diff options
| author | Christoph Helma <helma@in-silico.ch> | 2015-12-15 17:28:31 +0100 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2015-12-15 17:28:31 +0100 |
| commit | 9c785ea4c33001a88e801233bf3a7da505792c36 (patch) | |
| tree | 2a3329346544fe0946942ec2a6002bdd65c55679 | |
| parent | 7d094e529df126bba3f30c8a039972062678c39c (diff) | |
activity comparison of datasets
42 files changed, 12532 insertions, 1525 deletions
diff --git a/loael-dataset-comparison.rb b/loael-dataset-comparison.rb deleted file mode 100644 index ad708d3..0000000 --- a/loael-dataset-comparison.rb +++ /dev/null @@ -1,113 +0,0 @@ -require_relative '../lazar/lib/lazar' -include OpenTox -#$mongo.database.drop -#$gridfs = $mongo.database.fs # recreate GridFS indexes -# compare duplicates within datasets -old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mmol_corrected_smiles.csv") -new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL.csv") - -combined_compounds = old.compound_ids & new.compound_ids - -compound_vector = [] -value_vector = [] -dataset_vector = [] - -combined_compounds.each do |cid| - c = Compound.find cid - old.values(c,old.features.first).each do |v| - compound_vector << c.smiles - value_vector << -Math.log(v) - dataset_vector << old.name - end - new.values(c,new.features.first).each do |v| - compound_vector << c.smiles - value_vector << -Math.log(v) - dataset_vector << new.name - end -end - -R.assign "smi", compound_vector -R.assign "values", value_vector -R.assign "dataset", dataset_vector -R.eval "df <- data.frame(factor(smi),values,factor(dataset))" -R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))" -R.eval "img <- img + scale_x_discrete(breaks=NULL) + geom_point() + coord_flip() + ylab('-log(LOAEL)') + xlab('Compound')" -R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-dataset-comparison.svg', plot=img)" - -=begin - -vars = [] - -[old, new].each do |dataset| - vars << [] - #vars[dataset.name] = [] - p dataset.name - p dataset.compounds.size - p dataset.duplicates(dataset.features.first).size - dataset.duplicates.each do |cid,values| - R.assign "values", values - var = R.eval("var(-log(values))").to_f - vars.last << var - #smi = Compound.find(cid).smiles - smi = cid.to_s - values.each do |val| - compound_vector << smi - value_vector << - Math.log(val) - dataset_vector << dataset.name - end - #vars << { :var => var, :values => values, :smiles => smi } - end - #vars.sort!{|a,b| a[:var] <=> b[:var]} - #vars.each do |dup| - #dup[:values].each do |v| - #compound_vector << dup[:smiles] - #value_vector << v - #end - #end -end -#p vars -# TODO statistical test for variances -R.assign "vars1", vars[0] -R.assign "vars2", vars[1] -print "p-value: #{R.eval("t.test(vars1,vars2)$p.value").to_f}" - -R.assign "smi", compound_vector -R.assign "values", value_vector -R.assign "dataset", dataset_vector -R.eval "df <- data.frame(factor(smi),values,factor(dataset))" -R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))" -R.eval "img <- img + scale_x_discrete(breaks=NULL) + geom_point() + coord_flip()"# + xlab('-log(LOAEL)'), ylab('Compound')" -R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael_variance.svg', plot=img)" -#R.eval "print(img)" -#R.eval "write.csv(df,'/home/ch/opentox/lazar-nestec-data/loael.csv')" -#`inkview /home/ch/opentox/lazar-nestec-data/loael_variance.svg` -#R.eval "ggsave(file='test.svg', plot=img)" -# compare datasets -# compare combined datasets -file = File.join(File.dirname(__FILE__),"regression","LOAEL-rat-combined.csv") -d = Dataset.from_csv_file file -replicates = [] -compounds = d.compound_ids.uniq -sds = [] -compounds.each do |cid| - compound_idxs = d.compound_ids.each_index.select{|i| d.compound_ids[i] == cid} - if compound_idxs.size > 1 - vals = compound_idxs.collect{|i| d.data_entries[i].first } - R.assign "values", vals - #sd = R.eval("sd(-log(values))").to_f - sd = R.eval("var(values)").to_f - sds << { :sd => sd, :values => vals, :smiles => Compound.find(cid).smiles } - #replicates << compound_idxs.collect{|i| d.data_entries[i].first } - #replicates[Compound.find(cid).smiles] = compound_idxs.collect{|i| d.data_entries[i].first } - end -end -p sds.sort{|a,b| a[:sd] <=> b[:sd]} -#R.assign "replicates", replicates -#R.assign "compounds", compounds.collect{|id| Compound.find id } -#R.eval "df = data.frame(compounds,replicates)" -#library(ggplot2) -#qplot(compounds, replicates, data=df, geom="boxplot") -#p replicates.to_json -#p replicates.size -# http://www.unc.edu/courses/2008spring/psyc/270/001/variance.html -=end diff --git a/loael-dataset-comparison.svg b/loael-dataset-comparison.svg deleted file mode 100644 index 665c236..0000000 --- a/loael-dataset-comparison.svg +++ /dev/null @@ -1,796 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="503pt" height="503pt" viewBox="0 0 503 503" version="1.1"> -<defs> -<g> -<symbol overflow="visible" id="glyph0-0"> -<path style="stroke:none;" d=""/> -</symbol> -<symbol overflow="visible" id="glyph0-1"> -<path style="stroke:none;" d="M 2.71875 -3 L 0.4375 -3 L 0.4375 -2.296875 L 2.71875 -2.296875 Z M 2.71875 -3 "/> -</symbol> -<symbol 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File.join(File.dirname(__FILE__),"regression","LOAEL-rat-combined.csv") - -compound_vector = [] -value_vector = [] -dataset_vector = [] - -vars = [] - -[old, new].each do |dataset| - vars << [] - #vars[dataset.name] = [] - p dataset.name - p dataset.compounds.size - p dataset.duplicates(dataset.features.first).size - dataset.duplicates.each do |cid,values| - R.assign "values", values - var = R.eval("var(-log(values))").to_f - vars.last << var - #smi = Compound.find(cid).smiles - smi = cid.to_s - values.each do |val| - compound_vector << smi - value_vector << - Math.log(val) - dataset_vector << dataset.name - end - #vars << { :var => var, :values => values, :smiles => smi } - end - #vars.sort!{|a,b| a[:var] <=> b[:var]} - #vars.each do |dup| - #dup[:values].each do |v| - #compound_vector << dup[:smiles] - #value_vector << v - #end - #end -end -#p vars -# TODO statistical test for variances -R.assign "vars1", vars[0] -R.assign "vars2", vars[1] -print "p-value: #{R.eval("t.test(vars1,vars2)$p.value").to_f}" - -R.assign "smi", compound_vector -R.assign "values", value_vector -R.assign "dataset", dataset_vector -R.eval "df <- data.frame(factor(smi),values,factor(dataset))" -R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))" -R.eval "img <- img + scale_x_discrete(breaks=NULL) + geom_point() + coord_flip()"# + xlab('-log(LOAEL)'), ylab('Compound')" -R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael_variance.svg', plot=img)" -#R.eval "print(img)" -#R.eval "write.csv(df,'/home/ch/opentox/lazar-nestec-data/loael.csv')" -#`inkview /home/ch/opentox/lazar-nestec-data/loael_variance.svg` -#R.eval "ggsave(file='test.svg', plot=img)" -=begin -# compare datasets -# compare combined datasets -file = File.join(File.dirname(__FILE__),"regression","LOAEL-rat-combined.csv") -d = Dataset.from_csv_file file -replicates = [] -compounds = d.compound_ids.uniq -sds = [] -compounds.each do |cid| - compound_idxs = d.compound_ids.each_index.select{|i| d.compound_ids[i] == cid} - if compound_idxs.size > 1 - vals = compound_idxs.collect{|i| d.data_entries[i].first } - R.assign "values", vals - #sd = R.eval("sd(-log(values))").to_f - sd = R.eval("var(values)").to_f - sds << { :sd => sd, :values => vals, :smiles => Compound.find(cid).smiles } - #replicates << compound_idxs.collect{|i| d.data_entries[i].first } - #replicates[Compound.find(cid).smiles] = compound_idxs.collect{|i| d.data_entries[i].first } - end -end -p sds.sort{|a,b| a[:sd] <=> b[:sd]} -#R.assign "replicates", replicates -#R.assign "compounds", compounds.collect{|id| Compound.find id } -#R.eval "df = data.frame(compounds,replicates)" -#library(ggplot2) -#qplot(compounds, replicates, data=df, geom="boxplot") -#p replicates.to_json -#p replicates.size -# http://www.unc.edu/courses/2008spring/psyc/270/001/variance.html -=end diff --git a/loael_variance.svg b/loael_variance.svg index 8dd54db..657f50f 100644 --- a/loael_variance.svg +++ 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+'S=P(OC)(OC)SCN1N=Nc2ccccc2C1(=O)',2.58 +'CCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)Cl',1 +'CCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)C',5.8 +'CCC1=NC(=CC(=N1)OP(=S)(OC)OC)OCC',0.45 +'S=P(OC)(OC)SCN1C(=O)SC(OC)=N1',1.6 +'CCOP(=S)(OCC)SCN1C2=C(C=C(C=C2)Cl)OC1=O',2 +'COP(=S)(OC)SCN2C(=O)c1ccccc1C2(=O)',9 +'CCOC(=O)C1=CN2C(=CC(=N2)OP(=S)(OCC)OCC)N=C1C',4 +'CCOP(=S)(OCC)OC1=NN(C=N1)C2=CC=CC=C2',1.3 +'O=C(Oc(c(c(ccc1)cc2)c1)c2)NC',60 +'CC1=CC(=CC(=C1SC)C)OC(=O)NC',9.3 +'CNC(=O)ON=C(C)SC',20 +'CCCOC(=O)NCCCN(C)C',680 +'COC(=O)NC1=NC2=CC=CC=C2N1',75 +'CC1=C(N=C(N=C1OC(=O)N(C)C)N(C)C)C',12.3 +'CNC(=O)CCSCCSP(=O)(OC)OC',0.54 +'N(C(=S)SSC(N(C)C)=S)(C)C',12 +'C1=NNC(=N1)N',5 +'CCCCCCCCc1cc(N(=O)(=O))c(OC(=O)C=CC)c(c1)N(=O)(=O)',64 +'C1=CC=C(C=C1)[Sn](C2=CC=CC=C2)C3=CC=CC=C3',0.3 +'O=C(NC(=O)c(c(F)ccc1)c1F)Nc(ccc(c2)Cl)c2',7 +'N(C(=S)NC1)C1',1.25 +'C1=CC(=C(C(=C1)F)C(=O)NC(=O)NC2=CC(=C(C(=C2F)Cl)F)Cl)F',25 +'CCCSC1=CC2=C(C=C1)N=C(N2)NC(=O)OC',20 +'C1CN(CCN1CCCC(=O)C2=CC=C(C=C2)F)C3=CC=CC=N3',115 +'CC1(C2C(C3C(C(=O)C(=C(N)O)C(=O)C3(C(=O)C2=C(C4=C(C=CC(=C41)Cl)O)O)O)N(C)C)O)O',5200 +'CC1=CC(=C(C=C1NC(=O)C2=CC(=CC(=C2O)I)I)Cl)C(C#N)C3=CC=C(C=C3)Cl',10 +'CN1CC2CC1CN2C3=C(C=C4C(=C3)N(C=C(C4=O)C(=O)O)C5CC5)F',50 +'C1=CC(=CC=C1C(C#N)C2=C(C=CC(=C2Cl)N3C(=O)NC(=O)C=N3)Cl)Cl',15 +'CC1=NC=C(N1C)[N+](=O)[O-]',15 +'CCN1CCN(CC1)C2=C(C=C3C(=C2)N(C=C(C3=O)C(=O)O)C4CC4)F',26 +'CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)NC(=O)C)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O',1 +'COCC(=O)NC1=C(C=CC(=C1)SC2=CC=CC=C2)NC(=NC(=O)OC)NC(=O)OC',40 +'CC1CCC2=C3N1C=C(C(=O)C3=CC(=C2)F)C(=O)O',400 +'COC(=O)NC1=NC2=C(N1)C=C(C=C2)S(=O)C3=CC=CC=C3',2 +'CC1(C2CC3C(C(=O)C(=C(N)O)C(=O)C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)N(C)C)O',150 +'C1CN(CCN1CCCC(=O)C2=CC=C(C=C2)F)C3=CC=CC=N3',30 +'CC(C)NCC(COC1=CC=CC2=C1C3=CC=CC=C3N2)O',7 +'C1=CC(=CC=C1C(C#N)C2=C(C=CC(=C2Cl)N3C(=O)NC(=O)C=N3)Cl)Cl',23 +'CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)NC(=O)C)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O',2.5 +'COP(=S)(OC)Oc1ccc(SC)c(C)c1',0.45 +'C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl',8 +'C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl',4 +'CC(N(C)C)CN(C(=CC=C3)C1=C3)C(=CC=C2)C(=C2)S1',16.6 +'C1=C(C=C(C(=C1Cl)N)Cl)[N+](=O)[O-]',240 +'c(cccc1)(c1)C=C',400 diff --git a/regression/NOAEL-LOAEL_dv.xlsx b/original/NOAEL-LOAEL_dv.xlsx Binary files differindex 34361cf..34361cf 100644 --- a/regression/NOAEL-LOAEL_dv.xlsx +++ b/original/NOAEL-LOAEL_dv.xlsx diff --git a/regression/NOAEL-LOAEL_elena_email_20150306.xlsx b/original/NOAEL-LOAEL_elena_email_20150306.xlsx Binary files differindex be6065a..be6065a 100644 --- a/regression/NOAEL-LOAEL_elena_email_20150306.xlsx +++ b/original/NOAEL-LOAEL_elena_email_20150306.xlsx diff --git a/original/box.png b/original/box.png Binary files differnew file mode 100755 index 0000000..9b450e5 --- /dev/null +++ b/original/box.png diff --git a/original/deviation_analysis.R b/original/deviation_analysis.R new file mode 100755 index 0000000..7e94616 --- /dev/null +++ b/original/deviation_analysis.R @@ -0,0 +1,30 @@ +# GID ("group id") indicates groups (measurements per molecule) +# MMOL indicates measurements +mydata = read.csv("LOAEL-Duplicates-mmol.csv") + + +# list of per-group deviations from the means (errors) +group_deviation = lapply(split(mydata,mydata$GID),function(x) + +# list of per-group variances +group_var=lapply(group_deviation, function(x) var(x)) + +# list of per-group means +group_mean = lapply(split(mydata, mydata$GID), function(x) mean(x$MMOL)) + +# gr mean vs gr var +png("gr_m_var.png") +plot(log(unlist(lapply(group_deviation, function(x) var(x)))) ~ unlist(group_mean), ylab='Group variance of residuals (ln)', xlab='Group mean', main="Group mean vs Group variance") +dev.off() + +# pooled residuals (plot result shows no interaction) +pooled_residuals = as.vector(unlist(group_deviation)) + +# S-form indicates heavier tails of standard normal, but no skew visible +png("qq_resid.png") +qqnorm(pooled_residuals,main="QQ pooled residuals") +dev.off() + + +cat(paste("SD of pooled residuals:",sd(pooled_residuals),"\n")) + diff --git a/original/gr_m_var.png b/original/gr_m_var.png Binary files differnew file mode 100755 index 0000000..78e4df6 --- /dev/null +++ b/original/gr_m_var.png diff --git a/original/loael_in_drei_formaten.R b/original/loael_in_drei_formaten.R Binary files differnew file mode 100755 index 0000000..6d6ee47 --- /dev/null +++ b/original/loael_in_drei_formaten.R diff --git a/original/loael_in_drei_formaten_corrected_smiles.R b/original/loael_in_drei_formaten_corrected_smiles.R Binary files differnew file mode 100755 index 0000000..2d7f5f9 --- /dev/null +++ b/original/loael_in_drei_formaten_corrected_smiles.R diff --git a/original/qq.png b/original/qq.png Binary files differnew file mode 100755 index 0000000..d8aae52 --- /dev/null +++ b/original/qq.png diff --git a/original/qq_resid.png b/original/qq_resid.png Binary files differnew file mode 100755 index 0000000..c0ad8ce --- /dev/null +++ b/original/qq_resid.png diff --git a/paper/SMARTS_InteLigand.txt b/paper/SMARTS_InteLigand.txt new file mode 100644 index 0000000..23bc6e2 --- /dev/null +++ b/paper/SMARTS_InteLigand.txt @@ -0,0 +1,983 @@ +# +# SMARTS Patterns for Functional Group Classification +# +# written by Christian Laggner +# Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH +# +# Released under the Lesser General Public License (LGPL license) +# see http://www.gnu.org/copyleft/lesser.html +# Modified from Version 221105 +##################################################################################################### + +# General Stuff: +# These patters were written in an attempt to represent the classification of organic compounds +# from the viewpoint of an organic chemist. +# They are often very restrictive. This may be generally a good thing, but it also takes some time +# for filtering/indexing large compound sets. +# For filtering undesired groups (in druglike compounds) one will want to have more general patterns +# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...). +# + +# Part I: Carbon +# ============== + + +# I.1: Carbon-Carbon Bonds +# ------------------------ + +# I.1.1 Alkanes: + +Primary_carbon: [CX4H3][#6] + +Secondary_carbon: [CX4H2]([#6])[#6] + +Tertiary_carbon: [CX4H1]([#6])([#6])[#6] + +Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6] + + +# I.1.2 C-C double and Triple Bonds + +Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] +# sp2 C may be substituted only by C or H - +# does not hit ketenes and allenes, nor enamines, enols and the like + +Alkyne: [CX2]#[CX2] +# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination + +Allene: [CX3]=[CX2]=[CX3] + + +# I.2: One Carbon-Hetero Bond +# --------------------------- + + +# I.2.1 Alkyl Halogenides + +Alkylchloride: [ClX1][CX4] +# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats +# a more restrictive version can be obtained by modifying the Alcohol string. + +Alkylfluoride: [FX1][CX4] + +Alkylbromide: [BrX1][CX4] + +Alkyliodide: [IX1][CX4] + + +# I.2.2 Alcohols and Ethers + +Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] +# nonspecific definition, no acetals, aminals, and the like + +Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])] + +Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])] + +Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])] + +Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] +# no acetals and the like; no enolethers + +Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] +# no acetals and the like; no enolethers + +Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] +# no acetals and the like; no enolethers + +Diarylether: [c][OX2][c] + +Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] + +Diarylthioether: [c][SX2][c] + +Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])] +# can't be aromatic, thus O and not #8 + +# I.2.3 Amines + +Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])] +# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ... + +# the following amines include also the protonated forms + +Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Primary_arom_amine: [NX3H2+0,NX4H3+]c + +Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] + +Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] + +Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] + +Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])] + +Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])] + +Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])] + +Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])] +# only C and H substituents allowed. Quaternary or protonated amines +# NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present + + +# I.2.4 Others + +Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])] + +Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])] + +Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])] + +Disulfide: [SX2D2][SX2D2] + +1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])] +# does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc. + +1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H] +# does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc. + +1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H] + +Hydroperoxide: [OX2H][OX2] +#does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides + +Peroxo: [OX2D2][OX2D2] + +Organolithium_compounds: [LiX1][#6,#14] + +Organomagnesium_compounds: [MgX2][#6,#14] +# not restricted to Grignard compounds, also dialkyl Mg + +Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-] +# very general, includes all metals covalently bound to carbon + + +# I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives) +# ---------------------------- + +# I.3.1 Double Bond to Hetero + +Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1] +# hits aldehydes including formaldehyde + +Ketone: [#6][CX3](=[OX1])[#6] +# does not include oxo-groups connected to a (hetero-) aromatic ring + +Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1] + +Thioketone: [#6][CX3](=[SX1])[#6] +# does not include thioxo-groups connected to a (hetero-) aromatic ring + +Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])] +# nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar + +Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])] + +Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H] + +Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])] +# ether, not ester or amide; does not hit isoxazole + + +# I.3.2. Two Single Bonds to Hetero + +Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] +# does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc. + +Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] + +Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] +# Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups + +Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H] + +Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])] + +Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H] + +Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] +# hits chloromethylenethers and other reactive alkylating agents + +Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +# includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar + +Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] +# also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed + +NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +# Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side + +Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +# Combination of the last two patterns + +Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H] + + +# I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar) + +Chloroalkene: [ClX1][CX3]=[CX3] + +Fluoroalkene: [FX1][CX3]=[CX3] + +Bromoalkene: [BrX1][CX3]=[CX3] + +Iodoalkene: [IX1][CX3]=[CX3] + +Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3] +# no phenols + +Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H] +# no 1,2-diphenols, ketenacetals, ... + +Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3] +# finds also endiodiethers, but not enolesters, no aromats + +Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])] + + +Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3] +# does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic + +Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3] + +Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3] + + +# I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives) +# ------------------------------ + +Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] + +Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] + +Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] + +Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1] + +Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1] +# all of the above + + +# The following contains all simple carboxylic combinations of O, N, S, & Hal - +# - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...) +# Cyclic structures (including aromats) like lactones, lactames, ... got their own +# definitions. Structures where both heteroatoms are part of an aromatic ring +# (oxazoles, imidazoles, ...) were excluded. + +Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])] +# includes carboxylate anions + +Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])] +# does not hit anhydrides or lactones + +Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])] +# may also be aromatic + +Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1]) +# anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic + +Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6] +# includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole + +Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])] +# hits both tautomeric forms, as well as anions + +Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])] + +Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])] +# may also be aromatic + +Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])] + +Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])] + +Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1] + +Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])] + +Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])] + +Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])] + + +Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# does not hit lactames + +Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2] + +Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])] + +Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])] + +Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# cyclic amides, may also be aromatic + +Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) +# may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide + +N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) +# everything else than H or C at central N + +Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1]) +# can be deprotonated + +Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# does not hit thiolactames + +Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# cyclic thioamides, may also be aromatic + + +Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])] +# may also be part of a ring / aromatic + +Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])] +# only basic amidines, not as part of aromatic ring (e.g. imidazole) + +Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])] + +Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])] +# does not hit anhydrides of carboxylic acids withs hydroxamic acids + + +Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +# not cyclic + +Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +# the enamide-form of lactames. may be aromatic like 2-hydroxypyridine + +Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] +# esters of the above structures. no anhydrides. + +Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] +# no oxazoles and similar + +Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] +# not cyclic + +Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] +# the enamide-form of thiolactames. may be aromatic like 2-thiopyridine + +Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] +# thioesters of the above structures. no anhydrides. + +Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] +# no thioxazoles and similar + +Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])] +# only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring + +Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])] +# one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole + +Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] +# not cyclic + +Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] +# may also be aromatic + +# may be ring, aromatic, substituted with carbonyls, hetero, ... +# (everything else would get too complicated) + +Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])] +# hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ... + + +Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-] +# N may be alkylated, but not part of an amide (as in peptides), ionic forms are included +# includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C +# N may not be aromatic as in 1H-pyrrole-2-carboxylic acid + +Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-] + +Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] +# finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides + +Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-] +# finds C-terminal amino acids + +Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] +# finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond. + + +Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] +# hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues) + +Ketene: [CX3]=[CX2]=[OX1] + +Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3] +# includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be + +Nitrile: [NX1]#[CX2] +# includes cyanhydrines + +Isonitrile: [CX1-]#[NX2+] + + +Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I] +# may be part of a ring, even aromatic + +Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])] + +Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])] + +Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1] + + + +# I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives) +# ----------------------------- + +Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])] +# may be part of a ring, even aromatic + +Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1] + +Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])] +# unstable + +Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6] + + +Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])] +# may be part of a ring, even aromatic + +Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1] + +Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])] + + +Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])] +# no check whether part of imide, biuret, etc. Aromatic structures are only hit if +# both N share no double bonds, like in the dioxo-form of uracil + +Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])] + +Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])] +# O may be substituted. no check whether further amide-like bonds are present. Aromatic +# structures are only hit if single bonded N shares no additional double bond, like in +# the 1-hydroxy-3-oxo form of uracil + +Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])] + +Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+] +# also hits guanidinium salts. v3 and v4 to avoid nitroamidines + +Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-] +# quite unstable, unlikely to be found. Also hits salts + +Urethan: [#7X3][#6](=[OX1])[#8X2][#6] +# also hits when part of a ring, no check whether the last C is part of carbonyl + +Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3] + +Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] + +Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1] + +Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] + +Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1] + +Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] + +Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1] + +Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] + +Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1] + + +Isocyanate: [NX2]=[CX2]=[OX1] + +Cyanate: [OX2][CX2]#[NX1] + +Isothiocyanate: [NX2]=[CX2]=[SX1] + +Thiocyanate: [SX2][CX2]#[NX1] + +Carbodiimide: [NX2]=[CX2]=[NX2] + +Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I] +# halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more +# stable as for example C(OCH3)4) + + +# I.6 Aromatics +# ------------- + +# I know that this classification is not very logical, arylamines are found under I.2 ... + +Phenol: [OX2H][c] + +1,2-Diphenol: [OX2H][c][c][OX2H] + +Arylchloride: [Cl][c] + +Arylfluoride: [F][c] + +Arylbromide: [Br][c] + +Aryliodide: [I][c] + +Arylthiol: [SX2H][c] + +Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])] +# N may be substituted with H or C, but not carbonyl or similar +# aromatic atom is always C, not S or P (these are not planar when substituted) + +Oxoarene: [c]=[OX1] + +Thioarene: [c]=[SX1] + +Hetero_N_basic_H: [nX3H1+0] +# as in pyrole. uncharged to exclude pyridinium ions + +Hetero_N_basic_no_H: [nX3H0+0] +# as in N-methylpyrole. uncharged to exclude pyridinium ions + +Hetero_N_nonbasic: [nX2,nX3+] +# as in pyridine, pyridinium + +Hetero_O: [o] + +Hetero_S: [sX2] +# X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic +# (is not planar because of lonepair at S) + +Heteroaromatic: [a;!c] + + +# Part II: N, S, P, Si, B +# ======================= + + +# II.1 Nitrogen +# ------------- + +Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])] +# hits nitrous acid, its anion, esters, and other O-substituted derivatives + +Thionitrite: [SX2][NX2]=[OX1] + +Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] +# hits nitric acid, its anion, esters, and other O-substituted derivatives + +Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] +# hits nitro groups attached to C,N, ... but not nitrates + +Nitroso: [NX2](=[OX1])[!#7;!#8] +# no nitrites, no nitrosamines + +Azide: [NX1]~[NX2]~[NX2,NX1] +# hits both mesomeric forms, also anion + +Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1] + +Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] + +Diazonium: [#6][NX2+]#[NX1] + +Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1] + +Nitrosamide: [NX2](=[OX1])N-*=O +# includes nitrososulfonamides + +N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] +# Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate. + + +Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])] +# no hydrazides + +Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6] + +Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])] +# no discrimination between O-, N-, and O,N-substitution + + +# II.2 Sulfur +# ----------- + +Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])] +# can't be aromatic, thus S and not #16 + +Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])] + +Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])] +# can't be aromatic, thus S and not #16 + +Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +# includes anions + +Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] + +Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6] +# everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative +# than sulfur, but this should be very very rare, anyway) + + + +#### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + + + +Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])] + +Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])] + +Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1] + +Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6] +# includes all of the above and many more +# for comparison: this is what "all sulfonic derivatives but not the ones above" would look like: +# [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])] + + +Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])] + +Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] + +Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1] + +Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6] + +Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])] + +Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])] + +Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1] + +Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6] + + +# II.3 Phosphorous +# ---------------- + +Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])] +# similar to amine, but less restrictive: includes also amide- and aminal-analogues + +Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])] + +Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])] +# similar to Ammonium + +Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])] + + +# conventions for the following acids and derivatives: +# acids find protonated and deprotonated acids +# esters do not find mixed anhydrides ( ...P-O-C(=O)) +# derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O, +# thus including acids and esters) + +Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +# includes anions + +Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6] +# all of the above and much more + + +Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +# includes anions + +Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6] + + +Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])] + +Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] + +Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6] + + +Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] + +Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6] + + +Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])] + +Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])] + +Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6] + + +# II.4 Silicon +# ------------ + +Quart_silane: [SiX4]([#6])([#6])([#6])[#6] +# four C-substituents. non-reactive, non-toxic, in experimental phase for drug development + +Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])] +# has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to +# the free positions at Si, thus Hs had to be added implicitly + +Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6] +# reagents for inserting protection groups + +Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6] +# mostly acid-labile protection groups such as trimethylsilyl-ethers + +Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6] + +Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6] + +Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6] +# four substituent which are neither C nor H + + +# II.5 Boron +# ---------- + +Trialkylborane: [BX3]([#6])([#6])[#6] +# also carbonyls allowed + +Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6] +# includes acids, esters, amides, ... H-substituent at B is very rare. + +Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6] +# # includes acids, esters, amides, ... + +Borohydride: [BH1,BH2,BH3,BH4] +# at least one H attached to B + +Quaternary_boron: [BX4] +# mostly borates (negative charge), in complex with Lewis-base + + + +# Part III: Some Special Patterns +# =============================== + + +# III.1 Chains +# ------------ + +# some simple chains + + + +# III.2 Rings +# ----------- + +Aromatic: a + +Heterocyclic: [!#6;!R0] +# may be aromatic or not + +Epoxide: [OX2r3]1[#6r3][#6r3]1 +# toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione) + +NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1 +# toxic/reactive according to Maybridge's garbage filter + +Spiro: [D4R;$(*(@*)(@*)(@*)@*)] +# at least two different rings can be found which are sharing just one atom. +# these two rings can be connected by a third ring, so it matches also some +# bridged systems, like morphine + +Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])] +# two different rings sharing exactly two atoms + +Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])] +# part of two or more rings, not spiro, not annelated -> finds bridgehead atoms, +# but only if they are not annelated at the same time - otherwise impossible (?) +# to distinguish from non-bridgehead annelated atoms + +# some basic ring-patterns (just size, no other information): + + + + + +# III.3 Sugars and Nucleosides/Nucleotides, Steroids +# -------------------------------------------------- + +# because of the large variety of sugar derivatives, different patterns can be applied. +# The choice of patterns and their combinations will depend on the contents of the database +# e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the +# desired restriction + + +Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)] +# 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents. + +Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +# 5 or 6-membered ring containing one O and an acetal-like bond at postion 2. + +Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)] +# combination of the two above + +Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)] +# 5 or 6-membered cyclic hemi-acetal + +Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +# 5 or 6-membered cyclic hemi-acetal + +Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +# 5 or 6-membered cyclic hemi-acetal + +##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]) +# pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!) + +##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]) +# pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!) + + +# III.4 Everything else... +# ------------------------ + +Conjugated_double_bond: *=*[*]=,#,:[*] + +Conjugated_tripple_bond: *#*[*]=,#,:[*] + +Cis_double_bond: */[D2]=[D2]\* +# only one single-bonded substituent on each DB-atom. no aromats. +# only found when character of DB is explicitely stated. + +Trans_double_bond: */[D2]=[D2]/* +# analog + +Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))] +# should hits all combinations of two acids + +Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6] + +Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])] +# Halogen which is not mono-substituted nor an anion, e.g. chlorate. +# Most of these cases should be also filtered by Halogen_on_hetero. + +Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1]) +# C with three F attached, connected to anything which is not another halogen + +C_ONS_bond: [#6]~[#7,#8,#16] +# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter + +## Mixture: (*).(*) +# two or more seperate parts, may also be salt +# component-level grouping is not yet supported in Open Babel Version 2.0 + + +Charged: [!+0] + +Anion: [-1,-2,-3,-4,-5,-6,-7] + +Kation: [+1,+2,+3,+4,+5,+6,+7] + +Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7]) +# two or more seperate components with opposite charges + +##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7]) +# both negative and positive charges somewhere within the same molecule. + +1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)] +# 1,3 migration of H allowed. Includes keto/enol and amide/enamide. +# Aromatic rings must stay aromatic - no keto form of phenol + +1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)] + +Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1] +# taken from http://www.daylight.com/support/contrib/smarts/content.html + +Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])] +# the classical case: C=C near carbonyl, nitrile, nitro, or similar +# Oxo-heteroaromats and similar are not included. + +Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1]) +# Michael-like acceptor, see Mitsunobu reaction + +# H-Bond_donor: + +# H-Bond_acceptor: + +# Pos_ionizable: + +# Neg_ionizable: + +# Unlikely_ions: +# O+,N-,C+,C-, ... + +CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)] +# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed. +# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded. +# hits also CH-acidic_strong + +CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])] +# same as above (without pentadiene), but carbonyl or similar on two or three sides + +Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)] +# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string +# depictmach does not find oxonium, sulfonium, or sulfoxides! + +# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)] +# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string +# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0 +
\ No newline at end of file diff --git a/paper/functional-groups.csv b/paper/functional-groups.csv new file mode 100644 index 0000000..414c28c --- /dev/null +++ b/paper/functional-groups.csv @@ -0,0 +1,307 @@ +Primary_carbon, 303, 287 +Secondary_carbon, 147, 149 +Tertiary_carbon, 91, 73 +Quaternary_carbon, 58, 60 +Alkene, 39, 30 +Alkyne, 5, 8 +Allene, 0, 0 +Alkylchloride, 71, 41 +Alkylfluoride, 52, 74 +Alkylbromide, 5, 3 +Alkyliodide, 0, 0 +Alcohol, 44, 27 +Primary_alcohol, 12, 2 +Secondary_alcohol, 23, 10 +Tertiary_alcohol, 18, 21 +Dialkylether, 35, 32 +Dialkylthioether, 14, 6 +Alkylarylether, 62, 90 +Diarylether, 35, 47 +Alkylarylthioether, 11, 10 +Diarylthioether, 3, 0 +Oxonium, 0, 0 +Amine, 66, 41 +Primary_aliph_amine, 8, 3 +Secondary_aliph_amine, 2, 2 +Tertiary_aliph_amine, 16, 9 +Quaternary_aliph_ammonium, 1, 6 +Primary_arom_amine, 26, 15 +Secondary_arom_amine, 2, 1 +Tertiary_arom_amine, 19, 0 +Quaternary_arom_ammonium, 0, 0 +Secondary_mixed_amine, 8, 3 +Tertiary_mixed_amine, 14, 7 +Quaternary_mixed_ammonium, 0, 0 +Ammonium, 1, 6 +Alkylthiol, 0, 0 +Dialkylthioether, 10, 4 +Alkylarylthioether, 10, 10 +Disulfide, 4, 2 +1,2-Aminoalcohol, 5, 0 +1,2-Diol, 12, 3 +1,1-Diol, 1, 0 +Hydroperoxide, 0, 0 +Peroxo, 0, 0 +Organolithium_compounds, 0, 0 +Organomagnesium_compounds, 0, 0 +Organometallic_compounds, 1, 5 +Aldehyde, 3, 1 +Ketone, 21, 25 +Thioaldehyde, 0, 0 +Thioketone, 0, 0 +Imine, 0, 0 +Immonium, 0, 0 +Oxime, 0, 0 +Oximether, 7, 15 +Acetal, 13, 13 +Hemiacetal, 1, 0 +Aminal, 1, 0 +Hemiaminal, 0, 0 +Thioacetal, 0, 0 +Thiohemiacetal, 0, 0 +Halogen_acetal_like, 13, 14 +Acetal_like, 34, 30 +Halogenmethylen_ester_and_similar, 1, 0 +NOS_methylen_ester_and_similar, 18, 19 +Hetero_methylen_ester_and_similar, 19, 19 +Cyanhydrine, 0, 0 +Chloroalkene, 39, 21 +Fluoroalkene, 0, 1 +Bromoalkene, 1, 2 +Iodoalkene, 1, 0 +Enol, 4, 5 +Endiol, 2, 0 +Enolether, 2, 4 +Enolester, 0, 6 +Enamine, 0, 1 +Thioenol, 0, 0 +Thioenolether, 1, 1 +Acylchloride, 0, 0 +Acylfluoride, 0, 0 +Acylbromide, 0, 0 +Acyliodide, 0, 0 +Acylhalide, 0, 0 +Carboxylic_acid, 33, 38 +Carboxylic_ester, 0, 0 +Lactone, 11, 10 +Carboxylic_anhydride, 1, 0 +Carboxylic_acid_derivative, 215, 227 +Carbothioic_acid, 0, 0 +Carbothioic_S_ester, 1, 1 +Carbothioic_S_lactone, 0, 0 +Carbothioic_O_ester, 0, 0 +Carbothioic_O_lactone, 0, 0 +Carbothioic_halide, 0, 0 +Carbodithioic_acid, 0, 0 +Carbodithioic_ester, 0, 0 +Carbodithiolactone, 0, 0 +Amide, 38, 60 +Primary_amide, 2, 1 +Secondary_amide, 22, 36 +Tertiary_amide, 15, 23 +Lactam, 12, 18 +Alkyl_imide, 5, 4 +N_hetero_imide, 6, 3 +Imide_acidic, 0, 0 +Thioamide, 0, 0 +Thiolactam, 0, 0 +Oximester, 0, 0 +Amidine, 3, 4 +Hydroxamic_acid, 0, 0 +Hydroxamic_acid_ester, 1, 1 +Imidoacid, 0, 0 +Imidoacid_cyclic, 0, 2 +Imidoester, 0, 0 +Imidolactone, 13, 32 +Imidothioacid, 0, 0 +Imidothioacid_cyclic, 0, 0 +Imidothioester, 0, 0 +Imidothiolactone, 1, 1 +Amidine, 3, 5 +Imidolactam, 3, 2 +Imidoylhalide, 0, 0 +Imidoylhalide_cyclic, 10, 19 +Amidrazone, 0, 0 +Alpha_aminoacid, 1, 1 +Alpha_hydroxyacid, 0, 0 +Peptide_middle, 0, 0 +Peptide_C_term, 0, 0 +Peptide_N_term, 1, 0 +Carboxylic_orthoester, 0, 0 +Ketene, 0, 0 +Ketenacetal, 0, 0 +Nitrile, 35, 39 +Isonitrile, 0, 0 +Vinylogous_carbonyl_or_carboxyl_derivative, 70, 97 +Vinylogous_acid, 9, 8 +Vinylogous_ester, 113, 120 +Vinylogous_amide, 19, 24 +Vinylogous_halide, 11, 27 +Carbonic_acid_dieester, 0, 2 +Carbonic_acid_esterhalide, 0, 0 +Carbonic_acid_monoester, 0, 0 +Carbonic_acid_derivatives, 109, 131 +Thiocarbonic_acid_dieester, 0, 0 +Thiocarbonic_acid_esterhalide, 0, 0 +Thiocarbonic_acid_monoester, 0, 0 +Urea, 23, 21 +Thiourea, 4, 4 +Isourea, 0, 1 +Isothiourea, 1, 3 +Guanidine, 6, 7 +Carbaminic_acid, 0, 0 +Urethan, 34, 35 +Biuret, 1, 4 +Semicarbazide, 0, 0 +Carbazide, 0, 0 +Semicarbazone, 1, 3 +Carbazone, 0, 0 +Thiosemicarbazide, 1, 0 +Thiocarbazide, 0, 0 +Thiosemicarbazone, 0, 0 +Thiocarbazone, 0, 0 +Isocyanate, 0, 0 +Cyanate, 0, 0 +Isothiocyanate, 0, 0 +Thiocyanate, 0, 0 +Carbodiimide, 0, 0 +Orthocarbonic_derivatives, 0, 0 +Phenol, 27, 9 +1,2-Diphenol, 2, 0 +Arylchloride, 142, 163 +Arylfluoride, 22, 41 +Arylbromide, 4, 8 +Aryliodide, 1, 4 +Arylthiol, 0, 0 +Iminoarene, 0, 1 +Oxoarene, 32, 29 +Thioarene, 1, 2 +Hetero_N_basic_H, 17, 11 +Hetero_N_basic_no_H, 59, 90 +Hetero_N_nonbasic, 127, 191 +Hetero_O, 10, 12 +Hetero_S, 17, 18 +Heteroaromatic, 147, 205 +Nitrite, 0, 0 +Thionitrite, 0, 0 +Nitrate, 0, 0 +Nitro, 42, 31 +Nitroso, 0, 0 +Azide, 0, 0 +Acylazide, 0, 0 +Diazo, 0, 0 +Diazonium, 0, 0 +Nitrosamine, 0, 0 +Nitrosamide, 0, 0 +N-Oxide, 0, 1 +Hydrazine, 1, 0 +Hydrazone, 1, 0 +Hydroxylamine, 3, 0 +Sulfon, 3, 14 +Sulfoxide, 2, 3 +Sulfonium, 0, 0 +Sulfuric_acid, 0, 0 +Sulfuric_monoester, 0, 0 +Sulfuric_diester, 0, 0 +Sulfuric_monoamide, 1, 0 +Sulfuric_diamide, 0, 0 +Sulfuric_esteramide, 0, 1 +Sulfuric_derivative, 5, 8 +Sulfonic_acid, 4, 0 +Sulfonamide, 6, 9 +Sulfonic_ester, 1, 0 +Sulfonic_halide, 0, 0 +Sulfonic_derivative, 24, 29 +Sulfinic_acid, 0, 0 +Sulfinic_amide, 0, 0 +Sulfinic_ester, 0, 0 +Sulfinic_halide, 0, 0 +Sulfinic_derivative, 0, 0 +Sulfenic_acid, 0, 0 +Sulfenic_amide, 0, 0 +Sulfenic_ester, 0, 0 +Sulfenic_halide, 0, 0 +Sulfenic_derivative, 48, 34 +Phosphine, 0, 0 +Phosphine_oxide, 0, 0 +Phosphonium, 0, 0 +Phosphorylen, 0, 0 +Phosphonic_acid, 5, 5 +Phosphonic_monoester, 1, 1 +Phosphonic_diester, 2, 1 +Phosphonic_monoamide, 0, 0 +Phosphonic_diamide, 0, 0 +Phosphonic_esteramide, 0, 0 +Phosphonic_acid_derivative, 10, 7 +Phosphoric_acid, 0, 0 +Phosphoric_monoester, 0, 0 +Phosphoric_diester, 0, 0 +Phosphoric_triester, 10, 3 +Phosphoric_monoamide, 0, 0 +Phosphoric_diamide, 0, 0 +Phosphoric_triamide, 0, 0 +Phosphoric_monoestermonoamide, 0, 0 +Phosphoric_diestermonoamide, 3, 2 +Phosphoric_monoesterdiamide, 0, 0 +Phosphoric_acid_derivative, 70, 44 +Phosphinic_acid, 1, 1 +Phosphinic_ester, 0, 0 +Phosphinic_amide, 0, 0 +Phosphinic_acid_derivative, 1, 1 +Phosphonous_acid, 0, 0 +Phosphonous_monoester, 0, 0 +Phosphonous_diester, 0, 0 +Phosphonous_monoamide, 0, 0 +Phosphonous_diamide, 0, 0 +Phosphonous_esteramide, 0, 0 +Phosphonous_derivatives, 0, 0 +Phosphinous_acid, 0, 0 +Phosphinous_ester, 0, 0 +Phosphinous_amide, 0, 0 +Phosphinous_derivatives, 0, 0 +Quart_silane, 1, 2 +Non-quart_silane, 0, 0 +Silylmonohalide, 0, 0 +Het_trialkylsilane, 0, 0 +Dihet_dialkylsilane, 0, 0 +Trihet_alkylsilane, 0, 0 +Silicic_acid_derivative, 0, 0 +Trialkylborane, 0, 0 +Boric_acid_derivatives, 0, 0 +Boronic_acid_derivative, 0, 0 +Borohydride, 0, 0 +Quaternary_boron, 0, 0 +Aromatic, 402, 396 +Heterocyclic, 228, 272 +Epoxide, 11, 2 +NH_aziridine, 0, 0 +Spiro, 3, 10 +Annelated_rings, 97, 73 +Bridged_rings, 8, 4 +Sugar_pattern_1, 10, 9 +Sugar_pattern_2, 6, 7 +Sugar_pattern_combi, 4, 5 +Sugar_pattern_2_reducing, 1, 0 +Sugar_pattern_2_alpha, 1, 1 +Sugar_pattern_2_beta, 1, 1 +Conjugated_double_bond, 207, 213 +Conjugated_tripple_bond, 10, 19 +Cis_double_bond, 31, 19 +Trans_double_bond, 31, 19 +Mixed_anhydrides, 1, 0 +Halogen_on_hetero, 0, 0 +Halogen_multi_subst, 1, 6 +Trifluoromethyl, 44, 63 +C_ONS_bond, 520, 484 +Charged, 27, 51 +Anion, 26, 45 +Kation, 25, 51 +Salt, 26, 45 +1,3-Tautomerizable, 265, 296 +1,5-Tautomerizable, 124, 148 +Rotatable_bond, 488, 462 +Michael_acceptor, 33, 33 +Dicarbodiazene, 0, 0 +CH-acidic, 60, 73 +CH-acidic_strong, 1, 4 +Chiral_center_specified, 1, 2 diff --git a/paper/functional-groups.rb b/paper/functional-groups.rb new file mode 100644 index 0000000..e961b92 --- /dev/null +++ b/paper/functional-groups.rb @@ -0,0 +1,31 @@ +require_relative '../../lazar/lib/lazar' +include OpenTox +old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression","LOAEL_mg_corrected_smiles_mmol.csv") +new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression","swissRat_chron_LOAEL_mmol.csv") + +functional_groups = {} +#functional_groups[:old] = {} +#functional_groups[:new] = {} +table = [] +#File.open("functional-groups.csv","w+") do |file| + File.open("functional-groups.txt").each_line do |line| + name, smarts = line.chomp.split ": " + if smarts + smarts_feature = Smarts.from_smarts smarts + oldcount = 0 + old.compounds.each do |c| + oldcount += Algorithm::Descriptor.smarts_match(c,smarts_feature).first.to_i + end + newcount = 0 + new.compounds.each do |c| + newcount += Algorithm::Descriptor.smarts_match(c,smarts_feature).first.to_i + end + puts "#{name}, #{oldcount}, #{newcount}" + else + p name, smarts + end + #table << [name, oldcount, newcount] + end +#end +#print table.to_csv +#old_fp = old.compounds.collect{|c| c.fingerprint("FP4")} diff --git a/paper/functional-groups.txt b/paper/functional-groups.txt new file mode 100644 index 0000000..e14fd6c --- /dev/null +++ b/paper/functional-groups.txt @@ -0,0 +1,307 @@ +Primary_carbon: [CX4H3][#6] +Secondary_carbon: [CX4H2]([#6])[#6] +Tertiary_carbon: [CX4H1]([#6])([#6])[#6] +Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6] +Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] +Alkyne: [CX2]#[CX2] +Allene: [CX3]=[CX2]=[CX3] +Alkylchloride: [ClX1][CX4] +Alkylfluoride: [FX1][CX4] +Alkylbromide: [BrX1][CX4] +Alkyliodide: [IX1][CX4] +Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] +Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])] +Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])] +Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])] +Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] +Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] +Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] +Diarylether: [c][OX2][c] +Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] +Diarylthioether: [c][SX2][c] +Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])] +Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])] +Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] +Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] +Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] +Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] +Primary_arom_amine: [NX3H2+0,NX4H3+]c +Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] +Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] +Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] +Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])] +Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])] +Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])] +Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])] +Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])] +Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])] +Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])] +Disulfide: [SX2D2][SX2D2] +1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])] +1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H] +1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H] +Hydroperoxide: [OX2H][OX2] +Peroxo: [OX2D2][OX2D2] +Organolithium_compounds: [LiX1][#6,#14] +Organomagnesium_compounds: [MgX2][#6,#14] +Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-] +Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1] +Ketone: [#6][CX3](=[OX1])[#6] +Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1] +Thioketone: [#6][CX3](=[SX1])[#6] +Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])] +Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])] +Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H] +Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])] +Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] +Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] +Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] +Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H] +Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])] +Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H] +Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] +Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] +NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H] +Chloroalkene: [ClX1][CX3]=[CX3] +Fluoroalkene: [FX1][CX3]=[CX3] +Bromoalkene: [BrX1][CX3]=[CX3] +Iodoalkene: [IX1][CX3]=[CX3] +Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3] +Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H] +Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3] +Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])] +Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3] +Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3] +Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3] +Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] +Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] +Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] +Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1] +Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1] +Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])] +Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])] +Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])] +Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1]) +Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6] +Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])] +Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])] +Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])] +Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])] +Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])] +Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1] +Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])] +Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])] +Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])] +Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2] +Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])] +Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])] +Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) +N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) +Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1]) +Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])] +Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])] +Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])] +Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])] +Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] +Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] +Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] +Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] +Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] +Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] +Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])] +Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])] +Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] +Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] +Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])] +Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-] +Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-] +Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] +Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-] +Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] +Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] +Ketene: [CX3]=[CX2]=[OX1] +Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3] +Nitrile: [NX1]#[CX2] +Isonitrile: [CX1-]#[NX2+] +Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I] +Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])] +Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])] +Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1] +Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])] +Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1] +Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])] +Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6] +Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])] +Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1] +Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])] +Urea: [#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])] +Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])] +Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])] +Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])] +Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+] +Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-] +Urethan: [#7X3][#6](=[OX1])[#8X2][#6] +Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3] +Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] +Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1] +Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] +Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1] +Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] +Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1] +Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] +Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1] +Isocyanate: [NX2]=[CX2]=[OX1] +Cyanate: [OX2][CX2]#[NX1] +Isothiocyanate: [NX2]=[CX2]=[SX1] +Thiocyanate: [SX2][CX2]#[NX1] +Carbodiimide: [NX2]=[CX2]=[NX2] +Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I] +Phenol: [OX2H][c] +1,2-Diphenol: [OX2H][c][c][OX2H] +Arylchloride: [Cl][c] +Arylfluoride: [F][c] +Arylbromide: [Br][c] +Aryliodide: [I][c] +Arylthiol: [SX2H][c] +Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])] +Oxoarene: [c]=[OX1] +Thioarene: [c]=[SX1] +Hetero_N_basic_H: [nX3H1+0] +Hetero_N_basic_no_H: [nX3H0+0] +Hetero_N_nonbasic: [nX2,nX3+] +Hetero_O: [o] +Hetero_S: [sX2] +Heteroaromatic: [a;!c] +Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])] +Thionitrite: [SX2][NX2]=[OX1] +Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] +Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] +Nitroso: [NX2](=[OX1])[!#7;!#8] +Azide: [NX1]~[NX2]~[NX2,NX1] +Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1] +Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] +Diazonium: [#6][NX2+]#[NX1] +Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1] +Nitrosamide: [NX2](=[OX1])N-*=O +N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] +Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])] +Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6] +Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])] +Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])] +Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])] +Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])] +Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] +Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] +Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] +Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6] +Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])] +Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])] +Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1] +Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6] +Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])] +Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] +Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1] +Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6] +Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])] +Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])] +Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1] +Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6] +Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])] +Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])] +Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])] +Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])] +Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] +Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] +Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6] +Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] +Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] +Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] +Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6] +Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])] +Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] +Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6] +Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] +Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] +Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6] +Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])] +Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])] +Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6] +Quart_silane: [SiX4]([#6])([#6])([#6])[#6] +Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])] +Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6] +Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6] +Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6] +Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6] +Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6] +Trialkylborane: [BX3]([#6])([#6])[#6] +Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6] +Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6] +Borohydride: [BH1,BH2,BH3,BH4] +Quaternary_boron: [BX4] +Aromatic: a +Heterocyclic: [!#6;!R0] +Epoxide: [OX2r3]1[#6r3][#6r3]1 +NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1 +Spiro: [D4R;$(*(@*)(@*)(@*)@*)] +Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])] +Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])] +Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)] +Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)] +Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)] +Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +Conjugated_double_bond: *=*[*]=,#,:[*] +Conjugated_tripple_bond: *#*[*]=,#,:[*] +Cis_double_bond: */[D2]=[D2]\* +Trans_double_bond: */[D2]=[D2]/* +Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))] +Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6] +Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])] +Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1]) +C_ONS_bond: [#6]~[#7,#8,#16] +Charged: [!+0] +Anion: [-1,-2,-3,-4,-5,-6,-7] +Kation: [+1,+2,+3,+4,+5,+6,+7] +Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7]) +1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)] +1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)] +Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1] +Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])] +Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1]) +CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)] +CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])] +Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)] diff --git a/paper/functional-groups.yaml b/paper/functional-groups.yaml new file mode 100644 index 0000000..eb6e5f4 --- /dev/null +++ b/paper/functional-groups.yaml @@ -0,0 +1,309 @@ +Primary_carbon': '[CX4H3][#6]' +Secondary_carbon': '[CX4H2]([#6])[#6]' +Tertiary_carbon': '[CX4H1]([#6])([#6])[#6]' +Quaternary_carbon': '[CX4]([#6])([#6])([#6])[#6]' +Alkene': '[CX3;'([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]' +Alkyne': '[CX2]#[CX2]' +Allene': '[CX3]=[CX2]=[CX3]' +Alkylchloride': '[ClX1][CX4]' +Alkylfluoride': '[FX1][CX4]' +Alkylbromide': '[BrX1][CX4]' +Alkyliodide': '[IX1][CX4]' +Alcohol': '[OX2H][CX4;!'(C([OX2H])[O,S,#7,#15])]' +Primary_alcohol': '[OX2H][CX4H2;!'(C([OX2H])[O,S,#7,#15])]' +Secondary_alcohol': '[OX2H][CX4H;!'(C([OX2H])[O,S,#7,#15])]' +Tertiary_alcohol': '[OX2H][CX4D4;!'(C([OX2H])[O,S,#7,#15])]' +Dialkylether': '[OX2]([CX4;!'(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]' +Dialkylthioether': '[SX2]([CX4;!'(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]' +Alkylarylether': '[OX2](c)[CX4;!'(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]' +Diarylether': '[c][OX2][c]' +Alkylarylthioether': '[SX2](c)[CX4;!'(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]' +Diarylthioether': '[c][SX2][c]' +Oxonium': '[O+;!'([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]' +Amine': '[NX3+0,NX4+;!'([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]' +Primary_aliph_amine': '[NX3H2+0,NX4H3+;!'([N][!C]);!$([N]*~[#7,#8,#15,#16])]' +Secondary_aliph_amine': '[NX3H1+0,NX4H2+;!'([N][!C]);!$([N]*~[#7,#8,#15,#16])]' +Tertiary_aliph_amine': '[NX3H0+0,NX4H1+;!'([N][!C]);!$([N]*~[#7,#8,#15,#16])]' +Quaternary_aliph_ammonium': '[NX4H0+;!'([N][!C]);!$([N]*~[#7,#8,#15,#16])]' +Primary_arom_amine': '[NX3H2+0,NX4H3+]c' +Secondary_arom_amine': '[NX3H1+0,NX4H2+;!'([N][!c]);!$([N]*~[#7,#8,#15,#16])]' +Tertiary_arom_amine': '[NX3H0+0,NX4H1+;!'([N][!c]);!$([N]*~[#7,#8,#15,#16])]' +Quaternary_arom_ammonium': '[NX4H0+;!'([N][!c]);!$([N]*~[#7,#8,#15,#16])]' +Secondary_mixed_amine': '[NX3H1+0,NX4H2+;'([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]' +Tertiary_mixed_amine': '[NX3H0+0,NX4H1+;'([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]' +Quaternary_mixed_ammonium': '[NX4H0+;'([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]' +Ammonium': '[N+;!'([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]' +Alkylthiol': '[SX2H][CX4;!'(C([SX2H])~[O,S,#7,#15])]' +Dialkylthioether': '[SX2]([CX4;!'(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]' +Alkylarylthioether': '[SX2](c)[CX4;!'(C([SX2])[O,S,#7,#15])]' +Disulfide': '[SX2D2][SX2D2]' +1,2-Aminoalcohol': '[OX2H][CX4;!'(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]' +1,2-Diol': '[OX2H][CX4;!'(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]' +1,1-Diol': '[OX2H][CX4;!'(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]' +Hydroperoxide': '[OX2H][OX2]' +Peroxo': '[OX2D2][OX2D2]' +Organolithium_compounds': '[LiX1][#6,#14]' +Organomagnesium_compounds': '[MgX2][#6,#14]' +Organometallic_compounds': '[!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]' +Aldehyde': '['([CX3H][#6]),$([CX3H2])]=[OX1]' +Ketone': '[#6][CX3](=[OX1])[#6]' +Thioaldehyde': '['([CX3H][#6]),$([CX3H2])]=[SX1]' +Thioketone': '[#6][CX3](=[SX1])[#6]' +Imine': '[NX2;'([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]' +Immonium': '[NX3+;!'([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]' +Oxime': '[NX2](=[CX3;'([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]' +Oximether': '[NX2](=[CX3;'([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]' +Acetal': '[OX2]([#6;!'(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]' +Hemiacetal': '[OX2H][CX4;!'(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]' +Aminal': '[NX3v3;!'(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] ' +Hemiaminal': '[NX3v3;!'(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]' +Thioacetal': '[SX2]([#6;!'(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]' +Thiohemiacetal': '[SX2]([#6;!'(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]' +Halogen_acetal_like': '[NX3v3,SX2,OX2;!'(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]' +Acetal_like': '[NX3v3,SX2,OX2;!'(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]' +Halogenmethylen_ester_and_similar': '[NX3v3,SX2,OX2;'(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]' +NOS_methylen_ester_and_similar': '[NX3v3,SX2,OX2;'(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]' +Hetero_methylen_ester_and_similar': '[NX3v3,SX2,OX2;'(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]' +Cyanhydrine': '[NX1]#[CX2][CX4;'([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]' +Chloroalkene': '[ClX1][CX3]=[CX3]' +Fluoroalkene': '[FX1][CX3]=[CX3]' +Bromoalkene': '[BrX1][CX3]=[CX3]' +Iodoalkene': '[IX1][CX3]=[CX3]' +Enol': '[OX2H][CX3;'([H1]),$(C[#6])]=[CX3]' +Endiol': '[OX2H][CX3;'([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]' +Enolether': '[OX2]([#6;!'(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]' +Enolester': '[OX2]([CX3]=[OX1])[#6X3;'([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]' +Enamine': '[NX3;'([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]' +Thioenol': '[SX2H][CX3;'([H1]),$(C[#6])]=[CX3]' +Thioenolether': '[SX2]([#6;!'(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]' +Acylchloride': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[ClX1] ' +Acylfluoride': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[FX1] ' +Acylbromide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[BrX1] ' +Acyliodide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[IX1]' +Acylhalide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]' +Carboxylic_acid': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]' +Carboxylic_ester': ' [CX3;'([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]' +Lactone': '[#6][#6X3R](=[OX1])[#8X2][#6;!'(C=[O,N,S])]' +Carboxylic_anhydride': '[CX3;'([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])' +Carboxylic_acid_derivative': '['([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]' +Carbothioic_acid': '[CX3;!R;'([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]' +Carbothioic_S_ester': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]' +Carbothioic_S_lactone': '[#6][#6X3R](=[OX1])[#16X2][#6;!'(C=[O,N,S])]' +Carbothioic_O_ester': '[CX3;'([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]' +Carbothioic_O_lactone': '[#6][#6X3R](=[SX1])[#8X2][#6;!'(C=[O,N,S])]' +Carbothioic_halide': '[CX3;'([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]' +Carbodithioic_acid': '[CX3;!R;'([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]' +Carbodithioic_ester': '[CX3;!R;'([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]' +Carbodithiolactone': '[#6][#6X3R](=[SX1])[#16X2][#6;!'(C=[O,N,S])]' +Amide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Primary_amide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[NX3H2]' +Secondary_amide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]' +Tertiary_amide': '[CX3;'([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]' +Lactam': '[#6R][#6X3R](=[OX1])[#7X3;'([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Alkyl_imide': '[#6X3;'([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])' +N_hetero_imide': '[#6X3;'([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])' +Imide_acidic': '[#6X3;'([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])' +Thioamide': '['([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Thiolactam': '[#6R][#6X3R](=[SX1])[#7X3;'([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Oximester': '[#6X3;'([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]' +Amidine': '[NX3;!'(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]' +Hydroxamic_acid': '[CX3;'([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]' +Hydroxamic_acid_ester': '[CX3;'([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]' +Imidoacid': '[CX3R0;'([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]' +Imidoacid_cyclic': '[#6R][#6X3R](=,:[#7X2;'([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] ' +Imidoester': '[CX3R0;'([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]' +Imidolactone': '[#6R][#6X3R](=,:[#7X2;'([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]' +Imidothioacid': '[CX3R0;'([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]' +Imidothioacid_cyclic': '[#6R][#6X3R](=,:[#7X2;'([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] ' +Imidothioester': '[CX3R0;'([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]' +Imidothiolactone': '[#6R][#6X3R](=,:[#7X2;'([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]' +Amidine': '[#7X3v3;!'(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]' +Imidolactam': '[#6][#6X3R;'([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])] ' +Imidoylhalide': '[CX3R0;'([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]' +Imidoylhalide_cyclic': '[#6R][#6X3R](=,:[#7X2;'([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]' + ' +Amidrazone': '['([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]' +Alpha_aminoacid': '[NX3,NX4+;!'([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]' +Alpha_hydroxyacid': '[OX2H][C][CX3](=[OX1])[OX2H,OX1-]' +Peptide_middle': '[NX3;'([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]' +Peptide_C_term': '[NX3;'([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]' +Peptide_N_term': '[NX3,NX4+;!'([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]' +Carboxylic_orthoester': '[#6][OX2][CX4;'(C[#6]),$([CH])]([OX2][#6])[OX2][#6] ' +Ketene': '[CX3]=[CX2]=[OX1]' +Ketenacetal': '[#7X2,#8X3,#16X2;'(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]' +Nitrile': '[NX1]#[CX2]' +Isonitrile': '[CX1-]#[NX2+]' +Vinylogous_carbonyl_or_carboxyl_derivative': '[#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]' +Vinylogous_acid': '[#6X3](=[OX1])[#6X3]=,:[#6X3]['([OX2H]),$([OX1-])]' +Vinylogous_ester': '[#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!'(C=[O,N,S])]' +Vinylogous_amide': '[#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;'([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Vinylogous_halide': '[#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]' +Carbonic_acid_dieester': '[#6;!'(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]' +Carbonic_acid_esterhalide': '[#6;!'(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]' +Carbonic_acid_monoester': '[#6;!'(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]' +Carbonic_acid_derivatives': '[!#6][#6X3](=[!#6])[!#6]' +Thiocarbonic_acid_dieester': '[#6;!'(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]' +Thiocarbonic_acid_esterhalide': '[#6;!'(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]' +Thiocarbonic_acid_monoester': '[#6;!'(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]' +Urea:[#7X3;!'([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]' +Thiourea': '[#7X3;!'([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]' +Isourea': '[#7X2;!'([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]' +Isothiourea': '[#7X2;!'([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]' +Guanidine': '[N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]' +Carbaminic_acid': '[NX3]C(=[OX1])[O;X2H,X1-]' +Urethan': '[#7X3][#6](=[OX1])[#8X2][#6]' +Biuret': '[#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]' +Semicarbazide': '[#7X3][#7X3][#6X3]([#7X3;!'([#7][#7])])=[OX1]' +Carbazide': '[#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]' +Semicarbazone': '[#7X2](=[#6])[#7X3][#6X3]([#7X3;!'([#7][#7])])=[OX1]' +Carbazone': '[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]' +Thiosemicarbazide': '[#7X3][#7X3][#6X3]([#7X3;!'([#7][#7])])=[SX1]' +Thiocarbazide': '[#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]' +Thiosemicarbazone': '[#7X2](=[#6])[#7X3][#6X3]([#7X3;!'([#7][#7])])=[SX1]' +Thiocarbazone': '[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]' +Isocyanate': '[NX2]=[CX2]=[OX1]' +Cyanate': '[OX2][CX2]#[NX1]' +Isothiocyanate': '[NX2]=[CX2]=[SX1]' +Thiocyanate': '[SX2][CX2]#[NX1]' +Carbodiimide': '[NX2]=[CX2]=[NX2]' +Orthocarbonic_derivatives': '[CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]' +Phenol': '[OX2H][c]' +1,2-Diphenol': '[OX2H][c][c][OX2H]' +Arylchloride': '[Cl][c]' +Arylfluoride': '[F][c]' +Arylbromide': '[Br][c]' +Aryliodide': '[I][c]' +Arylthiol': '[SX2H][c]' +Iminoarene': '[c]=[NX2;'([H1]),$([H0][#6;!$([C]=[N,S,O])])]' +Oxoarene': '[c]=[OX1]' +Thioarene': '[c]=[SX1]' +Hetero_N_basic_H': '[nX3H1+0]' +Hetero_N_basic_no_H': '[nX3H0+0]' +Hetero_N_nonbasic': '[nX2,nX3+]' +Hetero_O': '[o]' +Hetero_S': '[sX2]' +Heteroaromatic': '[a;!c]' +Nitrite': '[NX2](=[OX1])[O;'([X2]),$([X1-])]' +Thionitrite': '[SX2][NX2]=[OX1]' +Nitrate': '['([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] ' +Nitro': '['([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]' +Nitroso': '[NX2](=[OX1])[!#7;!#8]' +Azide': '[NX1]~[NX2]~[NX2,NX1]' +Acylazide': '[CX3](=[OX1])[NX2]~[NX2]~[NX1]' +Diazo': '['([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] ' +Diazonium': '[#6][NX2+]#[NX1]' +Nitrosamine': '[#7;!'(N*=O)][NX2]=[OX1]' +Nitrosamide': '[NX2](=[OX1])N-*=O' +N-Oxide': '['([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] ' +Hydrazine': '[NX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]' +Hydrazone': '[NX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]' +Hydroxylamine': '[NX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]' +Sulfon': '['([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]' +Sulfoxide': '['([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]' +Sulfonium': '[S+;!'([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]' +Sulfuric_acid': '[SX4](=[OX1])(=[OX1])(['([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]' +Sulfuric_monoester': '[SX4](=[OX1])(=[OX1])(['([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]' +Sulfuric_diester': '[SX4](=[OX1])(=[OX1])([OX2][#6;!'(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' +Sulfuric_monoamide': '[SX4](=[OX1])(=[OX1])([#7X3;'([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]' +Sulfuric_diamide': '[SX4](=[OX1])(=[OX1])([#7X3;'([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Sulfuric_esteramide': '[SX4](=[OX1])(=[OX1])([#7X3][#6;!'(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' +Sulfuric_derivative': '[SX4D4](=[!#6])(=[!#6])([!#6])[!#6]' +Sulfonic_acid': '[SX4;'([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]' +Sulfonamide': '[SX4;'([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Sulfonic_ester': '[SX4;'([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]' +Sulfonic_halide': '[SX4;'([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]' +Sulfonic_derivative': '[SX4;'([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]' +Sulfinic_acid': '[SX3;'([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]' +Sulfinic_amide': '[SX3;'([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Sulfinic_ester': '[SX3;'([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]' +Sulfinic_halide': '[SX3;'([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]' +Sulfinic_derivative': '[SX3;'([H1]),$([H0][#6])](=[!#6])[!#6]' +Sulfenic_acid': '[SX2;'([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]' +Sulfenic_amide': '[SX2;'([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Sulfenic_ester': '[SX2;'([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]' +Sulfenic_halide': '[SX2;'([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]' +Sulfenic_derivative': '[SX2;'([H1]),$([H0][#6])][!#6]' +Phosphine': '[PX3;'([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]' +Phosphine_oxide': '[PX4;'([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]' +Phosphonium': '[P+;!'([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]' +Phosphorylen': '[PX4;'([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]' +Phosphonic_acid': '[PX4;'([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]' +Phosphonic_monoester': '[PX4;'([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]' +Phosphonic_diester': '[PX4;'([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' +Phosphonic_monoamide': '[PX4;'([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphonic_diamide': '[PX4;'([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphonic_esteramide': '[PX4;'([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphonic_acid_derivative': '[PX4;'([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]' +Phosphoric_acid': '[PX4D4](=[OX1])(['([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]' +Phosphoric_monoester': '[PX4D4](=[OX1])(['([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]' +Phosphoric_diester': '[PX4D4](=[OX1])(['([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' +Phosphoric_triester': '[PX4D4](=[OX1])([OX2][#6;!'(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' +Phosphoric_monoamide': '[PX4D4](=[OX1])(['([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphoric_diamide': '[PX4D4](=[OX1])(['([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphoric_triamide': '[PX4D4](=[OX1])([#7X3;'([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphoric_monoestermonoamide': '[PX4D4](=[OX1])(['([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphoric_diestermonoamide': '[PX4D4](=[OX1])([OX2][#6;!'(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphoric_monoesterdiamide': '[PX4D4](=[OX1])([OX2][#6;!'(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphoric_acid_derivative': '[PX4D4](=[!#6])([!#6])([!#6])[!#6]' +Phosphinic_acid': '[PX4;'([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]' +Phosphinic_ester': '[PX4;'([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]' +Phosphinic_amide': '[PX4;'([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphinic_acid_derivative': '[PX4;'([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]' +Phosphonous_acid': '[PX3;'([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]' +Phosphonous_monoester': '[PX3;'([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]' +Phosphonous_diester': '[PX3;'([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]' +Phosphonous_monoamide': '[PX3;'([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphonous_diamide': '[PX3;'([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphonous_esteramide': '[PX3;'([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphonous_derivatives': '[PX3;'([D2]),$([D3][#6])]([!#6])[!#6]' +Phosphinous_acid': '[PX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]' +Phosphinous_ester': '[PX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]' +Phosphinous_amide': '[PX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]' +Phosphinous_derivatives': '[PX3;'([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]' +Quart_silane': '[SiX4]([#6])([#6])([#6])[#6]' +Non-quart_silane': '[SiX4;'([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]' +Silylmonohalide': '[SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]' +Het_trialkylsilane': '[SiX4]([!#6])([#6])([#6])[#6]' +Dihet_dialkylsilane': '[SiX4]([!#6])([!#6])([#6])[#6]' +Trihet_alkylsilane': '[SiX4]([!#6])([!#6])([!#6])[#6]' +Silicic_acid_derivative': '[SiX4]([!#6])([!#6])([!#6])[!#6]' +Trialkylborane': '[BX3]([#6])([#6])[#6] ' +Boric_acid_derivatives': '[BX3]([!#6])([!#6])[!#6]' +Boronic_acid_derivative': '[BX3]([!#6])([!#6])[!#6]' +Borohydride': '[BH1,BH2,BH3,BH4]' +Quaternary_boron': '[BX4]' +Aromatic': 'a' +Heterocyclic': '[!#6;!R0]' +Epoxide': '[OX2r3]1[#6r3][#6r3]1' +NH_aziridine': '[NX3H1r3]1[#6r3][#6r3]1' +Spiro': '[D4R;'(*(@*)(@*)(@*)@*)]' +Annelated_rings': '[R;'(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]' +Bridged_rings': '[R;'(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]' +Sugar_pattern_1': '[OX2;'([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]' +Sugar_pattern_2': '[OX2;'([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]' +Sugar_pattern_combi': '[OX2;'([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]' +Sugar_pattern_2_reducing': '[OX2;'([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]' +Sugar_pattern_2_alpha': '[OX2;'([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]' +Sugar_pattern_2_beta': '[OX2;'([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]' +Conjugated_double_bond': '*=*[*]=,#,:[*]' +Conjugated_tripple_bond': '*#*[*]=,#,:[*]' +Cis_double_bond': '*/[D2]=[D2]\*' +Trans_double_bond': '*/[D2]=[D2]/*' +Mixed_anhydrides': '['(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]' +Halogen_on_hetero': '[FX1,ClX1,BrX1,IX1][!#6]' +Halogen_multi_subst': '[F,Cl,Br,I;!'([X1]);!$([X0-])]' +Trifluoromethyl': '[FX1][CX4;!'([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])' +C_ONS_bond': '[#6]~[#7,#8,#16]' +Charged': '[!+0]' +Anion': '[-1,-2,-3,-4,-5,-6,-7]' +Kation': '[+1,+2,+3,+4,+5,+6,+7]' +Salt': '([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])' +1,3-Tautomerizable': '['([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]' +1,5-Tautomerizable': '['([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]' +Rotatable_bond': '[!'(*#*)&!D1]-!@[!$(*#*)&!D1]' +Michael_acceptor': '[CX3]=[CX3]['([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]' +Dicarbodiazene': '[CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])' +CH-acidic': '['([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]' +CH-acidic_strong': '[CX4;!'([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]' +Chiral_center_specified': '['([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]' + ' diff --git a/paper/loael-dataset-comparison-all-compounds.pdf 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File.join(File.dirname(__FILE__),"..","regression","swissRat_chron_LOAEL_mmol.csv") + +combined_compounds = old.compound_ids & new.compound_ids + +compound_vector = [] +value_vector = [] +dataset_vector = [] + +old_median = [] +new_median = [] + +errors = [] +combined_compounds.each do |cid| + c = Compound.find cid + old_values = old.values(c,old.features.first) + old_median << -Math.log(old_values.mean) + old_values.each do |v| + compound_vector << c.smiles + value_vector << -Math.log(v.to_f) + dataset_vector << old.name + end + new_values = new.values(c,new.features.first) + new_median << -Math.log(new_values.mean) + new_values.each do |v| + compound_vector << c.smiles + value_vector << -Math.log(v) + dataset_vector << new.name + end +end +old_median.each_index do |i| + errors[i] = (old_median[i] - new_median[i]).abs unless old_median[i] == new_median[i] +end +rmse = 0 +mae = 0 +errors.compact.each do |e| + rmse += e**2 + mae += e +end +rmse = Math.sqrt(rmse/errors.size) +mae = mae/errors.size + +=begin +R.assign "smi", compound_vector +R.assign "values", value_vector +R.assign "dataset", dataset_vector +R.eval "df <- data.frame(factor(smi),values,factor(dataset))" +R.eval "df$smi <- reorder(df$factor.smi,df$values)" +R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))" +R.eval "img <- img + ylab('-log(LOAEL mg/kg_bw/day)') + xlab('Compound') + theme(axis.text.x = element_blank())" +R.eval "img <- img + geom_point()" + +R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-dataset-comparison-mmol_kg_day.svg', plot=img,width=12, height=8)" +=end + +R.assign "old", old_median +R.assign "new", new_median +=begin +R.eval "df <- data.frame(old,new)" +R.eval "img <- ggplot(df, aes(old,new))" +R.eval "img <- img + geom_point()" +#R.eval "img <- img + geom_smooth(method=lm) " +R.eval "img <- img + geom_abline(intercept=0.0) " +R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-dataset-correlation.svg', plot=img,width=12, height=8)" +=end +puts "Correlation old/new:" +puts "\tr^2: #{R.eval("cor(old,new,use='complete')").to_f**2}" +puts "\tRMSE: #{rmse}" +puts "\tMAE: #{mae}" diff --git a/paper/loael-dataset-correlation.pdf b/paper/loael-dataset-correlation.pdf Binary files differnew file mode 100644 index 0000000..3e0a042 --- /dev/null +++ b/paper/loael-dataset-correlation.pdf diff --git a/paper/loael-dataset-correlation.svg b/paper/loael-dataset-correlation.svg new file mode 100644 index 0000000..1ce514e --- /dev/null +++ b/paper/loael-dataset-correlation.svg @@ -0,0 +1,387 @@ +<?xml version="1.0" encoding="UTF-8"?> +<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="864pt" height="576pt" viewBox="0 0 864 576" version="1.1"> +<defs> +<g> +<symbol overflow="visible" id="glyph0-0"> +<path style="stroke:none;" d=""/> +</symbol> +<symbol overflow="visible" id="glyph0-1"> +<path style="stroke:none;" d="M 2.640625 -6.796875 C 2 -6.796875 1.421875 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+</g> +</svg> diff --git a/paper/loael-variability.rb b/paper/loael-variability.rb new file mode 100644 index 0000000..ae74c3f --- /dev/null +++ b/paper/loael-variability.rb @@ -0,0 +1,61 @@ +require_relative '../lazar/lib/lazar' +include OpenTox +#$mongo.database.drop +#$gridfs = $mongo.database.fs # recreate GridFS indexes +# compare duplicates within datasets +#old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mmol_corrected_smiles.csv") +old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mg_corrected_smiles_mmol.csv") +#new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL.csv") +new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL_mmol.csv") +#combined = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL-rat-combined.csv") + +compound_vector = [] +value_vector = [] +dataset_vector = [] + +vars = [] + +[old, new].each do |dataset| + vars << [] + #vars[dataset.name] = [] + p dataset.name + p dataset.compounds.size + p dataset.duplicates(dataset.features.first).size + dataset.duplicates.each do |cid,values| + R.assign "values", values + var = R.eval("var(-log(values))").to_f + vars.last << var + #smi = Compound.find(cid).smiles + smi = cid.to_s + values.each do |val| + compound_vector << smi + value_vector << - Math.log(val) + dataset_vector << dataset.name + end + #vars << { :var => var, :values => values, :smiles => smi } + end + #vars.sort!{|a,b| a[:var] <=> b[:var]} + #vars.each do |dup| + #dup[:values].each do |v| + #compound_vector << dup[:smiles] + #value_vector << v + #end + #end +end +#p vars +# TODO statistical test for variances +R.assign "vars1", vars[0] +R.assign "vars2", vars[1] +print "p-value: #{R.eval("t.test(vars1,vars2)$p.value").to_f}" + +R.assign "smi", compound_vector +R.assign "values", value_vector +R.assign "dataset", dataset_vector +R.eval "df <- data.frame(factor(smi),values,factor(dataset))" +R.eval "df$smi <- reorder(df$factor.smi,df$values)" +R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))" +R.eval "img <- img + ylab('-log(LOAEL mg/kg_bw/day)') + xlab('Compound') + theme(axis.text.x = element_blank())" +R.eval "img <- img + geom_point()" +#R.eval "img <- img + scale_x_discrete(breaks=NULL) + geom_point() + coord_flip()"# + xlab('-log(LOAEL)'), ylab('Compound')" +#R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael_variance.svg', plot=img)" +R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-variance.svg', plot=img,width=12, height=8)" diff --git a/paper/loael.html b/paper/loael.html new file mode 100644 index 0000000..c8c0a2d --- /dev/null +++ b/paper/loael.html @@ -0,0 +1,384 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html 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solid; + border-collapse: collapse; +} +table.docutils.booktabs * { + border: 0px; +} +table.docutils.booktabs th { + border-bottom: thin solid; + text-align: left; +} + +h1 tt.docutils, h2 tt.docutils, h3 tt.docutils, +h4 tt.docutils, h5 tt.docutils, h6 tt.docutils { + font-size: 100% } + +ul.auto-toc { + list-style-type: none } + +</style> +</head> +<body> +<div class="document"> + + +<div class="section" id="introduction"> +<h1>Introduction</h1> +</div> +<div class="section" id="data"> +<h1>Data</h1> +<div class="section" id="loael-values"> +<h2>LOAEL Values</h2> +<div class="section" id="comparison-of-variances-in-datasets"> +<h3>Comparison of variances in datasets</h3> +<p>p-value: 0.4750771581019402</p> +<object data="loael-variance.svg" type="image/svg+xml"> +loael-variance.svg</object> +</div> +<div class="section" id="comparison-of-compounds-in-both-datasets"> +<h3>Comparison of compounds in both datasets</h3> +<object data="loael-dataset-comparison-mmol_kg_day.svg" type="image/svg+xml"> +loael-dataset-comparison-mmol_kg_day.svg</object> +</div> +<div class="section" id="correlation-between-datasets"> +<h3>Correlation between datasets</h3> +<p>using means</p> +<object data="loael-dataset-correlation.svg" type="image/svg+xml"> +loael-dataset-correlation.svg</object> +<p>with "identical" values</p> +<blockquote> +r^2: 0.6106457754533314 +RMSE: 1.2228212261024438 +MAE: 0.801626064534318</blockquote> +</div> +</div> +</div> +<div class="section" id="models"> +<h1>Models</h1> +</div> +<div class="section" id="validation"> +<h1>Validation</h1> +<p>Discussion</p> +</div> +</div> +</body> +</html> diff --git a/paper/loael.pdf b/paper/loael.pdf new file mode 100644 index 0000000..e2edd82 --- /dev/null +++ b/paper/loael.pdf @@ -0,0 +1,205 @@ +%PDF-1.4
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diff --git a/paper/loael.rst b/paper/loael.rst index 2a5bbea..50b7a6a 100644 --- a/paper/loael.rst +++ b/paper/loael.rst @@ -1,9 +1,34 @@ Introduction +------------ Data +---- -Models +LOAEL Values +............ -Validation +Comparison of variances in datasets +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Discussion +p-value: 0.4750771581019402 + +.. image:: loael-variance.svg + + +Comparison of compounds in both datasets +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: loael-dataset-comparison-mmol_kg_day.svg + +Correlation between datasets +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +using means + +.. image:: loael-dataset-correlation.svg + +with "identical" values + + r^2: 0.6106457754533314 + RMSE: 1.2228212261024438 + MAE: 0.801626064534318 diff --git a/regression/LOAEL_mg_corrected_smiles.csv b/regression/LOAEL_mg_corrected_smiles.csv new file mode 100644 index 0000000..b71129c --- /dev/null +++ b/regression/LOAEL_mg_corrected_smiles.csv @@ -0,0 +1,568 @@ +SMILES,LOAEL_mg_kg_bw_day 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