Re: [Open Babel] Other ob tools

[Francois Berenger]

On 03/03/2020 17:46, Noel O'Boyle wrote:

Well, I don't really agree. They could just add it to obabel in the
first place and get the feedback from the development version. The
problem is that people find it easier to add new executables, rather
than spending a bit of time figuring out how to add a plugin for
obabel.


I once worked somewhere where there was a very big chemoinformatics 
executable

able to do many things; instead of having a nice library used by several
rather simple programs.

Trying to do any task using the big executable was a nightmare in terms 
of

finding the long list of options and values that you had to pass to it.

The one big program/executable approach is against the Unix philosophy 
of

having rather simple programs that can be combined easily.

For those interested in the Unix philosophy and its not so trivial many 
implications,

there is an interesting book:
---
Raymond, E. S. (2003). The art of Unix programming. Addison-Wesley 
Professional.

---

Regards,
F.


Regards,

- Noel

On Tue, 3 Mar 2020 at 07:52, Chris Swain  wrote:


Hi,

It is clear that a number of the obtools have been incorporated into
obabel, however I’m not sure they are all suitable for every file
type.

It is perhaps better to think of obtools as way to develop new tools
that others can hopefully try out and provide feedback. Tools that
are regularly used and prove to be robust and useful could then be
rolled into obabel.

And no I don’t know of a process to do this.

Cheers,

Chris

On 2 Mar 2020, at 20:11, Noel O'Boyle  wrote:

It's not a popular opinion, but I think we should have a single
robust executable. I've never used any of the others, and they are
mostly untested.

On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss,
 wrote:
Hi,

I’m working on an update to iBabel, and was hoping to clear out
the tools tab particularly as I’m not sure if some are now
supported with OpenBabel 3.0

Looking through the directory of openbabel tools that are installed
we have

obconformer  equiv to  obabel --conformer
obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
obenergy  equiv to obabel  --energy
obfit equiv to --obabel --align
obfitall not sure what this is?
obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
obgrep equiv to obabel structure searching
obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000
--sd)
obmm apparently this is a this is a 'full featured' MM program but
may not be generally useful
obprobe (create electrostatic probe grid)
obprop (print standard molecular properties), would be more useful
if we could get individual properties,e.g. obabel —props
  (MW LogP TPSA HBA  HBD RBC)
obrms (Calculate the heavy-atom RMSD between two chemically
identical structures) perhaps this should be an obabel option?
obrotamer (generate conformer/rotamer coordinates, not minimized)
better to use —conformer?
obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
obspectrophore (calculate spectrophore)
obsym (detect 3D point group symmetry, only cif files?) sounds like
it is to deprecated
obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
obthermo (extract the thermochemistry for a molecule, what file
format is needed?)

Any insights very welcome,

Cheers,

Chris

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Re: [Open Babel] Other ob tools

[Chris Swain via OpenBabel-discuss]

Out of curiosity how many users install the development version?

Cheers

Chris

> On 3 Mar 2020, at 08:46, Noel O'Boyle  wrote:
> 
> Well, I don't really agree. They could just add it to obabel in the first 
> place and get the feedback from the development version. The problem is that 
> people find it easier to add new executables, rather than spending a bit of 
> time figuring out how to add a plugin for obabel.
> 
> Regards,
> - Noel
> 
> On Tue, 3 Mar 2020 at 07:52, Chris Swain  > wrote:
> Hi,
> 
> It is clear that a number of the obtools have been incorporated into obabel, 
> however I’m not sure they are all suitable for every file type.
> 
> It is perhaps better to think of obtools as way to develop new tools that 
> others can hopefully try out and provide feedback. Tools that are regularly 
> used and prove to be robust and useful could then be rolled into obabel.
> 
> And no I don’t know of a process to do this.
> 
> Cheers,
> 
> Chris
> 
> 
>> On 2 Mar 2020, at 20:11, Noel O'Boyle > > wrote:
>> 
>> It's not a popular opinion, but I think we should have a single robust 
>> executable. I've never used any of the others, and they are mostly untested.
>> 
>> On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, 
>> > > wrote:
>> Hi,
>> 
>> I’m working on an update to iBabel, and was hoping to clear out the tools 
>> tab particularly as I’m not sure if some are now supported with OpenBabel 3.0
>> 
>> Looking through the directory of openbabel tools that are installed we have 
>> 
>> obconformer  equiv to  obabel --conformer
>> obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
>> obenergy  equiv to obabel  --energy
>> obfit equiv to --obabel --align
>> obfitall not sure what this is?
>> obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
>> obgrep equiv to obabel structure searching
>> obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000 --sd)
>> obmm apparently this is a this is a 'full featured' MM program but may not 
>> be generally useful
>> obprobe (create electrostatic probe grid)
>> obprop (print standard molecular properties), would be more useful if we 
>> could get individual properties,e.g. obabel —props   (MW LogP 
>> TPSA HBA  HBD RBC)
>> obrms (Calculate the heavy-atom RMSD between two chemically identical 
>> structures) perhaps this should be an obabel option?
>> obrotamer (generate conformer/rotamer coordinates, not minimized) better to 
>> use —conformer?
>> obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
>> obspectrophore (calculate spectrophore)
>> obsym (detect 3D point group symmetry, only cif files?) sounds like it is to 
>> deprecated
>> obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
>> obthermo (extract the thermochemistry for a molecule, what file format is 
>> needed?) 
>> 
>> Any insights very welcome,
>> 
>> Cheers,
>> 
>> Chris
>> 
>> 
>> 
>> 
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>> OpenBabel-discuss@lists.sourceforge.net 
>> 
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss 
>> 
> 

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Re: [Open Babel] Other ob tools

[Noel O'Boyle]

Well, I don't really agree. They could just add it to obabel in the first
place and get the feedback from the development version. The problem is
that people find it easier to add new executables, rather than spending a
bit of time figuring out how to add a plugin for obabel.

Regards,
- Noel

On Tue, 3 Mar 2020 at 07:52, Chris Swain  wrote:

> Hi,
>
> It is clear that a number of the obtools have been incorporated into
> obabel, however I’m not sure they are all suitable for every file type.
>
> It is perhaps better to think of obtools as way to develop new tools that
> others can hopefully try out and provide feedback. Tools that are regularly
> used and prove to be robust and useful could then be rolled into obabel.
>
> And no I don’t know of a process to do this.
>
> Cheers,
>
> Chris
>
>
> On 2 Mar 2020, at 20:11, Noel O'Boyle  wrote:
>
> It's not a popular opinion, but I think we should have a single robust
> executable. I've never used any of the others, and they are mostly untested.
>
> On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, <
> openbabel-discuss@lists.sourceforge.net> wrote:
>
>> Hi,
>>
>> I’m working on an update to iBabel, and was hoping to clear out the tools
>> tab particularly as I’m not sure if some are now supported with OpenBabel
>> 3.0
>>
>> Looking through the directory of openbabel tools that are installed we
>> have
>>
>> obconformer  equiv to  obabel --conformer
>> obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
>> obenergy  equiv to obabel  --energy
>> obfit equiv to --obabel --align
>> obfitall not sure what this is?
>> obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
>> obgrep equiv to obabel structure searching
>> obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000 --sd)
>> obmm apparently this is a this is a 'full featured' MM program but may
>> not be generally useful
>> obprobe (create electrostatic probe grid)
>> obprop (print standard molecular properties), would be more useful if we
>> could get individual properties,e.g. obabel —props   (MW LogP
>> TPSA HBA  HBD RBC)
>> obrms (Calculate the heavy-atom RMSD between two chemically identical
>> structures) perhaps this should be an obabel option?
>> obrotamer (generate conformer/rotamer coordinates, not minimized) better
>> to use —conformer?
>> obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
>> obspectrophore (calculate spectrophore)
>> obsym (detect 3D point group symmetry, only cif files?) sounds like it is
>> to deprecated
>> obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
>> obthermo (extract the thermochemistry for a molecule, what file format is
>> needed?)
>>
>> Any insights very welcome,
>>
>> Cheers,
>>
>> Chris
>>
>>
>>
>>
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
>
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Re: [Open Babel] Other ob tools

[Chris Swain via OpenBabel-discuss]

Hi,

It is clear that a number of the obtools have been incorporated into obabel, 
however I’m not sure they are all suitable for every file type.

It is perhaps better to think of obtools as way to develop new tools that 
others can hopefully try out and provide feedback. Tools that are regularly 
used and prove to be robust and useful could then be rolled into obabel.

And no I don’t know of a process to do this.

Cheers,

Chris


> On 2 Mar 2020, at 20:11, Noel O'Boyle  wrote:
> 
> It's not a popular opinion, but I think we should have a single robust 
> executable. I've never used any of the others, and they are mostly untested.
> 
> On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, 
>  > wrote:
> Hi,
> 
> I’m working on an update to iBabel, and was hoping to clear out the tools tab 
> particularly as I’m not sure if some are now supported with OpenBabel 3.0
> 
> Looking through the directory of openbabel tools that are installed we have 
> 
> obconformer  equiv to  obabel --conformer
> obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
> obenergy  equiv to obabel  --energy
> obfit equiv to --obabel --align
> obfitall not sure what this is?
> obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
> obgrep equiv to obabel structure searching
> obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000 --sd)
> obmm apparently this is a this is a 'full featured' MM program but may not be 
> generally useful
> obprobe (create electrostatic probe grid)
> obprop (print standard molecular properties), would be more useful if we 
> could get individual properties,e.g. obabel —props   (MW LogP 
> TPSA HBA  HBD RBC)
> obrms (Calculate the heavy-atom RMSD between two chemically identical 
> structures) perhaps this should be an obabel option?
> obrotamer (generate conformer/rotamer coordinates, not minimized) better to 
> use —conformer?
> obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
> obspectrophore (calculate spectrophore)
> obsym (detect 3D point group symmetry, only cif files?) sounds like it is to 
> deprecated
> obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
> obthermo (extract the thermochemistry for a molecule, what file format is 
> needed?) 
> 
> Any insights very welcome,
> 
> Cheers,
> 
> Chris
> 
> 
> 
> 
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> 
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Re: [Open Babel] Other ob tools

[Dmitri Maziuk via OpenBabel-discuss]

On 3/2/2020 3:17 PM, Pedro Lacerda wrote:

I'm just a humble user but agree to a single executable like git.


Single executable like that is usually a front-end to other binaries, 
not a single binary that has all the functionality. What you really want 
to know is if (e.g.) `obabel --gen3d` really just execs `obgen` or is a 
completely separate implementation with its own bugs, idiosyncrasies, etc.


Dima


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Re: [Open Babel] Other ob tools

[Pedro Lacerda]

I'm just a humble user but agree to a single executable like git.

Em seg, 2 de mar de 2020 17:12, Noel O'Boyle 
escreveu:

> It's not a popular opinion, but I think we should have a single robust
> executable. I've never used any of the others, and they are mostly untested.
>
> On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, <
> openbabel-discuss@lists.sourceforge.net> wrote:
>
>> Hi,
>>
>> I’m working on an update to iBabel, and was hoping to clear out the tools
>> tab particularly as I’m not sure if some are now supported with OpenBabel
>> 3.0
>>
>> Looking through the directory of openbabel tools that are installed we
>> have
>>
>> obconformer  equiv to  obabel --conformer
>> obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
>> obenergy  equiv to obabel  --energy
>> obfit equiv to --obabel --align
>> obfitall not sure what this is?
>> obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
>> obgrep equiv to obabel structure searching
>> obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000 --sd)
>> obmm apparently this is a this is a 'full featured' MM program but may
>> not be generally useful
>> obprobe (create electrostatic probe grid)
>> obprop (print standard molecular properties), would be more useful if we
>> could get individual properties,e.g. obabel —props   (MW LogP
>> TPSA HBA  HBD RBC)
>> obrms (Calculate the heavy-atom RMSD between two chemically identical
>> structures) perhaps this should be an obabel option?
>> obrotamer (generate conformer/rotamer coordinates, not minimized) better
>> to use —conformer?
>> obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
>> obspectrophore (calculate spectrophore)
>> obsym (detect 3D point group symmetry, only cif files?) sounds like it is
>> to deprecated
>> obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
>> obthermo (extract the thermochemistry for a molecule, what file format is
>> needed?)
>>
>> Any insights very welcome,
>>
>> Cheers,
>>
>> Chris
>>
>>
>>
>>
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>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
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Re: [Open Babel] Other ob tools

[Noel O'Boyle]

It's not a popular opinion, but I think we should have a single robust
executable. I've never used any of the others, and they are mostly untested.

On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, <
openbabel-discuss@lists.sourceforge.net> wrote:

> Hi,
>
> I’m working on an update to iBabel, and was hoping to clear out the tools
> tab particularly as I’m not sure if some are now supported with OpenBabel
> 3.0
>
> Looking through the directory of openbabel tools that are installed we
> have
>
> obconformer  equiv to  obabel --conformer
> obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
> obenergy  equiv to obabel  --energy
> obfit equiv to --obabel --align
> obfitall not sure what this is?
> obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
> obgrep equiv to obabel structure searching
> obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000 --sd)
> obmm apparently this is a this is a 'full featured' MM program but may not
> be generally useful
> obprobe (create electrostatic probe grid)
> obprop (print standard molecular properties), would be more useful if we
> could get individual properties,e.g. obabel —props   (MW LogP
> TPSA HBA  HBD RBC)
> obrms (Calculate the heavy-atom RMSD between two chemically identical
> structures) perhaps this should be an obabel option?
> obrotamer (generate conformer/rotamer coordinates, not minimized) better
> to use —conformer?
> obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
> obspectrophore (calculate spectrophore)
> obsym (detect 3D point group symmetry, only cif files?) sounds like it is
> to deprecated
> obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
> obthermo (extract the thermochemistry for a molecule, what file format is
> needed?)
>
> Any insights very welcome,
>
> Cheers,
>
> Chris
>
>
>
>
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[Open Babel] Other ob tools

[Chris Swain via OpenBabel-discuss]

Hi,

I’m working on an update to iBabel, and was hoping to clear out the tools tab 
particularly as I’m not sure if some are now supported with OpenBabel 3.0

Looking through the directory of openbabel tools that are installed we have 

obconformer  equiv to  obabel --conformer
obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
obenergy  equiv to obabel  --energy
obfit equiv to --obabel --align
obfitall not sure what this is?
obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
obgrep equiv to obabel structure searching
obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000 --sd)
obmm apparently this is a this is a 'full featured' MM program but may not be 
generally useful
obprobe (create electrostatic probe grid)
obprop (print standard molecular properties), would be more useful if we could 
get individual properties,e.g. obabel —props   (MW LogP TPSA HBA  
HBD RBC)
obrms (Calculate the heavy-atom RMSD between two chemically identical 
structures) perhaps this should be an obabel option?
obrotamer (generate conformer/rotamer coordinates, not minimized) better to use 
—conformer?
obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
obspectrophore (calculate spectrophore)
obsym (detect 3D point group symmetry, only cif files?) sounds like it is to 
deprecated
obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
obthermo (extract the thermochemistry for a molecule, what file format is 
needed?) 

Any insights very welcome,

Cheers,

Chris




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