Rdfile reader

.github/workflows/maven.yml

@@ -34,6 +34,7 @@ jobs:
   build-sonarcloud:
     name: Build sonarcloud
     runs-on: ubuntu-latest
+    environment: SonarCloud
     steps:
       - uses: actions/checkout@v3
         with:

base/dict/pom.xml

@@ -17,6 +17,16 @@
         <dependency>
             <groupId>xom</groupId>
             <artifactId>xom</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>xerces</groupId>
+                    <artifactId>xercesImpl</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>xalan</groupId>
+                    <artifactId>xalan</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>

base/interfaces/src/main/java/org/openscience/cdk/hash/MoleculeHashGenerator.java

@@ -27,7 +27,13 @@
 
 /**
  * A hash function which generates a single 64-bit hash code for a molecule.
- *
+ * <p>
+ *     Implementations of this interface are encouraged to be conservative about
+ *     introducing any changes to the generated hash values and to mention any
+ *     such changes in the release notes. However, please take into consideration
+ *     that the hash values generated by this class are <b>not</b> guaranteed to
+ *     remain unaltered over time.
+ * </p>
  * @author John May
  * @cdk.module interfaces
  * @cdk.githash

descriptor/qsarcml/pom.xml

@@ -17,11 +17,21 @@
         <dependency>
             <groupId>xom</groupId>
             <artifactId>xom</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>xerces</groupId>
+                    <artifactId>xercesImpl</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>xalan</groupId>
+                    <artifactId>xalan</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.blueobelisk</groupId>
             <artifactId>cmlxom</artifactId>
-            <version>4.3</version>
+            <version>4.4</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

descriptor/qsarmolecular/pom.xml

@@ -30,6 +30,16 @@
         <dependency>
             <groupId>xom</groupId>
             <artifactId>xom</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>xerces</groupId>
+                    <artifactId>xercesImpl</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>xalan</groupId>
+                    <artifactId>xalan</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>

doc/refs/cheminf.bibx

@@ -159,6 +159,15 @@
     </bibtex:article>
   </bibtex:entry>
 
+  <bibtex:entry id="Dassault20">
+      <bibtex:techreport>
+        <bibtex:title>CTFile Formats Biovia Databases 2020</bibtex:title>
+        <bibtex:institution>Dassault Systèmes</bibtex:institution>
+        <bibtex:year>2020</bibtex:year>
+        <bibtex:url>https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf</bibtex:url>
+      </bibtex:techreport>
+    </bibtex:entry>
+
   <bibtex:entry id="BLE91">
     <bibtex:article>
       <bibtex:author>Bley, K. and Brandt, J. and Dengler, A. and

pom.xml

@@ -518,7 +518,7 @@
             <dependency>
                 <groupId>xom</groupId>
                 <artifactId>xom</artifactId>
-                <version>1.3.7</version>
+                <version>1.3.8</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.felix</groupId>

storage/ctab/src/main/java/org/openscience/cdk/io/CharIter.java

@@ -0,0 +1,119 @@
+/*
+ * Copyright (C) 2022 NextMove Software
+ *               2022 John Mayfield
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ */
+package org.openscience.cdk.io;
+
+/**
+ * Helper class that facilitates the parsing of text data.
+ * @author John Mayfield
+ */
+final class CharIter {
+    private final String string;
+    private int position = 0;
+
+    CharIter(String str) {
+        this.string = str;
+    }
+
+    static boolean isSpace(char c) {
+        return c == ' ';
+    }
+
+    static boolean isDigit(char c) {
+        return c >= '0' && c <= '9';
+    }
+
+    int position() {
+        return position;
+    }
+
+    char next() {
+        return string.charAt(position++);
+    }
+
+    char peek() {
+        return position < string.length() ? string.charAt(position) : '\0';
+    }
+
+    boolean hasNext() {
+        return position < string.length();
+    }
+
+    String rest() {
+        return string.substring(position);
+    }
+
+    void skipWhiteSpace() {
+        while (hasNext()) {
+            if (isSpace(string.charAt(position)))
+                position++;
+            else
+                break;
+        }
+    }
+
+    int nextUnsignedNumber() {
+        if (!hasNext())
+            return -1;
+        if (!isDigit(peek()))
+            return -1;
+        int num = next() - '0';
+        while (hasNext() && isDigit(peek()))
+            num = (10 * num) + (next() - '0');
+        return num;
+    }
+
+    boolean consume(String substring) {
+        if (position + substring.length() > string.length())
+            return false;
+        int mark = position;
+        for (int i = 0; i < substring.length(); i++) {
+            if (substring.charAt(i) != string.charAt(position)) {
+                position = mark; // reset
+                break;
+            }
+            position++;
+        }
+        return position - mark == substring.length();
+    }
+
+    String substring(int beg, int end) {
+        return string.substring(beg, end);
+    }
+
+    void seek(int position) {
+        this.position = position;
+    }
+
+    boolean nextIf(char c) {
+        if (peek() == c) {
+            next();
+            return true;
+        }
+        return false;
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        sb.append(string, 0, position);
+        sb.append('|');
+        sb.append(string.substring(position));
+        return sb.toString();
+    }
+}

storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java

@@ -52,6 +52,7 @@
 import java.io.Reader;
 import java.io.StringReader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -160,6 +161,38 @@ private static final class ReadState {
         boolean chiral;
         Map<Integer,Integer> stereoflags = null;
         final Map<IAtom,Integer> stereo0d = new HashMap<>();
+
+        // atom/bond ids need not be sequential, we could use map but more
+        // common is the ids will be sequential
+        IAtom[] atomById = new IAtom[64];
+        IBond[] bondById = new IBond[64];
+
+        <T> T[] grow(T[] arr, int req)
+        {
+            int cap = arr.length;
+            return Arrays.copyOf(arr, Math.max(cap + cap >> 1,
+                                               req + 1));
+        }
+
+        void addAtom(int id, IAtom atom) {
+            if (id >= atomById.length)
+                atomById = grow(atomById, id);
+            atomById[id] = atom;
+        }
+
+        void addBond(int id, IBond bond) {
+            if (id >= bondById.length)
+                bondById = grow(bondById, id);
+            bondById[id] = bond;
+        }
+
+        public IAtom getAtom(int i) {
+            return atomById[i];
+        }
+
+        public IBond getBond(int i) {
+            return bondById[i];
+        }
     }
 
     public IAtomContainer readMolecule(IChemObjectBuilder builder) throws CDKException {
@@ -190,9 +223,9 @@ public IAtomContainer readConnectionTable(IChemObjectBuilder builder) throws CDK
             } else if ("BEGIN ATOM".equals(command)) {
                 readAtomBlock(state);
             } else if ("BEGIN BOND".equals(command)) {
-                readBondBlock(readData);
+                readBondBlock(state);
             } else if ("BEGIN SGROUP".equals(command)) {
-                readSGroup(readData);
+                readSGroup(state);
             } else if ("BEGIN COLLECTION".equals(command)) {
                 readCollection(state);
             } else {
@@ -277,9 +310,9 @@ private void finalizeStereochemistry(ReadState state, IAtomContainer readData) {
                     if (se.getConfigClass() != IStereoElement.TH)
                         continue;
                     IAtom focus = (IAtom) se.getFocus();
-                    int idx = readData.indexOf(focus);
-                    if (idx < 0)
+                    if (focus.getID() == null)
                         continue;
+                    int idx = Integer.parseInt(focus.getID());
                     Integer grpinfo = state.stereoflags.get(idx);
                     if (grpinfo != null)
                         se.setGroupInfo(grpinfo);
@@ -372,7 +405,7 @@ private void parseStereoGroup(Map<Integer,Integer> flags, String str, int type)
             }
             // val-1 since we store atom index instead of atom number
             if (val > 0)
-                flags.put(val-1, type);
+                flags.put(val, type);
             while (i < len && str.charAt(i) == ' ')
                 i++;
             if (i < len && str.charAt(i) == ')')
@@ -455,6 +488,7 @@ public void readAtomBlock(ReadState state) throws CDKException {
 
         int RGroupCounter = 1;
         int Rnumber;
+        String id;
         String[] rGroup;
 
         boolean foundEND = false;
@@ -469,7 +503,7 @@ public void readAtomBlock(ReadState state) throws CDKException {
                 StringTokenizer tokenizer = new StringTokenizer(command);
                 // parse the index
                 try {
-                    atom.setID(tokenizer.nextToken());
+                    id = tokenizer.nextToken();
                 } catch (Exception exception) {
                     String error = "Error while parsing atom index";
                     logger.error(error);
@@ -607,7 +641,9 @@ public void readAtomBlock(ReadState state) throws CDKException {
                 }
 
                 // store atom
+                atom.setID(id);
                 readData.addAtom(atom);
+                state.addAtom(Integer.parseInt(id), readData.getAtom(readData.getAtomCount()-1));
                 logger.debug("Added atom: " + atom);
             }
         }
@@ -616,7 +652,8 @@ public void readAtomBlock(ReadState state) throws CDKException {
     /**
      * Reads the bond atoms, order and stereo configuration.
      */
-    public void readBondBlock(IAtomContainer readData) throws CDKException {
+    public void readBondBlock(ReadState state) throws CDKException {
+        IAtomContainer readData = state.mol;
         logger.info("Reading BOND block");
         boolean foundEND = false;
         while (isReady() && !foundEND) {
@@ -657,7 +694,7 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
                 try {
                     String indexAtom1String = tokenizer.nextToken();
                     int indexAtom1 = Integer.parseInt(indexAtom1String);
-                    IAtom atom1 = readData.getAtom(indexAtom1 - 1);
+                    IAtom atom1 = state.getAtom(indexAtom1);
                     bond.setAtom(atom1, 0);
                 } catch (Exception exception) {
                     String error = "Error while parsing index atom 1 in bond";
@@ -669,7 +706,7 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
                 try {
                     String indexAtom2String = tokenizer.nextToken();
                     int indexAtom2 = Integer.parseInt(indexAtom2String);
-                    IAtom atom2 = readData.getAtom(indexAtom2 - 1);
+                    IAtom atom2 = state.getAtom(indexAtom2);
                     bond.setAtom(atom2, 1);
                 } catch (Exception exception) {
                     String error = "Error while parsing index atom 2 in bond";
@@ -726,6 +763,8 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
 
                 // storing bond
                 readData.addBond(bond);
+                state.addBond(Integer.parseInt(bond.getID()),
+                              readData.getBond(readData.getBondCount()-1));
 
                 // storing positional variation
                 if ("ANY".equals(attach)) {
@@ -750,7 +789,8 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
     /**
      * Reads labels.
      */
-    public void readSGroup(IAtomContainer readData) throws CDKException {
+    public void readSGroup(ReadState state) throws CDKException {
+        IAtomContainer readData = state.mol;
         boolean foundEND = false;
         while (isReady() && !foundEND) {
             String command = readCommand(readLine());
@@ -788,13 +828,13 @@ public void readSGroup(IAtomContainer readData) throws CDKException {
                                 StringTokenizer atomsTokenizer = new StringTokenizer(value);
                                 int nExpected = Integer.parseInt(atomsTokenizer.nextToken());
                                 while (atomsTokenizer.hasMoreTokens()) {
-                                    sgroup.addAtom(readData.getAtom(Integer.parseInt(atomsTokenizer.nextToken()) - 1));
+                                    sgroup.addAtom(state.getAtom(Integer.parseInt(atomsTokenizer.nextToken())));
                                 }
                             } else if (key.equals("XBONDS")) {
                                 StringTokenizer xbonds = new StringTokenizer(value);
                                 int nExpected = Integer.parseInt(xbonds.nextToken());
                                 while (xbonds.hasMoreTokens()) {
-                                    sgroup.addBond(readData.getBond(Integer.parseInt(xbonds.nextToken()) - 1));
+                                    sgroup.addBond(state.getBond(Integer.parseInt(xbonds.nextToken())));
                                 }
                             } else if (key.equals("LABEL")) {
                                 label = value;