Using pybel.readstring() and using pybel in Python 2.7

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Using pybel.readstring() and using pybel in Python 2.7

Quim Aguirre
Hello,

I am new at using Open Babel software. My intention is to use "Pybel" to calculate structural similarity.

First, I have installed Pybel for Python 3 this way:

$> pip3 install pybel

However, I cannot use the function "readstring":

$> python3
>>> import pybel
>>> smiles = ['CCCC', 'CCCN']
>>> mols = [pybel.readstring("smi", x) for x in smiles] # Create a list of two molecules
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<stdin>", line 1, in <listcomp>
AttributeError: module 'pybel' has no attribute 'readstring'

Do you know why is this happening?

The other problem is that I am interested in using Pybel in Python 2.7. However, I cannot successfully run it. I install it properly this way:

$> pip install pybel

But then, when importing it, I get the following error:

$> python
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/pybel/__init__.py", line 54, in <module>
    from . import io
  File "/Library/Python/2.7/site-packages/pybel/io.py", line 31, in <module>
    from .canonicalize import decanonicalize_node
  File "/Library/Python/2.7/site-packages/pybel/canonicalize.py", line 9, in <module>
    from .parser.language import rev_abundance_labels
  File "/Library/Python/2.7/site-packages/pybel/parser/__init__.py", line 8, in <module>
    from .parse_bel import BelParser
  File "/Library/Python/2.7/site-packages/pybel/parser/parse_bel.py", line 15, in <module>
    from .baseparser import BaseParser, WCW, nest, one_of_tags, triple
  File "/Library/Python/2.7/site-packages/pybel/parser/baseparser.py", line 22, in <module>
    quote = dblQuotedString().setParseAction(removeQuotes)
TypeError: __call__() takes exactly 2 arguments (1 given)

Do you know what could be the reason of these errors? It would be very interesting for me to be able to use this package.

Thank you very much,

Quim

--
Joaquim Aguirre Plans
Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
[Tel.] +34 692 352 112
[hidden email]

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Re: Using pybel.readstring() and using pybel in Python 2.7

David Hall
Quoting from Matt Swain a couple weeks ago:

pip install pybel is not correct. That's an unrelated package. Instead, do pip install openbabel


-David

On Mar 9, 2017, at 8:29 AM, Quim Aguirre <[hidden email]> wrote:

Hello,

I am new at using Open Babel software. My intention is to use "Pybel" to calculate structural similarity.

First, I have installed Pybel for Python 3 this way:

$> pip3 install pybel

However, I cannot use the function "readstring":

$> python3
>>> import pybel
>>> smiles = ['CCCC', 'CCCN']
>>> mols = [pybel.readstring("smi", x) for x in smiles] # Create a list of two molecules
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<stdin>", line 1, in <listcomp>
AttributeError: module 'pybel' has no attribute 'readstring'

Do you know why is this happening?

The other problem is that I am interested in using Pybel in Python 2.7. However, I cannot successfully run it. I install it properly this way:

$> pip install pybel

But then, when importing it, I get the following error:

$> python
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/pybel/__init__.py", line 54, in <module>
    from . import io
  File "/Library/Python/2.7/site-packages/pybel/io.py", line 31, in <module>
    from .canonicalize import decanonicalize_node
  File "/Library/Python/2.7/site-packages/pybel/canonicalize.py", line 9, in <module>
    from .parser.language import rev_abundance_labels
  File "/Library/Python/2.7/site-packages/pybel/parser/__init__.py", line 8, in <module>
    from .parse_bel import BelParser
  File "/Library/Python/2.7/site-packages/pybel/parser/parse_bel.py", line 15, in <module>
    from .baseparser import BaseParser, WCW, nest, one_of_tags, triple
  File "/Library/Python/2.7/site-packages/pybel/parser/baseparser.py", line 22, in <module>
    quote = dblQuotedString().setParseAction(removeQuotes)
TypeError: __call__() takes exactly 2 arguments (1 given)

Do you know what could be the reason of these errors? It would be very interesting for me to be able to use this package.

Thank you very much,

Quim

--
Joaquim Aguirre Plans
Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
[Tel.] +34 692 352 112
[hidden email]
------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
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dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
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Re: Using pybel.readstring() and using pybel in Python 2.7

Quim Aguirre
Thank you David!

I have also tried installing openbabel, but I get the following error:

$> pip install openbabel

Collecting openbabel
  Downloading openbabel-2.4.1.tar.gz (74kB)
    100% |████████████████████████████████| 81kB 1.1MB/s
Installing collected packages: openbabel
  Running setup.py install for openbabel ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-7qwutX/openbabel/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-q5ZfA0-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build_ext
    Open Babel location automatically determined by pkg-config:
    - include_dirs: ['/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7', '/usr/local/Cellar/open-babel/2.4.0/include/openbabel-2.0']
    - library_dirs: ['/usr/local/Cellar/open-babel/2.4.0/lib']
    building '_openbabel' extension
    swigging openbabel-python.i to openbabel-python_wrap.cpp
    swig -python -c++ -small -O -templatereduce -naturalvar -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/Cellar/open-babel/2.4.0/include/openbabel-2.0 -o openbabel-python_wrap.cpp openbabel-python.i
    unable to execute 'swig': No such file or directory
   
    Error: SWIG failed. Is Open Babel installed?
    You may need to manually specify the location of Open Babel include and library directories. For example:
      python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib
      python setup.py install
   
    ----------------------------------------

Do you know why is this error occurring?

Thank you very much for your help,

Quim

2017-03-09 15:29 GMT+01:00 David Hall <[hidden email]>:
Quoting from Matt Swain a couple weeks ago:

pip install pybel is not correct. That's an unrelated package. Instead, do pip install openbabel


-David

On Mar 9, 2017, at 8:29 AM, Quim Aguirre <[hidden email]> wrote:

Hello,

I am new at using Open Babel software. My intention is to use "Pybel" to calculate structural similarity.

First, I have installed Pybel for Python 3 this way:

$> pip3 install pybel

However, I cannot use the function "readstring":

$> python3
>>> import pybel
>>> smiles = ['CCCC', 'CCCN']
>>> mols = [pybel.readstring("smi", x) for x in smiles] # Create a list of two molecules
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<stdin>", line 1, in <listcomp>
AttributeError: module 'pybel' has no attribute 'readstring'

Do you know why is this happening?

The other problem is that I am interested in using Pybel in Python 2.7. However, I cannot successfully run it. I install it properly this way:

$> pip install pybel

But then, when importing it, I get the following error:

$> python
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/pybel/__init__.py", line 54, in <module>
    from . import io
  File "/Library/Python/2.7/site-packages/pybel/io.py", line 31, in <module>
    from .canonicalize import decanonicalize_node
  File "/Library/Python/2.7/site-packages/pybel/canonicalize.py", line 9, in <module>
    from .parser.language import rev_abundance_labels
  File "/Library/Python/2.7/site-packages/pybel/parser/__init__.py", line 8, in <module>
    from .parse_bel import BelParser
  File "/Library/Python/2.7/site-packages/pybel/parser/parse_bel.py", line 15, in <module>
    from .baseparser import BaseParser, WCW, nest, one_of_tags, triple
  File "/Library/Python/2.7/site-packages/pybel/parser/baseparser.py", line 22, in <module>
    quote = dblQuotedString().setParseAction(removeQuotes)
TypeError: __call__() takes exactly 2 arguments (1 given)

Do you know what could be the reason of these errors? It would be very interesting for me to be able to use this package.

Thank you very much,

Quim

--
Joaquim Aguirre Plans
Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
[Tel.] <a href="tel:+34%20692%2035%2021%2012" value="+34692352112" target="_blank">+34 692 352 112
[hidden email]
------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
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--
Joaquim Aguirre Plans
Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
[Tel.] +34 692 352 112
[hidden email]

------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
_______________________________________________
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Re: Using pybel.readstring() and using pybel in Python 2.7

Fredrik Wallner
Looking at the error message it looks like you could solve the problem by installing Swig. However, there might be easier ways to do it. It looks like you installed OpenBabel through Homebrew on a Mac, is that right? If so, did you specify "--with-python", that is run the command as "brew install open-babel --with-python"?
I think that would be the best way to install the python library on your system.
You can also try "conda install openbabel" to use OpenBabel in the Anaconda python distribution.

Kind regards,
Fredrik

On 9 mars 2017 16:01 +0100, Quim Aguirre <[hidden email]>, wrote:
Thank you David!

I have also tried installing openbabel, but I get the following error:

$> pip install openbabel

Collecting openbabel
  Downloading openbabel-2.4.1.tar.gz (74kB)
    100% |████████████████████████████████| 81kB 1.1MB/s
Installing collected packages: openbabel
  Running setup.py install for openbabel ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-7qwutX/openbabel/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-q5ZfA0-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build_ext
    Open Babel location automatically determined by pkg-config:
    - include_dirs: ['/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7', '/usr/local/Cellar/open-babel/2.4.0/include/openbabel-2.0']
    - library_dirs: ['/usr/local/Cellar/open-babel/2.4.0/lib']
    building '_openbabel' extension
    swigging openbabel-python.i to openbabel-python_wrap.cpp
    swig -python -c++ -small -O -templatereduce -naturalvar -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/Cellar/open-babel/2.4.0/include/openbabel-2.0 -o openbabel-python_wrap.cpp openbabel-python.i
    unable to execute 'swig': No such file or directory
   
    Error: SWIG failed. Is Open Babel installed?
    You may need to manually specify the location of Open Babel include and library directories. For example:
      python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib
      python setup.py install
   
    ----------------------------------------

Do you know why is this error occurring?

Thank you very much for your help,

Quim

2017-03-09 15:29 GMT+01:00 David Hall <[hidden email]>:
Quoting from Matt Swain a couple weeks ago:

pip install pybel is not correct. That's an unrelated package. Instead, do pip install openbabel


-David

On Mar 9, 2017, at 8:29 AM, Quim Aguirre <[hidden email]> wrote:

Hello,

I am new at using Open Babel software. My intention is to use "Pybel" to calculate structural similarity.

First, I have installed Pybel for Python 3 this way:

$> pip3 install pybel

However, I cannot use the function "readstring":

$> python3
>>> import pybel
>>> smiles = ['CCCC', 'CCCN']
>>> mols = [pybel.readstring("smi", x) for x in smiles] # Create a list of two molecules
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<stdin>", line 1, in <listcomp>
AttributeError: module 'pybel' has no attribute 'readstring'

Do you know why is this happening?

The other problem is that I am interested in using Pybel in Python 2.7. However, I cannot successfully run it. I install it properly this way:

$> pip install pybel

But then, when importing it, I get the following error:

$> python
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/pybel/__init__.py", line 54, in <module>
    from . import io
  File "/Library/Python/2.7/site-packages/pybel/io.py", line 31, in <module>
    from .canonicalize import decanonicalize_node
  File "/Library/Python/2.7/site-packages/pybel/canonicalize.py", line 9, in <module>
    from .parser.language import rev_abundance_labels
  File "/Library/Python/2.7/site-packages/pybel/parser/__init__.py", line 8, in <module>
    from .parse_bel import BelParser
  File "/Library/Python/2.7/site-packages/pybel/parser/parse_bel.py", line 15, in <module>
    from .baseparser import BaseParser, WCW, nest, one_of_tags, triple
  File "/Library/Python/2.7/site-packages/pybel/parser/baseparser.py", line 22, in <module>
    quote = dblQuotedString().setParseAction(removeQuotes)
TypeError: __call__() takes exactly 2 arguments (1 given)

Do you know what could be the reason of these errors? It would be very interesting for me to be able to use this package.

Thank you very much,

Quim

--
Joaquim Aguirre Plans
Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
[Tel.] <a href="tel:+34%20692%2035%2021%2012" value="+34692352112" target="_blank">+34 692 352 112
[hidden email]
------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
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--
Joaquim Aguirre Plans
Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
[Tel.] <a dir="ltr" href="tel:+34%20692%20352%20112" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="12">+34 692 352 112
[hidden email]
------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
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Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
_______________________________________________
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