Right-click anywhere on this window, and then choose “Set” > “Properties of atoms”. You will obtain a new window (gray by default). Another option would be to select the Geometry/Draw drop down menu. Prepare GABEDIT so that you can draw your lanthanide complexįrom the main menu of Gabedit, click on the "Draw Geometry" icon.
Determine the total charge of your complex.Determine the coordination number of your lanthanide ion in your complex of interest, e.g, 8, 9, 10, 11, 12, etc.
#CHEM DRAW TUTORIAL HOW TO#
Thus, please, download, install, and learn how to use GABEDIT. While you wait for the MOPAC2012 password to arrive (it takes about three days), it is a good idea to practice drawing complexes in GABEDIT. GetDrawingText () return pngĭisplacement of B-Alexa-Fluor647 from CDK2 (un.Ĭyclin-dependent kinase of B-Alexa-Fluor647 from CDK2 (un.Using GABEDIT to draw Lanthanide Complexes and run MOPAC2012 DrawMoleculeWithHighlights ( tmol, legend, dict ( highlightatoms ), dict ( highlightbonds ), atomrads, widthmults ) d2d. clearBackground = False #- # now draw the molecule, with highlights: d2d. GetConformer () for ( aring, color ) in rings : ps = for aidx in aring : pos = Geometry.
useBWAtomPalette () #- # if we are filling rings, go ahead and do that first so that we draw # the molecule on top of the filled rings if fillRings and rings : # a hack to set the molecule scale d2d. MolDraw2DCairo ( width, height ) dos = d2d. append ( color ) widthmults = 2 d2d = rdMolDraw2D. GetBondBetweenAtoms ( oldNewAtomMap, oldNewAtomMap ) bndIdx = origBnd. HasProp ( sourceIdxProperty ): origBnd = tmol. append (( tring, color )) for qbnd in rquery. append ( oldNewAtomMap ) if allFound : rings. HasProp ( sourceIdxProperty ): allFound = False break tring. AtomRings (): tring = allFound = True for aid in aring : at = rquery. append ( color ) atomrads = 0.4 if fillRings : for aring in rinfo. HasProp ( sourceIdxProperty ): origIdx = oldNewAtomMap highlightatoms. GenerateDepictionMatching2DStructure ( tmol, core ) oldNewAtomMap = rings = for i, lbl in enumerate ( lbls ): color = colors GetAtomMapNum ()) # remove unmapped hs so that they don't mess up the depiction rhps = Chem. GetIntProp ( sourceIdxProperty )) if mAt. HasProp ( sourceIdxProperty ): mAt = mol. the atoms connected to this # should be from the molecule for nbr in at. GetProp ( 'dummyLabel' ) = lbl : # attachment point. GetAtomMapNum ())) for lbl in row : if lbl = 'Core' : continue rg = row for at in rg. Mol ( core ) # - # include the atom map numbers in the substructure search in order to # try to ensure a good alignment of the molecule to symmetric cores for at in core. Inhibitory activity against human CDK2 (Cyclin.īinding affinity for human cyclin-dependent ki.Ĭc1ccc2c(c3ccnc(Nc4cccc(c4)C(F)(F)F)n3)c(nn2n1.Ĭc1ccc2c(c3ccnc(Nc4ccc(F)c(F)c4)n3)c(nn2n1)c5c.Ĭc1ccc2c(c3ccnc(Nc4ccc5OCCOc5c4)n3)c(nn2n1)c6c.Ĭc1ccc2c(c3ccnc(Nc4ccc(Cl)c(c4)C(F)(F)F)n3)c(n.įrom collections import defaultdict def highlight_rgroups ( mol, row, core, width = 350, height = 200, fillRings = True, legend = "", sourceIdxProperty = "SourceAtomIdx", lbls = ( 'R1', 'R2', 'R3', 'R4' )): # copy the molecule and core mol = Chem.