diff --git a/gnu/local.mk b/gnu/local.mk
index ab63bd5881..b5d61eb4dd 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -63,6 +63,7 @@
 # Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 # Copyright © 2023 Herman Rimm <herman@rimm.ee>
 # Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
+# Copyright © 2024 David Elsing <david.elsing@posteo.net>
 #
 # This file is part of GNU Guix.
 #
@@ -952,6 +953,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/audiofile-function-signature.patch	\
   %D%/packages/patches/automake-skip-amhello-tests.patch	\
   %D%/packages/patches/avahi-localstatedir.patch		\
+  %D%/packages/patches/avalon-toolkit-rdkit-fixes.patch		\
   %D%/packages/patches/avidemux-install-to-lib.patch		\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/awesome-4.3-fno-common.patch		\
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 4a9dd97c5b..5e19bdf182 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -917,90 +917,67 @@ (define-public yaehmop
 (define-public avalon-toolkit
   (package
     (name "avalon-toolkit")
-    (version "1.2.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "mirror://sourceforge/avalontoolkit/"
-             "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
-             version ".source.tar"))
-       (sha256
-        (base32
-         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
-       (modules '((guix build utils) (ice-9 ftw)))
-       (snippet
-        #~(begin
-            (delete-file-recursively "../SourceDistribution/java")))))
+    (version "2.0.5a")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rohdebe1/ava-formake")
+                    (commit (string-append "AvalonToolkit_" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1mfg40y5xc17sm59zdfc5sk22n9zm5zk0z1aw47chvl6hp465szk"))
+              (patches
+               (search-patches "avalon-toolkit-rdkit-fixes.patch"))
+              (modules '((guix build utils) (ice-9 ftw)))
+              (snippet
+               #~(begin
+                   (delete-file-recursively "src/main/java")
+                   (delete-file-recursively "src/test/target")))))
     (build-system gnu-build-system)
     (arguments
      (list
-      ;; There are no intended tests
+      ;; There is only one test, which is missing a file
       #:tests? #f
       #:phases
-      #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk")))
-          (modify-phases %standard-phases
-            (add-after 'unpack 'chdir
-              (lambda _ (chdir "common")))
-            (delete 'configure)
-            (add-before 'build 'dont-free-static-memory
-              (lambda _
-                (substitute* "reaccsio.c"
-                  (("MyFree\\(.*tempdir\\)" m)
-                   (string-append "/* freeing memory from getenv is bad */"
-                                  "// " m)))))
-            ;; The makefile has incorrect compiler flags and is missing some
-            ;; object files, so we build it ourselves.
-            (replace 'build
-              (lambda _
-                (for-each
-                 (lambda (part)
-                   (format #t "Compiling ~a.c ~~> ~a.o~%" part part)
-                   (invoke #$(cc-for-target) "-c" "-fPIC" "-O2"
-                           (string-append part ".c")
-                           "-o" (string-append part ".o")))
-                 (list "aacheck" "casutils" "denormal" "depictutil"
-                       "didepict" "fixcharges" "forio" "geometry"
-                       "graph" "hashcode" "layout" "local" "pattern"
-                       "perceive" "reaccsio" "rtutils" "set" "shortcut"
-                       "sketch" "ssmatch" "stereo" "symbol_lists"
-                       "symboltable" "utilities"))
-                (display "Building libavalontoolkit.so\n")
-                (apply invoke "gcc" "-fPIC" "-shared" "-lm"
-                       "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c"
-                       "struchk.c" "patclean.c" (find-files "." "\\.o$"))
-                ;; patclean is not built here as there is an undeclared
-                ;; variable in main().
-                (for-each
-                 (lambda (program)
-                   (display (string-append "Building " program "\n"))
-                   (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
-                           (string-append "-Wl,-rpath=" #$output "/lib")
-                           "-DMAIN" (string-append program ".c") "-o" program))
-                 programs)))
-            (replace 'install
-              (lambda _
-                ;; Executables
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (replace 'build
+            (lambda* (#:key parallel-build? #:allow-other-keys)
+              (mkdir "build")
+              (mkdir-p "target/executables")
+              (mkdir-p "target/libraries")
+              (invoke "make" "programs" "-j"
+                      (if parallel-build?
+                          (number->string (parallel-job-count))
+                          "1"))))
+          (replace 'install
+            (lambda _
+              ;; Executables
+              (let ((programs '("canonizer" "matchtest" "smi2mol" "struchk")))
                 (for-each
                  (lambda (program)
-                   (install-file program (string-append #$output "/bin")))
-                 programs)
-                (for-each
-                 (lambda (name)
-                   (symlink (string-append #$output "/bin/smi2mol")
-                            (string-append #$output "/bin/" name)))
-                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
-                ;; Library
-                (install-file "libavalontoolkit.so"
-                              (string-append #$output "/lib"))
-                (for-each
-                 (lambda (file)
-                   (install-file file (string-append #$output
-                                                    "/include/avalontoolkit")))
-                 (find-files "." "\\.h$"))
-                (install-file "../license.txt"
-                              (string-append #$output "/share/doc/"
-                                             #$name "-" #$version "/"))))))))
+                   (install-file (string-append "target/executables/" program)
+                                 (string-append #$output "/bin")))
+                 programs))
+              (for-each
+               (lambda (name)
+                 (symlink (string-append #$output "/bin/smi2mol")
+                          (string-append #$output "/bin/" name)))
+               '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
+              ;; Library
+              (install-file "target/libraries/libavalon_tools.a"
+                            (string-append #$output "/lib"))
+              (install-file "target/libraries/libavalon4rdkit.a"
+                            (string-append #$output "/lib"))
+              (for-each
+               (lambda (file)
+                 (install-file file (string-append #$output
+                                                   "/include/avalontoolkit")))
+               (find-files "src/main/C/include" "\\.h$"))
+              (install-file "license.txt"
+                            (string-append #$output "/share/doc/"
+                                           #$name "-" #$version "/")))))))
     (home-page "https://sourceforge.net/projects/avalontoolkit/")
     (synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
     (description "This package contains a library and programs for
diff --git a/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch
new file mode 100644
index 0000000000..c93a9869ed
--- /dev/null
+++ b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch
@@ -0,0 +1,110 @@
+Patches taken from the rdkit fork at this commit (there version
+AvalonToolkit_2.0.6-pre.2):
+https://github.com/rdkit/ava-formake/commit/d05bee0382b8f4696b2b4b05b0038fb7d559520a
+
+diff -ur a/src/main/C/common/reaccsio.c b/src/main/C/common/reaccsio.c
+--- a/src/main/C/common/reaccsio.c
++++ b/src/main/C/common/reaccsio.c
+@@ -322,34 +322,49 @@
+       fprintf(fp,"\n");
+ }
+ 
++#define MAX_BONDLINE_FIELDS 7
++#define BONDLINE_FIELD_LEN 3
++
+ int ReadREACCSBond(Fortran_FILE *fp, struct reaccs_bond_t *bp)
+ {
+-   int nitems, i;
+-   char buffer[MAX_BUFFER+1];
++   int nitems, i, j, k;
++   int bond_line_len, n_chars, pos;
++   int *ptrarray[MAX_BONDLINE_FIELDS];
++   char c;
++   char buffer[BONDLINE_FIELD_LEN+1];
+ 
+    if (fp->status != FORTRAN_NORMAL) return(fp->status);
+ 
+-   strncpy(buffer,fp->buffer,MAX_BUFFER);
+-   /* zero pad only atom numbers! */
+-   for (i=0; i<6; i++) if (buffer[i] == ' ') buffer[i] = '0';
+-
+    bp->stereo_symbol = 0;
+    bp->dummy = 0;
+    bp->topography = 0;
+    bp->reaction_mark = NONE;
+-   // make sure spaces are interpreted the Fortran-way
+-   for (i=9; i<strlen(buffer)  &&  i<21; i+=3)
+-   {
+-       if ((i+1)<strlen(buffer)  &&  buffer[i+1]==' ') buffer[i+1] = '0';
+-       if ((i+2)<strlen(buffer)  &&  buffer[i+2]==' ') buffer[i+2] = '0';
++   ptrarray[0] = &bp->atoms[0];
++   ptrarray[1] = &bp->atoms[1];
++   ptrarray[2] = &bp->bond_type;
++   ptrarray[3] = &bp->stereo_symbol;
++   ptrarray[4] = &bp->dummy;
++   ptrarray[5] = &bp->topography;
++   ptrarray[6] = &bp->reaction_mark;
++   bond_line_len = strlen(fp->buffer);
++   nitems = bond_line_len ? (bond_line_len - 1) / BONDLINE_FIELD_LEN + 1 : 0;
++   if (nitems > MAX_BONDLINE_FIELDS)
++      nitems = MAX_BONDLINE_FIELDS;
++   for (i = 0; i < nitems; ++i)
++   {
++      pos = i * BONDLINE_FIELD_LEN;
++      memset(buffer, 0, BONDLINE_FIELD_LEN + 1);
++      n_chars = bond_line_len - pos;
++      if (n_chars > BONDLINE_FIELD_LEN)
++         n_chars = BONDLINE_FIELD_LEN;
++      for (j = 0, k = 0; j < n_chars; ++j)
++      {
++         c = fp->buffer[pos + j];
++         if (c != ' ')
++            buffer[k++] = c;
++      }
++      sscanf(buffer, "%3d", ptrarray[i]);
+    }
+-   nitems = sscanf(buffer,
+-                   "%3d%3d%3d%3d%3d%3d%3d",
+-                   &bp->atoms[0],   &bp->atoms[1],
+-                   &bp->bond_type,  &bp->stereo_symbol,
+-                   &bp->dummy,
+-                   &bp->topography, &bp->reaction_mark);
+-
+    if (nitems >= 3)
+    {
+       GetBuffer(fp);
+@@ -1582,6 +1597,8 @@
+ 
+    PrintREACCSMolecule(fp, mp,"");
+ 
++   fputc('\0', fp);
++   fflush(fp);
+    rewind(fp);
+ 
+    MolStr = _ReadFile(fp);
+diff -ur a/src/main/C/programs/struchk.c b/src/main/C/programs/struchk.c
+--- a/src/main/C/programs/struchk.c
++++ b/src/main/C/programs/struchk.c
+@@ -1581,6 +1581,22 @@
+ 
+    if ((result & SIZE_CHECK_FAILED) == 0)
+    {
++      for (i = 0; i < mp->n_bonds; ++i) {
++         for (j = 0; j < 2; ++j) {
++            if (mp->bond_array[i].atoms[j] < 1 || mp->bond_array[i].atoms[j] > mp->n_atoms)
++            {
++               snprintf(msg_buffer, MAXMSG,
++                  "%10s    : illegal atom # (%d, max allowed is %d) in bond %d",
++                  mp->name, mp->bond_array[i].atoms[j], mp->n_atoms, i + 1);
++               AddMsgToList(msg_buffer);
++               result |= SIZE_CHECK_FAILED;
++            }
++         }
++      }
++   }
++
++   if ((result & SIZE_CHECK_FAILED) == 0)
++   {
+       if (convert_atom_texts)
+       {
+          tmp = ConvertAtomAliases(mp);
