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From 26351733bde20eb16aedd62b4b64a2417615020e Mon Sep 17 00:00:00 2001
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From: Mamoru TASAKA <mtasaka@fedoraproject.org>
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Date: Thu, 25 Nov 2021 23:07:31 +0900
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Subject: [PATCH] MolfileReadCountsLine: fix storing n_atoms, n_bonds members
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after reading short size
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In MolfileReadCountsLine() (in INCHI_BASE/src/mol_fmt1.c), currently
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ctab->n_atoms and ctab->n_bonds, which have int type (as defined in src/mol_fmt.h),
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are passed to be MolfileReadField(), and to be treated there as if they have
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short size (as MOL_FMT_SHORT_INT_DATA is also passed to the argument of
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MolfileReadField(), and also the comment shows).
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This causes a error on big endian system such as s390x, where for example
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reading the line:
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1 0 0 0 0 0 0 0 0 0999 V2000
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On little endian (64bit) system, ctab->n_atoms is correctly stored as 1, but on
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s390x (big endian 64bit) system, ctab->n_atoms gets 65536 (= 1<<16), which is
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unexpected.
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To fix this, once store the read value to short size local variable, then
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copy the value to ctab->n_atoms or so later.
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---
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INCHI_BASE/src/mol_fmt1.c | 7 +++++--
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1 file changed, 5 insertions(+), 2 deletions(-)
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diff --git a/INCHI_BASE/src/mol_fmt1.c b/INCHI_BASE/src/mol_fmt1.c
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index 41ed15e..c2ad11a 100644
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--- a/INCHI_BASE/src/mol_fmt1.c
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+++ b/INCHI_BASE/src/mol_fmt1.c
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@@ -572,6 +572,7 @@ int MolfileReadCountsLine( MOL_FMT_CTAB* ctab,
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char line[MOL_FMT_INPLINELEN];
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const int line_len = sizeof( line );
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int err = 0, len;
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+ short n_atoms, n_bonds;
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p = inchi_fgetsLf( line, line_len, inp_file );
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@@ -588,8 +589,8 @@ int MolfileReadCountsLine( MOL_FMT_CTAB* ctab,
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TREAT_ERR( err, 0, "Too long counts line" ); /* too long input file line */
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}
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- if (0 > MolfileReadField( &ctab->n_atoms, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */
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- || 0 > MolfileReadField( &ctab->n_bonds, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */
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+ if (0 > MolfileReadField( &n_atoms, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */
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+ || 0 > MolfileReadField( &n_bonds, 3, MOL_FMT_SHORT_INT_DATA, &p ) /* V2000 only: short int */
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#if ( MOL_FMT_QUERY == MOL_FMT_PRESENT )
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|| 0 > MolfileReadField( &ctab->n_atom_lists, 3, MOL_FMT_SHORT_INT_DATA, &p )
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@@ -621,6 +622,8 @@ int MolfileReadCountsLine( MOL_FMT_CTAB* ctab,
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AddErrorMessage( pStrErr, line );
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goto err_fin;
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}
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+ ctab->n_atoms = n_atoms;
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+ ctab->n_bonds = n_bonds;
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/* Get CTFile version (V2000 or other) */
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len = MolfileReadField( ctab->version_string,
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--
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2.33.1
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