labelSizeOffset[0] * (p1[1] - p2[1]) / (p2[0] - p1[0])) < labelSizeOffset[1]:
          newpos[1] = p1[1] + cmp(p2[1], p1[1]) * abs(labelSizeOffset[0] * (p1[1] - p2[1]) / (p2[0] - p1[0]))
        else:
          newpos[1] = p1[1] + cmp(p2[1], p1[1]) * labelSizeOffset[1]
    else:
      newpos = copy.deepcopy(p1)
    return newpos

  def _drawWedgedBond(self,bond,pos,nbrPos,
                      width=None,color=None,
                      dash=None):
    if width is None:
        width = self.drawingOptions.bondLineWidth
    if color is None:
        color = self.drawingOptions.defaultColor
    perp,offsetX,offsetY = self._getBondOffset(pos,nbrPos)
    offsetX *=.75
    offsetY *=.75
    poly = ((pos[0],pos[1]),
            (nbrPos[0]+offsetX,nbrPos[1]+offsetY),
            (nbrPos[0]-offsetX,nbrPos[1]-offsetY))
    #canvas.drawPolygon(poly,edgeColor=color,edgeWidth=1,fillColor=color,closed=1)
    if not dash:
      self.canvas.addCanvasPolygon(poly,color=color)
    elif self.drawingOptions.wedgeDashedBonds and self.canvas.addCanvasDashedWedge:
      self.canvas.addCanvasDashedWedge(poly[0],poly[1],poly[2],color=color)
    else:
      self.canvas.addCanvasLine(pos,nbrPos,linewidth=width*2,color=color,
                    dashes=dash)
    
  def _drawBond(self,bond,atom,nbr,pos,nbrPos,conf,
                width=None,color=None,color2=None,labelSize1=None,labelSize2=None):
    if width is None:
      width = self.drawingOptions.bondLineWidth
    if color is None:
      color = self.drawingOptions.defaultColor
    p1_raw = copy.deepcopy(pos)
    p2_raw = copy.deepcopy(nbrPos)
    newpos = self._getBondAttachmentCoordinates(p1_raw, p2_raw, labelSize1)
    newnbrPos = self._getBondAttachmentCoordinates(p2_raw, p1_raw, labelSize2)
    bType=bond.GetBondType()
    if bType == Chem.BondType.SINGLE:
      bDir = bond.GetBondDir()
      if bDir in (Chem.BondDir.BEGINWEDGE,Chem.BondDir.BEGINDASH):
        # if the bond is "backwards", change the drawing direction:
        if bond.GetBeginAtom().GetChiralTag() in (Chem.ChiralType.CHI_TETRAHEDRAL_CW,
                                                  Chem.ChiralType.CHI_TETRAHEDRAL_CCW):
          p1,p2 = newpos,newnbrPos
          wcolor=color
        else:
          p2,p1 = newpos,newnbrPos
          if color2 is not None:
            wcolor=color2
          else:
            wcolor=self.drawingOptions.defaultColor
        if bDir==Chem.BondDir.BEGINWEDGE:
          self._drawWedgedBond(bond,p1,p2,color=wcolor,width=width)
        elif bDir==Chem.BondDir.BEGINDASH:
          self._drawWedgedBond(bond,p1,p2,color=wcolor,width=width,
                               dash=self.drawingOptions.dash)

      else:
        self.canvas.addCanvasLine(newpos, newnbrPos, linewidth=width, color=color, color2=color2)
    elif bType == Chem.BondType.DOUBLE:
      crossBond = (self.drawingOptions.showUnknownDoubleBonds and \
                     bond.GetStereo() == Chem.BondStereo.STEREOANY)
      if not crossBond and \
            ( bond.IsInRing() or (atom.GetDegree()!=1 and bond.GetOtherAtom(atom).GetDegree()!=1) ):
        self.canvas.addCanvasLine(newpos,newnbrPos,linewidth=width,color=color,color2=color2)
        fp1,fp2 = self._offsetDblBond(newpos,newnbrPos,bond,atom,nbr,conf)
        self.canvas.addCanvasLine(fp1,fp2,linewidth=width,color=color,color2=color2)
      else:
        fp1,fp2 = self._offsetDblBond(newpos,newnbrPos,bond,atom,nbr,conf,dir=.5,
                                      lenFrac=1.0)
        fp3,fp4 = self._offsetDblBond(newpos,newnbrPos,bond,atom,nbr,conf,dir=-.5,
                                      lenFrac=1.0)
        if crossBond:
          fp2,fp4=fp4,fp2
        self.canvas.addCanvasLine(fp1,fp2,linewidth=width,color=color,color2=color2)
        self.canvas.addCanvasLine(fp3,fp4,linewidth=width,color=color,color2=color2)
          
    elif bType == Chem.BondType.AROMATIC:
      self.canvas.addCanvasLine(newpos,newnbrPos,linewidth=width,color=color,color2=color2)
      fp1,fp2 = self._offsetDblBond(newpos,newnbrPos,bond,atom,nbr,conf)
      self.canvas.addCanvasLine(fp1,fp2,linewidth=width,color=color,color2=color2,
                    dash=self.drawingOptions.dash)
    elif bType == Chem.BondType.TRIPLE:
      self.canvas.addCanvasLine(newpos,newnbrPos,linewidth=width,color=color,color2=color2)
      fp1,fp2 = self._offsetDblBond(newpos,newnbrPos,bond,atom,nbr,conf)
      self.canvas.addCanvasLine(fp1,fp2,linewidth=width,color=color,color2=color2)
      fp1,fp2 = self._offsetDblBond(newpos,newnbrPos,bond,atom,nbr,conf,dir=-1)
      self.canvas.addCanvasLine(fp1,fp2,linewidth=width,color=color,color2=color2)
    else:
      self.canvas.addCanvasLine(newpos, newnbrPos, linewidth=width, color=color, color2=color2,
                                dash=(1,2))
      
  def scaleAndCenter(self,mol,conf,coordCenter=False,canvasSize=None,ignoreHs=False):
    if canvasSize is None:
      canvasSize=self.canvasSize
    xAccum = 0
    yAccum = 0
    minX = 1e8
    minY = 1e8
    maxX = -1e8
    maxY = -1e8

    nAts = mol.GetNumAtoms()
    for i in range(nAts):
      if ignoreHs and mol.GetAtomWithIdx(i).GetAtomicNum()==1: continue
      pos = conf.GetAtomPosition(i)*self.drawingOptions.coordScale
      xAccum += pos[0]
      yAccum += pos[1]
      minX = min(minX,pos[0])
      minY = min(minY,pos[1])
      maxX = max(maxX,pos[0])
      maxY = max(maxY,pos[1])

    dx = abs(maxX-minX)
    dy = abs(maxY-minY)
    xSize = dx*self.currDotsPerAngstrom
    ySize = dy*self.currDotsPerAngstrom

    if coordCenter:
      molTrans = -xAccum/nAts,-yAccum/nAts
    else:
      molTrans = -(minX+(maxX-minX)/2),-(minY+(maxY-minY)/2)
    self.molTrans = molTrans

    if xSize>=.95*canvasSize[0]:
      scale = .9*canvasSize[0]/xSize
      xSize*=scale
      ySize*=scale
      self.currDotsPerAngstrom*=scale
      self.currAtomLabelFontSize = max(self.currAtomLabelFontSize*scale,
                                       self.drawingOptions.atomLabelMinFontSize)
    if ySize>=.95*canvasSize[1]:
      scale = .9*canvasSize[1]/ySize
      xSize*=scale
      ySize*=scale
      self.currDotsPerAngstrom*=scale
      self.currAtomLabelFontSize = max(self.currAtomLabelFontSize*scale,
                                       self.drawingOptions.atomLabelMinFontSize)
    drawingTrans = canvasSize[0]/2,canvasSize[1]/2
    self.drawingTrans = drawingTrans

  def _drawLabel(self,label,pos,baseOffset,font,color=None,**kwargs):
    if color is None:
      color = self.drawingOptions.defaultColor
    x1 = pos[0]
    y1 = pos[1]
    labelP = x1,y1
    labelSize = self.canvas.addCanvasText(label,(x1,y1,baseOffset),font,color,**kwargs)
    return labelSize
    
  def AddMol(self,mol,centerIt=True,molTrans=None,drawingTrans=None,
             highlightAtoms=[],confId=-1,flagCloseContactsDist=2,
             highlightMap=None, ignoreHs=False,highlightBonds=[],**kwargs):
    """Set the molecule to be drawn.

    Parameters:
      hightlightAtoms -- list of atoms to highlight (default [])
      highlightMap -- dictionary of (atom, color) pairs (default None)

    Notes:
      - specifying centerIt will cause molTrans and drawingTrans to be ignored
    """
    conf = mol.GetConformer(confId)
    if 'coordScale' in kwargs:
      self.drawingOptions.coordScale=kwargs['coordScale']

    self.currDotsPerAngstrom=self.drawingOptions.dotsPerAngstrom
    self.currAtomLabelFontSize=self.drawingOptions.atomLabelFontSize
    if centerIt:
      self.scaleAndCenter(mol,conf,ignoreHs=ignoreHs)
    else:
      if molTrans is None:
        molTrans = (0,0)
      self.molTrans = molTrans
      if drawingTrans is None:
        drawingTrans = (0,0)
      self.drawingTrans = drawingTrans

    font = Font(face=self.drawingOptions.atomLabelFontFace,size=self.currAtomLabelFontSize)

    obds=None
    if not mol.HasProp('_drawingBondsWedged'):
      # this is going to modify the molecule, get ready to undo that
      obds=[x.GetBondDir() for x in mol.GetBonds()]
      Chem.WedgeMolBonds(mol,conf)
      
    includeAtomNumbers = kwargs.get('includeAtomNumbers',self.drawingOptions.includeAtomNumbers)
    self.atomPs[mol] = {}
    self.boundingBoxes[mol] = [0]*4
    self.activeMol = mol
    self.bondRings = mol.GetRingInfo().BondRings()
    labelSizes = {}
    for atom in mol.GetAtoms():
      labelSizes[atom.GetIdx()] = None
      if ignoreHs and atom.GetAtomicNum()==1:
        drawAtom=False
      else:
        drawAtom=True
      idx = atom.GetIdx()
      pos = self.atomPs[mol].get(idx,None)
      if pos is None:
        pos = self.transformPoint(conf.GetAtomPosition(idx)*self.drawingOptions.coordScale)
        self.atomPs[mol][idx] = pos
        if drawAtom:
          self.boundingBoxes[mol][0]=min(self.boundingBoxes[mol][0],pos[0])
          self.boundingBoxes[mol][1]=min(self.boundingBoxes[mol][1],pos[1])
          self.boundingBoxes[mol][2]=max(self.boundingBoxes[mol][2],pos[0])
          self.boundingBoxes[mol][3]=max(self.boundingBoxes[mol][3],pos[1])

      if not drawAtom: continue
      nbrSum = [0,0]
      for bond in atom.GetBonds():
        nbr = bond.GetOtherAtom(atom)
        if ignoreHs and nbr.GetAtomicNum()==1: continue
        nbrIdx = nbr.GetIdx()
        if nbrIdx > idx:
          nbrPos = self.atomPs[mol].get(nbrIdx,None)
          if nbrPos is None:
            nbrPos = self.transformPoint(conf.GetAtomPosition(nbrIdx)*self.drawingOptions.coordScale)
            self.atomPs[mol][nbrIdx] = nbrPos
            self.boundingBoxes[mol][0]=min(self.boundingBoxes[mol][0],nbrPos[0])
            self.boundingBoxes[mol][1]=min(self.boundingBoxes[mol][1],nbrPos[1])
            self.boundingBoxes[mol][2]=max(self.boundingBoxes[mol][2],nbrPos[0])
            self.boundingBoxes[mol][3]=max(self.boundingBoxes[mol][3],nbrPos[1])
            
        else:
          nbrPos = self.atomPs[mol][nbrIdx]
        nbrSum[0] += nbrPos[0]-pos[0]
        nbrSum[1] += nbrPos[1]-pos[1]
  
      iso = atom.GetIsotope()

      labelIt= not self.drawingOptions.noCarbonSymbols or \
               atom.GetAtomicNum()!=6 or \
               atom.GetFormalCharge()!=0 or \
               atom.GetNumRadicalElectrons() or \
               includeAtomNumbers or \
               iso or \
               atom.HasProp('molAtomMapNumber') or \
               atom.GetDegree()==0
      orient=''
      if labelIt:
        baseOffset = 0
        if includeAtomNumbers:
          symbol = str(atom.GetIdx())
          symbolLength = len(symbol)
        else:
          base = atom.GetSymbol()
          symbolLength = len(base)  
          nHs = atom.GetTotalNumHs()
          if nHs>0:
            if nHs>1:
              hs='H<sub>%d</sub>'%nHs
              symbolLength += 1 + len(str(nHs))
            else:
              hs ='H'
              symbolLength += 1
          else:
            hs = ''
          chg = atom.GetFormalCharge()
          if chg!=0:
            if chg==1:
              chg = '+'
            elif chg==-1:
              chg = '-'
            elif chg>1:
              chg = '+%d'%chg
            elif chg<-1:
              chg = '-%d'%chg
            symbolLength += len(chg) 
          else:
            chg = ''
          if chg:
            chg = '<sup>%s</sup>'%chg

          if atom.GetNumRadicalElectrons():
            rad = self.drawingOptions.radicalSymbol*atom.GetNumRadicalElectrons()
            rad = '<sup>%s</sup>'%rad
            symbolLength += atom.GetNumRadicalElectrons()
          else:
            rad = ''

          isotope=''
          isotopeLength = 0
          if iso:
            isotope='<sup>%d</sup>'%atom.GetIsotope()
            isotopeLength = len(str(atom.GetIsotope()))
            symbolLength += isotopeLength
          mapNum=''
          mapNumLength = 0
          if atom.HasProp('molAtomMapNumber'):
            mapNum=':'+atom.GetProp('molAtomMapNumber')
            mapNumLength = 1 + len(str(atom.GetProp('molAtomMapNumber')))
            symbolLength += mapNumLength
          deg = atom.GetDegree()
          # This should be done in a better way in the future:
          # 'baseOffset' should be determined by getting the size of 'isotope' and the size of 'base', or the size of 'mapNum' and the size of 'base'
          # (depending on 'deg' and 'nbrSum[0]') in order to determine the exact position of the base
          if deg==0:
            if periodicTable.GetElementSymbol(atom.GetAtomicNum()) in ('O','S','Se','Te','F','Cl','Br','I','At'):
              symbol = '%s%s%s%s%s%s'%(hs,isotope,base,chg,rad,mapNum)
            else:
              symbol = '%s%s%s%s%s%s'%(isotope,base,hs,chg,rad,mapNum)
          elif deg>1 or nbrSum[0]<1:
            symbol = '%s%s%s%s%s%s'%(isotope,base,hs,chg,rad,mapNum)
            baseOffset = 0.5 - (isotopeLength + len(base) / 2.) / symbolLength
          else:
            symbol = '%s%s%s%s%s%s'%(rad,chg,hs,isotope,base,mapNum)
            baseOffset = -0.5 + (mapNumLength + len(base) / 2.) / symbolLength
          if deg==1:
            if abs(nbrSum[1])>1:
              islope=nbrSum[0]/abs(nbrSum[1])
            else:
              islope=nbrSum[0]
            if abs(islope)>.3:
              if islope>0:
                orient='W'
              else:
                orient='E'
            elif abs(nbrSum[1])>10:
              if nbrSum[1]>0:
                orient='N'
              else :
                orient='S'
          else:
            orient = 'C'
        if highlightMap and idx in highlightMap:
          color = highlightMap[idx]
        elif highlightAtoms and idx in highlightAtoms:
          color = self.drawingOptions.selectColor
        else:
          color = self.drawingOptions.elemDict.get(atom.GetAtomicNum(),(0,0,0))
        labelSize = self._drawLabel(symbol, pos, baseOffset, font, color=color,orientation=orient)
        labelSizes[atom.GetIdx()] = [labelSize, orient]

    for bond in mol.GetBonds():
          atom, idx = bond.GetBeginAtom(), bond.GetBeginAtomIdx()
          nbr, nbrIdx = bond.GetEndAtom(), bond.GetEndAtomIdx()
          pos = self.atomPs[mol].get(idx,None)
          nbrPos = self.atomPs[mol].get(nbrIdx,None)
          if highlightBonds and bond.GetIdx() in highlightBonds:
            width=2.0*self.drawingOptions.bondLineWidth
            color = self.drawingOptions.selectColor
            color2 = self.drawingOptions.selectColor
          elif highlightAtoms and idx in highlightAtoms and nbrIdx in highlightAtoms:
            width=2.0*self.drawingOptions.bondLineWidth
            color = self.drawingOptions.selectColor
            color2 = self.drawingOptions.selectColor
          elif highlightMap is not None and idx in highlightMap and nbrIdx in highlightMap:
            width=2.0*self.drawingOptions.bondLineWidth
            color = highlightMap[idx]
            color2 = highlightMap[nbrIdx]
          else:
            width=self.drawingOptions.bondLineWidth
            if self.drawingOptions.colorBonds:
              color = self.drawingOptions.elemDict.get(atom.GetAtomicNum(),(0,0,0))
              color2 = self.drawingOptions.elemDict.get(nbr.GetAtomicNum(),(0,0,0))
            else:
              color = self.drawingOptions.defaultColor
              color2= color
          self._drawBond(bond,atom,nbr,pos,nbrPos,conf,
                           color=color,width=width,color2=color2,labelSize1=labelSizes[idx],labelSize2=labelSizes[nbrIdx])
  
    # if we modified the bond wedging state, undo those changes now
    if obds:
      for i,d in enumerate(obds):
        mol.GetBondWithIdx(i).SetBondDir(d)
      
      
    if flagCloseContactsDist>0:
      tol = flagCloseContactsDist*flagCloseContactsDist
      for i,atomi in enumerate(mol.GetAtoms()):
        pi = numpy.array(self.atomPs[mol][i])
        for j in range(i+1,mol.GetNumAtoms()):
          pj = numpy.array(self.atomPs[mol][j])
          d = pj-pi
          dist2 = d[0]*d[0]+d[1]*d[1]
          if dist2<=tol:
            self.canvas.addCanvasPolygon(((pi[0]-2*flagCloseContactsDist,
                                      pi[1]-2*flagCloseContactsDist),
                                     (pi[0]+2*flagCloseContactsDist,
                                      pi[1]-2*flagCloseContactsDist),
                                     (pi[0]+2*flagCloseContactsDist,
                                      pi[1]+2*flagCloseContactsDist),
                                     (pi[0]-2*flagCloseContactsDist,
                                      pi[1]+2*flagCloseContactsDist)),
                             color=(1.,0,0),
                             fill=False,stroke=True)
