openbabel-ruby 3.1.1.2-arm64-darwin

data/lib/openbabel/3.2.0/data/3.1.1/superatom.txt

@@ -0,0 +1,227 @@
+# Translations of superatom labels to SMILES.
+# First atom of SMILES string should be the one connected to the rest of
+# the molecule.
+# Empty lines and lines starting with # are ignored.
+# Originally from http://cactus.nci.nih.gov/osra/
+# The left-aligned form is the one recognized in MDL alias lines;
+# the right-aligned form may be used in 2D depiction.
+# The whole list is used to look up alias names;
+# only the part up to a line starting with ## is used to generate aliases.
+# and here the largest fragments should be first;
+#left    right    SMILES		color
+CO2Et    EtO2C    C(=O)OCC
+COOEt    EtOOC    C(=O)OCC
+OiBu     iBuO     OCC(C)C
+tBu      tBu      C(C)(C)C
+nBu      nBu      CCCC
+iPr      iPr      C(C)C
+nPr      nPr      CCC
+Et       Et       CC
+NCF3     F3CN     NC(F)(F)F
+CF3      F3C      C(F)(F)F
+CCl3     Cl3C     C(Cl)(Cl)Cl
+CN       NC       C#N
+NC       CN       [N+]#[C-]
+N(OH)CH3 CH3(OH)N N(O)C
+NO2      O2N      N(=O)=O
+NO2    O2N      [N+]([O-])=O
+NO       ON       N=O
+SO3H     HO3S     S(=O)(=O)O
+COOH     HOOC     C(=O)O		blue
+OEt      EtO      OCC
+OAc      AcO      OC(=O)C
+NHAc     AcNH     NC(=O)C
+Ac       Ac       C(=O)C
+CHO      OHC      C=O
+NMe      MeN      NC
+SMe      MeS      SC
+OMe      MeO      OC
+COO-     -OOC     C(=O)[O-]
+## Only entries above this line are used to *generate* aliases.
+Ph       Ph       c1ccccc1
+OR       RO       O*
+OBz      BzO      OCc1ccccc1
+THPO     THPO     O[C@@H]1OCCCC1
+NOH      HON      NO
+CO2H     HO2C     C(=O)O
+CO2Me    MeO2C    C(=O)OC
+COOMe    MeOOC    C(=O)OC
+SO2Me    MeO2S    S(=O)(=O)C
+NMe2     Me2N     N(C)C
+CO2R     RO2C     C(=O)O*
+COOR     ROOC     C(=O)O*
+NHZ      ZNH      NC(=O)OCC1=CC=CC=C1
+CH2OH    HOCH2    CO
+CH2NH2   H2NCH2   CN
+Me       Me       C
+OBn      BnO      OCC1=CC=CC=C1
+NHAm     AmNH     NCCCCC
+OAm      AmO      OCCCCC
+CO2Am    AmO2C    C(=O)OCCCCC
+COOAm    AmOOC    C(=O)OCCCCC
+SAm      AmS      SCCCCC
+NHBn     BnNH     NCC1=CC=CC=C1
+CO2Bn    BnO2C    C(=O)OCC1=CC=CC=C1
+SnBu3    Bu3Sn    [Sn](CCCC)(CCCC)CCCC
+NHBu     BuNH     NCCCC
+OBu      BuO      OCCCC
+CO2Bu    BuO2C    C(=O)OCCCC
+COOBu    BuOOC    C(=O)OCCCC
+SBu      BuS      SCCCC
+CBr3     Br3C     C(Br)(Br)Br
+NHCbz    CbzNH    NC(=O)OCC1=CC=CC=C1
+SO2Cl    ClSO2    S(Cl)(=O)=O
+COBr     BrCO     C(=O)Br
+COBu     BuCO     C(=O)CCCC
+COCF3    F3CCO    C(=O)C(F)(F)F
+COCl     ClCO     C(=O)Cl
+COCO     COCO     C(=O)C=O
+COEt     EtCO     C(=O)CC
+COF      FCO      C(=O)F
+COMe     MeCO     C(=O)C
+CONEt2   Et2NCO   C(=O)(CC)NCC
+CONH2    H2NCO    C(=O)N
+CONHEt   EtHNCO   C(=O)NCC
+CONHMe   MeHNCO   C(=O)NC
+CONMe2   Me2NCO   C(=O)(C)NC
+COSH     HSOC     C(=O)S
+NEt2     Et2N     N(CC)CC
+NEt3     Et3N     N(CC)(CC)CC
+NHEt     EtNH     NCC
+SO2NH2   H2NSO2   S(=O)(N)=O
+NHOH     HONH     ON
+NMe2     Me2N     N(C)C
+OMs      MsO      CS(O)(=O)=O
+OCN      NCO      N=C=O
+SCN      NCS      N=C=S
+NHAm     AmHN     NCCCCC
+NHBn     BnHN     NCC1=CC=CC=C1
+NHBu     BuHN     NCCCC
+NHEt     EtHB     NCC
+NHOH     HOHN     NO
+NHPr     PrHN     NCCC
+NO       ON       N=O
+POEt2    EtO2P    P(OCC)OCC
+POEt3    EtO3P    P(OCC)(OCC)OCC
+POOEt2   Et2OOP   P(=O)(OCC)OCC
+PrNH     HNPr     CCCN
+SEt      CCS      SCC
+#Aliases from samples provided with InChI
+CH       HC       [CH]
+CH-      HC-      [CH-]
+D        D        [2H]
+ND2      D2N      [N]([2H])[2H]
+DS       SD       [S][2H]
+CH3      H3C      C
+C2H5     C2H5     CC
+#Updates 3 Dec 2012 from Chris Swain
+Ace      Ace      C(=O)C
+Acetyl   Acetyl   C(=O)C
+Acyl     Acyl     C(=O)C
+AcAc     AcAc     C(=O)CC(C)=O
+Ad       Ad       C1(C2)CC3CC2CC(C3)C1
+AOC      AOC      C(=O)OC=C
+Alloc    Alloc    C(=O)OC=C
+Allyl    Allyl    CC=C
+All      All      CC=C
+BDMS     BDMS     [Si](C)(C)c1ccc(c2ccccc2)cc1
+Boc      Boc      C(=O)OC(C)(C)C
+BOC      BOC      C(=O)OC(C)(C)C
+t-Boc    t-Boc    C(=O)OC(C)(C)C
+BOM      BOM      COCc1ccccc1
+Bn       Bn       Cc1ccccc1
+Benzyl   Benzyl   Cc1ccccc1
+Bz       Bz       C(=O)c1ccccc1
+Benzoyl  Benzoyl  C(=O)c1ccccc1
+Bromo    Bromo    Br
+n-Bu     n-Bu     CCCC
+t-Bu     t-Bu     CC(C)(C)
+cBu      cBu      C1CCC1
+c-Bu     c-Bu     C1CCC1
+c-But    c-But    C1CCC1
+nButyl   nButyl   CCCC
+n-Butyl  n-Butyl  CCCC
+n-But    n-But    CCCC
+t-Butyl  t-Butyl  CC(C)(C)
+cButyl   cButyl   C1CCC1
+c-Butyl  c-Butyl  C1CCC1
+Bs       Bs       S(=O)(=O)C1=CC=C(Br)C=C1
+Cbz      Cbz      C(=O)OCC1=CC=CC=C1
+Z        Z        C(=O)OCC1=CC=CC=C1
+CE       CE       CCC#N
+cinnamyl cinnamyl C/C=C/C1=CC=CC=C1
+Chloro   Chloro   Cl
+Dansyl   Dansyl   S(=O)(=O)C(C=CC=C12)=C1C=CC=C2N(C)C
+Dan      Dan      S(=O)(=O)C(C=CC=C12)=C1C=CC=C2N(C)C
+DEM      DEM      CC(OC)OC
+DEIPS    DEIPS    [Si](CC)(CC)C(C)C
+Dip      Dip      OC1=C(C(C)C)C=CC=C1(C(C)C)
+Dmb      Dmb      CC1=CC=C(OC)C=C1OC
+DPA      DPA      C(C=O)(C1=CC=CC=C1)C2=CC=CC=C2
+DPhAc    DPhAc    C(C=O)(C1=CC=CC=C1)C2=CC=CC=C2
+DTBMS    DTBMS    [Si](C)(C(C)(C)C)C(C)(C)C
+Et       Et       CC
+Ethyl    Ethyl    CC
+EE       EE       CCOCC
+EOM      EOM      COCC
+Fluoro   Fluoro   F
+Formyl   Formyl   C=O
+FMOC     FMOC     C(=O)OCC1C2=CC=CC=C2C3=CC=CC=C13
+nHeptyl  nHeptyl  CCCCCCC
+n-Heptyl n-Heptyl CCCCCCC
+cHeptyl  cHeptyl  C1CCCCCC1
+c-Heptyl c-Heptyl C1CCCCCC1
+nHexyl   nHexyl   CCCCCC
+n-Hexyl  n-Hexyl  CCCCCC
+cHexyl   cHexyl   C1CCCCC1
+c-Hexyl  c-Hexyl  C1CCCCC1
+Iodo     Iodo     I
+IPDMS    IPDMS    [Si](C)(C(C)C)C
+Methoxy  Methoxy  OC
+MEM      MEM      COCCOC
+Mesityl  Mesityl  C1=C(C)C=C(C)C=C1(C)
+MOM      MOM      COC
+Mesyl    Mesyl    S(=O)(C)=O
+Ms       Ms       S(=O)(C)=O
+Nitro    Nitro    N(=O)[O-]
+nOctyl   nOctyl   CCC
+n-Octyl  n-Octyl  CCC
+n-Oct    n-Oct    CCC
+PAB      PAB      CC1=CC=C(N)C=C1
+nPentyl  nPentyl  CCCCC
+n-Pentyl n-Pentyl CCCCC
+cPentyl  cPentyl  C1CCCC1
+c-Pentyl c-Pentyl C1CCCC1
+Phenyl   Phenyl   c1ccccc1
+PMB      PMB      CC1=CC=C(OC)C=C1
+Pv       Pv       C(=O)C(C)(C)C
+Pivaloyl Pivaloyl C(=O)C(C)(C)C
+Propargyl Propargyl CC#C
+nPropyl  nPropyl  CCC
+n-Propyl n-Propyl CCC
+n-Pr     n-Pr     CCC
+n-Pro    n-Pro    CCC
+cPropyl  cPropyl  C1CC1
+c-Propyl c-Propyl C1CC1
+c-Pr     c-Pr     C1CC1
+c-Pro    c-Pro    C1CC1
+cPr      cPr      C1CC1
+i-Propyl i-Propyl C(C)C
+i-Pr     i-Pr     C(C)C
+i-Pro    i-Pro    C(C)C
+SEM      SEM      ClCOCC[Si](C)(C)C
+THP      THP      C1OCCCC1
+TMS      TMS      [Si](C)(C)C
+TBDMS    TBDMS    [Si](C)(C)C(C)(C)C
+TBDPS    TBDPS    [Si](c1ccccc1)(c1ccccc1)C(C)(C)C
+TES      TES      [Si](CC)(CC)CC
+Tf       Tf       S(=O)(C(F)(F)F)=O
+TIPS     TIPS     [Si](C(C)C)(C(C)C)C(C)C
+Tos      Tos      S(=O)(=O)c1ccc(C)cc1
+p-Tos    p-Tos    S(=O)(=O)c1ccc(C)cc1
+p-Tosyl  p-Tosyl  S(=O)(=O)c1ccc(C)cc1
+4-Tosyl  4-Tosyl  S(=O)(=O)c1ccc(C)cc1
+Tr       Tr       C(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3
+Troc     Troc     C(=O)OCC(Cl)(Cl)Cl
+Vinyl    Vinyl    C=C
+Voc      Voc      C(=O)OC=C

data/lib/openbabel/3.2.0/data/3.1.1/svgformat.script

@@ -0,0 +1,51 @@
+<script type="text/ecmascript">
+  <![CDATA[
+    var svgEl = document.getElementById("topsvg");
+    svgEl.addEventListener('DOMMouseScroll', wheel, false);
+    svgEl.addEventListener('mousewheel', wheel, false);
+    var startx=0;
+    var starty=0;
+    function wheel(evt){
+      evt = evt ? evt : window.event;
+      var normal = evt.detail ? evt.detail * -1 : evt.wheelDelta / 40;
+      var vb = new Array(4);
+      var vbtext = svgEl.getAttributeNS(null,"viewBox");
+      vb = vbtext.split(" ");
+      var zoom = (normal<0)? 1.41 : 0.71;
+      //var dwidth = parseFloat(Math.max(vb[2],vb[3])) * (1-zoom);
+      vb[0] = parseFloat(vb[0]) + parseFloat(vb[2])*(1-zoom) * evt.clientX/innerWidth;
+      vb[1] = parseFloat(vb[1]) + parseFloat(vb[3])*(1-zoom) * evt.clientY/innerHeight;
+      vb[2] = parseFloat(vb[2]) * zoom;
+      vb[3] = parseFloat(vb[3]) * zoom;
+      svgEl.setAttributeNS(null, "viewBox", vb.join(" "));
+      if (evt.preventDefault)
+        evt.preventDefault(); // Don't scroll the page when zooming
+    }
+   svgEl.onmousedown = function(evt) {
+      startx = evt.clientX;
+      starty = evt.clientY;
+    }
+    svgEl.onmousemove=function(evt) {
+      if(startx!=0 && starty!=0 
+        && ((evt.clientX - startx)*(evt.clientX - startx)+(evt.clientY - starty)*(evt.clientY - starty)>100))
+      {
+        var vbtext = svgEl.getAttributeNS(null,"viewBox");
+        vb = vbtext.split(" ");
+        var maxwh = Math.max(parseFloat(vb[2]),parseFloat(vb[3]));
+        vb[0] = parseFloat(vb[0]) - (evt.clientX - startx)*maxwh/innerWidth;
+        vb[1] = parseFloat(vb[1]) - (evt.clientY - starty)*maxwh/innerHeight;
+        svgEl.setAttributeNS(null, "viewBox", vb.join(" "));
+        startx = evt.clientX;
+        starty = evt.clientY;
+      }
+    } 
+    svgEl.onmouseup=function() {
+      startx=0;
+      starty=0;
+    }
+    svgEl.ondblclick=function() {
+      location.reload();
+    }
+  ]]>
+</script>
+

data/lib/openbabel/3.2.0/data/3.1.1/templates.sdf

@@ -0,0 +1,51 @@
+
+  ACD/Labs10200816283D
+
+ 10 12  0  0  0  0  0  0  0  0  1 V2000
+   11.7466   -9.2167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0827  -10.5962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.4479  -11.8018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8589  -12.6696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3767  -11.8246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.5800  -10.5556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.9565   -9.1175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8891   -8.7118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.5532   -9.6158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.4814  -11.1730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  8  1  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  3  5  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4 10  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  7  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  2  0  0  0  0
+M  END
+$$$$
+
+  ChemDraw06061415082D
+
+  8  9  0  0  0  0  0  0  0  0999 V2000
+   -1.0031   -0.8765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2062   -0.6630    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    0.5906   -0.8765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5906   -0.1620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0031   -0.1620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2062    0.0515    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2062    0.1620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2062    0.8765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0      
+  2  3  1  0      
+  1  4  1  0      
+  3  5  1  0      
+  4  6  1  0      
+  6  5  1  0      
+  2  7  1  0      
+  6  8  1  0      
+  8  7  1  0      
+M  END
+$$$$

data/lib/openbabel/3.2.0/data/3.1.1/torlib.txt

@@ -0,0 +1,231 @@
+##############################################################################
+#                                                                            #
+#                       Open Babel file: torlib.txt                          #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison            #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  First three lines represent: (used by rotor.cpp::OBRotorRules             #
+#  Hybridization pair (atom types around a rotatable bond)                   #
+#   followed by a list of default bond rotation angles (in degrees)          #
+#                                                                            #
+#  Later lines should specify:                                               #
+#   * A SMARTS pattern for the rotor rule                                    #
+#   * A set of 4 "reference atoms" (as integers, numbered from 1             #
+#      in the specified SMARTS pattern                                       #
+#   * At least one torsion value (in degrees)                                #
+#   * Optionally ending with "Delta" and a delta value                       #
+#      (i.e., the resolution of a dihedral step                              #
+#                                                                            #
+#  SMARTS rules will be attempted first, then hybridization                  #
+#                                                                            #
+##############################################################################
+
+SP3-SP3  60.0  -60.0 180.0
+SP2-SP2   0.0  180.0 -30.0 30.0 150.0 -150.0
+SP3-SP2   0.0   30.0 -30.0 60.0 -60.0  120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0
+
+# ring bonds
+[r4]-[r4]-[r4]-[r4] 1 2 3 4 0.0 25.0 -25.0
+[r5]-[r5]-[r5]-[r5] 1 2 3 4 0.0 15.0 -15.0 35.0 -35.0
+[r6]-[r6]-[r6]-[r6] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
+[r7]-[r7]-[r7]-[r7] 1 2 3 4 0.0
+[r8]-[r8]-[r8]-[r8] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0
+
+# Many of these rules came from the Supporting Information
+# from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801
+
+#polysaccaride bridges
+O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0
+O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0
+
+#acids
+[OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0
+[a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0
+[OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0
+
+#sulfonamides
+NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0
+c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0
+O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0
+O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0
+[c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0
+*=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0
+O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0
+[aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0
+[aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0
+[aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0
+[aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0
+[a]cS(=O)(=O)[C,N] 1 2 3 6 60.0 -60.0 90.0 -90.0 120.0 -120.0 0.0 180.0
+aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0
+aaNS(=O)(=O) 1 2 3 4 90.0 -90.0
+
+#sulfone
+O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0
+
+#hydrazides
+[O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0
+[O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0
+
+#cyclopropyl-ketones
+O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0
+O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0
+O=CC1([*])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 120.0 -120.0 90.0 -90.0 30.0 -30.0
+
+#epoxy-ketone
+O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0
+
+#opposite end of tert amide
+O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0
+O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0
+O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0
+
+#misc
+[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0
+[cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.0 -110.0
+c[CD2][ND3](C)c 1 2 3 4 90.0 -90.0 60.0 -60.0 120.0 -120.0
+
+#carbonyls
+O=CC=O 1 2 3 4 180.0 0.0 120.0 -120.0 90.0 -90.0
+C=CC=O 1 2 3 4 0.0 180.0 20.0 -20.0 160.0 -160.0
+O=C[CD2][ND2] 1 2 3 4 0.0 -30.0 30.0 150.0 -150.0 180.0
+O=C[CD2]C=O 1 2 3 4 0.0 -30.0 30.0 60.0 -60.0 130.0 -130.0
+O=C(c)[ND2][CD3][#1] 2 4 5 6 0.0 -30.0 30.0
+O=C[ND2][CD3]* 2 3 4 5 20.0 -20.0 120 -120.0 60.0 -60.0 0.0
+O=CN[CD2]* 2 3 4 5 180.0 150.0 -150.0 -120.0 120.0 0.0 30.0 -30.0
+O=Ccc[OD1] 1 2 3 4 0.0 180.0 90.0 -90.0 30.0 -30.0
+O=C[CD4][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
+O=C[CD3][OD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
+O=C[CD2][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0
+O=C[CD3][#1] 1 2 3 4 0.0 30.0 -30.0 180.0
+#O=C[CD3]* 1 2 3 4 0.0 90.0 -90.0 30.0 -30.0 -120.0 120.0 60.0 -60.0
+
+#amidene and guanidine
+[aD3]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
+[a]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
+*[ND2]~C(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
+[CD2][CD2][ND2]~C(~[ND1])~[ND1] 1 2 3 4 -70.0 70.0 90.0 -90.0 110.0 -110.0
+
+#ether
+aCO[CD2] 1 2 3 4 180.0 100.0 -100.0
+
+#isoprene
+C=C[CX4D2]* 1 2 3 4 0.0 180.0 90.0 -90.0 60.0 -60.0 30.0 -30.0
+C=Cc[a] 1 2 3 4 0.0 90.0 -90.0 180.0 30.0 -30.0 150.0 -150.0
+
+#aryl secondary amines
+[aD2]c([aD2])[ND2][CD2] 1 2 4 5 0.0 180.0
+[aD2]c([aD3])[ND2][CD2] 1 2 4 5 0.0
+[aD2]c([aD2])[ND2][CD1] 1 2 4 5 0.0 90.0 -90.0 180.0
+ac[ND2][CD2] 1 2 3 4 90.0 -90.0 160.0 -160.0 20.0 -20.0
+
+#aromatic subtituents
+[aD3]c([aD3])[CD2]C 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
+[aD2]c([aD2])[ND3]([CD1])[CD2] 1 2 4 5 0.0 180.0
+[aD3][c,n]([aD2])[C^3D3][#1] 1 2 4 5 0.0 -30.0 30.0 60.0 -60.0 160.0 -160.0
+a[CD2X4][ND3^3]* 1 2 3 4 60.0 -60.0 180.0 160.0 -160.0 90.0 -90.0 120.0 -120.0
+an[CD2X4][CD1] 1 2 3 4 90.0 -90.0
+[aD3]c([aD2])C(=O)[C^3] 1 2 4 5 0.0 20.0 -20.0 150.0 -150.0 180.0
+[aD3]c([aD2])O[CD2] 1 2 3 4 180.0
+a[ND2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0
+[ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0
+[aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0
+[a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0
+[a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0
+[a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
+[a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
+
+#borderline low-res
+[CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0
+
+#conjugated substituents
+a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0
+C=CC=C 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 60.0 -60.0 120.0 -120.0
+cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0
+C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0
+c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0
+C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0
+
+#ureas
+[ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0
+[ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0
+
+#carbamates
+C[ND2]C(=O)O 1 2 3 4 0.0 180.0
+[ND2]C(=O)OC 3 2 4 5 0.0
+OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0
+
+#piperidine amide
+O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0
+
+#amides and esters
+[*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0
+[OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0
+[O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0
+[O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0
+[O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0
+[O,SD1]=C(C)cn 1 2 4 5 0.0 180.0
+[O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0
+[O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180
+O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0
+O=CNc([aD2,aD3])[aD3] 2 3 4 5 20.0 -20.0 -90.0 90.0 60.0 -60.0 120.0 -120.0 0.0
+O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0
+O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0
+O=C([CD1])O[CD1] 1 2 4 5 0.0
+[O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0
+O=CO[CD2][CD1] 2 3 4 5 0.0 180.0
+O=CO[CD2]* 2 3 4 5 180.0 60.0 0.0 -60.0 90.0 -90.0
+O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0
+O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0
+O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
+O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 180.0
+O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0
+O=C[ND3]* 1 2 3 4 0.0 180.0
+CC[ND3](CC)[CD2,CD3]* 2 3 6 7 180.0 60.0 -60.0 120.0 -120.0 0.0 180.0 30.0 -30.0
+[a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0
+[ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
+[CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0
+
+#t-butyl
+C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0
+**C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0
+
+#propyl
+[CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0
+
+#highly substituted alkane
+#[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6
+*[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0
+c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0
+[CD2^3][CD2^3][CD3^3][#1] 1 2 3 4 60.0 -60.0 180.0 30.0 -30.0 0.0 160.0 -160.0 120.0 -120.0
+[*D2][CD2][CRH]([*R])[*R] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 0.0
+[*D2][CD2][CX4D3][*D2] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0
+*[CHD3][CH2D2]* 1 2 3 4 150.0 -150.0 60.0 -60.0 180.0 -90.0 90.0 0.0 30.0 -30.0
+[CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0
+
+#long unsubstituted alkanes
+[CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0
+[CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0
+[CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0
+[*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0
+
+#nitro
+[aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0
+[a]cN(~[OD1])~[OD1] 1 2 3 4 0.0
+
+#trihalides
+**C(F)(F)F 1 2 3 4 0.0
+**C(I)(I)I 1 2 3 4 0.0
+**C(Cl)(Cl)Cl 1 2 3 4 0.0
+**C(Br)(Br)Br 1 2 3 4 0.0
+
+#CSD SPECIFIC RULES
+a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0
+PPcc 1 2 3 4 60.0 -60.0
+
+#phosphorus containing groups
+#[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0
+#[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0
+#S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0
+#[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0