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Re: [OpenBabel-scripting] [Open Babel] how to access getAlias() in perl

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

On 29 March 2011 18:07, Geoffrey Hutchison <ge...@ge...> wrote:
>> TypeError in method 'toSetData', argument 1 of type
>> 'OpenBabel::OBGenericData *'
>>
>> Does it mean that the argument should not be an object returned by
>> GetData()? What should it be then?
>
> It's been a while since I've used the Perl bindings. What does ref($ad) return?
>
> Do you need to use the SetData hierarchy? I'm wondering if the extra redirection is the issue.

With the example file in the bug, I have:

C:\Users\Noel\Downloads>babel example.sdf -osmi
==============================
*** Open Babel Warning  in OpenBabel::AliasData::Expand
  Alias Xx Could not be interpreted.
 Output may not be correct.
C1=NCC(C(/C=C\C/*=C(/C(c2c(C=C)ccc(c2)NC(=N)c2cc(C)c(c(C)c2)*)C)\C)C)C=C1

1 molecule converted
1 warnings 50 audit log messages

...so I don't think it's related to the Perl bindings.

- Noel

Re: [OpenBabel-scripting] [Open Babel] how to access getAlias() in perl

[Geoffrey H. <ge...@ge...>]

> TypeError in method 'toSetData', argument 1 of type
> 'OpenBabel::OBGenericData *'
> 
> Does it mean that the argument should not be an object returned by
> GetData()? What should it be then? 

It's been a while since I've used the Perl bindings. What does ref($ad) return?

Do you need to use the SetData hierarchy? I'm wondering if the extra redirection is the issue.

-Geoff

Re: [OpenBabel-scripting] Duplicate Molecules

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

You should find a specific example where your script disagrees with
Open Babel and use it to determine which is wrong... (I don't think
you expect us to debug your Python scripts on this list, right?)

- Noel

On 29 March 2011 13:43, Jurgens de Bruin <deb...@gm...> wrote:
> Hi All,
> I do hope some light can be shed on the following...
> I have a .sdf file that contains 2483 molecules when I run the following
> command ">babel in.sdf out.sdf --unique" it finds 255 duplicated, which is
> possible.
> When I try and do the same using python code by calculating the Tanimoto
> coefficient between two compounds (Tc = 1 would indicate a duplicate) I
> don't find any duplicated. How is this possible?
> Python code below:
> mport openbabel
> import pybel
> import csv
> from pybel import *
>
> def createFPS():
>
>     before = 0
>     Phytochemicals = []
>
>     for phyto in readfile("sdf","./phyto3000.sdf"):
>         Phytochemical = {}
>         before += 1
>         fps = phyto.calcfp()
>         Phytochemical["Name"] = phyto.title
>         Phytochemical["FPS"] = fps
>         Phytochemicals.append(Phytochemical)
>
>     print "Phytochemicals in original sdf:",before
>
>     return Phytochemicals
>
>
> def fDuplicated(Phytochemicals):
>
>     stop = len(Phytochemicals)
>     count = 0
>     for x in range(0, stop):
>         for z in range(0, stop):
>             if x != z:
>                 Tc = Phytochemicals[x]['FPS'] | Phytochemicals[z]['FPS']
>         if Tc == 1:
>             print "Tc equalto 1"
>             count += 1
>
>     print "Total Tc equal to 1",count
>
> Phytochemicals = createFPS()
> fDuplicated(Phytochemicals)
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
>
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[OpenBabel-scripting] Duplicate Molecules

[Jurgens de B. <deb...@gm...>]

Hi All,

I do hope some light can be shed on the following...

I have a .sdf file that contains 2483 molecules when I run the following
command ">babel in.sdf out.sdf --unique" it finds 255 duplicated, which is
possible.

When I try and do the same using python code by calculating the Tanimoto
coefficient between two compounds (Tc = 1 would indicate a duplicate) I
don't find any duplicated. How is this possible?
Python code below:

mport openbabel
import pybel
import csv
from pybel import *


def createFPS():

    before = 0
    Phytochemicals = []

    for phyto in readfile("sdf","./phyto3000.sdf"):
        Phytochemical = {}
        before += 1
        fps = phyto.calcfp()
        Phytochemical["Name"] = phyto.title
        Phytochemical["FPS"] = fps
        Phytochemicals.append(Phytochemical)

    print "Phytochemicals in original sdf:",before

    return Phytochemicals


def fDuplicated(Phytochemicals):

    stop = len(Phytochemicals)
    count = 0
    for x in range(0, stop):
        for z in range(0, stop):
            if x != z:
                Tc = Phytochemicals[x]['FPS'] | Phytochemicals[z]['FPS']
        if Tc == 1:
            print "Tc equalto 1"
            count += 1

    print "Total Tc equal to 1",count


Phytochemicals = createFPS()
fDuplicated(Phytochemicals)

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

Re: [OpenBabel-scripting] Problems with openbabel/pybel installation on MacOS X 10.6.6

[Geoffrey H. <ge...@pi...>]

> and build THAT, I ended up with 2.0.2.  Is there a reason that the 2.0.0 version is so critical?


We have had problems with the 2.0.2 release. Either 2.0.0 or 2.0.1 is recommended, and definitely better than the older 1.3 versions.

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office: (412) 648-0492

Re: [OpenBabel-scripting] Problems with openbabel/pybel installation on MacOS X 10.6.6

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

On 23 March 2011 22:44, Andrew Fant <fa...@mo...> wrote:
> I'm having problems building the python extensions for openbabel on essentially virgin installation of snowleopard (thanks to a corrupted boot disk).  When I build and install openbabel-2.3.0 itself, everything is fine, and I can use babel from the command line without any difficulty, but when I include the python extensions, I can import pybel just fine, but as soon as I actually make a call to the libraries, it segfaults and generates a crash report for the nice people in Cupertino.  This isn't tied to how I install it, because when I enable testing, make tests returns with 6 failed tests, all of the python tests.  The others are all fine.  I checked with google, and I saw the note about mac builds binding to the wrong dynamic library, but in the traceback from the segfault, there are no references to my home directory, and all attempts to find _openbabel.so are to where it should be (/Library/Python/2.6/site-packages ).
>
> The code that generates the segfault is:
>
> import pybel
>
> mymol=pybel.readstring( "smi", "CCCC")
>
> (the segfault actually claims to be coming from the smilesformat.so plugin, for what it's worth)
>
> Can anyone make any suggestions?
>
> Also, as an FYI, the way that the cmake files notify people about whether the GUI will be built and where libxml2 is found is parsed as an error by ccmake, which prevents using that tool to configure the build.  Is there any chance that the notification method can be made more ccmake friendly?

Could you provide a patch to our CMakeLists.txt that would correct the
behaviour? Or else specify the desired format of the messages?

> Thanks,
>        Andy
>
>
> ------------------------------------------------------------------------------
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Re: [OpenBabel-scripting] Problems with openbabel/pybel installation on MacOS X 10.6.6

[Geoffrey H. <ge...@pi...>]

>> I'm having problems building the python extensions for openbabel on essentially virgin installation of snowleopard (thanks to a corrupted boot disk).  When I build and install openbabel-2.3.0 itself, everything is fine, and I can use babel from the command line without any difficulty, but when I include the python extensions, I can import pybel just fine, but as soon as I actually make a call to the libraries, it segfaults
> 
> I'm aware of the problem. The new CMake bindings don't correctly link the Python extension with the newly-installed libopenbabel.dylib.

OK, the SVN trunk should now have a CMake that properly updates the _openbabel.so compiled for the Python bindings. I became aware of this issue recently, so I hope the fix works -- it seems to do the trick on my MacBook.

If you have a chance, could you try grabbing the latest version from SVN?

Thanks very much,
-Geoff

Re: [OpenBabel-scripting] Problems with openbabel/pybel installation on MacOS X 10.6.6

[Geoffrey H. <ge...@ge...>]

On Mar 23, 2011, at 6:44 PM, Andrew Fant wrote:

> I'm having problems building the python extensions for openbabel on essentially virgin installation of snowleopard (thanks to a corrupted boot disk).  When I build and install openbabel-2.3.0 itself, everything is fine, and I can use babel from the command line without any difficulty, but when I include the python extensions, I can import pybel just fine, but as soon as I actually make a call to the libraries, it segfaults

I'm aware of the problem. The new CMake bindings don't correctly link the Python extension with the newly-installed libopenbabel.dylib.

I'm going to see if I can work up the fix tonight -- thanks for the reminder.

-Geoff

[OpenBabel-scripting] Problems with openbabel/pybel installation on MacOS X 10.6.6

[Andrew F. <fa...@mo...>]

I'm having problems building the python extensions for openbabel on essentially virgin installation of snowleopard (thanks to a corrupted boot disk).  When I build and install openbabel-2.3.0 itself, everything is fine, and I can use babel from the command line without any difficulty, but when I include the python extensions, I can import pybel just fine, but as soon as I actually make a call to the libraries, it segfaults and generates a crash report for the nice people in Cupertino.  This isn't tied to how I install it, because when I enable testing, make tests returns with 6 failed tests, all of the python tests.  The others are all fine.  I checked with google, and I saw the note about mac builds binding to the wrong dynamic library, but in the traceback from the segfault, there are no references to my home directory, and all attempts to find _openbabel.so are to where it should be (/Library/Python/2.6/site-packages ). 

The code that generates the segfault is:

import pybel

mymol=pybel.readstring( "smi", "CCCC")

(the segfault actually claims to be coming from the smilesformat.so plugin, for what it's worth)

Can anyone make any suggestions?

Also, as an FYI, the way that the cmake files notify people about whether the GUI will be built and where libxml2 is found is parsed as an error by ccmake, which prevents using that tool to configure the build.  Is there any chance that the notification method can be made more ccmake friendly?

Thanks,
	Andy

Re: [OpenBabel-scripting] openbabel for sdf to mol conversion

[nms_uk <nou...@ya...>]

Thanks a lot Chris 

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Re: [OpenBabel-scripting] openbabel for sdf to mol conversion

[Chris M. <c.m...@ga...>]

OpenBabel's current implementation for V3000 mol and sdf files does not 
support the S group block contained in this file, and causes the 
conversion to fail. I have altered the development code so that the rest 
of the molecule is converted properly.

With the current code, a work around would be to use the (far more 
common) V2000 mol file or prevent the generating program from using an S 
group (aka alias, abbreviated group), which just controls the display. 
The S group block could be manually deleted, which would affect the 
display, e.g. the C and O of the OCH3 group would have the same coordinates.

The properties towards the end of the file do not look right and are 
ignored.

Chris

On 10/03/2011 10:11, nms_uk wrote:
> Hi all,
> I'm trying to use babel to convert a valid sdf file to mol file but it
> doesn't work.
> Can anyone take a look and help please?
> here are the contents of the sdf file:
>
>
>
>    0  0  0     0  0            999 V3000
> M  V30 BEGIN CTAB
> M  V30 COUNTS 13 13 3 0 0
> M  V30 BEGIN ATOM
> M  V30 1 C 7.90196 6.19608 0.00000 0
> M  V30 2 C 9.29412 5.37255 0.00000 0
> M  V30 3 C 6.50980 5.37255 0.00000 0
> M  V30 4 C 6.50980 3.76471 0.00000 0
> M  V30 5 C 9.31373 3.78431 0.00000 0
> M  V30 6 C 7.90196 2.94118 0.00000 0
> M  V30 7 C 7.90196 1.35294 0.00000 0
> M  V30 8 C 9.21569 0.52941 0.00000 0
> M  V30 9 O 7.58824 8.09804 0.00000 0
> M  V30 10 H 7.58824 8.09804 0.00000 0
> M  V30 11 C 10.27451 1.78431 0.00000 0
> M  V30 12 C 10.37255 6.49020 0.00000 0
> M  V30 13 O 10.37255 6.49020 0.00000 0
> M  V30 END ATOM
> M  V30 BEGIN BOND
> M  V30 1 1 2 1
> M  V30 2 1 3 4
> M  V30 3 1 5 6
> M  V30 4 1 6 7
> M  V30 5 1 8 7
> M  V30 6 2 3 1
> M  V30 7 2 5 2
> M  V30 8 2 6 4
> M  V30 9 1 9 10
> M  V30 10 1 1 9
> M  V30 11 2 8 11
> M  V30 12 1 12 13
> M  V30 13 1 2 13
> M  V30 END BOND
> M  V30 BEGIN SGROUP
> M  V30 1 SUP 0 ATOMS=(2 9 10) XBONDS=(1 10) LABEL=OH
> M  V30 2 SUP 0 ATOMS=(1 11) XBONDS=(1 11) LABEL=CH2
> M  V30 3 SUP 0 ATOMS=(2 12 13) XBONDS=(1 13) LABEL=OCH3
> M  V30 END SGROUP
> M  V30 END CTAB
> M  END
>>
> 51.00000
>
>>
> 000300@
>
> $$$$
>
> --

[OpenBabel-scripting] openbabel for sdf to mol conversion

[nms_uk <nou...@ya...>]

Hi all,
I'm trying to use babel to convert a valid sdf file to mol file but it
doesn't work.
Can anyone take a look and help please?
here are the contents of the sdf file:



  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 13 13 3 0 0 
M  V30 BEGIN ATOM
M  V30 1 C 7.90196 6.19608 0.00000 0 
M  V30 2 C 9.29412 5.37255 0.00000 0 
M  V30 3 C 6.50980 5.37255 0.00000 0 
M  V30 4 C 6.50980 3.76471 0.00000 0 
M  V30 5 C 9.31373 3.78431 0.00000 0 
M  V30 6 C 7.90196 2.94118 0.00000 0 
M  V30 7 C 7.90196 1.35294 0.00000 0 
M  V30 8 C 9.21569 0.52941 0.00000 0 
M  V30 9 O 7.58824 8.09804 0.00000 0 
M  V30 10 H 7.58824 8.09804 0.00000 0 
M  V30 11 C 10.27451 1.78431 0.00000 0 
M  V30 12 C 10.37255 6.49020 0.00000 0 
M  V30 13 O 10.37255 6.49020 0.00000 0 
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 1 
M  V30 2 1 3 4 
M  V30 3 1 5 6 
M  V30 4 1 6 7 
M  V30 5 1 8 7 
M  V30 6 2 3 1 
M  V30 7 2 5 2 
M  V30 8 2 6 4 
M  V30 9 1 9 10 
M  V30 10 1 1 9 
M  V30 11 2 8 11 
M  V30 12 1 12 13 
M  V30 13 1 2 13 
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 SUP 0 ATOMS=(2 9 10) XBONDS=(1 10) LABEL=OH
M  V30 2 SUP 0 ATOMS=(1 11) XBONDS=(1 11) LABEL=CH2
M  V30 3 SUP 0 ATOMS=(2 12 13) XBONDS=(1 13) LABEL=OCH3
M  V30 END SGROUP
M  V30 END CTAB
M  END
> 
51.00000

> 
000300@

$$$$

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Re: [OpenBabel-scripting] openbabel for comparing molfiles

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

There's no known bug.

Can you ask a chemist to check whether the two molecules are the same?
If they are, please send us the structures.

- Noel

On 24 February 2011 10:52, nms_uk <nou...@ya...> wrote:
>
> i have 2 molfiles molfile1.mol and molfile2.molfile
> i run:
> babel molfile1.mol molfile2.mol -ok
> in my terminal
> this gives me whether they're identical or not
> apparently the way it works is by generating a unique InChl string for both
> files and then doing string matching.
>
> correct me if i'm wrong please
> --
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Re: [OpenBabel-scripting] openbabel for comparing molfiles

[nms_uk <nou...@ya...>]

i have 2 molfiles molfile1.mol and molfile2.molfile
i run:
babel molfile1.mol molfile2.mol -ok
in my terminal
this gives me whether they're identical or not
apparently the way it works is by generating a unique InChl string for both
files and then doing string matching.

correct me if i'm wrong please
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Re: [OpenBabel-scripting] openbabel for comparing molfiles

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

How did you compare molfiles using OpenBabel? I'm not aware of any
module to do this.

- Noel

On 23 February 2011 20:32, nms_uk <nou...@ya...> wrote:
> Hi all, does anyone know whether openbabel has a bug in its comparison
> moldules. I'm not a chemist but I'm running openbabel to compare two
> molfiles and it tells me they're different. When I display these two
> molfiles using pubchem's sketcher, they look exactly identical. Any help
> would be appreciated!
> ________________________________
> View this message in context: openbabel for comparing molfiles
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>
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Re: [OpenBabel-scripting] The type initializer for 'OpenBabel.openbabelcsharpPINVOKE' threw an exception.

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

As I said to the last comment on this thread, you forgot to cc the
person who knows the answer. He may not be on this list.

- Noel

On 21 February 2011 08:48, redswan <lal...@ya...> wrote:
>
> Hello,
> I am using the same dll. but facing the same issue that you was facing. How
> can i resolve this issue ?
> please guide me .
> --
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>
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[OpenBabel-scripting] openbabel for comparing molfiles

[nms_uk <nou...@ya...>]

Hi all,
does anyone know whether openbabel has a bug in its comparison moldules.
I'm not a chemist but I'm running openbabel to compare two molfiles and it
tells me they're different.
When I display these two molfiles using pubchem's sketcher, they look
exactly identical.

Any help would be appreciated!
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Re: [OpenBabel-scripting] The type initializer for 'OpenBabel.openbabelcsharpPINVOKE' threw an exception.

[redswan <lal...@ya...>]

Hello,
I am using the same dll. but facing the same issue that you was facing. How
can i resolve this issue ?
please guide me .
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Re: [OpenBabel-scripting] import error

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

You need to compile with Eigen2 as described in the docs.

- Noel

On 17 February 2011 09:27, Jurgens de Bruin <deb...@gm...> wrote:
> Hi
>
> I get the following error after installing openbabel:
>
>>>> import openbabel
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/usr/local/lib/python2.6/site-packages/openbabel.py", line 91,
> in <module>
>    _openbabel = swig_import_helper()
>  File "/usr/local/lib/python2.6/site-packages/openbabel.py", line 87,
> in swig_import_helper
>    _mod = imp.load_module('_openbabel', fp, pathname, description)
> ImportError: /usr/local/lib/python2.6/site-packages/_openbabel.so:
> undefined symbol: _ZTVN9OpenBabel22OBEnergyConformerScoreE
>
> Can anyone please help me...
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
>
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[OpenBabel-scripting] import error

[Jurgens de B. <deb...@gm...>]

Hi

I get the following error after installing openbabel:

>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/site-packages/openbabel.py", line 91,
in <module>
    _openbabel = swig_import_helper()
  File "/usr/local/lib/python2.6/site-packages/openbabel.py", line 87,
in swig_import_helper
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: /usr/local/lib/python2.6/site-packages/_openbabel.so:
undefined symbol: _ZTVN9OpenBabel22OBEnergyConformerScoreE

Can anyone please help me...

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

Re: [OpenBabel-scripting] Smiles to 3D SDF

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

Hi Jurgens,

If you wrap the OBMol with a Pybel Molecule, you can access the
property fields with the .data attribute.

pmol = pybel.Molecule(mol)
pmol.data["Name"] = "My Title"

This changes the underlying OBMol, so 'mol' now has the property
fields. It's probably a good idea to set the molecule title also
(pmol.title = "My Title").

To understand how this all works, just see the code in pybel.py (it's
really quite short).

- Noel

On 16 February 2011 11:56, Jurgens de Bruin <deb...@gm...> wrote:
> Hi Noel,
>
> I am trying to create 3D sdf from smiles using python and openbabel
> but I am having a bit of a snag:
>
> obConversion = openbabel.OBConversion()
> mol = openbabel.OBMol()
> conv.SetInFormat("smi")
> conv.ReadString(mol, "C(Cl)(=O)CCC(=O)Cl")
> conv.SetOutFormat("sdf")
> OBOp gen3d = OBOp.FindType("Gen3D")
> gen3d.Do(mol)
> obConversion.WriteFile(mol, 'Name.sdf')
>
> Then I would also like to add the molecule name as property to the SDF
> can this be done?
>
>
> Thanks in advance
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Smiles to 3D SDF

[Geoffrey H. <ge...@ge...>]

> I am trying to create 3D sdf from smiles using python and openbabel
> but I am having a bit of a snag:

Can you be a bit more specific about your "snag?" What doesn't work?

> Then I would also like to add the molecule name as property to the SDF
> can this be done?

Sure. Where do you want to get the name of the molecule? Is it in the title? The filename? Somewhere else?

Thanks,
-Geoff

[OpenBabel-scripting] Smiles to 3D SDF

[Jurgens de B. <deb...@gm...>]

Hi Noel,

I am trying to create 3D sdf from smiles using python and openbabel
but I am having a bit of a snag:

obConversion = openbabel.OBConversion()
mol = openbabel.OBMol()
conv.SetInFormat("smi")
conv.ReadString(mol, "C(Cl)(=O)CCC(=O)Cl")
conv.SetOutFormat("sdf")
OBOp gen3d = OBOp.FindType("Gen3D")
gen3d.Do(mol)
obConversion.WriteFile(mol, 'Name.sdf')

Then I would also like to add the molecule name as property to the SDF
can this be done?


Thanks in advance

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

Re: [OpenBabel-scripting] MOL file as string by parameter and JME

[kohai.raul <koh...@gm...>]

Oops,

pasted wrong version of perl script:

>From PERL (OBConverter.pl):

#!/usr/bin/perl

use Chemistry::OpenBabel;

 $chemdata = shift;
 $serviceIn = shift;
 $serviceOut = shift;

  my $obMolIn = new Chemistry::OpenBabel::OBMol;
  my $obConv = new Chemistry::OpenBabel::OBConversion;

  $obConv->SetInAndOutFormats($serviceIn, $serviceOut);
  $obConv->ReadString($obMolIn, $chemdata);
  my $obOut=$obConv->WriteString($obMolIn);

  print ("$obOut");


2011/1/25 kohai.raul [via Open Babel] <
ml-...@n4...<ml-node%2B3...@n4...>
>

> Hi all,
>
> problem Solved! ... if it could to help someone:
>
> From PHP:
>
>
>
>   public function largeDataConverter($chemData,$inFormat,$outFormat){
>
>     $file="OBConverter.pl @'$chemData' '$inFormat' '$outFormat'";
>     $myVar = "";
>
>     ob_start();
>     passthru("$file");
>     $myVar = ob_get_contents();
>     ob_end_clean ();
>
>     if (substr_count(strtolower($myVar), 'error')>0)
>       $myVar="";
>
>     return $myVar;
>
>   //$myVar contains the conversion result from perl script.
>
>   }
>
>
>
> From PERL (OBConverter.pl):
>
>
> #!/usr/bin/perl
>
> use Chemistry::OpenBabel;
>
>  @chemdata = shift;
>  $serviceIn = shift;
>  $serviceOut = shift;
>
>   my $obMolIn = new Chemistry::OpenBabel::OBMol;
>   my $obConv = new Chemistry::OpenBabel::OBConversion;
>
>   $obConv->SetInAndOutFormats($serviceIn, $serviceOut);
>   $obConv->Read($obMolIn, @chemdata);
>   my $obOut=$obConv->WriteString($obMolIn);
>
>   print ("$obOut");
>
>
> This way, Perl admits $chemdata as SMI or MOL, all in string format, no
> external files needed.
>
> Thanks to this, I found that   JME-SMI->MOL / or CML / or VMOL, etc.. have
> not the same results as JME-MOL->CML / or VMOL, etc ... because to spatial
> data??... maybe...  as I said, I'm not chemist, but now I understand that
> SMI doesn't express the same information such as MOL, and there will be more
> resulting data in MOL->CML than SMI->CML
>
> Now, I can not only make use of JME.smiles() (from javascript), but
> JME.molFile() and obtain via "php-ob-bridge" conversions to CML, VMOL, INCHI
> .... through the flux:
>
> Web-Client (JME ->javascript molFile -> AJAX ) -> SERVER ( php +
> "ob-bridge" -> chem results available on php -> to DB or anything ) ->
> callback (JSON) -> javascript (on web client)
>
> Best Regards,
>
> ------------------------------
>  If you reply to this email, your message will be added to the discussion
> below:
>
> http://forums.openbabel.org/MOL-file-as-string-by-parameter-and-JME-tp3233189p3236634.html
>  To unsubscribe from MOL file as string by parameter and JME, click here<http://forums.openbabel.org/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3233189&code=a29oYWkucmF1bEBnbWFpbC5jb218MzIzMzE4OXwtMTg3MTk2NzAx>.
>
>



-- 
--
Raúl Cruz
foro.fuentedepermacultura.org
"pro-curando..."

-- 
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Re: [OpenBabel-scripting] MOL file as string by parameter and JME

[kohai.raul <koh...@gm...>]

Hi all,

problem Solved! ... if it could to help someone:

>From PHP:



  public function largeDataConverter($chemData,$inFormat,$outFormat){
  
    $file="OBConverter.pl @'$chemData' '$inFormat' '$outFormat'";
    $myVar = "";

    ob_start();
    passthru("$file");
    $myVar = ob_get_contents();
    ob_end_clean ();
  
    if (substr_count(strtolower($myVar), 'error')>0)
      $myVar="";

    return $myVar;

  //$myVar contains the conversion result from perl script.

  }



>From PERL (OBConverter.pl):


#!/usr/bin/perl

use Chemistry::OpenBabel;

 @chemdata = shift;
 $serviceIn = shift;
 $serviceOut = shift;

  my $obMolIn = new Chemistry::OpenBabel::OBMol;
  my $obConv = new Chemistry::OpenBabel::OBConversion;
 
  $obConv->SetInAndOutFormats($serviceIn, $serviceOut);  
  $obConv->Read($obMolIn, @chemdata);
  my $obOut=$obConv->WriteString($obMolIn);
    
  print ("$obOut");  
 

This way, Perl admits $chemdata as SMI or MOL, all in string format, no
external files needed.

Thanks to this, I found that   JME-SMI->MOL / or CML / or VMOL, etc.. have
not the same results as JME-MOL->CML / or VMOL, etc ... because to spatial
data??... maybe...  as I said, I'm not chemist, but now I understand that
SMI doesn't express the same information such as MOL, and there will be more
resulting data in MOL->CML than SMI->CML

Now, I can not only make use of JME.smiles() (from javascript), but
JME.molFile() and obtain via "php-ob-bridge" conversions to CML, VMOL, INCHI
.... through the flux:

Web-Client (JME ->javascript molFile -> AJAX ) -> SERVER ( php + "ob-bridge"
-> chem results available on php -> to DB or anything ) -> callback (JSON)
-> javascript (on web client)

Best Regards,
-- 
View this message in context: http://forums.openbabel.org/MOL-file-as-string-by-parameter-and-JME-tp3233189p3236634.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.