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Merged
PiTrem merged 2 commits into from
Dec 8, 2025
Merged

build: update InChI version to official 1.07.4 #3

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040895e
Add devcontainer
JanCBrammer Nov 12, 2025
e8bcd17
Update InChI sources
JanCBrammer Nov 13, 2025
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24 changes: 24 additions & 0 deletions .devcontainer.json
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{
"name": "inchi-gem",
"image": "ruby:3.3.10",
"features": {
"ghcr.io/devcontainers/features/common-utils:2": {
"installZsh": true,
"configureZshAsDefaultShell": true,
"installOhMyZsh": true,
"installOhMyZshConfig": true,
"upgradePackages": true,
"username": "automatic",
"userUid": "automatic",
"userGid": "automatic"
}
},
"customizations": {
"vscode": {
"extensions": [
"eamodio.gitlens"
]
}
},
"postCreateCommand": "apt-get update && apt-get install cmake -y"
}
7 changes: 3 additions & 4 deletions .gitignore
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Expand Up @@ -4,10 +4,9 @@ Gemfile.lock
pkg/*

# ignore build artifacts
ext/inchi-gem/Makefile
ext/inchi-gem/inchi/
ext/inchi-gem/inchi.o
ext/inchi-gem/inchi_wrap.*
ext/inchi-gem/*

!ext/inchi-gem/extconf.rb
!ext/inchi-gem/inchi.c

.tool-versions
163 changes: 19 additions & 144 deletions ext/inchi-gem/extconf.rb
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Expand Up @@ -2,153 +2,28 @@
require 'rbconfig'
require 'mkmf'

# current dir
main_dir = File.expand_path(File.join(File.dirname(__FILE__)))
inchi_src = File.join(main_dir, "inchi_src")
libinchi_src = File.join(inchi_src, "INCHI-1-SRC/INCHI_API/libinchi/src")
libinchi_build = File.join(inchi_src, "build")
inchi_version = "d124ee52b4de0ed3d608d2a3d522b939f01f2549"

# ext/inchi-gem/inchi
inchi_src_dir = File.join(main_dir, "inchi")

FileUtils.rm_rf inchi_src_dir

### Download InChI source
FileUtils.rm_rf inchi_src
Dir.chdir main_dir
puts "Downloading InChI sources"
# ext/inchi-gem/inchi/
system "git clone https://github.com/CamAnNguyen/inchi" or abort

# ext/inchi-gem/inchi/INCHI_BASE/src -> inchi-gem/build/inchi/INCHI_API/libinchi/src
FileUtils.cp_r("#{inchi_src_dir}/INCHI_BASE/src/.", "#{inchi_src_dir}/INCHI_API/libinchi/src")

inc_dirs = '-I. -I./inchi/INCHI_API/libinchi/src'
system("git clone --no-checkout --filter=tree:0 https://github.com/IUPAC-InChI/InChI.git #{inchi_src}") or abort
Dir.chdir inchi_src
system("git fetch --depth 1 origin #{inchi_version}") or abort
system("git sparse-checkout set --no-cone /INCHI-1-SRC") or abort
system("git checkout #{inchi_version}") or abort

system("swig #{inc_dirs} -c++ -ruby inchi.i") or abort
### Compile InChI
system("cmake -B #{libinchi_build} -S #{libinchi_src}") or abort
system("cmake --build #{libinchi_build}") or abort

$INCFLAGS << inc_dirs
$CFLAGS << " -DTARGET_API_LIB"
### Configure Ruby extension
find_library('inchi', "MakeINCHIFromMolfileText", File.join(libinchi_build, "lib"))
find_header('inchi_api.h', File.join(inchi_src, "/INCHI-1-SRC/INCHI_BASE/src"))

$srcs = [
'inchi.cpp',
'inchi_wrap.cxx',
'./inchi/INCHI_API/libinchi/src/ichi_bns.c',
'./inchi/INCHI_API/libinchi/src/ichi_io.c',
'./inchi/INCHI_API/libinchi/src/ichican2.c',
'./inchi/INCHI_API/libinchi/src/ichicano.c',
'./inchi/INCHI_API/libinchi/src/ichicans.c',
'./inchi/INCHI_API/libinchi/src/ichierr.c',
'./inchi/INCHI_API/libinchi/src/ichiisot.c',
'./inchi/INCHI_API/libinchi/src/ichilnct.c',
'./inchi/INCHI_API/libinchi/src/ichimak2.c',
'./inchi/INCHI_API/libinchi/src/ichimake.c',
'./inchi/INCHI_API/libinchi/src/ichimap1.c',
'./inchi/INCHI_API/libinchi/src/ichimap2.c',
'./inchi/INCHI_API/libinchi/src/ichimap4.c',
'./inchi/INCHI_API/libinchi/src/ichinorm.c',
'./inchi/INCHI_API/libinchi/src/ichiparm.c',
'./inchi/INCHI_API/libinchi/src/ichiprt1.c',
'./inchi/INCHI_API/libinchi/src/ichiprt2.c',
'./inchi/INCHI_API/libinchi/src/ichiprt3.c',
'./inchi/INCHI_API/libinchi/src/ichiqueu.c',
'./inchi/INCHI_API/libinchi/src/ichiread.c',
'./inchi/INCHI_API/libinchi/src/ichiring.c',
'./inchi/INCHI_API/libinchi/src/ichirvr1.c',
'./inchi/INCHI_API/libinchi/src/ichirvr2.c',
'./inchi/INCHI_API/libinchi/src/ichirvr3.c',
'./inchi/INCHI_API/libinchi/src/ichirvr4.c',
'./inchi/INCHI_API/libinchi/src/ichirvr5.c',
'./inchi/INCHI_API/libinchi/src/ichirvr6.c',
'./inchi/INCHI_API/libinchi/src/ichirvr7.c',
'./inchi/INCHI_API/libinchi/src/ichisort.c',
'./inchi/INCHI_API/libinchi/src/ichister.c',
'./inchi/INCHI_API/libinchi/src/ichitaut.c',
'./inchi/INCHI_API/libinchi/src/ikey_base26.c',
'./inchi/INCHI_API/libinchi/src/ikey_dll.c',
'./inchi/INCHI_API/libinchi/src/inchi_dll.c',
'./inchi/INCHI_API/libinchi/src/inchi_dll_a.c',
'./inchi/INCHI_API/libinchi/src/inchi_dll_a2.c',
'./inchi/INCHI_API/libinchi/src/inchi_dll_b.c',
'./inchi/INCHI_API/libinchi/src/inchi_dll_main.c',
'./inchi/INCHI_API/libinchi/src/inchi_gui.c',
'./inchi/INCHI_API/libinchi/src/mol2atom.c',
'./inchi/INCHI_API/libinchi/src/mol_fmt1.c',
'./inchi/INCHI_API/libinchi/src/mol_fmt2.c',
'./inchi/INCHI_API/libinchi/src/mol_fmt3.c',
'./inchi/INCHI_API/libinchi/src/mol_fmt4.c',
'./inchi/INCHI_API/libinchi/src/readinch.c',
'./inchi/INCHI_API/libinchi/src/runichi.c',
'./inchi/INCHI_API/libinchi/src/runichi2.c',
'./inchi/INCHI_API/libinchi/src/runichi3.c',
'./inchi/INCHI_API/libinchi/src/runichi4.c',
'./inchi/INCHI_API/libinchi/src/sha2.c',
'./inchi/INCHI_API/libinchi/src/strutil.c',
'./inchi/INCHI_API/libinchi/src/util.c',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_builder.c',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_inchikey_builder.c',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_mol.c',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_read_inchi.c',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_read_mol.c',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_status.c',
]

$objs = [
'inchi.o',
'inchi_wrap.o',
'./inchi/INCHI_API/libinchi/src/ichi_bns.o',
'./inchi/INCHI_API/libinchi/src/ichi_io.o',
'./inchi/INCHI_API/libinchi/src/ichican2.o',
'./inchi/INCHI_API/libinchi/src/ichicano.o',
'./inchi/INCHI_API/libinchi/src/ichicans.o',
'./inchi/INCHI_API/libinchi/src/ichierr.o',
'./inchi/INCHI_API/libinchi/src/ichiisot.o',
'./inchi/INCHI_API/libinchi/src/ichilnct.o',
'./inchi/INCHI_API/libinchi/src/ichimak2.o',
'./inchi/INCHI_API/libinchi/src/ichimake.o',
'./inchi/INCHI_API/libinchi/src/ichimap1.o',
'./inchi/INCHI_API/libinchi/src/ichimap2.o',
'./inchi/INCHI_API/libinchi/src/ichimap4.o',
'./inchi/INCHI_API/libinchi/src/ichinorm.o',
'./inchi/INCHI_API/libinchi/src/ichiparm.o',
'./inchi/INCHI_API/libinchi/src/ichiprt1.o',
'./inchi/INCHI_API/libinchi/src/ichiprt2.o',
'./inchi/INCHI_API/libinchi/src/ichiprt3.o',
'./inchi/INCHI_API/libinchi/src/ichiqueu.o',
'./inchi/INCHI_API/libinchi/src/ichiread.o',
'./inchi/INCHI_API/libinchi/src/ichiring.o',
'./inchi/INCHI_API/libinchi/src/ichirvr1.o',
'./inchi/INCHI_API/libinchi/src/ichirvr2.o',
'./inchi/INCHI_API/libinchi/src/ichirvr3.o',
'./inchi/INCHI_API/libinchi/src/ichirvr4.o',
'./inchi/INCHI_API/libinchi/src/ichirvr5.o',
'./inchi/INCHI_API/libinchi/src/ichirvr6.o',
'./inchi/INCHI_API/libinchi/src/ichirvr7.o',
'./inchi/INCHI_API/libinchi/src/ichisort.o',
'./inchi/INCHI_API/libinchi/src/ichister.o',
'./inchi/INCHI_API/libinchi/src/ichitaut.o',
'./inchi/INCHI_API/libinchi/src/ikey_base26.o',
'./inchi/INCHI_API/libinchi/src/ikey_dll.o',
'./inchi/INCHI_API/libinchi/src/inchi_dll.o',
'./inchi/INCHI_API/libinchi/src/inchi_dll_a.o',
'./inchi/INCHI_API/libinchi/src/inchi_dll_a2.o',
'./inchi/INCHI_API/libinchi/src/inchi_dll_b.o',
'./inchi/INCHI_API/libinchi/src/inchi_dll_main.o',
'./inchi/INCHI_API/libinchi/src/inchi_gui.o',
'./inchi/INCHI_API/libinchi/src/mol2atom.o',
'./inchi/INCHI_API/libinchi/src/mol_fmt1.o',
'./inchi/INCHI_API/libinchi/src/mol_fmt2.o',
'./inchi/INCHI_API/libinchi/src/mol_fmt3.o',
'./inchi/INCHI_API/libinchi/src/mol_fmt4.o',
'./inchi/INCHI_API/libinchi/src/readinch.o',
'./inchi/INCHI_API/libinchi/src/runichi.o',
'./inchi/INCHI_API/libinchi/src/runichi2.o',
'./inchi/INCHI_API/libinchi/src/runichi3.o',
'./inchi/INCHI_API/libinchi/src/runichi4.o',
'./inchi/INCHI_API/libinchi/src/sha2.o',
'./inchi/INCHI_API/libinchi/src/strutil.o',
'./inchi/INCHI_API/libinchi/src/util.o',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_builder.o',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_inchikey_builder.o',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_mol.o',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_read_inchi.o',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_read_mol.o',
'./inchi/INCHI_API/libinchi/src/ixa/ixa_status.o',
]

create_makefile('inchi')
Dir.chdir main_dir
create_makefile("inchi")
122 changes: 122 additions & 0 deletions ext/inchi-gem/inchi.c
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#include <ruby.h>
#include <inchi_api.h>
#include <string.h>


typedef struct {
int returnCode;
VALUE message;
VALUE log;
VALUE auxInfo;
} rb_ExtraInchiReturnValues;

static void
rb_eirv_free(void *ptr)
{
ruby_xfree(ptr);
}

static const rb_data_type_t rb_eirv_type = {
"ExtraInchiReturnValues",
{0, rb_eirv_free, 0},
0, 0,
RUBY_TYPED_FREE_IMMEDIATELY
};

static VALUE
rb_eirv_alloc(VALUE klass)
{
rb_ExtraInchiReturnValues *p;
VALUE obj = TypedData_Make_Struct(klass, rb_ExtraInchiReturnValues,
&rb_eirv_type, p);
p->returnCode = 0;
p->message = Qnil;
p->log = Qnil;
p->auxInfo = Qnil;
return obj;
}

static void
fix_option_symbols(const char *in, char *out)
{
const char *s = in;
char *d = out;
while ((*d = *s)) {
#ifdef _WIN32
if (*d == '-') *d = '/';
#else
if (*d == '/') *d = '-';
#endif
++d; ++s;
}
}

static VALUE
rb_molfile_to_inchi(int argc, VALUE *argv, VALUE self)
{
VALUE rb_mol, rb_rv, rb_opts;
rb_scan_args(argc, argv, "21", &rb_mol, &rb_rv, &rb_opts);
if (NIL_P(rb_opts)) rb_opts = rb_str_new2("");

Check_Type(rb_mol, T_STRING);
Check_Type(rb_opts, T_STRING);

rb_ExtraInchiReturnValues *rv;
TypedData_Get_Struct(rb_rv, rb_ExtraInchiReturnValues,
&rb_eirv_type, rv);

const char *mol_text = RSTRING_PTR(rb_mol);
const char *opts_in = RSTRING_LEN(rb_opts) ? RSTRING_PTR(rb_opts) : NULL;

char *opts_copy = NULL;
if (opts_in) {
opts_copy = ALLOCA_N(char, RSTRING_LEN(rb_opts) + 1);
fix_option_symbols(opts_in, opts_copy);
}

inchi_Output out;
memset(&out, 0, sizeof(out));

int ret = MakeINCHIFromMolfileText(mol_text, opts_copy, &out);

rv->returnCode = ret;
rv->message = (out.szMessage ? rb_str_new2(out.szMessage) : Qnil);
rv->log = (out.szLog ? rb_str_new2(out.szLog) : Qnil);
rv->auxInfo = (out.szAuxInfo ? rb_str_new2(out.szAuxInfo) : Qnil);
VALUE result = out.szInChI ? rb_str_new2(out.szInChI) : rb_str_new2("");
FreeINCHI(&out);
return result;
}

static VALUE
rb_inchi_to_inchi_key(VALUE self, VALUE rb_inchi)
{
Check_Type(rb_inchi, T_STRING);
const char *inchi = RSTRING_PTR(rb_inchi);

char inchi_key[29], xtra1[65], xtra2[65];
int rc = GetINCHIKeyFromINCHI(inchi, 0, 0, inchi_key, xtra1, xtra2);

if (rc == INCHIKEY_OK)
return rb_str_new2(inchi_key);

return Qnil;
}

void
Init_inchi(void)
{
VALUE mInchi = rb_define_module("Inchi");

VALUE cRV = rb_define_class_under(mInchi, "ExtraInchiReturnValues", rb_cObject);
rb_define_alloc_func(cRV, rb_eirv_alloc);
rb_define_attr(cRV, "returnCode", 1, 1);
rb_define_attr(cRV, "message", 1, 1);
rb_define_attr(cRV, "log", 1, 1);
rb_define_attr(cRV, "auxInfo", 1, 1);

rb_define_module_function(mInchi, "molfileToInchi",
rb_molfile_to_inchi, -1);
rb_define_module_function(mInchi, "InchiToInchiKey",
rb_inchi_to_inchi_key, 1);
}
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