From dab18279dcc3a47b0e1b10adb222e16673a6c6a5 Mon Sep 17 00:00:00 2001 From: Greg Landrum Date: Sun, 22 Feb 2015 04:57:02 +0100 Subject: [PATCH] update docs as part of #432 --- Docs/Book/RDKit_Book.rst | 26 +++++++++++++++++++++++++- Docs/Book/images/picture_10.png | Bin 0 -> 3300 bytes Docs/Book/images/picture_11.png | Bin 0 -> 3263 bytes 3 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 Docs/Book/images/picture_10.png create mode 100644 Docs/Book/images/picture_11.png diff --git a/Docs/Book/RDKit_Book.rst b/Docs/Book/RDKit_Book.rst index 46744fa90..a46c0c6f6 100644 --- a/Docs/Book/RDKit_Book.rst +++ b/Docs/Book/RDKit_Book.rst @@ -20,7 +20,6 @@ The rules are relatively straightforward. Aromaticity is a property of atoms and bonds in rings. An aromatic bond must be between aromatic atoms, but a bond between aromatic atoms does not need to be aromatic. - For example the fusing bonds here are not considered to be aromatic by the RDKit: .. image:: images/picture_9.png @@ -83,6 +82,31 @@ True >>> m.GetBondBetweenAtoms(6,7).GetIsAromatic() False +A special case, heteroatoms with radicals are not considered candidates for aromaticity: + +.. image:: images/picture_10.png + +>>> m = Chem.MolFromSmiles('C1=C[N]C=C1') +>>> m.GetAtomWithIdx(0).GetIsAromatic() +False +>>> m.GetAtomWithIdx(2).GetIsAromatic() +False +>>> m.GetAtomWithIdx(2).GetNumRadicalElectrons() +1 + +Carbons with radicals, however, are still considered: + +.. image:: images/picture_11.png + +>>> m = Chem.MolFromSmiles('C1=[C]NC=C1') +>>> m.GetAtomWithIdx(0).GetIsAromatic() +True +>>> m.GetAtomWithIdx(1).GetIsAromatic() +True +>>> m.GetAtomWithIdx(1).GetNumRadicalElectrons() +1 + + **Note:** For reasons of computation expediency, aromaticity perception is only done for fused-ring systems where all members are at most 24 atoms in size. diff --git a/Docs/Book/images/picture_10.png b/Docs/Book/images/picture_10.png new file mode 100644 index 0000000000000000000000000000000000000000..7a66a2be7ac3ed4e99baa0e036ab721468c8c87b GIT binary patch literal 3300 zcmds4i9b|r6rLfIWSK0(ScW8#Z5Wj7+0tUqGKMkwELp~$K}MFC5Y1;v$XZ6Wl5CkF zGEK=^F@#3RE_-(RZvV!2fA_xc{oUXD-gEAAp7We@?^#)x@o$1U@6OYdB;%F+C4Fl2 z#Ad!qTvA9-?+&%$kdrv`x-~Cq`L%LQ;cQ8!jg)j9rXF#}Tm6QVF&pHfjNAWyx;4>x zPe4vi?#0Tz5~dj`My`} z?(Nma{2>Yo2^GJ10i{?x?x04j7k!?C3JGywu`KYy=;)|w$n;g}=2u@wT4cSct+p`4 z{f4Z7)pZU*LAlJ#gvr@~KNGbK#M=~=R+6wQ0W5IFLQo%TV-uH?Ba)ewby7|3lctfj zD#V>#Rv>T!^ukxzO`XlF7i6h-tdrq@`$nB>noQG945c=*h+>d~@gb590-l{OgvM6EIk! zS3v{>4u`{-r)6Y{%E}-~e3FS2%1lpT4rC(g0q*iOj_JOmXmkzHze{jo+%zI0;-tR5 zWS*w~MQdv^J?!rd7AyI0Mn-jryXd8bE5qI)%e2c8Q3_$x-Gk4krq60bZ4Ulps2C&*mV7d{ex$=u`SCG zj7uz;C`1M#w6YS|$zV9&jz<7qfB9mk=t>od*B~$ z-w%4#$bMWnZBbEKS$UWmff5xHBNr6lgIt1x)jB#likJ({LiA){-^r5?i8?L#$5R?N z7;FNv!=4Czef`DZT6W)|s`g@|r0$xaurQNbw=~lby2ZfW=7^9u3=Q9un7sK~kG2dR zOp+vW#>B)>cjqf%Or3*`&yKCPwOoli9{UGdEY190RaIzv)H1la`OR{hukMG_cszc% zHClUfX*|V$w807UFgqK9#bR4=jcgEUPVOVwir|E;P)%V$!Gz~+hoS-0RfwplXm<_# z99|s2+8T{c4rtwZ_fFsf45CH~{|4?YWJV^(hF*{W&L5ML1EZt9x2^>SBGphRGLU*K z;$9E1m=~{6Yx}UV#Ms0H_coCS#-uYCr8PCYgM))($!grxxM6t}6_uYqf4WV+yZ^&J zQ>AU6e|&u0vEC<(hY})%ZtIe~zq^<9_4V~ ziP`W(z2)((X^~rO(DxaUD;pnE3K;&n3|drL3yT*ge?qJ8%0K5@bU2pWV(cp z5H9c04Z2@Y3_wMtrR*rLUSoH6X&W1x?i$rcR|)gaD1iX`7e^cW+%Ks^3k}8J+{c@Y z0091FL3Xz1_JeYk>r1KbCbKeE{j=u7ZOrD5^3Y^E<-FDEFu)XbU4QW>(u{TqNo<4bU#L3AC#;nG+AzE8o9UJ@}@lfh4xjWl2-;!V6 z-U(LM)Xa53;m6J|jx`HJZ7tEKd-D8silcE-ymHFQyz4W4j1rR+MZ8J#OhMEGGP%84 zE`9<8~lfxf=&_lSIw#!wa)unhT_Bd zS|JY}KfVt~dFC7tJw0W4B`zf7=8BH;dYb+HqEln;Jk#&VrwA+UN68r(@ef@i%@=}9 zmA<)a75Da9bkgaD&zYz+LnO3LP}Wip;=t6aJ_%90d7|bgK1CNBBv2t}yv((!;;^E=J zJowlwGpUpvuN}Rs&d<;PB6#Yu&hBg}I{ikt2#MYHGH&$;Jx9}D)W+7f9>Gvvh53@u zf3`-e*xA`N0HR@UuX0pWR9HDXA3t~Q(3`X`~cW3H%NN{yQ0ir%? 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