Bump - another patch.
On 20 July 2011 20:29, Izhar Wallach <izh...@cs.toronto.edu> wrote:
> I just noticed that my suggested code below has a bug...
> currConf should hold the index of the current conformation and not a pointer
> to it (because that memory address belongs to the source object).
> So, below is the corrected code. Hopefully no noticeable bugs this time ;-)
>
> Cheers,
> Izhar
>
> ----------------
> //Copy conformer
> information
> if (src.NumConformers() >
> 1)
> {
> int
> k,l;
> vector<double*>
> conf;
> int currConf =
> -1;
> double* xyz =
> NULL;
> for (k=0 ; k<src.NumConformers() ; ++k)
> {
> xyz = new double
> [3*src.NumAtoms()];
> memcpy( xyz, src.GetConformer(k), sizeof( double )*3*src.NumAtoms()
> );
>
> conf.push_back(xyz);
>
> if( src.GetConformer(k) == src._c )
> {
> currConf =
> k;
>
> }
> }
>
>
> SetConformers(conf);
> if( currConf >= 0 && _vconf.size() )
> {
> _c =
> _vconf[currConf];
>
> }
> }
>
>
> On Wed, Jul 13, 2011 at 2:31 PM, Izhar Wallach <izh...@cs.toronto.edu>
> wrote:
>>
>> Hi all,
>>
>> I noticed that when a molecule has multiple conformations the assignment
>> operator in OBMol does not copy properly the active conformation but rather
>> sets it to be the first one in the conformation set.
>> I guess this happens because the molecule object does not "remember" the
>> index of the currently active one but rather just points to it.
>>
>> It seems to me this is more of a bug than a feature because when copying a
>> molecule one expects to copy its full state and not resets it to some
>> arbitrary configuration.
>>
>> Below are my suggested small modifications to the code in mol.cpp (line
>> #~1300) that solve this issue (given the right commit permissions I will
>> modify the code directly...).
>>
>> Thanks,
>> Izhar
>> --------------------------
>> //Copy conformer
>> information
>> if (src.NumConformers() > 1) {
>> int k,l;
>> vector<double*> conf;
>> double* currConf = NULL; // NEW
>>
>> double* xyz = NULL;
>> for (k=0 ; k<src.NumConformers() ; ++k) {
>> xyz = new double [3*src.NumAtoms()];
>> //for (l=0 ; l<(int) (3*src.NumAtoms()) ;
>> ++l)
>> // xyz[l] = src.GetConformer(k)[l];
>> memcpy( xyz, src.GetConformer(k), sizeof( double
>> )*3*src.NumAtoms() ); // while we are here, this is more efficient than the
>> above loop
>> conf.push_back(xyz);
>>
>> if( src.GetConformer(k) == src._c ) { // NEW
>>
>> currConf =
>> src._c;
>>
>> }
>> }
>>
>> SetConformers(conf);
>> if( currConf ) { // NEW
>>
>> _c =
>> currConf;
>>
>> }
>> }
>>
>
>
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