lazar 0.0.4 → 0.0.5

data/README.md

@@ -1,44 +0,0 @@
-lazar
-=====
-
-Ruby libraries for the lazar framework
-
-Dependencies
-------------
-
-  lazar depends on a couple of external programs and libraries. On Debian 7 "Wheezy" systems you can install them with
-
-   `sudo apt-get install build-essential ruby ruby-dev git cmake swig r-base r-base-dev r-cran-rserve openjdk-7-jre libgsl0-dev libxml2-dev zlib1g-dev libcairo2-dev`
-  
-  You will also need at least mongodb version 3.0, but Debian "Wheezy" provides version 2.4. Please follow the instructions at http://docs.mongodb.org/manual/tutorial/install-mongodb-on-debian/:
-
-  ```
-  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10
-  echo "deb http://repo.mongodb.org/apt/debian wheezy/mongodb-org/3.0 main" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.0.list
-  sudo apt-get update
-  sudo apt-get install -y mongodb-org
-  ```
-
-Installation
-------------
-
-  `gem install lazar`
-
-  Please be patient, the compilation of OpenBabel and Fminer libraries can be very time consuming. If installation fails you can try to install manually:
-
-  ```
-  git clone https://github.com/opentox/lazar.git
-  cd lazar
-  ruby ext/lazar/extconf.rb
-  bundle install
-  ```
-
-  The output should give you more verbose information that can help in debugging (e.g. to identify missing libraries).
-
-Documentation
--------------
-* [API documentation](http://rdoc.info/gems/lazar)
-
-Copyright
----------
-Copyright (c) 2009-2015 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.

data/Rakefile

@@ -1 +0,0 @@
-require "bundler/gem_tasks"

data/VERSION

@@ -1 +0,0 @@
-0.0.4

data/ext/lazar/Makefile

@@ -1,5 +0,0 @@
-all:
-	true
-
-install:
-	true

data/java/CdkDescriptorInfo.java

@@ -1,22 +0,0 @@
-import java.util.*;
-import org.openscience.cdk.qsar.descriptors.molecular.*;
-import org.openscience.cdk.qsar.*;
-
-class CdkDescriptorInfo {
-  public static void main(String[] args) {
-
-    DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
-
-    for (Iterator<IDescriptor> it = engine.getDescriptorInstances().iterator(); it.hasNext(); ) {
-      IDescriptor descriptor = it.next();
-      String cdk_class = descriptor.getClass().toString().replaceAll("class ","");
-      System.out.println("- :java_class: \""+cdk_class+"\"");
-      String description = engine.getDictionaryDefinition(cdk_class).replaceAll("^\\s+", "" ).replaceAll("\\s+$", "").replaceAll("\\s+", " ");
-      System.out.println("  :description: \""+description+"\"");
-      System.out.println("  :names:");
-      for (String name : descriptor.getDescriptorNames()) {
-        System.out.println("    - \""+name+"\"");
-      }
-    }
-  }
-}

data/java/CdkDescriptors.java

@@ -1,141 +0,0 @@
-import java.util.*;
-import java.io.*;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.io.iterator.IteratingMDLReader;
-import org.openscience.cdk.qsar.*;
-import org.openscience.cdk.qsar.DescriptorValue;
-import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.exception.NoSuchAtomTypeException;
-
-class CdkDescriptors {
-  public static void main(String[] args) {
-
-    if (args==null || args.length<2) {
-	System.err.println("required params: <sd-file> <descriptor1> <descriptor2(optional)> <descriptor3(optional)> ...");
-	System.exit(1);
-    }
-    if (! new File(args[0]).exists()){
-	System.err.println("file not found "+args[0]);
-	System.exit(1);
-    }
-
-    // command line descriptor params can be either "descriptorName" or "descriptorValueName"
-    // terminology:
-    // A descriptor can calculate serveral values, e.g., ALOGP produces ALOGP.ALogP, ALOGP.ALogp2, ALOGP.AMR
-    // "descriptorName" ALOGP
-    // "valueName" AMR
-    // "descriptorValueName" ALOGP.AMR
-    DescriptorEngine engine;
-    Set<String> classNames = new LinkedHashSet<String>(); // descriptors to be computed
-    Set<String> descriptorNames = new LinkedHashSet<String>(); // all values of this descriptor will be printed
-    Set<String> descriptorValueNames = new LinkedHashSet<String>(); // only these values of a descriptor will be printed
-    for (int i =1; i < args.length; i++) {
-      String descriptorName;
-      if (args[i].indexOf(".")!=-1) {
-          descriptorValueNames.add(args[i]);
-	  descriptorName = args[i].substring(0,args[i].indexOf("."));
-      }
-      else {
-	  descriptorNames.add(args[i]);
-          descriptorName = args[i];
-      }
-      classNames.add(getDescriptorClassName(descriptorName));
-    }
-
-    engine = new DescriptorEngine(new ArrayList<String>(classNames));
-    List<IDescriptor> instances =  engine.instantiateDescriptors(new ArrayList<String>(classNames));
-    List<DescriptorSpecification> specs = engine.initializeSpecifications(instances);
-    engine.setDescriptorInstances(instances);
-    engine.setDescriptorSpecifications(specs);
-
-    try {
-      BufferedReader br = new BufferedReader(new FileReader(args[0]));
-      PrintWriter yaml = new PrintWriter(new FileWriter(args[0]+"cdk.yaml"));
-      // parse 3d sdf from file and calculate descriptors
-      IteratingMDLReader reader = new IteratingMDLReader( br, DefaultChemObjectBuilder.getInstance());
-      int c = 0;
-      while (reader.hasNext()) {
-        try {
-          System.out.println("computing "+(args.length-1)+" descriptors for compound "+(++c));
-          IMolecule molecule = (IMolecule)reader.next();
-          molecule = (IMolecule) AtomContainerManipulator.removeHydrogens(molecule);
-          try {
-            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-          }
-	      catch (NoSuchAtomTypeException e) {
-            e.printStackTrace();
-          }
-          CDKHueckelAromaticityDetector.detectAromaticity(molecule);
-
-          engine.process(molecule);
-          Map<Object,Object> properties = molecule.getProperties();
-          Boolean first = true;
-          for (Map.Entry<Object, Object> entry : properties.entrySet()) {
-            try {
-              if ((entry.getKey() instanceof DescriptorSpecification) && (entry.getValue() instanceof DescriptorValue)) {
-                DescriptorSpecification property = (DescriptorSpecification)entry.getKey();
-                DescriptorValue value = (DescriptorValue)entry.getValue();
-                String[] values = value.getValue().toString().split(",");
-                for (int i = 0; i < values.length; i++) {
-                  String cdk_class = property.getImplementationTitle();
-                  String descriptorName = cdk_class.substring(cdk_class.lastIndexOf(".")+1).replace("Descriptor","");
-                  String descriptorValueName = descriptorName + "." + value.getNames()[i];
-		  if (descriptorNames.contains(descriptorName) || descriptorValueNames.contains(descriptorValueName)) {
-		      if (first) { yaml.print("- "); first = false; }
-		      else { yaml.print("  "); }
-                      yaml.println("Cdk." + descriptorValueName  + ": " + values[i]);
-		  }
-                }
-              }
-            }
-            catch (ClassCastException e) { } // sdf properties are stored as molecules properties (strings), ignore them
-            catch (Exception e) { e.printStackTrace(); } // output nothing to yaml
-          }
-        }
-        catch (Exception e) {
-          yaml.println("- {}");
-          e.printStackTrace();
-          continue;
-        }
-      }
-      yaml.close();
-    }
-    catch (Exception e) { e.printStackTrace(); }
-  }
-    
-
-    /** HACK to find the class for a descriptor
-     * problem: Descriptor is not always at the end of the class (APolDescriptor), but may be in the middle (AutocorrelationDescriptorPolarizability)
-     * this method makes a class-lookup using trial and error */
-    static String getDescriptorClassName(String descriptorName) {
-	String split = splitCamelCase(descriptorName)+" "; // space mark possible positions for 'Descriptor'
-	for(int i = split.length()-1; i>0; i--) {
-	    if (split.charAt(i)==' ') { // iterate over all spaces, starting with the trailing one
-		String test = split.substring(0,i)+"Descriptor"+split.substring(i+1,split.length()); // replace current space with 'Descriptor' ..
-		test = test.replaceAll("\\s",""); // .. and remove other spaces
-		String className = "org.openscience.cdk.qsar.descriptors.molecular." + test;
-		try {
-		    Class.forName(className);
-		    return className;
-		} catch (ClassNotFoundException e) {}
-	    }
-        }
-	System.err.println("Descriptor not found: "+descriptorName);
-	System.exit(1);
-	return null;
-    }
-
-    /** inserts space in between camel words */
-  static String splitCamelCase(String s) {
-   return s.replaceAll(
-      String.format("%s|%s|%s",
-         "(?<=[A-Z])(?=[A-Z][a-z])",
-         "(?<=[^A-Z])(?=[A-Z])",
-         "(?<=[A-Za-z])(?=[^A-Za-z])"
-      ),
-      " "
-   );
-  }
-}

data/java/JoelibDescriptorInfo.java

@@ -1,15 +0,0 @@
-import joelib2.feature.FeatureHelper;
-
-class JoelibDescriptorInfo {
-  public static void main(String[] args) {
-    FeatureHelper helper = FeatureHelper.instance();
-    System.out.println("---"); // document separator for Joelib debug messages
-    for (Object feature : helper.getNativeFeatures() ) {
-      System.out.println("- :java_class: \""+feature.toString()+"\"");
-      // methods for accessing feature descriptions e.g. with 
-      // FeatureFactory.instance().getFeature(feature.toString()).getDescription().getText() or
-      // FeatureFactory.instance().getFeature(feature.toString()).getDescription().getHtml()
-      // are defunct
-    }
-  }
-}

data/java/JoelibDescriptors.java

@@ -1,60 +0,0 @@
-import java.util.*;
-import java.io.*;
-import joelib2.feature.Feature;
-import joelib2.feature.FeatureHelper;
-import joelib2.feature.FeatureFactory;
-import joelib2.feature.FeatureResult;
-import joelib2.io.BasicIOType;
-import joelib2.io.BasicIOTypeHolder;
-import joelib2.io.BasicReader;
-import joelib2.io.MoleculeFileHelper;
-import joelib2.io.MoleculeFileIO;
-import joelib2.io.MoleculeIOException;
-import joelib2.molecule.BasicConformerMolecule;
-
-class JoelibDescriptors {
-  public static void main(String[] args) {
-
-    String[] features = null;
-    features = new String[args.length-1];
-    System.arraycopy(args,1,features,0,args.length-1);
-
-    FeatureFactory factory = FeatureFactory.instance();
-    MoleculeFileIO loader = null;
-    String line = new String();
-    String sdf = new String();
-    try {
-      // parse 3d sdf from file and calculate descriptors
-      InputStream is = new FileInputStream(args[0]);
-      PrintWriter yaml = new PrintWriter(new FileWriter(args[0]+"joelib.yaml"));
-      BasicIOType inType = BasicIOTypeHolder.instance().getIOType("SDF");
-      loader = MoleculeFileHelper.getMolReader(is, inType);
-      BasicConformerMolecule mol = new BasicConformerMolecule(inType, inType);
-      while (true) {
-        try {
-          Boolean success = loader.read(mol);
-          if (!success) { break; } // last molecule
-          for (int i =0; i < features.length; i++) {
-            String name = "joelib2.feature.types." + features[i];
-            Feature feature = factory.getFeature(name);
-            FeatureResult result = feature.calculate(mol);
-            if (i == 0) { yaml.print("- "); }
-            else { yaml.print("  "); }
-            yaml.print( "Joelib."+features[i]+": " );
-            yaml.println( result.toString() );
-          }
-
-        }
-        catch (Exception e) { 
-          System.err.println(e.toString());
-          e.printStackTrace();
-        }
-      }
-      yaml.close();
-    }
-    catch (Exception e) {
-      System.err.println(e.toString());
-      e.printStackTrace();
-    }
-  }
-}

data/java/Rakefile

@@ -1,15 +0,0 @@
-# Java class, classpath
-java_classes = [
-  ["CdkDescriptors", "cdk-1.4.19.jar"],
-  ["CdkDescriptorInfo", "cdk-1.4.19.jar"],
-  ["JoelibDescriptors", "joelib2.jar:."],
-  ["JoelibDescriptorInfo", "joelib2.jar:."],
-]
-  
-task :default => java_classes.collect{|c| "#{c.first}.class"}
-
-java_classes.each do |c|
-  file "#{c.first}.class" => "#{c.first}.java" do
-    puts `javac -classpath #{c.last} #{c.first}.java`
-  end
-end

data/lazar.gemspec

@@ -1,29 +0,0 @@
-# -*- encoding: utf-8 -*-
-$:.push File.expand_path("../lib", __FILE__)
-
-Gem::Specification.new do |s|
-  s.name        = "lazar"
-  s.version     = File.read("./VERSION").strip
-  s.authors     = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler, Denis Gebele"]
-  s.email       = ["helma@in-silico.ch"]
-  s.homepage    = "http://github.com/opentox/lazar"
-  s.summary     = %q{Lazar framework}
-  s.description = %q{Libraries for lazy structure-activity relationships and read-across.}
-  s.license     = 'GPL-3'
-
-  s.rubyforge_project = "lazar"
-
-  s.files         = `git ls-files`.split("\n")
-  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.extensions    = %w[ext/lazar/extconf.rb]
-  s.require_paths = ["lib"]
-
-  # specify any dependencies here; for example:
-  s.add_runtime_dependency "bundler"
-  s.add_runtime_dependency "rest-client"
-  s.add_runtime_dependency 'nokogiri'
-  #s.add_runtime_dependency "openbabel"
-  s.add_runtime_dependency 'rserve-client'
-  s.add_runtime_dependency "mongoid", '~> 5.0beta'  
-
-end

data/lib/SMARTS_InteLigand.txt

@@ -1,983 +0,0 @@
-#
-#              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 
-