rdworks 0.25.7__py3-none-any.whl

rdworks/predefined/ionized/simple_smarts_pattern.csv

@@ -0,0 +1,57 @@
+Substructure,SMARTS,Index,Acid_or_base
+Sulfate monoether,[SX4:0](=[O:1])(=[O:2])(-[O:3])-[OX2:4]-[H:5],4,A
+Sulfate monoether,[SX4:0](=[O:1])(=[O:2])(-[O:3])-[O-1:4],4,B
+Sulfonic acid,"[SX4:0](=[O:1])(=[O:2])(-[#6,#7:3])-[OX2:4]-[H:5]",4,A
+Sulfonic acid,"[SX4:0](=[O:1])(=[O:2])(-[#6,#7:3])-[O-1:4]",4,B
+Sulfinic acid,"[SX3:0](=[O:1])(-[#6,#7:2])-[OX2:3]-[H:4]",3,A
+Sulfinic acid,"[SX3:0](=[O:1])(-[0#6,#7:2])-[O-1:3]",3,B
+Seleninic acid,"[SeX3:0](=[O:1])(-[#6,#7:2])-[OX2:3]-[H:4]",3,A
+Seleninic acid,"[SeX3:0](=[O:1])(-[#6,#7:2])-[O-1:3]",3,B
+Selenenic acid,[SeX2:0]-[OX2:1]-[H:2],1,A
+Selenenic acid,[SeX2:0]-[O-1:1],1,B
+Arsonic acid,"[AsX4:0](=[O:1])(-[#6,#7:2])-[OX2:3]-[H:4]",3,A
+Arsonic acid,"[AsX4:0](=[O:1])(-[#6,#7:2])-[O-1:3]",3,B
+Thiosulfuric acid,[S:0]~[SX4:1](~[O:2])(~[O:3])-[O:4]-[H:5],4,A
+Thiosulfuric acid,[S:0]~[SX4:1](~[O:2])(~[O:3])-[O-1:4],4,B
+Phosph(o/i)nic acid,"[PX4:0](=[O:1])(-[OX2:2]-[H:5])(-[#1,#6,#7,#8:3])(-[#1,#6,#7,#8:4])",2,A
+Phosph(o/i)nic acid,"[PX4:0](=[O:1])(-[O-1:2])(-[#1,#6,#7,#8:3])(-[#1,#6,#7,#8:4])",2,B
+Phosphate (mono/di)ether,[PX4:0](=[O:1])(-[O:2])(-[O:3])-[OX2:4]-[H:5],4,A
+Phosphate (mono/di)ether,[PX4:0](=[O:1])(-[O:2])(-[O:3])-[O-1:4],4,B
+Carboxyl acid,"[$([#6]=[#8,#7]),$(C#N):0]-[OX2:1]-[H:2]",1,A
+Carboxyl acid,"[$([#6]=[#8,#7]),$(C#N):0]-[O-1:1]",1,B
+Carboxyl acid enol,[C:0]=[C:1](-[OX2:2]-[H:3])-[OX2:4]-[H:5],4,A
+Carboxyl acid enol,[C:0]=[C:1](-[OX2:2]-[H:3])-[O-1:4],4,B
+Carbo(di)thioic acid,"[CX3:0](=[O,S:1])-[SX2,OX2:2]-[H:3]",2,A
+Carbo(di)thioic acid,"[CX3:0](=[O,S:1])-[S-1,O-1:2]",2,B
+Carboxyl acid vinylogue ,[O:0]=[C:1]-[C:2]=[C:3]-[OX2:4]-[H:5],4,A
+Carboxyl acid vinylogue,[O:0]=[C:1]-[C:2]=[C:3]-[O-1:4],4,B
+Thiol/Thiophenol,"[#6,#7:0]-[SX2:1]-[H:2]",1,A
+Thiol/Thiophenol,"[#6,#7:0]-[S-1:1]",1,B
+Phenol,"[c,n:0]-[OX2:1]-[H:2]",1,A
+Phenol,"[c,n:0]-[O-1:1]",1,B
+Hydroperoxide/Hydroxyl amine,"[O,N:0]-[OX2:1]-[H:2]",1,A
+Hydroperoxide/Hydroxyl amine,"[O,N:0]-[O-1:1]",1,B
+Azole,"[#7:0]1(-[H:5])-,:[#7,#6:1]=,:[#7,#6:2]-,:[#7,#6:3]=,:[#7,#6:4]-,:1",0,A
+Azole,"[#7-1:0]1-,:[#7,#6:1]=,:[#7,#6:2]-,:[#7,#6:3]=,:[#7,#6:4]-,:1",0,B
+Aza-aromatics,[n:0]-[H:1],0,A
+Aza-aromatics,"[n-1,n+0X2:0]",0,B
+Oxime,"[$([#7]:,=[#6,#7]),$([#7]:,=[#6,#7]:,-[#6,#7]:,=[#6,#7]):0]-[OX2,NX3:1]-[H:2]",1,A
+Oxime,"[$([#7]:,=[#6,#7]),$([#7]:,=[#6,#7]:,-[#6,#7]:,=[#6,#7]):0]-[O-1,NX2-1:1]",1,B
+Amine,"[NX4+1:0](-[H:4])(-[CX4,c,#7,#8,#1,S,$(C=C),Cl:1])(-[CX4,c,#7,#8,#1,S,$(C=C):2])(-[CX4,c,#7,#8,#1,S,$(C=C):3])",0,A
+Amine,"[NX3:0](-[CX4,c,#7,#8,#1,S,$(C=C),Cl:1])(-[CX4,c,#7,#8,#1,S,$(C=C):2])(-[CX4,c,#7,#8,#1,S,$(C=C):3])",0,B
+Imine,"[#6,#7,P,S:0]=[NX3+1:1](-[H:2])",1,A
+Imine,"[#6,#7,P,S:0]=[NX2:1]",1,B
+Amide,"[$([#7]=[#7,#8]),$(c:c:c:c:[#7+1]):0]-[NX3:1]-[H:2]",1,A
+Amide,"[$([#7]=[#7,#8]),$(c:c:c:c:[#7+1]):0]-[NX2-1:1]",1,B
+Amide imine,"[$([#6]-,:[O,S,#7]),N+1:0]=,:[NX2:1]-[H:2]",1,A
+Amide imine,"[$([#6]-,:[O,S,#7]),N+1:0]=,:[NX1-1:1]",1,B
+Sulfamide,[SX4:0](=[O:1])(=[O:2])-[NX3:3]-[H:4],3,A
+Sulfamide,[SX4:0](=[O:1])(=[O:2])-[NX2-1:3],3,B
+Phosphamide,[PX4:0](=[O:1])-[NX3:2]-[H:3],2,A
+Phosphamide,[PX4:0](=[O:1])-[NX2-1:2],2,B
+Enol,"[$([#6]=,:[#7,#8]),$(C#N),#7+1,$([S]=[O]),OH1:0]-[#6:1]:,=[#6:2]-[OX2:3]-[H:4]",3,A
+Enol,"[$([#6]=,:[#7,#8]),$(C#N),#7+1,$([S]=[O]),OH1:0]-[#6:1]:,=[#6:2]-[O-1:3]",3,B
+Hydrocyanic acid,[N:0]#[C:1]-[H:2],1,A
+Hydrocyanic acid,[N:0]#[C-1:1],1,B
+Selenol,[SeX2:0]-[H:1],0,A
+Selenol,[SeX1-1:0],0,B

rdworks/predefined/ionized/smarts_pattern.csv

@@ -0,0 +1,107 @@
+Substructure,SMARTS,Index,Acid_or_base
+Sulfate monoether,[SX4:0](=[O:1])(=[O:2])(-[O:3])-[OX2:4]-[H:5],4,A
+Sulfate monoether,[SX4:0](=[O:1])(=[O:2])(-[O:3])-[O-1:4],4,B
+Sulfonic acid,"[SX4:0](=[O:1])(=[O:2])(-[#6,#7:3])-[OX2:4]-[H:5]",4,A
+Sulfonic acid,"[SX4:0](=[O:1])(=[O:2])(-[#6,#7:3])-[O-1:4]",4,B
+Sulfinic acid,"[SX3:0](=[O:1])(-[#6,#7:2])-[OX2:3]-[H:4]",3,A
+Sulfinic acid,"[SX3:0](=[O:1])(-[0#6,#7:2])-[O-1:3]",3,B
+Seleninic acid,"[SeX3:0](=[O:1])(-[#6,#7:2])-[OX2:3]-[H:4]",3,A
+Seleninic acid,"[SeX3:0](=[O:1])(-[#6,#7:2])-[O-1:3]",3,B
+Selenenic acid,[SeX2:0]-[OX2:1]-[H:2],1,A
+Selenenic acid,[SeX2:0]-[O-1:1],1,B
+Arsonic acid,"[AsX4:0](=[O:1])(-[#6,#7:2])-[OX2:3]-[H:4]",3,A
+Arsonic acid,"[AsX4:0](=[O:1])(-[#6,#7:2])-[O-1:3]",3,B
+Thiosulfuric acid,[S:0]~[SX4:1](~[O:2])(~[O:3])-[O:4]-[H:5],4,A
+Thiosulfuric acid,[S:0]~[SX4:1](~[O:2])(~[O:3])-[O-1:4],4,B
+Phosph(o/i)nic acid,"[PX4:0](=[O:1])(-[OX2:2]-[H:5])(-[#1,#6,#7,#8:3])(-[#1,#6,#7,#8:4])",2,A
+Phosph(o/i)nic acid,"[PX4:0](=[O:1])(-[O-1:2])(-[#1,#6,#7,#8:3])(-[#1,#6,#7,#8:4])",2,B
+Phosphate (mono/di)ether,[PX4:0](=[O:1])(-[O:2])(-[O:3])-[OX2:4]-[H:5],4,A
+Phosphate (mono/di)ether,[PX4:0](=[O:1])(-[O:2])(-[O:3])-[O-1:4],4,B
+Carboxyl acid,"[$([#6]=[#8,#7]),$(C#N):0]-[OX2:1]-[H:2]",1,A
+Carboxyl acid,"[$([#6]=[#8,#7]),$(C#N):0]-[O-1:1]",1,B
+Carboxyl acid enol,[C:0]=[C:1](-[OX2:2]-[H:3])-[OX2:4]-[H:5],4,A
+Carboxyl acid enol,[C:0]=[C:1](-[OX2:2]-[H:3])-[O-1:4],4,B
+Carbo(di)thioic acid,"[CX3:0](=[O,S:1])-[SX2,OX2:2]-[H:3]",2,A
+Carbo(di)thioic acid,"[CX3:0](=[O,S:1])-[S-1,O-1:2]",2,B
+Carboxyl acid vinylogue ,[O:0]=[C:1]-[C:2]=[C:3]-[OX2:4]-[H:5],4,A
+Carboxyl acid vinylogue,[O:0]=[C:1]-[C:2]=[C:3]-[O-1:4],4,B
+Thiol/Thiophenol,"[#6,#7:0]-[SX2:1]-[H:2]",1,A
+Thiol/Thiophenol,"[#6,#7:0]-[S-1:1]",1,B
+Phenol,"[c,n:0]-[OX2:1]-[H:2]",1,A
+Phenol,"[c,n:0]-[O-1:1]",1,B
+Alcohol,"[$([CX4]-[$([#6]=,:[#7,#8]),$([#6]=,:[#6]-,:[#6]=,:[#7,#8]),$(C#N),O,#7+1,$(C-Cl),$(C#C),$(C-O),S:0]),$([CH2]-[#1,CH3]):0]-[OX2:1]-[H:2]",1,A
+Alcohol,"[$([CX4]-[$([#6]=,:[#7,#8]),$([#6]=,:[#6]-,:[#6]=,:[#7,#8]),$(C#N),O,#7+1,$(C-Cl),$(C#C),$(C-O),S:0]),$([CH2]-[#1,CH3]):0]-[O-1:1]",1,B
+Hydroxypyridine,[n:0]:[c:1]-[OH2+1:2]-[H:3],2,A
+Hydroxypyridine,[n:0]:[c:1]-[OX2H1:2],2,B
+Methylpyridine,[n:0](-[C:1]=[O:2]):[c:3]:[c:4]:[c:5]-[CX4:6]-[H:7],6,A
+Methylpyridine,[n:0](-[C:1]=[O:2]):[c:3]:[c:4]:[c:5]-[CX3-1:6],6,B
+Hydroperoxide/Hydroxyl amine,"[O,N:0]-[OX2:1]-[H:2]",1,A
+Hydroperoxide/Hydroxyl amine,"[O,N:0]-[O-1:1]",1,B
+Azole,"[#7:0]1(-[H:5])-,:[#7,#6:1]=,:[#7,#6:2]-,:[#7,#6:3]=,:[#7,#6:4]-,:1",0,A
+Azole,"[#7-1:0]1-,:[#7,#6:1]=,:[#7,#6:2]-,:[#7,#6:3]=,:[#7,#6:4]-,:1",0,B
+Aza-aromatics,[n:0]-[H:1],0,A
+Aza-aromatics,"[n-1,n+0X2:0]",0,B
+N-substitute aza-aromatics,[n+1:0]-[CX4:1]-[H:2],1,A
+N-substitute aza-aromatics,[n+1:0]-[CX3-1:1],1,B
+Oxime,"[$([#7]:,=[#6,#7]),$([#7]:,=[#6,#7]:,-[#6,#7]:,=[#6,#7]):0]-[OX2,NX3:1]-[H:2]",1,A
+Oxime,"[$([#7]:,=[#6,#7]),$([#7]:,=[#6,#7]:,-[#6,#7]:,=[#6,#7]):0]-[O-1,NX2-1:1]",1,B
+Amine,"[NX4+1:0](-[H:4])(-[CX4,c,#7,#8,#1,S,$(C=C),Cl:1])(-[CX4,c,#7,#8,#1,S,$(C=C):2])(-[CX4,c,#7,#8,#1,S,$(C=C):3])",0,A
+Amine,"[NX3:0](-[CX4,c,#7,#8,#1,S,$(C=C),Cl:1])(-[CX4,c,#7,#8,#1,S,$(C=C):2])(-[CX4,c,#7,#8,#1,S,$(C=C):3])",0,B
+Imine,"[#6,#7,P,S:0]=[NX3+1:1](-[H:2])",1,A
+Imine,"[#6,#7,P,S:0]=[NX2:1]",1,B
+Amide,"[$([#6]=,:[O,S,#7:0]),$([#7]=[#7,#8]),$([#6]:,=[#6]:,-[#7]=[#7,#8]),$(c:c:c:c:[#7+1]):0]-[NX3:1]-[H:2]",1,A
+Amide,"[$([#6]=,:[O,S,#7:0]),$([#7]=[#7,#8]),$([#6]:,=[#6]:,-[#7]=[#7,#8]),$(c:c:c:c:[#7+1]):0]-[NX2-1:1]",1,B
+Amide imine,"[$([#6]-,:[O,S,#7]),N+1:0]=,:[NX2:1]-[H:2]",1,A
+Amide imine,"[$([#6]-,:[O,S,#7]),N+1:0]=,:[NX1-1:1]",1,B
+Sulfamide,[SX4:0](=[O:1])(=[O:2])-[NX3:3]-[H:4],3,A
+Sulfamide,[SX4:0](=[O:1])(=[O:2])-[NX2-1:3],3,B
+Phosphamide,[PX4:0](=[O:1])-[NX3:2]-[H:3],2,A
+Phosphamide,[PX4:0](=[O:1])-[NX2-1:2],2,B
+Amide vinylogue,"[NX3:0](-[H:5])-,:[#6:1]=,:[#6:2]-,:[$([#6]=,:[#7,#8]),$(C#N):3]",0,A
+Amide vinylogue,"[NX2-1:0]-,:[#6:1]=,:[#6:2]-,:[$([#6]=,:[#7,#8]),$(C#N):3]",0,B
+Di Carbonyl βH,"[$([#6,#7]=,:[#7,#8]),$(C#N),$([#6]=,:[#6]-,:[$([#6]=,:[#7,#8]),$(C#N)]),$(P=O),$(S=O),S+1,Cl,F,O,c:0]-,:[#6X4:1](-[H:3])-,:[$([#6]=,:[#7,#8]),$(C#N),$(P=O),$(S=O):2]",1,A
+Di Carbonyl βH,"[$([#6,#7]=,:[#7,#8]),$(C#N),$([#6]=,:[#6]-,:[$([#6]=,:[#7,#8]),$(C#N)]),$(P=O),$(S=O),S+1,Cl,F,O,c:0]-,:[#6X3-1:1]-,:[$([#6]=,:[#7,#8]),$(C#N),$(P=O),$(S=O):2]",1,B
+Carbonyl βH,"[$([#6](=O)(-,:[#7+1,#6,#1])(-,:[#6,#1])),$([N](=O)(-O)),$(P=O),$(C=C-C(=O)-[#6,#1]):0]-,:[#6X4:1]-[H:2]",1,A
+Carbonyl βH,"[$([#6](=O)(-,:[#7+1,#6,#1])(-,:[#6,#1])),$([N](=O)(-O)),$(P=O),$(C=C-C(=O)-[#6,#1]):0]-,:[#6X3-1:1]",1,B
+Carbonyl allene,[O:0]=[C:1]-[C:2]=[C:3]=[CX3:4]-[H:5],4,A
+Carbonyl allene,[O:0]=[C:1]-[C:2]=[C:3]=[CX2-1:4],4,B
+Enol,"[$([#6]=,:[#7,#8]),$(C#N),#7+1,$([S]=[O]),c,$(C=C),OH1:0]-[#6:1]:,=[#6:2]-[OX2:3]-[H:4]",3,A
+Enol,"[$([#6]=,:[#7,#8]),$(C#N),#7+1,$([S]=[O]),c,$(C=C),OH1:0]-[#6:1]:,=[#6:2]-[O-1:3]",3,B
+Enol,"[#6:0]=[#6:1](-[$(C=O),$(C(=C)-[OH1]):2])-[OX2:3]-[H:4]",3,A
+Enol,"[#6:0]=[#6:1](-[$(C=O),$(C(=C)-[OH1]):2])-[O-1:3]",3,B
+Acyl group,"[#6:0](-[O,N:1])=[OX2+1:2]-[H:3]",2,A
+Acyl group,"[#6:0](-[O,N:1])=[OX1:2]",2,B
+Sulfoxide,[S+1:0](-[OX2:1]-[H:4])(-[#6:2])(-[#6:3]),1,A
+Sulfoxide,[S+1:0](-[O-1:1])(-[#6:2])(-[#6:3]),1,B
+Sulfoxide,[S:0](=[OX2+1:1]-[H:4])(-[#6:2])(-[#6:3]),1,A
+Sulfoxide,[S:0](=[OX1:1])(-[#6:2])(-[#6:3]),1,B
+Sulfoxide,[S:0](=[OX2+1:1]-[H:3])(=[#6:2]),1,A
+Sulfoxide,[S:0](=[OX1:1])(=[#6:2]),1,B
+Hydrocyanic acid,[N:0]#[C:1]-[H:2],1,A
+Hydrocyanic acid,[N:0]#[C-1:1],1,B
+Phosphoryl group,[PX4:0]=[OX2+1:1]-[H:3],1,A
+Phosphoryl group,[PX4:0]=[OX1:1],1,B
+Selenonyl group,[Se:0]=[OX2+1:1]-[H:3],1,A
+Selenonyl group,[Se:0]=[OX1:1],1,B
+Arsenyl group,[AsX4:0]=[OX2+1:1]-[H:2],1,A
+Arsenyl group,[AsX4:0]=[OX1:1],1,B
+Carboxyl group,"[#6X3:0](:,-[O,#7,S:1])=[OX2+1,SX2+1:2]-[H:3]",2,A
+Carboxyl group,"[#6X3:0](:,-[O,#7,S:1])=[OX1,SX1:2]",2,B
+Carboxyl group vinylogue,"[#6X3:0](:,-[#6:1]:,=[#6:2]:,-[O,#7,S:3])=[OX2+1,SX2+1:4]-[H:5]",4,A
+Carboxyl group vinylogue,"[#6X3:0](:,-[#6:1]:,=[#6:2]:,-[O,#7,S:3])=[OX1,SX1:4]",4,B
+Carbonyl group,"[#6X3:0](:,-[#1,#6:1])(:,-[#1,#6:2])=[OX2+1:3]-[H:4]",3,A
+Carbonyl group,"[#6X3:0](:,-[#1,#6:1])(:,-[#1,#6:2])=[OX1:3]",3,B
+Cyano group,[C:0]#[N:1]-[H:2],1,A
+Cyano group,[C:0]#[NX1:1],1,B
+Hydroxyl group,"[CX4:0](-[#6,#1:1])(-[#6,#1:2])(-[#6,#1:3])-[OH2+1:4]",4,A
+Hydroxyl group,"[CX4:0](-[#6,#1:1])(-[#6,#1:2])(-[#6,#1:3])-[OX2:4]-[H:5]",4,B
+Selenol,[SeX2:0]-[H:1],0,A
+Selenol,[SeX1-1:0],0,B
+Borate,[BX3:0]-[OX2:1]-[H:2],1,A
+Borate,[BX3:0]-[O-1:1],1,B
+Bromomethane,[Br:0]-[CH3:1]-[H:2],1,A
+Bromomethane,[Br:0]-[CH2-1:1],1,B
+Cyclopentadiene,"[#6X4:0](-[#1:5])1-,:[#6:1]=,:[#6:2]-,:[#6:3]=,:[#6:4]-,:1",0,A
+Cyclopentadiene,"[#6X3-1:0]1-,:[#6:1]=,:[#6:2]-,:[#6:3]=,:[#6:4]-,:1",0,B
+Tin alkyl,[N+:0]-[CX4:1](-[H:3])-[SnX4:2],1,A
+Tin alkyl,[N+:0]-[CX3-1:1]-[SnX4:2],1,B

rdworks/predefined/misc/makexml.py

@@ -0,0 +1,119 @@
+from xml.etree.ElementTree import Element,SubElement,Comment,tostring,parse
+from xml.dom import minidom
+
+count= 0
+A= Element('reactive')
+
+for (name, smarts) in [
+  ["4-Nitrophenyl Ester","[O-][N+](=O)c1ccc(OC=O)cc1"],
+  ["Acid Chloride","C(=O)Cl"],
+  ["Acid Bromide","C(=O)Br"],
+  ["Acid Iodide","C(=O)I"],
+  ["Acid Fluoride","C(=O)F"],
+  ["Acyl Cyanide","N#CC(=O)"],
+  ["Acyl hydrazine","NNC=O"],
+  ["Anhydride","C(=O)OC(=O)"],
+  ["Allyl Bromide","BrCC=C"],
+  ["Allyl Chloride","ClCC=C"],
+  ["Allyl Fluoride","FCC=C"],
+  ["Allyl iodide","ICC=C"],
+  ["Alpha_HaloCarbonyl","[F,Cl,Br,I]CC=O"],
+  ["Beta_HaloCarbonyl","[F,Cl,Br,I]CCC=O"],
+  ["Azide","N=[N+]=[N-]"],
+  ["Aziridine","C1CN1"],
+  ["Azo","[N;X2]=[N;X2]"],
+  ["Benzyl Bromide","[H]C([H])(Br)c"],
+  ["Benzyl Chloride","[H]C([H])(Cl)c"],
+  ["Benzyl Iodide","[H]C([H])(I)c"],
+  ["Beta ammonium carbonyl","C[N+](C)(C)CCC=O"],
+  ["Carbazide","O=*N=[N+]=[N-]"],
+  ["Carbodimide","N=C=N"],
+  ["Chloramine","[N;X3](Cl)"],
+  ["Chloro Silane","Cl[Si]"],
+  ["Cyanohydrin","N#CC[OH]"],
+  ["cyanamides","N[CH2]C#N"],
+  ["Cyanate","O=C=N"],
+  ["diazo","cN=Nc"],
+  ["Diazonium","[N+]#N"],
+  ["Dichloramine","[N;X3](Cl)Cl"],
+  ["Disulphide","SS"],
+  ["Epoxide","C1CO1"],
+  ["HaloAmine","[F,Cl,Br,I]N"],
+  ["Beta_HaloAmine","[F,Cl,Br,I]CCN"],
+  ["HaloMethylEther","[F,Cl,Br,I]C[OH0;X2]"],
+  ["HaloMethylThioEther","[F,Cl,Br,I]C[SH0;X2]"],
+  ["HydroxyBenzoylTriazole","C(=O)Onnn"],
+  ["Imidoyl Chloride","ClC=N"],
+  ["Imidoyl Bromide","BrC=N"],
+  ["Iodoso","I(=O)"],
+  ["Iodoxy","O=I=O"],
+  ["Isocyanate","N=C=O"],
+  ["Isothiocyanate","N=C=S"],
+  ["isonitriles","[N+]#[C-]"],
+  ["Ketene","C=C=O"],
+  ["Lawesson's_reagents","P(=S)(S)S"],
+  ["Nitroso","[N;X2]=O"],
+  ["Oxaziridine","C1NO1"],
+  ["Pentafluorophenyl Ester","Fc1c(F)c(F)c(OC=O)c(F)c1F"],
+  ["Peroxide","OO"],
+  ["Phosphine Chloride","PCl"],
+  ["Phosphine Bromide","PBr"],
+  ["Phosphine Fluoride","PF"],
+  ["Phosphine Iodide","PI"],
+  ["Cationic Br","[Br+]"],
+  ["Cationic Cl","[Cl+]"],
+  ["Cationic I","[I+]"],
+  ["Cationic O","[O+,o+]"],
+  ["Cationic P","[P+]"],
+  ["Cationic S","[S+]"],
+  ["Sulphonyl Chloride","S(=O)(=O)[Cl]"],
+  ["Sulphonyl Bromide","S(=O)(=O)[Br]"],
+  ["Sulphonyl Fluoride","S(=O)(=O)[F]"],
+  ["Sulphonate Ester","COS(c)(=O)=O"],
+  ["Sulphonyl Cyanide","S(=O)(=O)C#N"],
+  ["Thioacyl Chloride","C(=S)Cl"],
+  ["Thioacyl  Bromide","C(=S)Br"],
+  ["Thio Halides","[S][Cl,Br,F,I]"],
+  ["Thiocyanate","SC#N"],
+  ["Triflate","OS(=O)(=O)C(F)(F)F"],
+  ["Vinylous Acid Chloride","ClC=CC=O"]
+  ]:
+     count += 1
+     entry= SubElement (A, 'group')
+     entry.set('name', '('+str(count)+') '+name)
+     node= SubElement(entry, "SMARTS")
+     node.text= smarts
+   
+with open('reactive-part1.xml','rt') as f :
+	treeA= parse(f)
+
+with open('reactive-part2.xml','rt') as g :
+	treeB= parse(g)
+
+
+for node in treeA.iter() :
+	if node.tag == 'SMART' :
+		smarts= node.text.strip()
+	if node.tag == 'name' :
+		name= node.text.strip()
+		count += 1
+		entry= SubElement (A, 'group')
+		entry.set('name', '('+str(count)+') '+name)
+		node= SubElement (entry, "SMARTS")
+		node.text= smarts
+
+for node in treeB.iter() :
+	if node.tag == 'SMART' :
+		smarts= node.text.strip()
+	if node.tag == 'name' :
+		name= node.text.strip()
+		count += 1
+		entry= SubElement (A, 'group')
+		entry.set('name', '('+str(count)+') '+name)
+		node= SubElement (entry, "SMARTS")
+		node.text= smarts
+
+g=open('reactive.xml','wt')
+coarse= tostring(A,'utf-8')
+g.write( minidom.parseString( coarse ).toprettyxml(indent="  ") )
+g.close()

rdworks/predefined/misc/reactive-part-2.xml

@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SMARTPatterns>
+    <pattern active="true">
+        <SMART>[F,Cl,Br,I]-[SX4](=[OX1])(=[OX1])-[#6]</SMART>
+        <name>sulfonyl-alide</name>
+        <desc>sulfonyl-alide</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[F,Cl,Br,I]-[CX3](=[OX1])-[#6]</SMART>
+        <name>acyl-halide</name>
+        <desc>acyl-halide</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[F,Cl,Br,I]-[CX4H2]-[#6]</SMART>
+        <name>alkyl-halide</name>
+        <desc>alkyl-halide</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[F,Cl,Br,I]-c1ncccn1</SMART>
+        <name>halopyrimidine</name>
+        <desc>halopyrimidine</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX3](=[OX1])-[OX2]-[CX3](=O)-[#6]</SMART>
+        <name>anhydride</name>
+        <desc>anhydride</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX3](=[OX1])-[CX3](=[OX1])-[#6]</SMART>
+        <name>1,2-dicarbonyl</name>
+        <desc>1,2-dicarbonyl</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[F,Cl,Br,I]-[CX4]([F,Cl,Br,I])([F,Cl,Br,I])-[CX3](=[OX1])-[CX4H2]-[#6]</SMART>
+        <name>perhalo-ketone</name>
+        <desc>perhalo-ketone</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[CH3]-[CX3](=[OX1])([CH2])-[#6]</SMART>
+        <name>aliphatic ketone</name>
+        <desc>aliphatic ketone</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4]1-[OX2]-[CX4]1</SMART>
+        <name>epoxide</name>
+        <desc>epoxide</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4]1-[NX3](-[#6])-[CX4]1-[#6]</SMART>
+        <name>aziridine</name>
+        <desc>aziridine</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4H2]-[CX3](=[OX1])-[OX2]-[#6]</SMART>
+        <name>aliphatic ester</name>
+        <desc>aliphatic ester</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4H2]-[CX3](=[OX1])-[SX2]-[#6]</SMART>
+        <name>aliphatic thioester</name>
+        <desc>aliphatic thioester</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4H2]-[SX4](=[OX1])(=[OX1])-[OX2]-[#6]</SMART>
+        <name>sulphonate ester</name>
+        <desc>sulphonate ester</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4H2]-[PX4](=[OX1])(-O)-[OX2]-[#6]</SMART>
+        <name>phosphonate ester</name>
+        <desc>phosphonate ester</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[CX4H2]-[CX3](=[NX2]-[#6])-[#6]</SMART>
+        <name>imine</name>
+        <desc>imine</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[CX3H1](=[OX1])-[#6]</SMART>
+        <name>aldehyde</name>
+        <desc>aldehyde</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-[C](-[#1])=[C](-[#1,C])-[CX3](=O)-[#6]</SMART>
+        <name>Michael acceptor</name>
+        <desc>Michael acceptor</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-[CX4H1](-[F,Cl,Br,I])-[CX4H2]-[CX3](=O)-[#6]</SMART>
+        <name>b-heterosubstitued carbonyl</name>
+        <desc>b-heterosubstitued carbonyl</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[#6]-[#7,#8,#16;X2]-[#7,#8,#16;X2]-[#6]</SMART>
+        <name>heteroatom-heteroatom single bonds</name>
+        <desc>heteroatom-heteroatom single bonds</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[$([#16X4](=[OX1])(=[OX1])-[C](-[#1,C])=[C](-[#1,C])),$([#16X4+2]([OX1-])([OX1-])-[C](-[#1,C])=[C](-[#1,C]))]</SMART>
+        <name>vinyl sulfone</name>
+        <desc>vinyl sulfone</desc>
+    </pattern>
+</SMARTPatterns>
+

rdworks/predefined/misc/reactive-part-3.xml

@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SMARTPatterns>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-C(=[OX1])-[CH2]-[F,Cl,Br,I]</SMART>
+        <name>alpha-Haloketones</name>
+        <desc>alpha-Haloketones</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-[BX3](-[OX2]-[*,#1])-[OX2]-[*,#1]</SMART>
+        <name>boronic acids boronic esters</name>
+        <desc>boronic acids boronic esters</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-[CH1]=[OX1]</SMART>
+        <name>aldehydes</name>
+        <desc>aldehydes</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-C(=[OX1])-C(-F)(-F)F</SMART>
+        <name>TFMKs</name>
+        <desc>TFMKs</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-C(=[OX1])-C(=[OX1])-*</SMART>
+        <name>1,2-dicarbonyls</name>
+        <desc>1,2-dicarbonyls</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=O)N-C(=C-*)c1cc2c(cc1)S(N(C2=O)*)(=O)=O</SMART>
+        <name>saccharinoids</name>
+        <desc>saccharinoids</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=C-O-[P](=[OX1])(-[O-])-[O-])-C(=[OX1])-[NH]-*</SMART>
+        <name>phosphoryl-serine phosphoryl-threonine</name>
+        <desc>phosphoryl-serine phosphoryl-threonine</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=C-c1ccc(-O-[PX4](=[OX1])(-[O-])-[O-])cc1)-C(=[OX1])-[NH]-*</SMART>
+        <name>phosphoryl-tyrosine</name>
+        <desc>phosphoryl-tyrosine</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=C-c1ccc(-O-[PX4](=[OX1])(-[O-])-[OX2]-*)cc1)-C(=[OX1])-[NH]-*</SMART>
+        <name>phosphate esters as "in vitro prodrugs"</name>
+        <desc>phosphate esters as "in vitro prodrugs"</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=C-c1ccc(-O-[*X4-3;!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#34;!#35;!#53](=[OX1])(-[O-])-[O])cc1)-C(=[OX1])-[NH]-*</SMART>
+        <name>various metal substitutes for phosphorous</name>
+        <desc>various metal substitutes for phosphorous</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-C(=[OX1])-[NH]-[O-,OH]</SMART>
+        <name>Hydroxamates</name>
+        <desc>Hydroxamates</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-[SH])-C(=[OX1])-[NH]-*</SMART>
+        <name>thiols</name>
+        <desc>thiols</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-[SH])-C(=[OX1])-[NH]-[OH]</SMART>
+        <name>double trouble</name>
+        <desc>double trouble</desc>
+    </pattern>
+    <pattern active="true">
+        <SMART>[*]-C(=[OX1])-[NH]-C(=[CH1]-*)-C(=N-[OH])-*</SMART>
+        <name>oximes</name>
+        <desc>oximes</desc>
+    </pattern>
+</SMARTPatterns>
+