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gnu: avalon-toolkit: Update to 2.0.5a.

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The bug freeing static memory and the makefile have been improved upstream, so
we don't have to work around them anymore. Now, two static libraries are built
instead.

* gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a.
[source]: Switch to git reference from GitHub. Adjust snippet. Add patch from
the RDKit fork.
[arguments]: Remove 'dont-free-static-memory phase. Use provided
makefile. Adjust 'install phase.
* gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Christopher Baines <mail@cbaines.net>
This commit is contained in:
David Elsing 2024-01-28 23:02:00 +00:00 committed by Christopher Baines
parent baa711441a
commit 52cca41c6f
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GPG key ID: 5E28A33B0B84F577
3 changed files with 166 additions and 77 deletions
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2
gnu/local.mk
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@ -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.
#
@ -957,6 +958,7 @@ 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 \

131
gnu/packages/chemistry.scm
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@ -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().
#~(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)
(display (string-append "Building " program "\n"))
(invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
(string-append "-Wl,-rpath=" #$output "/lib")
"-DMAIN" (string-append program ".c") "-o" program))
programs)))
(replace 'install
(lambda _
;; Executables
(for-each
(lambda (program)
(install-file program (string-append #$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

110
gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch Normal file
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@ -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);