Re: [O3Q] Open3DTools Openbabel Issue

[Matthew L. <ml...@gm...>]

Things are working well now.  I'm sure that I've got somethings that are
causing issues with OB.  :)

Thanks for your help Paolo!
Matthew

On Mon, Nov 21, 2016 at 12:17 PM, Matthew Lardy <ml...@gm...> wrote:

> I'll add, that a dummy example works fine:
>
> > calc_field type=MM_ELE
>
> Number of fields:      1
>
> -------------------------
> Field    Attribute
> -------------------------
>     1    INCLUDED
>
> Number of objects:   4
>
> Number of Y variables:   1
>
> Y variable full names:
>   y1: pIC50
>
> ------------------------------------------------------------
> -----------------------------------
>
>                                  y1
>     N   ID  Str    Object name
> Attribute             Weight       pIC50
> ------------------------------------------------------------
> -----------------------------------
>     1    1    1    omega_1                             TRAINING
> SET          1.0000      8.0000
>     2    2    2    omega_2                             TRAINING
> SET          1.0000      4.0000
>     3    3    3    omega_3                             TRAINING
> SET          1.0000      5.0000
>     4    4    4    omega_4                             TRAINING
> SET          1.0000      6.0000
>
> x variables:           5168
> y variables:           1
>
> TYPE    STATUS      TOTAL         ACTIVE               MIN
> MAX           WEIGHT
> x1      INCLUDED    5168          5168     (100%)      -293.4798
> 965.2949      1.0000
> y1      INCLUDED    1             1        (100%)      4.0000
> 8.0000        1.0000
>
> Active x variables:        5168 (100%)
> Zero x values:                0 (  0%)
> Active y variables:           1
> Zero y values:                0 (  0%)
>
> END COMMAND #00.0003 - CALC_MM_FIELD tool succeeded.
>
> So I guess I have to guess what is causing my problems, unless someone has
> a way to pull out bad actors for this flavor of OpenBabel.
>
> Thanks!
> Matthew
>
>
> On Mon, Nov 21, 2016 at 11:14 AM, Matthew Lardy <ml...@gm...> wrote:
>
>> Hi Paolo,
>>
>> That's unfortunate, as I was hopeful that the CoMFA code had been
>> ported.  I unfortunately cannot share these structures.  Worse, the version
>> of obenergy that is in the Openbabel-for-open3dtools gives me this when I
>> pass it the sd file:
>>
>> open3dtools/bin/obenergy -v -ff mmff94 file.sdf
>> open3dtools/bin/obenergy: cannot read input format!
>>
>> I've played with OB for a long time; so I am not surprised by the error
>> but it is a showstopper.
>>
>> Matthew
>>
>> On Mon, Nov 21, 2016 at 10:49 AM, Paolo Tosco <pao...@un...>
>> wrote:
>>
>>> Hi Matthew,
>>>
>>> unfortunately there is no Open3DQSAR implementation in the RDKit as of
>>> now. Can you share your input structures with me? So I can have a look and
>>> see what's wrong.
>>>
>>> Thanks, cheers
>>> p.
>>>
>>>
>>> On 11/21/16 18:42, Matthew Lardy wrote:
>>>
>>> Hi Paolo,
>>>
>>> Unfortunately, the shell script is written in Bash so I have to re-write
>>> it to use the tools.  Which after doing so, still fails:
>>>
>>> OpenBabel reported the error message which follows:
>>> obenergy: could not setup force field.
>>>
>>> CALC_FIELD failed.
>>>
>>>
>>> Job finished on Mon Nov 21 10:40:56 2016
>>>
>>> Abnormal exit.
>>>
>>> I see Open3DAlign in RDKit, but I don't see the CoMFA stuff (which I am
>>> assuming is the Open3DQSAR package).  Would you mind pointing me towards
>>> it, as I'd rather use the RDKit implementation anyway!
>>>
>>> Thanks!
>>> Matthew
>>>
>>> On Fri, Nov 18, 2016 at 10:42 PM, Paolo Tosco <pao...@un...>
>>> wrote:
>>>
>>>> Hi Matthew,
>>>>
>>>> It looks like you are using obenergy from the openbabel_for_open3dtools
>>>> package (which is 32-bit), but that it's picking the 64-bit library from
>>>> your own installation.
>>>> Please make sure that you install both open3dalign
>>>> and openbabel_for_open3dtools in the same open3dtools folder, and prior to
>>>> running open3dalign, issue this command in the same shell where you are
>>>> going to run open3dalign:
>>>>
>>>> source /path/to/open3dtools/bin/env_babel.sh
>>>>
>>>> where /path/to depends on where you installed open3dtools.
>>>>
>>>> This should fix it.
>>>>
>>>> In case you didn't know, the Open3DALIGN algorithm is also implemented
>>>> in the RDKit.
>>>>
>>>> Cheers,
>>>> p.
>>>>
>>>>
>>>> On 19 Nov 2016, at 00:30, Matthew Lardy < <ml...@gm...>
>>>> ml...@gm...>wrote:
>>>>
>>>> Hi!  I am trying to give your Open3DAlign tools a go, but I am having a
>>>> problem with the openbabel_for_open3dtools:
>>>>
>>>> obenergy: error while loading shared libraries: libopenbabel.so.4:
>>>> wrong ELF class: ELFCLASS64
>>>>
>>>> When I compile my own version and use it (I grabbed the most recent
>>>> copy), I get a different error:
>>>>
>>>> obenergy: could not setup force field.
>>>>
>>>> CALC_FIELD failed.
>>>>
>>>> Is there a specific version that I should be using?
>>>>
>>>> Thanks!
>>>> Matthew
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>>
>>>> _______________________________________________
>>>> Open3dqsar-discuss mailing list
>>>> Ope...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss
>>>>
>>>>
>>>
>>>
>>
>