For what it's worth, I value reproducibility for conformer generation,
and I use
the same random seed every time I run it. Out of curiosity, what
exactly is the
issue with minstd_rand?
Greg
Quoting Greg Landrum <greg.land...@gmail.com>:
> Sorry for the slow reply, I'm travelling.
>
> On Tue, Apr 12, 2011 at 10:24 PM, Andrew Dalke
> <da...@dalkescientific.com> wrote:
>>
>> I was curious about the choice of rng_type. utils.h says:
>>
>> namespace RDKit{
>> ...
>> typedef boost::uniform_int<> uniform_int;
>>
>>
>> where
>>
>> typedef random::linear_congruential< int32_t, 48271, 0, 2147483647,
>> 399268537 > minstd_rand;
>>
>>
>> I don't think minstd_rand is a good standard default, and I see that
>> other RDKit code agrees:
>>
>> Fingerprints.cpp: typedef boost::mt19937 rng_type;
>> Code/SimDivPickers/MaxMinPicker.h: typedef boost::mt19937 rng_type;
>>
>>
>> Is it time to revisit the choice of minstd_rand for conformation
>> generation?
>
> It easy enough to do if the community thinks it's worthwhile.
>
> One possible cost is that it will break any existing code or analyses
> that people have done that rely on the conformations that come from a
> particular seed.
>
> Best Regards,
> -greg
>
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