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From: Dmitry K. <d.k...@qu...> - 2021-08-26 10:05:56
|
Good morning, everyone I want to add an additional external descriptor column in the QSAR equation. For example, the number of rotatable bonds. Is it possible to do? At first glance at the manual I did not find this possibility. Thank you. Dmitry S. Karlov, PhD research fellow School of Pharmacy, Rm 02.061 Queen’s University Belfast 97 Lisburn Road, BT9 7BL, UK Email: d.k...@qu... Tel: +44 (0)78 5985 9078 |
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From: Paolo T. <pao...@un...> - 2017-11-28 13:23:44
|
Dear Cosmas, 1) what tutorial are you referring to? 2) The dollar symbol makes me think that command should be typed in the normal shell rather than in the Open3DALIGN shell. Even in a normal Linux shell you shouldn't be typing the $ symbol though, as it is part of the shell prompt. Best, Paolo On 11/27/17 22:13, Okoro, Cosmas wrote: > > I am in 3dalign shell. The tutorial asks to type: $ cd a4b2. I > did but I keep getting parsing error. I don’t know what I did wrong. > I was just trying to go through the tutorial. > > Cosmas > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Open3dqsar-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss |
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From: Okoro, C. <co...@Tn...> - 2017-11-27 22:57:03
|
I am in 3dalign shell. The tutorial asks to type: $ cd a4b2. I did but I keep getting parsing error. I don't know what I did wrong. I was just trying to go through the tutorial. Cosmas |
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From: Paolo T. <pao...@un...> - 2017-11-25 06:23:46
|
Dear Cosmas, Are you using Windows, Linux or macOS? If you are on Windows, did you download the correct binary package? I have the impression that you downloaded either the source code package or the installer for Linux or macOS; all of these three have extensions which are not recognised by Windows, which would explain the behaviour you are describing. Windows binary packages are here: https://sourceforge.net/projects/open3dqsar/files/binaries/windows/openbabel_for_open3dtools_windows_setup.exe/download https://sourceforge.net/projects/open3dqsar/files/binaries/windows/open3dqsar-2.3_windows_64_sse3_setup.exe/download HTH, kind regards Paolo > On 25 Nov 2017, at 06:38, Okoro, Cosmas <co...@Tn...> wrote: > > Hi, I have completed download but having problem starting the program. When I double click on the icon I get folders instead that tells me to look for a program in my computer that can be used to open the file. I am not getting a command line to start the program. Can anyone please email me a practical step by step procedure. I want to take activity data and use it to make prediction using Comfa and Comsia. Thanks > > Cosmas > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Open3dqsar-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss |
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From: Okoro, C. <co...@Tn...> - 2017-11-25 05:50:56
|
Hi, I have completed download but having problem starting the program. When I double click on the icon I get folders instead that tells me to look for a program in my computer that can be used to open the file. I am not getting a command line to start the program. Can anyone please email me a practical step by step procedure. I want to take activity data and use it to make prediction using Comfa and Comsia. Thanks Cosmas |
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From: Paolo T. <pao...@un...> - 2016-11-21 23:02:44
|
Hi Matthew, Glad to hear that it's working now. Usually these issues are due to OB not finding it's libraries/plugins or picking those from a different installation on the same machine. Cheers, p. > On 21 Nov 2016, at 22:14, Matthew Lardy <ml...@gm...> wrote: > > 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...>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 >>>>> >>>> >>> >> > |
|
From: Matthew L. <ml...@gm...> - 2016-11-21 22:15:04
|
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 >>>> >>>> >>> >>> >> > |
|
From: Matthew L. <ml...@gm...> - 2016-11-21 20:17:42
|
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
>>>
>>>
>>
>>
>
|
|
From: Matthew L. <ml...@gm...> - 2016-11-21 19:14:50
|
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 >> >> > > |
|
From: Paolo T. <pao...@un...> - 2016-11-21 18:49:26
|
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... > <mailto: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... > <mailto: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... >> <mailto:Ope...@li...> >> https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss >> <https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss> > > |
|
From: Matthew L. <ml...@gm...> - 2016-11-21 18:42:09
|
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...>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 > > |
|
From: Paolo T. <pao...@un...> - 2016-11-19 07:04:28
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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...>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 |
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From: Matthew L. <ml...@gm...> - 2016-11-19 00:30:50
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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 |
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From: stalin a. <a.s...@gm...> - 2014-11-22 15:00:54
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Dear Sir/Madam Wishes and greetings... I am Stalin Antony. I am trying to work on open3dQSAR software on my windows7 64bit OS. I have followed all the instructions given by the open3dQSAR website and i checked the installations. But, still i cant run the software. while i am trying to run, the error message i got is "Open3DQSAR has stopped working" and the pymol has not been open. Even i have set the environmental variable path. please help me -- STALIN ANTONY, SRF, ICMR - NEW DELHI, ENTOMOLOGY RESEARCH INSTITUTE, LOYOLA COLLEGE, CHENNAI-600 034 CELL: +91 7200785830, +91 9942823461 |
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From: Conrad H. <con...@ar...> - 2014-08-03 23:02:02
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Dear open3DTools Developers, I have problems opening imported sdf files in pymol. It seems any open3dtool creates simple *.mol files. The pymol console says, that the *.mol2 failed to load. Thank you in advance, best regards Conrad |
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From: Paolo T. <pao...@un...> - 2013-08-07 17:23:18
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Dear Rafael, I have just released Open3DQSAR 2.25 which implements a "tanimoto" keyword to do what you suggested. Best regards, Paolo On 06/19/2013 06:10 PM, Rafael Doležal wrote: > Hello! > > Would it be possible to add into Open3DQSAR a function for computing the Tanimoto similarity index? Then, the correlation between two MIFs bearing the same information could be revealed. > > The Taminoto similartity index Tj of the j-th molecule is calculated by this formula: > > Tj(x,y) = Σni XijYij / (Σni X2ij + Σni Y2ij - Σni XijYij) > > Xij and Yij are the field values at i-th grid point. > > The Tanimoto T-vector may be described by max, min, mean values. > > Thank you, > Rafael Doležal. > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Open3dqsar-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: pao...@un... http://open3dqsar.org | http://open3dalign.org ========================================================== |
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From: Paolo T. <pao...@un...> - 2013-08-07 17:21:26
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Dear Philip, I have just released Open3DQSAR 2.25 which implements the stdev * coeff and mean * coeff features. Regarding the problem that you mentioned with Mac OS X/PyMOL, I think it depends on a faulty OpenBabel installation. Did you check whether Open3DQSAR complains about non-working OpenBabel binaries when it starts? In any case, did you try to run from your command line the following command: babel -imol sample.mol -omol2 sample.mol2 using any .mol file as input? It should run without errors. If it doesn't, this explains the problems you are experiencing with PyMOL. To avoid trouble, I suggest to install openbabel_for_open3dtools for Mac OS X (see Open3DQSAR website). Please let me know if this solves your problems. Best regards, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: pao...@un... http://open3dqsar.org | http://open3dalign.org ========================================================== |
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From: Renato Q. P. <rpo...@ya...> - 2013-08-04 01:33:52
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Renato Queiroga Pordeus Graduando do curso de Química Universidade Federal da Bahia - UFBA --- Em sáb, 3/8/13, Renato Queiroga Pordeus <rpo...@ya...> escreveu: > De: Renato Queiroga Pordeus <rpo...@ya...> > Assunto: install and use open3dqsar > Para: "Paolo Tosco" <pao...@un...> > Cc: ope...@li... > Data: Sábado, 3 de Agosto de 2013, 22:28 > Good evening, Mr. Paolo and members. > join a project in molecular docking Federal University of > Bahia - Brazil. This project includes the use of Open3d > Qsar. However I could not make it work. What format and how > to use? . mol, pdb, pdbqt if there is a tutorial or passoa > by step video demo and ask please answer me. On the website > I found something. Make available to me to make a video > tutor on my tongue with your authorization. > In anexo > Thank outset. > > Renato Queiroga Pordeus > Graduando do curso de Química > Universidade Federal da Bahia - UFBA |
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From: Paolo T. <pao...@un...> - 2013-08-01 21:41:46
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Dear Philip, Thanks for reporting this. I'll try to fix it by the next release, which will include the stdev * coeff feature and a few other things; however, I won't be able to build it until Monday. Best regards, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: pao...@un... http://open3dqsar.org | http://open3dalign.org ========================================================== On 1 Aug 2013, at 21:26, Phillip Cruz <pm...@me...> wrote: > Regarding the bug reported in the interface to pymol on the Mac, I am seeing the same thing. The problem appears to be that the pymol interface is expecting to read .mol2 files from the temporary directory within /var/tmp, but what is actually in the temporary directory is .mol files (single molecule MDL files). Pymol is reporting lots of errors similar to: > > PyMOL>load /var/tmp//O3Q.33565.mol_dir.FGauZv/0001.mol2, 0001, 0, mol2 > ExecutiveLoad-Error: Unable to open file '/var/tmp//O3Q.33565.mol_dir.FGauZv/0001.mol2'. > > Thanks. > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > _______________________________________________ > Open3dqsar-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss > |
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From: Phillip C. <pm...@me...> - 2013-08-01 19:27:00
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Regarding the bug reported in the interface to pymol on the Mac, I am seeing the same thing. The problem appears to be that the pymol interface is expecting to read .mol2 files from the temporary directory within /var/tmp, but what is actually in the temporary directory is .mol files (single molecule MDL files). Pymol is reporting lots of errors similar to: PyMOL>load /var/tmp//O3Q.33565.mol_dir.FGauZv/0001.mol2, 0001, 0, mol2 ExecutiveLoad-Error: Unable to open file '/var/tmp//O3Q.33565.mol_dir.FGauZv/0001.mol2'. Thanks. |
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From: Paolo T. <pao...@un...> - 2013-08-01 10:07:09
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Dear Lukas, thank for your message. I will look into this and provide a fix ASAP. Best regards, Paolo On 08/01/2013 11:44 AM, Lukas Linden wrote: > Dear all, > > I was trying to use open3DQSAR with the COSMOsar program, the > turbomole calculation for the input sdf-files worked fine. But then > the there was a problem with the data path, because the program wasn't > able to read it any more. In my opinion the problem is that the data > path is placed in quotes by the program and cs3d.inp-file. Could you > help me somehow? In the attachment you can find my output file and the > cs3d input file. > > Thank you in advance, > best regards > > Lukas > > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > > > _______________________________________________ > Open3dqsar-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: pao...@un... http://open3dqsar.org | http://open3dalign.org ========================================================== |
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From: Lukas L. <luk...@uf...> - 2013-08-01 09:44:34
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Dear all, I was trying to use open3DQSAR with the COSMOsar program, the turbomole calculation for the input sdf-files worked fine. But then the there was a problem with the data path, because the program wasn't able to read it any more. In my opinion the problem is that the data path is placed in quotes by the program and cs3d.inp-file. Could you help me somehow? In the attachment you can find my output file and the cs3d input file. Thank you in advance, best regards Lukas |
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From: Paolo T. <pao...@un...> - 2013-07-26 14:40:27
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Dear Rafael, you may compute RMSDs using Open3DALIGN with the "align" command together with the undocumented option "print_rmsd=y". Then in the aligned SDF file you will find two additional scores: "ORIGINAL_RMSD" and "ALIGNED_RMSD". I guess what you want to look at is "ORIGINAL_RMSD", that is RMSD before re-alignment by Open3DALIGN. Please note that RMSD calculation between non-identical molecules requires finding matches between similar atoms, which may be more or less appropriate dipending on the matching algorithm. Best regards, Paolo On 07/26/2013 04:06 PM, Rafael Doležal wrote: > Is there any way how to calucate RMSDs within an alignment set in Opend3DQSAR? > Thank you. > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > Open3dqsar-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dqsar-discuss > -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: pao...@un... http://open3dqsar.org | http://open3dalign.org ========================================================== |
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From: Rafael D. <raf...@ce...> - 2013-07-26 14:29:12
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Is there any way how to calucate RMSDs within an alignment set in Opend3DQSAR? Thank you. |
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From: Paolo T. <pao...@un...> - 2013-07-25 21:20:24
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Dear Phil, currently it is not implemented but it'll be straightforward to add that feature. I'll let you know as soon as it is ready, I guess by Monday it should be done. Best regards, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: pao...@un... http://open3dqsar.org | http://open3dalign.org ========================================================== |
