Actually that sizeof in Translate (data.cpp) is plain wrong, since it
refers to sizeof(char *) which is 8 on a 64-bit OS and 4 on a 32-bit OS;
build the attached test.c with -m64 and -m32 and run to verify that:
$ gcc -m64 test.c -o test64
$ ./test64
This is really 6: 6
This is machine-dependent: 8
$ gcc -m32 test.c -o test32
$ ./test32
This is really 6: 6
This is machine-dependent: 4
Probably Chris has a 32-bit Windows machine, that's why it works.
So the rel fix is not increasing to 8 the size of _type in OBAtom
(atom.h), but rather defining OBATOM_TYPE_LEN = 6 in atom.h, setting
_type[OBATOM_TYPE_LEN] in OBAtom and replacing sizeof(to) with
OBATOM_TYPE_LEN in bool OBTypeTable::Translate(char *to, const char
*from). A new patch is attached.
Cheers,
p.
--
==========================================================
Paolo Tosco, Ph.D. Phone: +39 011 6707680
Department of Drug Science Fax: +39 011 6707687
and Technology Mob: +39 348 5537206
Via Pietro Giuria, 9
10125 Torino, Italy
http://open3dalign.org
E-mail: paolo.to...@unito.it http://open3dqsar.org
==========================================================
#include <stdio.h>
int sizeof_in_function(char *type) {
return sizeof(type);
}
int main(int argc, char **argv)
{
char type[6];
printf("This is really 6: %d\n", sizeof(type));
printf("This is machine-dependent: %d\n", sizeof_in_function(type));
return 0;
}
*** src/forcefield.cpp.orig 2012-05-18 00:22:20.875386817 +0200
--- src/forcefield.cpp 2012-05-18 00:26:12.030386712 +0200
***************
*** 779,788 ****
{
IF_OBFF_LOGLVL_LOW {
OBFFLog("\nA T O M T Y P E S\n\n");
! OBFFLog("IDX\tTYPE\n");
FOR_ATOMS_OF_MOL (a, _mol) {
! snprintf(_logbuf, BUFF_SIZE, "%d\t%s\n", a->GetIdx(), a->GetType());
OBFFLog(_logbuf);
}
}
--- 779,789 ----
{
IF_OBFF_LOGLVL_LOW {
OBFFLog("\nA T O M T Y P E S\n\n");
! OBFFLog("IDX\tTYPE\tRING\n");
FOR_ATOMS_OF_MOL (a, _mol) {
! snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(),
a->GetType(),
! (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO"));
OBFFLog(_logbuf);
}
}
***************
*** 855,875 ****
}
if (IsSetupNeeded(mol)) {
- int *formal_charge = new int[mol.NumAtoms()];
- int i;
-
- i = 0;
- FOR_ATOMS_OF_MOL (atom, mol) {
- formal_charge[i] = atom->GetFormalCharge();
- ++i;
- }
_mol = mol;
- i = 0;
- FOR_ATOMS_OF_MOL (atom, _mol) {
- atom->SetFormalCharge(formal_charge[i]);
- ++i;
- }
- delete [] formal_charge;
_ncoords = _mol.NumAtoms() * 3;
if (_velocityPtr)
--- 856,862 ----
***************
*** 925,945 ****
}
if (IsSetupNeeded(mol)) {
- int *formal_charge = new int[mol.NumAtoms()];
- int i;
-
- i = 0;
- FOR_ATOMS_OF_MOL (atom, mol) {
- formal_charge[i] = atom->GetFormalCharge();
- ++i;
- }
_mol = mol;
- i = 0;
- FOR_ATOMS_OF_MOL (atom, _mol) {
- atom->SetFormalCharge(formal_charge[i]);
- ++i;
- }
- delete [] formal_charge;
_ncoords = _mol.NumAtoms() * 3;
if (_velocityPtr)
--- 912,918 ----
*** src/data.cpp.orig 2012-05-18 01:04:55.818907112 +0200
--- src/data.cpp 2012-05-18 01:05:05.358819367 +0200
***************
*** 568,576 ****
string sto,sfrom;
sfrom = from;
rval = Translate(sto,sfrom);
! strncpy(to,(char*)sto.c_str(), sizeof(to) - 1);
! to[sizeof(to) - 1] = '\0';
!
return(rval);
}
--- 568,576 ----
string sto,sfrom;
sfrom = from;
rval = Translate(sto,sfrom);
! strncpy(to,(char*)sto.c_str(), OBATOM_TYPE_LEN - 1);
! to[OBATOM_TYPE_LEN - 1] = '\0';
!
return(rval);
}
*** include/openbabel/atom.h.orig 2012-05-18 00:20:06.932510403 +0200
--- include/openbabel/atom.h 2012-05-18 00:55:56.804975387 +0200
***************
*** 77,88 ****
// Class OBAtom
// class introduction in atom.cpp
class OBAPI OBAtom: public OBBase
{
protected:
unsigned char _ele; //!< atomic number (type
unsigned char to minimize space -- allows for 0..255 elements)
char _impval; //!< implicit valence
! char _type[6]; //!< atomic type
short _fcharge; //!< formal charge
unsigned short _isotope; //!< isotope (0 = most
abundant)
short _spinmultiplicity;//!< atomic spin, e.g.,
2 for radical 1 or 3 for carbene
--- 77,89 ----
// Class OBAtom
// class introduction in atom.cpp
+ #define OBATOM_TYPE_LEN 6
class OBAPI OBAtom: public OBBase
{
protected:
unsigned char _ele; //!< atomic number (type
unsigned char to minimize space -- allows for 0..255 elements)
char _impval; //!< implicit valence
! char _type[OBATOM_TYPE_LEN]; //!< atomic type
short _fcharge; //!< formal charge
unsigned short _isotope; //!< isotope (0 = most
abundant)
short _spinmultiplicity;//!< atomic spin, e.g.,
2 for radical 1 or 3 for carbene
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