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Re: [OpenBabel-scripting] dihedral angles in G09 output

[Noel O'B. <bao...@gm...>]

I just realised that you are posting to a mailing list that I thought I had
closed down! Can you resend your email instead to
ope...@li...? This will have a greater reach.

By the way, right now my only thoughts are to check whether there's an IOP
to convince G09 to write out more info. Or to do each of the scan manually
using separate G09 calculations (if there's a way).

Also, maybe put together a small example and attached the G09 logfile to
your email?

- Noel

On Thu, 28 Feb 2019 at 11:49, Kenneth Irving <ke...@fq...> wrote:

> Noel: thanks for the reply. In fact the problem is slightly more
> complicated than the description I gave.
>
> What I'm actually trying to do is extract molecular coordinates from a
> G09 surface scan.
>
> I know that G09 publishes the cartesian coordinates of the molecule at the
> end of the output file and, as you say, I could use that info to get build
> the internal coordinates.
>
> But the in which G09 does a scan calculation is this:
>
> For each point to be calculated, G09 publishes the initial cartesian
> coordinates of the molecule.
>
> Having established a fixed distance bewteen two atoms (the scan
> coordinate), G09 optimizes the rest of the coordinates and reports the
> result... in internal coordinates!!!
>
> Then it changes the scan coordinate, reports the new initial coordinates
> in cartesian (Input orientation), and proceeds to optimize the rest,
> reportin the optimized result again in internal coordinates. The output
> doesn't report optimized cartesian coordinates for each point, only
> internal coordinates.
>
> It repeats this procedure for each of the scan values.
>
> For each point the optimized geometry is always reported in internal
> coordinates, which are not exactly the ones I need to further prepare a
> barrierless calculation using another program (multiwell).
>
> That is my problem: how can I use the internal coordinates information
> given in G09 scan output to make useful (internal or cartesian)
> coordinates I can use with multiwell.
>
> The way G09 is reporting the dihedral angle, is not exactly the one I need
> to build the input for the other program.
>
> I reckon all the information is there: bond distances, bond angles and
> dihedral angle. The problem is the way in which G09 particularly reports
> the dihedral angle: 1,2,4,3 or 2,1,4,3 instead of 1,2,3,4
>
> I havent' got a clue why G09 reports internal coodinates in this manner.
> There must be a very good reason, but I haven't been able to find out.
>
> If I can transform the dihedral angle value to the original numbering, I
> would be able to solve the problem.
>
> That's what I'm trying to find out. Or maybe I'm missing something quite
> obvious. Any help is appreciated.
>
> best regards
>
> Kenneth
>
> On Thu, 28 Feb 2019, Noel O'Boyle wrote:
>
> > Are the atoms in the cartesian gaussian output in the same order as your
> input atoms? If so, then you could use the library to calculate
> > the dihedral angle yourself since you know which atom is which and their
> cartesian coordinates.
> >
> > On Wed, 27 Feb 2019 at 18:59, Kenneth Irving via OpenBabel-scripting <
> ope...@li...> wrote:
> >
> >       I have this simple molecule I'm studying: H2SCl
> >
> >       The Gaussian 2009 (G09) input file is this:
> >
> >       ---------- cut here -------------
> >       #ub2plyp/6-31g(d,p) freq OPT
> >
> >         adducto H2S--Cl
> >
> >       0  2
> >       Cl
> >       S, 1, r1
> >       H, 2, r2, 1, a1
> >       H, 2, r3, 1, a2, 3, d1
> >          Variables:
> >       r1=1.9
> >       r2=1.0
> >       r3=1.0
> >       a1=120.0
> >       a2=120.0
> >       d1=120.0
> >
> >       ---------- cut here -------------
> >
> >       After running g09, I get these internal coordinate values in the
> output
> >
> >       ---------- cut here -------------
> >         ! Name  Definition              Value          Derivative Info.
> >
>  --------------------------------------------------------------------------------
> >         ! R1    R(1,2)                  2.7341         -DE/DX =    0.0
> >         ! R2    R(2,3)                  1.3401         -DE/DX =   -0.0001
> >         ! R3    R(2,4)                  1.3401         -DE/DX =   -0.0001
> >         ! A1    A(1,2,3)               89.758          -DE/DX =    0.0
> >         ! A2    A(1,2,4)               89.758          -DE/DX =    0.0
> >         ! A3    A(3,2,4)               93.213          -DE/DX =    0.0
> >         ! D1    D(1,2,4,3)            -89.744          -DE/DX =    0.0
> >
>  --------------------------------------------------------------------------------
> >       ---------- cut here -------------
> >
> >       It's easy to see that G09 is not printing the same internal
> coordinates
> >       I used in the input
> >
> >       If I redefine the initial internal coordinates, putting sulphur as
> >       the first atom:
> >
> >       ---------- cut here -------------
> >       #ub2plyp/6-31g(d,p) freq OPT
> >
> >         adducto H2S--Cl
> >
> >       0  2
> >       S
> >       Cl, 1, r1
> >       H, 1, r2, 2, a1
> >       H, 1, r3, 2, a2, 3, d1
> >          Variables:
> >       r1=2.9
> >       r2=1.0
> >       r3=1.0
> >       a1=120.0
> >       a2=120.0
> >       d1=120.0
> >
> >       ---------- cut here -------------
> >
> >       ...I get these final internal coordinates:
> >
> >       ---------- cut here -------------
> >         ! Name  Definition              Value          Derivative Info.
> >
>  --------------------------------------------------------------------------------
> >         ! R1    R(1,2)                  2.7349         -DE/DX =    0.0
> >         ! R2    R(1,3)                  1.3399         -DE/DX =    0.0
> >         ! R3    R(1,4)                  1.3399         -DE/DX =    0.0
> >         ! A1    A(2,1,3)               89.7451         -DE/DX =    0.0
> >         ! A2    A(2,1,4)               89.7451         -DE/DX =    0.0
> >         ! A3    A(3,1,4)               93.2202         -DE/DX =    0.0
> >         ! D1    D(2,1,4,3)            -89.7303         -DE/DX =    0.0
> >
> >       ---------- cut here -------------
> >
> >       Distances and bond angles are no problem. The problem I'm having
> is with
> >       the dihedral angle.
> >
> >       In both cases the numbering in the dihedral angle is different
> from the
> >       one I used in the input file.
> >
> >       In the first case the dihedral angle in the input is numbered:
> 4,2,1,3 but
> >       in the output I get: 1,2,4,3
> >
> >       In the second case the dihedral angle in the input numbered:
> 4,1,2,3 but
> >       in the output I get: 2,1,4,3
> >
> >       For a different calculation I need to take these internal
> coordinates
> >       results from G09 output and recreate the geometry in internal
> coordinates
> >       but with the original numbering. As I said, distances and bond
> angles are
> >       no problem. The problem is getting the original dihedral angle
> from the
> >       internal coordinates data provided in the output.
> >
> >       I was wondering whether I could do this with openbabel?
> >
> >       I haven't been able to find a way that works for all cases:
> depending on
> >       the atomic numbers, G09 displays different numbering of dihedral
> angles.
> >       Apparently it lists atoms from the highest to lowest atomic number.
> >
> >       Maybe there's a way I can use the internal coordinates in the
> output to
> >       convert to cartesian coordinates and from there calculate the
> internal
> >       coordinates with the original numbering.
> >
> >       Maybe there's a simple way to convert dihedral angles based on
> their
> >       numbering, but I haven't been able to come up with a solution, nor
> have I
> >       found any literature on this topic.
> >
> >       If someone could provide me with some guidance or has any idea,
> I'd be
> >       very grateful. Thanks in advance.
> >
> >       Best regards
> >
> >       Kenneth
> >
> >
> >
> >
> >       _______________________________________________
> >       OpenBabel-scripting mailing list
> >       Ope...@li...
> >       https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
> >

Re: [OpenBabel-scripting] dihedral angles in G09 output

[Kenneth I. <ke...@fq...>]

Noel: thanks for the reply. In fact the problem is slightly more 
complicated than the description I gave.

What I'm actually trying to do is extract molecular coordinates from a 
G09 surface scan.

I know that G09 publishes the cartesian coordinates of the molecule at the 
end of the output file and, as you say, I could use that info to get build 
the internal coordinates.

But the in which G09 does a scan calculation is this:

For each point to be calculated, G09 publishes the initial cartesian 
coordinates of the molecule.

Having established a fixed distance bewteen two atoms (the scan 
coordinate), G09 optimizes the rest of the coordinates and reports the 
result... in internal coordinates!!!

Then it changes the scan coordinate, reports the new initial coordinates 
in cartesian (Input orientation), and proceeds to optimize the rest, 
reportin the optimized result again in internal coordinates. The output 
doesn't report optimized cartesian coordinates for each point, only 
internal coordinates.

It repeats this procedure for each of the scan values.

For each point the optimized geometry is always reported in internal 
coordinates, which are not exactly the ones I need to further prepare a 
barrierless calculation using another program (multiwell).

That is my problem: how can I use the internal coordinates information 
given in G09 scan output to make useful (internal or cartesian) 
coordinates I can use with multiwell.

The way G09 is reporting the dihedral angle, is not exactly the one I need 
to build the input for the other program.

I reckon all the information is there: bond distances, bond angles and 
dihedral angle. The problem is the way in which G09 particularly reports 
the dihedral angle: 1,2,4,3 or 2,1,4,3 instead of 1,2,3,4

I havent' got a clue why G09 reports internal coodinates in this manner. 
There must be a very good reason, but I haven't been able to find out.

If I can transform the dihedral angle value to the original numbering, I 
would be able to solve the problem.

That's what I'm trying to find out. Or maybe I'm missing something quite 
obvious. Any help is appreciated.

best regards

Kenneth

On Thu, 28 Feb 2019, Noel O'Boyle wrote:

> Are the atoms in the cartesian gaussian output in the same order as your input atoms? If so, then you could use the library to calculate
> the dihedral angle yourself since you know which atom is which and their cartesian coordinates.
> 
> On Wed, 27 Feb 2019 at 18:59, Kenneth Irving via OpenBabel-scripting <ope...@li...> wrote:
>
>       I have this simple molecule I'm studying: H2SCl
>
>       The Gaussian 2009 (G09) input file is this:
>
>       ---------- cut here -------------
>       #ub2plyp/6-31g(d,p) freq OPT
>
>         adducto H2S--Cl
>
>       0  2
>       Cl
>       S, 1, r1
>       H, 2, r2, 1, a1
>       H, 2, r3, 1, a2, 3, d1
>          Variables:
>       r1=1.9
>       r2=1.0
>       r3=1.0
>       a1=120.0
>       a2=120.0
>       d1=120.0
>
>       ---------- cut here -------------
>
>       After running g09, I get these internal coordinate values in the output
>
>       ---------- cut here -------------
>         ! Name  Definition              Value          Derivative Info.
>       --------------------------------------------------------------------------------
>         ! R1    R(1,2)                  2.7341         -DE/DX =    0.0
>         ! R2    R(2,3)                  1.3401         -DE/DX =   -0.0001
>         ! R3    R(2,4)                  1.3401         -DE/DX =   -0.0001
>         ! A1    A(1,2,3)               89.758          -DE/DX =    0.0
>         ! A2    A(1,2,4)               89.758          -DE/DX =    0.0
>         ! A3    A(3,2,4)               93.213          -DE/DX =    0.0
>         ! D1    D(1,2,4,3)            -89.744          -DE/DX =    0.0
>       --------------------------------------------------------------------------------
>       ---------- cut here -------------
>
>       It's easy to see that G09 is not printing the same internal coordinates
>       I used in the input
>
>       If I redefine the initial internal coordinates, putting sulphur as
>       the first atom:
>
>       ---------- cut here -------------
>       #ub2plyp/6-31g(d,p) freq OPT
>
>         adducto H2S--Cl
>
>       0  2
>       S
>       Cl, 1, r1
>       H, 1, r2, 2, a1
>       H, 1, r3, 2, a2, 3, d1
>          Variables:
>       r1=2.9
>       r2=1.0
>       r3=1.0
>       a1=120.0
>       a2=120.0
>       d1=120.0
>
>       ---------- cut here -------------
>
>       ...I get these final internal coordinates:
>
>       ---------- cut here -------------
>         ! Name  Definition              Value          Derivative Info.
>       --------------------------------------------------------------------------------
>         ! R1    R(1,2)                  2.7349         -DE/DX =    0.0
>         ! R2    R(1,3)                  1.3399         -DE/DX =    0.0
>         ! R3    R(1,4)                  1.3399         -DE/DX =    0.0
>         ! A1    A(2,1,3)               89.7451         -DE/DX =    0.0
>         ! A2    A(2,1,4)               89.7451         -DE/DX =    0.0
>         ! A3    A(3,1,4)               93.2202         -DE/DX =    0.0
>         ! D1    D(2,1,4,3)            -89.7303         -DE/DX =    0.0
>
>       ---------- cut here -------------
>
>       Distances and bond angles are no problem. The problem I'm having is with
>       the dihedral angle.
>
>       In both cases the numbering in the dihedral angle is different from the
>       one I used in the input file.
>
>       In the first case the dihedral angle in the input is numbered: 4,2,1,3 but
>       in the output I get: 1,2,4,3
>
>       In the second case the dihedral angle in the input numbered: 4,1,2,3 but
>       in the output I get: 2,1,4,3
>
>       For a different calculation I need to take these internal coordinates
>       results from G09 output and recreate the geometry in internal coordinates
>       but with the original numbering. As I said, distances and bond angles are
>       no problem. The problem is getting the original dihedral angle from the
>       internal coordinates data provided in the output.
>
>       I was wondering whether I could do this with openbabel?
>
>       I haven't been able to find a way that works for all cases: depending on
>       the atomic numbers, G09 displays different numbering of dihedral angles.
>       Apparently it lists atoms from the highest to lowest atomic number.
>
>       Maybe there's a way I can use the internal coordinates in the output to
>       convert to cartesian coordinates and from there calculate the internal
>       coordinates with the original numbering.
>
>       Maybe there's a simple way to convert dihedral angles based on their
>       numbering, but I haven't been able to come up with a solution, nor have I
>       found any literature on this topic.
>
>       If someone could provide me with some guidance or has any idea, I'd be
>       very grateful. Thanks in advance.
>
>       Best regards
>
>       Kenneth
> 
> 
> 
>
>       _______________________________________________
>       OpenBabel-scripting mailing list
>       Ope...@li...
>       https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 
>

Re: [OpenBabel-scripting] dihedral angles in G09 output

[Noel O'B. <bao...@gm...>]

Are the atoms in the cartesian gaussian output in the same order as your
input atoms? If so, then you could use the library to calculate the
dihedral angle yourself since you know which atom is which and their
cartesian coordinates.

On Wed, 27 Feb 2019 at 18:59, Kenneth Irving via OpenBabel-scripting <
ope...@li...> wrote:

>
> I have this simple molecule I'm studying: H2SCl
>
> The Gaussian 2009 (G09) input file is this:
>
> ---------- cut here -------------
> #ub2plyp/6-31g(d,p) freq OPT
>
>   adducto H2S--Cl
>
> 0  2
> Cl
> S, 1, r1
> H, 2, r2, 1, a1
> H, 2, r3, 1, a2, 3, d1
>    Variables:
> r1=1.9
> r2=1.0
> r3=1.0
> a1=120.0
> a2=120.0
> d1=120.0
>
> ---------- cut here -------------
>
> After running g09, I get these internal coordinate values in the output
>
> ---------- cut here -------------
>   ! Name  Definition              Value          Derivative Info.
>
> --------------------------------------------------------------------------------
>   ! R1    R(1,2)                  2.7341         -DE/DX =    0.0
>   ! R2    R(2,3)                  1.3401         -DE/DX =   -0.0001
>   ! R3    R(2,4)                  1.3401         -DE/DX =   -0.0001
>   ! A1    A(1,2,3)               89.758          -DE/DX =    0.0
>   ! A2    A(1,2,4)               89.758          -DE/DX =    0.0
>   ! A3    A(3,2,4)               93.213          -DE/DX =    0.0
>   ! D1    D(1,2,4,3)            -89.744          -DE/DX =    0.0
>
> --------------------------------------------------------------------------------
> ---------- cut here -------------
>
> It's easy to see that G09 is not printing the same internal coordinates
> I used in the input
>
> If I redefine the initial internal coordinates, putting sulphur as
> the first atom:
>
> ---------- cut here -------------
> #ub2plyp/6-31g(d,p) freq OPT
>
>   adducto H2S--Cl
>
> 0  2
> S
> Cl, 1, r1
> H, 1, r2, 2, a1
> H, 1, r3, 2, a2, 3, d1
>    Variables:
> r1=2.9
> r2=1.0
> r3=1.0
> a1=120.0
> a2=120.0
> d1=120.0
>
> ---------- cut here -------------
>
> ...I get these final internal coordinates:
>
> ---------- cut here -------------
>   ! Name  Definition              Value          Derivative Info.
>
> --------------------------------------------------------------------------------
>   ! R1    R(1,2)                  2.7349         -DE/DX =    0.0
>   ! R2    R(1,3)                  1.3399         -DE/DX =    0.0
>   ! R3    R(1,4)                  1.3399         -DE/DX =    0.0
>   ! A1    A(2,1,3)               89.7451         -DE/DX =    0.0
>   ! A2    A(2,1,4)               89.7451         -DE/DX =    0.0
>   ! A3    A(3,1,4)               93.2202         -DE/DX =    0.0
>   ! D1    D(2,1,4,3)            -89.7303         -DE/DX =    0.0
>
> ---------- cut here -------------
>
> Distances and bond angles are no problem. The problem I'm having is with
> the dihedral angle.
>
> In both cases the numbering in the dihedral angle is different from the
> one I used in the input file.
>
> In the first case the dihedral angle in the input is numbered: 4,2,1,3 but
> in the output I get: 1,2,4,3
>
> In the second case the dihedral angle in the input numbered: 4,1,2,3 but
> in the output I get: 2,1,4,3
>
> For a different calculation I need to take these internal coordinates
> results from G09 output and recreate the geometry in internal coordinates
> but with the original numbering. As I said, distances and bond angles are
> no problem. The problem is getting the original dihedral angle from the
> internal coordinates data provided in the output.
>
> I was wondering whether I could do this with openbabel?
>
> I haven't been able to find a way that works for all cases: depending on
> the atomic numbers, G09 displays different numbering of dihedral angles.
> Apparently it lists atoms from the highest to lowest atomic number.
>
> Maybe there's a way I can use the internal coordinates in the output to
> convert to cartesian coordinates and from there calculate the internal
> coordinates with the original numbering.
>
> Maybe there's a simple way to convert dihedral angles based on their
> numbering, but I haven't been able to come up with a solution, nor have I
> found any literature on this topic.
>
> If someone could provide me with some guidance or has any idea, I'd be
> very grateful. Thanks in advance.
>
> Best regards
>
> Kenneth
>
>
>
>
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] dihedral angles in G09 output

[Kenneth I. <ke...@fq...>]

I have this simple molecule I'm studying: H2SCl

The Gaussian 2009 (G09) input file is this:

---------- cut here -------------
#ub2plyp/6-31g(d,p) freq OPT

  adducto H2S--Cl

0  2
Cl
S, 1, r1
H, 2, r2, 1, a1
H, 2, r3, 1, a2, 3, d1
   Variables:
r1=1.9
r2=1.0
r3=1.0
a1=120.0
a2=120.0
d1=120.0

---------- cut here -------------

After running g09, I get these internal coordinate values in the output

---------- cut here -------------
  ! Name  Definition              Value          Derivative Info. 
--------------------------------------------------------------------------------
  ! R1    R(1,2)                  2.7341         -DE/DX =    0.0
  ! R2    R(2,3)                  1.3401         -DE/DX =   -0.0001
  ! R3    R(2,4)                  1.3401         -DE/DX =   -0.0001
  ! A1    A(1,2,3)               89.758          -DE/DX =    0.0
  ! A2    A(1,2,4)               89.758          -DE/DX =    0.0
  ! A3    A(3,2,4)               93.213          -DE/DX =    0.0
  ! D1    D(1,2,4,3)            -89.744          -DE/DX =    0.0 
--------------------------------------------------------------------------------
---------- cut here -------------

It's easy to see that G09 is not printing the same internal coordinates
I used in the input

If I redefine the initial internal coordinates, putting sulphur as
the first atom:

---------- cut here -------------
#ub2plyp/6-31g(d,p) freq OPT

  adducto H2S--Cl

0  2
S
Cl, 1, r1
H, 1, r2, 2, a1
H, 1, r3, 2, a2, 3, d1
   Variables:
r1=2.9
r2=1.0
r3=1.0
a1=120.0
a2=120.0
d1=120.0

---------- cut here -------------

...I get these final internal coordinates:

---------- cut here -------------
  ! Name  Definition              Value          Derivative Info. 
--------------------------------------------------------------------------------
  ! R1    R(1,2)                  2.7349         -DE/DX =    0.0
  ! R2    R(1,3)                  1.3399         -DE/DX =    0.0
  ! R3    R(1,4)                  1.3399         -DE/DX =    0.0
  ! A1    A(2,1,3)               89.7451         -DE/DX =    0.0
  ! A2    A(2,1,4)               89.7451         -DE/DX =    0.0
  ! A3    A(3,1,4)               93.2202         -DE/DX =    0.0
  ! D1    D(2,1,4,3)            -89.7303         -DE/DX =    0.0

---------- cut here -------------

Distances and bond angles are no problem. The problem I'm having is with
the dihedral angle.

In both cases the numbering in the dihedral angle is different from the 
one I used in the input file.

In the first case the dihedral angle in the input is numbered: 4,2,1,3 but 
in the output I get: 1,2,4,3

In the second case the dihedral angle in the input numbered: 4,1,2,3 but 
in the output I get: 2,1,4,3

For a different calculation I need to take these internal coordinates 
results from G09 output and recreate the geometry in internal coordinates 
but with the original numbering. As I said, distances and bond angles are 
no problem. The problem is getting the original dihedral angle from the 
internal coordinates data provided in the output.

I was wondering whether I could do this with openbabel?

I haven't been able to find a way that works for all cases: depending on 
the atomic numbers, G09 displays different numbering of dihedral angles. 
Apparently it lists atoms from the highest to lowest atomic number.

Maybe there's a way I can use the internal coordinates in the output to 
convert to cartesian coordinates and from there calculate the internal 
coordinates with the original numbering.

Maybe there's a simple way to convert dihedral angles based on their 
numbering, but I haven't been able to come up with a solution, nor have I 
found any literature on this topic.

If someone could provide me with some guidance or has any idea, I'd be 
very grateful. Thanks in advance.

Best regards

Kenneth

[OpenBabel-scripting] Help needed with OpenBabel in python3

[Nitish G. <nit...@gm...>]

Hi,

I was looking to install OpenBabel bindings for python3. I tried the steps
mentioned at
http://openbabel.org/docs/dev/Installation/install.html#compile-language-bindings

However, after the installation was done, running 'import openbabel' works
fine while nothing is getting imported from openbabel library.
Checking dir(openbabel) shows that the imported library object does not
include any modules.

Any idea on what might have gone wrong or what other ways are there to
install openbabel for python3 ? I had tried pip also but it was not working.

Thanks and regards,
Nitish Garg

Re: [OpenBabel-scripting] smi support problem in pybel/openbabel python

[Noel O'B. <bao...@gm...>]

Great. Good to know what the problem was too.

On 29 Sep 2016 5:43 p.m., "Jianshu Hu" <huj...@gm...> wrote:

> Problem solved!!!!
>
> DO NOT USE THE WHEEL FROM http://www.lfd.uci.edu/~
> gohlke/pythonlibs!!!!!!!!!!!
>
> USE THE ONE FROM PYTHON PIP!!!!!!
>
> They have the same names but not the same contents.
>
> 😤😤😤😤
>
> On Fri, Sep 30, 2016 at 12:03 AM, Jianshu Hu <huj...@gm...>
> wrote:
>
>> Yes, I install the 32-bit openbabel.
>> And yes, a lot of formats are missing.
>> However the GUI version can handle these format very well.
>> I think there is something wrong when binding the obabel to python in " pythong-binding:
>> openbabel-2.4.0-cp27-cp27m-win32.whl"
>> However, I am not familiar with this part. So I don't know where goes
>> wrong.
>> The only thing I can ensure is that the binding is for 2.40 version and
>> python2.7
>>
>> I have no idea what is going on in pybel.
>>
>> Sad. :(
>>
>> On Thu, Sep 29, 2016 at 11:00 PM, Noel O'Boyle <bao...@gm...>
>> wrote:
>>
>>> (ccing to openbabel-discuss as this mailing list is closed)
>>>
>>> I notice that others formats are missing such as Mol file. There are 6
>>> or 7 common formats loaded from formats_common.obf and these are all
>>> missing. It must be that your virus checker or Windows firewall is
>>> blocking that .obf file. I don't understand how the GUI can handle it
>>> correctly though in that case. ??
>>>
>>> - Noel
>>>
>>> On 29 September 2016 at 15:54, Noel O'Boyle <bao...@gm...>
>>> wrote:
>>> > Did you install the 32-bit version of Open Babel?
>>> >
>>> > - Noel
>>> >
>>> > On 29 September 2016 at 15:07, Jianshu Hu <huj...@gm...>
>>> wrote:
>>> >> Hi everyone,
>>> >>
>>> >>      I met a problem while trying to use openbabel in Python.
>>> >>
>>> >>     Env:
>>> >>         python: Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016,
>>> 15:19:22)
>>> >> [MSC v.1500 32 bit (Intel)] on win32
>>> >>         obabel: Open Babel 2.4.0 -- Sep 22 2016 -- 18:19:48
>>> >>         OS: win10
>>> >>         pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl
>>> >>
>>> >>     Problem:
>>> >>>>> from pybel import *
>>> >>>>> mymol=readstring("smi","CCCC")
>>> >> Traceback (most recent call last):
>>> >>   File "<stdin>", line 1, in <module>
>>> >>   File "C:\Python27\lib\site-packages\pybel.py", line 199, in
>>> readstring
>>> >>     raise ValueError("%s is not a recognised Open Babel format" %
>>> format)
>>> >> ValueError: smi is not a recognised Open Babel format
>>> >>
>>> >>     Trying to find out what happend:
>>> >>         >>> sorted(informats)
>>> >> ['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF',
>>> >> 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'aoforce', 'arc',
>>> >> 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car',
>>> >> 'castep', 'ccc', 'cdx', 'cif', 'ck', 'crk2d', 'crk3d', 'ct', 'cub',
>>> 'cube',
>>> >> 'dallog', 'dalmol', 'dat', 'dmol', 'dx', 'exyz', 'fa', 'fasta', 'fch',
>>> >> 'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09',
>>> 'g92',
>>> >> 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got', 'gpr',
>>> >> 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inp', 'ins', 'jin', 'jout',
>>> >> 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold',
>>> 'molden',
>>> >> 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo',
>>> 'mpqc',
>>> >> 'msi', 'nwo', 'orca', 'out', 'outmol', 'output', 'pcm', 'pdbqt',
>>> 'png',
>>> >> 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn',
>>> >> 'siesta', 'smy', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz',
>>> >> 'unixyz', 'vmol', 'xsf', 'xyz', 'yob']
>>> >>
>>> >>     I found there is no smi in pybel.informats, however the Openbabel
>>> GUI
>>> >> can read or write smi format correctly.
>>> >>
>>> >>     Where goes wrong? The pybel no loner support smi format?
>>> >>
>>> >>     PS: the openbabel in python has the same problem
>>> >>
>>> >>     Thank you for helps,
>>> >>
>>> >>     JS Hu
>>> >>
>>> >> ------------------------------------------------------------
>>> ------------------
>>> >>
>>> >> _______________________________________________
>>> >> OpenBabel-scripting mailing list
>>> >> Ope...@li...
>>> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>> >>
>>>
>>
>>
>

Re: [OpenBabel-scripting] smi support problem in pybel/openbabel python

[Jianshu Hu <huj...@gm...>]

Problem solved!!!!

DO NOT USE THE WHEEL FROM http://www.lfd.uci.edu/~gohlke/pythonlibs!!!!!!!!!
!!

USE THE ONE FROM PYTHON PIP!!!!!!

They have the same names but not the same contents.

😤😤😤😤

On Fri, Sep 30, 2016 at 12:03 AM, Jianshu Hu <huj...@gm...> wrote:

> Yes, I install the 32-bit openbabel.
> And yes, a lot of formats are missing.
> However the GUI version can handle these format very well.
> I think there is something wrong when binding the obabel to python in " pythong-binding:
> openbabel-2.4.0-cp27-cp27m-win32.whl"
> However, I am not familiar with this part. So I don't know where goes
> wrong.
> The only thing I can ensure is that the binding is for 2.40 version and
> python2.7
>
> I have no idea what is going on in pybel.
>
> Sad. :(
>
> On Thu, Sep 29, 2016 at 11:00 PM, Noel O'Boyle <bao...@gm...>
> wrote:
>
>> (ccing to openbabel-discuss as this mailing list is closed)
>>
>> I notice that others formats are missing such as Mol file. There are 6
>> or 7 common formats loaded from formats_common.obf and these are all
>> missing. It must be that your virus checker or Windows firewall is
>> blocking that .obf file. I don't understand how the GUI can handle it
>> correctly though in that case. ??
>>
>> - Noel
>>
>> On 29 September 2016 at 15:54, Noel O'Boyle <bao...@gm...> wrote:
>> > Did you install the 32-bit version of Open Babel?
>> >
>> > - Noel
>> >
>> > On 29 September 2016 at 15:07, Jianshu Hu <huj...@gm...>
>> wrote:
>> >> Hi everyone,
>> >>
>> >>      I met a problem while trying to use openbabel in Python.
>> >>
>> >>     Env:
>> >>         python: Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016,
>> 15:19:22)
>> >> [MSC v.1500 32 bit (Intel)] on win32
>> >>         obabel: Open Babel 2.4.0 -- Sep 22 2016 -- 18:19:48
>> >>         OS: win10
>> >>         pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl
>> >>
>> >>     Problem:
>> >>>>> from pybel import *
>> >>>>> mymol=readstring("smi","CCCC")
>> >> Traceback (most recent call last):
>> >>   File "<stdin>", line 1, in <module>
>> >>   File "C:\Python27\lib\site-packages\pybel.py", line 199, in
>> readstring
>> >>     raise ValueError("%s is not a recognised Open Babel format" %
>> format)
>> >> ValueError: smi is not a recognised Open Babel format
>> >>
>> >>     Trying to find out what happend:
>> >>         >>> sorted(informats)
>> >> ['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF',
>> >> 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'aoforce', 'arc',
>> >> 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car',
>> >> 'castep', 'ccc', 'cdx', 'cif', 'ck', 'crk2d', 'crk3d', 'ct', 'cub',
>> 'cube',
>> >> 'dallog', 'dalmol', 'dat', 'dmol', 'dx', 'exyz', 'fa', 'fasta', 'fch',
>> >> 'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09',
>> 'g92',
>> >> 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got', 'gpr',
>> >> 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inp', 'ins', 'jin', 'jout',
>> >> 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold',
>> 'molden',
>> >> 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo',
>> 'mpqc',
>> >> 'msi', 'nwo', 'orca', 'out', 'outmol', 'output', 'pcm', 'pdbqt', 'png',
>> >> 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn',
>> >> 'siesta', 'smy', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz',
>> >> 'unixyz', 'vmol', 'xsf', 'xyz', 'yob']
>> >>
>> >>     I found there is no smi in pybel.informats, however the Openbabel
>> GUI
>> >> can read or write smi format correctly.
>> >>
>> >>     Where goes wrong? The pybel no loner support smi format?
>> >>
>> >>     PS: the openbabel in python has the same problem
>> >>
>> >>     Thank you for helps,
>> >>
>> >>     JS Hu
>> >>
>> >> ------------------------------------------------------------
>> ------------------
>> >>
>> >> _______________________________________________
>> >> OpenBabel-scripting mailing list
>> >> Ope...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >>
>>
>
>

Re: [OpenBabel-scripting] smi support problem in pybel/openbabel python

[Jianshu Hu <huj...@gm...>]

Yes, I install the 32-bit openbabel.
And yes, a lot of formats are missing.
However the GUI version can handle these format very well.
I think there is something wrong when binding the obabel to python in
" pythong-binding:
openbabel-2.4.0-cp27-cp27m-win32.whl"
However, I am not familiar with this part. So I don't know where goes wrong.
The only thing I can ensure is that the binding is for 2.40 version and
python2.7

I have no idea what is going on in pybel.

Sad. :(

On Thu, Sep 29, 2016 at 11:00 PM, Noel O'Boyle <bao...@gm...> wrote:

> (ccing to openbabel-discuss as this mailing list is closed)
>
> I notice that others formats are missing such as Mol file. There are 6
> or 7 common formats loaded from formats_common.obf and these are all
> missing. It must be that your virus checker or Windows firewall is
> blocking that .obf file. I don't understand how the GUI can handle it
> correctly though in that case. ??
>
> - Noel
>
> On 29 September 2016 at 15:54, Noel O'Boyle <bao...@gm...> wrote:
> > Did you install the 32-bit version of Open Babel?
> >
> > - Noel
> >
> > On 29 September 2016 at 15:07, Jianshu Hu <huj...@gm...>
> wrote:
> >> Hi everyone,
> >>
> >>      I met a problem while trying to use openbabel in Python.
> >>
> >>     Env:
> >>         python: Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016,
> 15:19:22)
> >> [MSC v.1500 32 bit (Intel)] on win32
> >>         obabel: Open Babel 2.4.0 -- Sep 22 2016 -- 18:19:48
> >>         OS: win10
> >>         pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl
> >>
> >>     Problem:
> >>>>> from pybel import *
> >>>>> mymol=readstring("smi","CCCC")
> >> Traceback (most recent call last):
> >>   File "<stdin>", line 1, in <module>
> >>   File "C:\Python27\lib\site-packages\pybel.py", line 199, in
> readstring
> >>     raise ValueError("%s is not a recognised Open Babel format" %
> format)
> >> ValueError: smi is not a recognised Open Babel format
> >>
> >>     Trying to find out what happend:
> >>         >>> sorted(informats)
> >> ['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF',
> >> 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'aoforce', 'arc',
> >> 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car',
> >> 'castep', 'ccc', 'cdx', 'cif', 'ck', 'crk2d', 'crk3d', 'ct', 'cub',
> 'cube',
> >> 'dallog', 'dalmol', 'dat', 'dmol', 'dx', 'exyz', 'fa', 'fasta', 'fch',
> >> 'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09',
> 'g92',
> >> 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got', 'gpr',
> >> 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inp', 'ins', 'jin', 'jout',
> >> 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold', 'molden',
> >> 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo', 'mpqc',
> >> 'msi', 'nwo', 'orca', 'out', 'outmol', 'output', 'pcm', 'pdbqt', 'png',
> >> 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn',
> >> 'siesta', 'smy', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz',
> >> 'unixyz', 'vmol', 'xsf', 'xyz', 'yob']
> >>
> >>     I found there is no smi in pybel.informats, however the Openbabel
> GUI
> >> can read or write smi format correctly.
> >>
> >>     Where goes wrong? The pybel no loner support smi format?
> >>
> >>     PS: the openbabel in python has the same problem
> >>
> >>     Thank you for helps,
> >>
> >>     JS Hu
> >>
> >> ------------------------------------------------------------
> ------------------
> >>
> >> _______________________________________________
> >> OpenBabel-scripting mailing list
> >> Ope...@li...
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
>

Re: [OpenBabel-scripting] smi support problem in pybel/openbabel python

[Noel O'B. <bao...@gm...>]

Did you install the 32-bit version of Open Babel?

- Noel

On 29 September 2016 at 15:07, Jianshu Hu <huj...@gm...> wrote:
> Hi everyone,
>
>      I met a problem while trying to use openbabel in Python.
>
>     Env:
>         python: Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22)
> [MSC v.1500 32 bit (Intel)] on win32
>         obabel: Open Babel 2.4.0 -- Sep 22 2016 -- 18:19:48
>         OS: win10
>         pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl
>
>     Problem:
>>>> from pybel import *
>>>> mymol=readstring("smi","CCCC")
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "C:\Python27\lib\site-packages\pybel.py", line 199, in readstring
>     raise ValueError("%s is not a recognised Open Babel format" % format)
> ValueError: smi is not a recognised Open Babel format
>
>     Trying to find out what happend:
>         >>> sorted(informats)
> ['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF',
> 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'aoforce', 'arc',
> 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car',
> 'castep', 'ccc', 'cdx', 'cif', 'ck', 'crk2d', 'crk3d', 'ct', 'cub', 'cube',
> 'dallog', 'dalmol', 'dat', 'dmol', 'dx', 'exyz', 'fa', 'fasta', 'fch',
> 'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09', 'g92',
> 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got', 'gpr',
> 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inp', 'ins', 'jin', 'jout',
> 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold', 'molden',
> 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo', 'mpqc',
> 'msi', 'nwo', 'orca', 'out', 'outmol', 'output', 'pcm', 'pdbqt', 'png',
> 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn',
> 'siesta', 'smy', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz',
> 'unixyz', 'vmol', 'xsf', 'xyz', 'yob']
>
>     I found there is no smi in pybel.informats, however the Openbabel GUI
> can read or write smi format correctly.
>
>     Where goes wrong? The pybel no loner support smi format?
>
>     PS: the openbabel in python has the same problem
>
>     Thank you for helps,
>
>     JS Hu
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] smi support problem in pybel/openbabel python

[Jianshu Hu <huj...@gm...>]

Hi everyone,

     I met a problem while trying to use openbabel in Python.

    Env:
        python: Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, 15:19:22)
[MSC v.1500 32 bit (Intel)] on win32
        obabel: Open Babel 2.4.0 -- Sep 22 2016 -- 18:19:48
        OS: win10
        pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl

    Problem:
>>> from pybel import *
>>> mymol=readstring("smi","CCCC")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\pybel.py", line 199, in readstring
    raise ValueError("%s is not a recognised Open Babel format" % format)
ValueError: smi is not a recognised Open Babel format

    Trying to find out what happend:
        >>> sorted(informats)
['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF',
'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'aoforce', 'arc',
'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car',
'castep', 'ccc', 'cdx', 'cif', 'ck', 'crk2d', 'crk3d', 'ct', 'cub', 'cube',
'dallog', 'dalmol', 'dat', 'dmol', 'dx', 'exyz', 'fa', 'fasta', 'fch',
'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09',
'g92', 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got',
'gpr', 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inp', 'ins', 'jin',
'jout', 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold',
'molden', 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo',
'mpqc', 'msi', 'nwo', 'orca', 'out', 'outmol', 'output', 'pcm', 'pdbqt',
'png', 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn',
'siesta', 'smy', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz',
'unixyz', 'vmol', 'xsf', 'xyz', 'yob']

    I found there is no smi in pybel.informats, however the Openbabel GUI
can read or write smi format correctly.

    Where goes wrong? The pybel no loner support smi format?

    PS: the openbabel in python has the same problem

    Thank you for helps,

    JS Hu

Re: [OpenBabel-scripting] Using Chemistry::OpenBabel::OBDescriptor::FindType in Perl

[David R. <tom...@gm...>]

Hi Fredrik:

  I tried that, and it solved my problem.   Thanks for your help!

Dave  

Sent from my iPhone

> On Jul 14, 2016, at 3:42 AM, Fredrik Wallner <fr...@wa...> wrote:
> 
> Hi,
> 
> Due to how the plugins work in OpenBabel, they are sometimes not loaded until an OBConversion object has been instantiated, so my suggestion would be to add ”my $obconv = new Chemistry::OpenBabel::OBConversion;” as line 3 in your script.
> 
> Kind regards,
> Fredrik
> 
>> 12 juli 2016 kl. 20:52 skrev David Rose <tom...@gm...>:
>> 
>> Hi:
>> 
>> I'm trying to obtain some descriptors (e.g. TPSA, logP) using the Chemistry::OpenBabel perl bindings.  I can get TPSA and logP values from the command line using obprop, but when I try to do so programmatically, I find that no matter what I ask for, FindType() returns undef.  For example:
>> 
>> use strict;
>> use Chemistry::OpenBabel;
>> my $oblogp = Chemistry::OpenBabel::OBDescriptor::FindType("logP");
>> 
>> If I run this, there are no errors reported but $oblogp always has the value undef.  This is true for every descriptor type I've tried ('TPSA','atoms','bonds','L5', etc.).  Sort-of-similar methods on OBMol (e.g. NumAtoms) work fine, so it is not the case that Chemistry::OpenBabel is not working at all. 
>> 
>> I would be grateful for any ideas why this might be the case.
>> 
>> Thanks,
>> David Rose
>> ------------------------------------------------------------------------------
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols are 
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
>> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
>> reports.http://sdm.link/zohodev2dev_______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 

Re: [OpenBabel-scripting] Using Chemistry::OpenBabel::OBDescriptor::FindType in Perl

[Noel O'B. <bao...@gm...>]

No problem, but best to cc the list to avoid Fredrik answering too :-)
By the way, openbabel-scripting is now obsolete and you should use
openbabel-discuss in future.

On 13 July 2016 at 15:25, David Rose <tom...@gm...> wrote:
> That did it.  Thanks for you help.
>
> Dave.
>
> On Wed, Jul 13, 2016 at 7:37 AM, Noel O'Boyle <bao...@gm...> wrote:
>>
>> I think you need to force the plugins to be loaded. I typically do
>> this by instantiating an OBConversion object first.
>>
>> On 12 July 2016 at 19:52, David Rose <tom...@gm...> wrote:
>> > Hi:
>> >
>> >  I'm trying to obtain some descriptors (e.g. TPSA, logP) using the
>> > Chemistry::OpenBabel perl bindings.  I can get TPSA and logP values from
>> > the
>> > command line using obprop, but when I try to do so programmatically, I
>> > find
>> > that no matter what I ask for, FindType() returns undef.  For example:
>> >
>> > use strict;
>> > use Chemistry::OpenBabel;
>> > my $oblogp = Chemistry::OpenBabel::OBDescriptor::FindType("logP");
>> >
>> > If I run this, there are no errors reported but $oblogp always has the
>> > value
>> > undef.  This is true for every descriptor type I've tried
>> > ('TPSA','atoms','bonds','L5', etc.).  Sort-of-similar methods on OBMol
>> > (e.g.
>> > NumAtoms) work fine, so it is not the case that Chemistry::OpenBabel is
>> > not
>> > working at all.
>> >
>> > I would be grateful for any ideas why this might be the case.
>> >
>> > Thanks,
>> > David Rose
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> > traffic
>> > patterns at an interface-level. Reveals which users, apps, and protocols
>> > are
>> > consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> > J-Flow, sFlow and other flows. Make informed decisions using capacity
>> > planning
>> > reports.http://sdm.link/zohodev2dev
>> > _______________________________________________
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>> >
>
>

Re: [OpenBabel-scripting] Using Chemistry::OpenBabel::OBDescriptor::FindType in Perl

[Fredrik W. <fr...@wa...>]

Hi,

Due to how the plugins work in OpenBabel, they are sometimes not loaded until an OBConversion object has been instantiated, so my suggestion would be to add ”my $obconv = new Chemistry::OpenBabel::OBConversion;” as line 3 in your script.

Kind regards,
Fredrik

> 12 juli 2016 kl. 20:52 skrev David Rose <tom...@gm...>:
> 
> Hi:
> 
>  I'm trying to obtain some descriptors (e.g. TPSA, logP) using the Chemistry::OpenBabel perl bindings.  I can get TPSA and logP values from the command line using obprop, but when I try to do so programmatically, I find that no matter what I ask for, FindType() returns undef.  For example:
> 
> use strict;
> use Chemistry::OpenBabel;
> my $oblogp = Chemistry::OpenBabel::OBDescriptor::FindType("logP");
> 
> If I run this, there are no errors reported but $oblogp always has the value undef.  This is true for every descriptor type I've tried ('TPSA','atoms','bonds','L5', etc.).  Sort-of-similar methods on OBMol (e.g. NumAtoms) work fine, so it is not the case that Chemistry::OpenBabel is not working at all. 
> 
> I would be grateful for any ideas why this might be the case.
> 
> Thanks,
> David Rose
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are 
> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
> reports.http://sdm.link/zohodev2dev_______________________________________________
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[OpenBabel-scripting] Using Chemistry::OpenBabel::OBDescriptor::FindType in Perl

[David R. <tom...@gm...>]

Hi:

 I'm trying to obtain some descriptors (e.g. TPSA, logP) using the
Chemistry::OpenBabel perl bindings.  I can get TPSA and logP values from
the command line using obprop, but when I try to do so programmatically, I
find that no matter what I ask for, FindType() returns undef.  For example:

use strict;
use Chemistry::OpenBabel;
my $oblogp = Chemistry::OpenBabel::OBDescriptor::FindType("logP");

If I run this, there are no errors reported but $oblogp always has the
value undef.  This is true for every descriptor type I've tried
('TPSA','atoms','bonds','L5', etc.).  Sort-of-similar methods on OBMol
(e.g. NumAtoms) work fine, so it is not the case that Chemistry::OpenBabel
is not working at all.

I would be grateful for any ideas why this might be the case.

Thanks,
David Rose

Re: [OpenBabel-scripting] chiral bug in openbabel

[Noel O'B. <bao...@gm...>]

Not a bug, but ....

(a) The SMILES format supports atom-based stereochemistry. This type
of stereochemistry is axial.

(b) In any case, Open Babel does not detect axial stereochemistry

- Noel

On 17 September 2015 at 12:45, qiancheng shen <qia...@gm...> wrote:
> Dear Openbabel group:
>
>               I found a molecule which should have chiral atoms, but when I
> tried to convert it from SDF to canonical SMILES with babel , the chiral
> atoms disappeared.
>
>               Is this a bug?
>
>
>               The mol file of this molecule is attached. Thank you very
> much!!
>
>
> Best,
>
> Qiancheng
>
>
>
>
> ------------------------------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] chiral bug in openbabel

[qiancheng s. <qia...@gm...>]

Dear Openbabel group:

              I found a molecule which should have chiral atoms, but when I
tried to convert it from SDF to canonical SMILES with babel , the chiral
atoms disappeared.

              Is this a bug?


              The mol file of this molecule is attached. Thank you very
much!!


Best,

Qiancheng

[OpenBabel-scripting] question about pybel for python 3.x

[S J. S. <swa...@gm...>]

Hello,

Hope you are well. I'm trying to figure out how to install python bindings
for Python 3. Is this functional yet?

Thanks!

S Joshua Swamidass
http://swami.wustl.edu/

[OpenBabel-scripting] considering new SWIG binding for R

[Kevin H. <kh...@cs...>]

I am considering using SWIG to create a new language binding for the R 
language (http://www.r-project.org/). I have so far just been wrapping a 
few functions from openbabel that I needed in C++ code and using R's 
normal interface to C/C++ (.Call). As I understand SWIG, there should be 
one general "openbabel.i" file and then any language binding can be 
created from that. But when I looked in the source tarball for R I found 
instead a swig file for each existing language binding (ie, 
openbabel-java.i, openbabel-python.i, etc. ), and no plain "openbabel.i" 
file. So my first question is, is there such a file? Or else, where 
should I start in creating an "openbabel-R.i" file? Also, any other 
general information anyone things I should know before trying this? Thanks.

Kevin

[OpenBabel-scripting] Hola Scripters!

[Roscoe C. <ros...@gm...>]

Just thought I would say hello, and thank you to all the support and
awesomeness that is OpenBabel!

-- 
Thanks in advance,
Roscoe Casita

[OpenBabel-scripting] Pybel : compute L5 return nan

[Quentin D. <que...@gm...>]

Dear openbabel scripting list,

I was trying in a script to compute the descriptor known as lipinski 
rule of five or 'L5' but the result is not a number. I know that would 
be a boolean normally. How to get it right?

FI i use :

         lipinski =  molecule.calcdesc(['L5'])



Thanks

Re: [OpenBabel-scripting] split structures into new objects

[Noel O'B. <bao...@gm...>]

I've filed a bug at https://sourceforge.net/p/openbabel/bugs/847/. It
should be fairly easy to copy the residue info to the separated
molecules; I've just done this for stereo info.

Please note for future reference that openbabel-scripting is obsolete.
Please send emails to openbabel-discuss instead.

- Noel

On 8 November 2012 12:37, Stefan Henrich <ste...@h-...> wrote:
> Hi Noel,
>
> Thank you for the fast answer. Actually, OBMol can be split into separated
> OBMol objects but the order of residues of a protein will be mixed up at
> least if unknown residue names are present or the protein is disconnected.
> Furthermore, for ligands the residue name, residue numbering and the atom
> names will not be copied to the new OBMol object. It seems that 'Separate'
> just copy atoms from one OBMol to a new ones.
>
> Best,
> Stefan
>
>
>
>
> On 11/07/2012 04:16 PM, Noel O'Boyle wrote:
>>
>> Does OBMol::Separate work for this? See the API at
>>
>> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a
>>
>> - Noel
>>
>> On 7 November 2012 13:53, Stefan Henrich <ste...@h-...> wrote:
>>>
>>> Hi OpenBabel users,
>>>
>>> Is there an easy way to read a complex structure as a molecule using
>>> openbabel (python-API) and to split it afterwards into different
>>> molecules (e.g., protein, ligand, cofactor,...) to handle/write it as
>>> different objects? Here, it would be helpful not loosing information
>>> like residue names what happens if you just copy atoms to a new molecule
>>> object.
>>> Thank you for your help!
>>>
>>> Best,
>>> Stefan
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> LogMeIn Central: Instant, anywhere, Remote PC access and management.
>>> Stay in control, update software, and manage PCs from one command center
>>> Diagnose problems and improve visibility into emerging IT issues
>>> Automate, monitor and manage. Do more in less time with Central
>>> http://p.sf.net/sfu/logmein12331_d2d
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
> --
> Dr. Stefan Henrich
> Research Associate
>
> HITS gGmbH Schloss-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
>
> phone: +49 6221 533 223
> fax:   +49 6221 533 298
> email:Ste...@h-...
> http://www.h-its.org
>
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h. c. Dr.-Ing. E. h. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
>

Re: [OpenBabel-scripting] split structures into new objects

[Stefan H. <ste...@h-...>]

Hi Noel,

Thank you for the fast answer. Actually, OBMol can be split into 
separated OBMol objects but the order of residues of a protein will be 
mixed up at least if unknown residue names are present or the protein is 
disconnected. Furthermore, for ligands the residue name, residue 
numbering and the atom names will not be copied to the new OBMol object. 
It seems that 'Separate' just copy atoms from one OBMol to a new ones.

Best,
Stefan



On 11/07/2012 04:16 PM, Noel O'Boyle wrote:
> Does OBMol::Separate work for this? See the API at
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a
>
> - Noel
>
> On 7 November 2012 13:53, Stefan Henrich <ste...@h-...> wrote:
>> Hi OpenBabel users,
>>
>> Is there an easy way to read a complex structure as a molecule using
>> openbabel (python-API) and to split it afterwards into different
>> molecules (e.g., protein, ligand, cofactor,...) to handle/write it as
>> different objects? Here, it would be helpful not loosing information
>> like residue names what happens if you just copy atoms to a new molecule
>> object.
>> Thank you for your help!
>>
>> Best,
>> Stefan
>>
>>
>> ------------------------------------------------------------------------------
>> LogMeIn Central: Instant, anywhere, Remote PC access and management.
>> Stay in control, update software, and manage PCs from one command center
>> Diagnose problems and improve visibility into emerging IT issues
>> Automate, monitor and manage. Do more in less time with Central
>> http://p.sf.net/sfu/logmein12331_d2d
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting

-- 
Dr. Stefan Henrich
Research Associate

HITS gGmbH Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Germany

phone: +49 6221 533 223
fax:   +49 6221 533 298
email:Ste...@h-...
http://www.h-its.org

Amtsgericht Mannheim / HRB 337446
Managing Directors:
Dr. h. c. Dr.-Ing. E. h. Klaus Tschira
Prof. Dr.-Ing. Andreas Reuter

Re: [OpenBabel-scripting] split structures into new objects

[Noel O'B. <bao...@gm...>]

Does OBMol::Separate work for this? See the API at
http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a

- Noel

On 7 November 2012 13:53, Stefan Henrich <ste...@h-...> wrote:
> Hi OpenBabel users,
>
> Is there an easy way to read a complex structure as a molecule using
> openbabel (python-API) and to split it afterwards into different
> molecules (e.g., protein, ligand, cofactor,...) to handle/write it as
> different objects? Here, it would be helpful not loosing information
> like residue names what happens if you just copy atoms to a new molecule
> object.
> Thank you for your help!
>
> Best,
> Stefan
>
>
> ------------------------------------------------------------------------------
> LogMeIn Central: Instant, anywhere, Remote PC access and management.
> Stay in control, update software, and manage PCs from one command center
> Diagnose problems and improve visibility into emerging IT issues
> Automate, monitor and manage. Do more in less time with Central
> http://p.sf.net/sfu/logmein12331_d2d
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting

[OpenBabel-scripting] split structures into new objects

[Stefan H. <ste...@h-...>]

Hi OpenBabel users,

Is there an easy way to read a complex structure as a molecule using 
openbabel (python-API) and to split it afterwards into different 
molecules (e.g., protein, ligand, cofactor,...) to handle/write it as 
different objects? Here, it would be helpful not loosing information 
like residue names what happens if you just copy atoms to a new molecule 
object.
Thank you for your help!

Best,
Stefan

[OpenBabel-scripting] Data directory missing from Open Babel 2.3.1 Installation?

[Richard M. R. <rma...@gm...>]

Hi

I was trying to install Open Babel version 2.3.1 on a machine running
Windows 7.

I ran OpenBabel2.3.1_Windows_Installer.exe and was informed the
installation had finished successfully, allowing me to start the GUI.

Since BABEL_DATADIR had not been created, I went to manually set this to
the location of the directory containing mr.txt (based upon the
instructions for testing the installation presented here:
http://openbabel.org/docs/2.3.0/UseTheLibrary/PythonInstall.html).

However, the \data\ subdirectory had not been created under C:\Program
Files (x86)\OpenBabel 2.3.1\
Indeed, I could not locate mr.txt anywhere.

A quick Google search does not seem to suggest that this has been removed
from version 2.3.1.... so I assume there was a problem with running the
installer.

Any clarification / suggestions as to why this might have occured /
possible ways to fix this would be greatly appreciated.

Thanks in advance.

Regards

Richard Marchese Robinson