Re: [Rdkit-discuss] Error if run Draw in Python
Hi I'm no Python expert, but I think the problem is that Python doesn't (by default) do filename globbing. As a result it doesn't understand the significance of the ~ character in your directory path and tries to interpret it literally. The simple solution is to just give a path that can be interpreted directly (e.g. /home/your_username/Desktop/rest_of_the_path), alternatively install the Python glob module to parse your current path. The former seems to be a much simpler solution! Best regards, Chris On 11 July 2018 at 00:28, Phuong Chau wrote: > Thank you so much! > > On Tue, Jul 10, 2018 at 4:33 PM, Malitha Kabir > wrote: > >> Hi, >> >> Probably the designated folder is missing. So, rdkit cannot create the >> file in specified path. Thanks. >> >> - malitha >> >> On Wed, Jul 11, 2018, 5:46 AM Phuong Chau wrote: >> >>> Hello, >>> >>> I was trying to draw the 2D structure of a molecule inside a python >>> script (.py). It works with other functions such as MolToSmiles, >>> FingerPrintMol(),... but somehow the Draw.MolToSmile() function does not >>> work. It kept throw errors of: >>> File "PairsFinder.py", line 53, in >>> Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/ >>> Chem1_avg7.png') >>> File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/__init__.py", >>> line 182, in MolToFile >>> canvas.save() >>> File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/spingCanvas.py", >>> line 111, in save >>> self.canvas.save() >>> File "/usr/lib/python2.7/dist-packages/rdkit/sping/PIL/pidPIL.py", >>> line 166, in save >>> self._image.save(filename, format=format) >>> File "/usr/lib/python2.7/dist-packages/PIL/Image.py", line 1672, in >>> save >>> fp = builtins.open(filename, "wb") >>> IOError: [Errno 2] No such file or directory: >>> '~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png' >>> My script is : >>> chem = Chem.MolFromSmiles('Nc1c1F') >>> Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png') >>> >>> Would anyone help me please? How do I run Draw in python script? >>> >>> Thank you so much for your help >>> -- >>> Phuong Chau >>> Smith College '20 >>> Engineering Major >>> >>> -- >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot__ >>> _ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> > > > -- > Phuong Chau > Smith College '20 > Engineering Major > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error if run Draw in Python
Thank you so much! On Tue, Jul 10, 2018 at 4:33 PM, Malitha Kabir wrote: > Hi, > > Probably the designated folder is missing. So, rdkit cannot create the > file in specified path. Thanks. > > - malitha > > On Wed, Jul 11, 2018, 5:46 AM Phuong Chau wrote: > >> Hello, >> >> I was trying to draw the 2D structure of a molecule inside a python >> script (.py). It works with other functions such as MolToSmiles, >> FingerPrintMol(),... but somehow the Draw.MolToSmile() function does not >> work. It kept throw errors of: >> File "PairsFinder.py", line 53, in >> Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_ >> v2/Chem1_avg7.png') >> File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/__init__.py", >> line 182, in MolToFile >> canvas.save() >> File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/spingCanvas.py", >> line 111, in save >> self.canvas.save() >> File "/usr/lib/python2.7/dist-packages/rdkit/sping/PIL/pidPIL.py", >> line 166, in save >> self._image.save(filename, format=format) >> File "/usr/lib/python2.7/dist-packages/PIL/Image.py", line 1672, in >> save >> fp = builtins.open(filename, "wb") >> IOError: [Errno 2] No such file or directory: >> '~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png' >> My script is : >> chem = Chem.MolFromSmiles('Nc1c1F') >> Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png') >> >> Would anyone help me please? How do I run Draw in python script? >> >> Thank you so much for your help >> -- >> Phuong Chau >> Smith College '20 >> Engineering Major >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot__ >> _ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > -- Phuong Chau Smith College '20 Engineering Major -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error if run Draw in Python
Hi, Probably the designated folder is missing. So, rdkit cannot create the file in specified path. Thanks. - malitha On Wed, Jul 11, 2018, 5:46 AM Phuong Chau wrote: > Hello, > > I was trying to draw the 2D structure of a molecule inside a python script > (.py). It works with other functions such as MolToSmiles, > FingerPrintMol(),... but somehow the Draw.MolToSmile() function does not > work. It kept throw errors of: > File "PairsFinder.py", line 53, in > > Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png') > File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/__init__.py", > line 182, in MolToFile > canvas.save() > File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/spingCanvas.py", > line 111, in save > self.canvas.save() > File "/usr/lib/python2.7/dist-packages/rdkit/sping/PIL/pidPIL.py", line > 166, in save > self._image.save(filename, format=format) > File "/usr/lib/python2.7/dist-packages/PIL/Image.py", line 1672, in save > fp = builtins.open(filename, "wb") > IOError: [Errno 2] No such file or directory: > '~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png' > My script is : > chem = Chem.MolFromSmiles('Nc1c1F') > Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png') > > Would anyone help me please? How do I run Draw in python script? > > Thank you so much for your help > -- > Phuong Chau > Smith College '20 > Engineering Major > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss