[Rdkit-discuss] read 2 SDF files in the loop
Hello all,
I have a little question.
I don't arrive to read 2 SDF files with RDKIT when I use the for loop.
I explain
I have a first sdf files with 1 property and a second with another properties.
I put the second SDMolSupplier instead of suppl and load a sdf file ( look
exemple)
If I replace the SDMolSupplier by a text file the program don't have a problem.
I just search a writer to read 2 SDF
Tks
Cedric
reader1 = Chem.SDMolSupplier(C:\Data\scaffold/Total/totalscaffold.sdf.sdf)
writer = Chem.SDWriter(C:\Data\scaffold/Eval/evalcount.sdf)
z = 0
for mol in reader1:
h = Chem.MolToSmiles(mol)
suppl = open('C:\Data\scaffold/Total/total.txt','r')
for a in suppl:
r = 0
r+=1
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Re: [Rdkit-discuss] Q2 2010 Release
On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, looking like it cannot be done with cmake without python installed. I have cygwin installed but cmake cannot find BISON and FLEX and complaining about python executable. Any suggestions? The python part should be easy: after you configure the first time, untick the RDK_BUILD_PYTHON_WRAPPERS box and then configure again. flex and bison should be found if they are in your PATH. Please check that they are. -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q2 2010 Release
Dear Greg, I was sure bison and flex are part of cygwin installation but cannot find executables. Can you suggest anything? Regards, Evgueni On 1 July 2010 13:06, Greg Landrum greg.land...@gmail.com wrote: On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, looking like it cannot be done with cmake without python installed. I have cygwin installed but cmake cannot find BISON and FLEX and complaining about python executable. Any suggestions? The python part should be easy: after you configure the first time, untick the RDK_BUILD_PYTHON_WRAPPERS box and then configure again. flex and bison should be found if they are in your PATH. Please check that they are. -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q2 2010 Release
On 1 July 2010 13:43, Evgueni Kolossov ekolos...@gmail.com wrote: Dear Greg, I was sure bison and flex are part of cygwin installation but cannot find executables. Can you suggest anything? Run cygwin setup, and type bison into the search box. Regards, Evgueni On 1 July 2010 13:06, Greg Landrum greg.land...@gmail.com wrote: On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, looking like it cannot be done with cmake without python installed. I have cygwin installed but cmake cannot find BISON and FLEX and complaining about python executable. Any suggestions? The python part should be easy: after you configure the first time, untick the RDK_BUILD_PYTHON_WRAPPERS box and then configure again. flex and bison should be found if they are in your PATH. Please check that they are. -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q2 2010 Release
Dear Noel, Thank you very much - done upgrade anyway and now can find bison and flex Regards, Evgueni On 1 July 2010 13:45, Noel O'Boyle baoille...@gmail.com wrote: On 1 July 2010 13:43, Evgueni Kolossov ekolos...@gmail.com wrote: Dear Greg, I was sure bison and flex are part of cygwin installation but cannot find executables. Can you suggest anything? Run cygwin setup, and type bison into the search box. Regards, Evgueni On 1 July 2010 13:06, Greg Landrum greg.land...@gmail.com wrote: On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, looking like it cannot be done with cmake without python installed. I have cygwin installed but cmake cannot find BISON and FLEX and complaining about python executable. Any suggestions? The python part should be easy: after you configure the first time, untick the RDK_BUILD_PYTHON_WRAPPERS box and then configure again. flex and bison should be found if they are in your PATH. Please check that they are. -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] read 2 SDF files in the loop
On 1 July 2010 19:52, Greg Landrum greg.land...@gmail.com wrote:
Dear Cedric,
On Thu, Jul 1, 2010 at 10:52 AM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
Hello all,
I have a little question.
I don’t arrive to read 2 SDF files with RDKIT when I use the for loop.
I explain
I have a first sdf files with 1 property and a second with another
properties.
I put the second SDMolSupplier instead of “suppl” and load a sdf file ( look
exemple)
I think what you want is something like the following:
suppl1 = Chem.SDMolSupplier('file1.sdf')
suppl2 = Chem.SDMolSupplier('file2.sdf')
for mol1 in suppl1:
mol2 = suppl2.next()
# do something with the two molecules
Maybe for mol1, mol2 in zip(suppl1, suppl2): ?
Best Regards,
-greg
If I replace the SDMolSupplier by a text file the program don’t have a
problem.
I just search a writer to read 2 SDF ….
Tks
Cedric
reader1 = Chem.SDMolSupplier(C:\Data\scaffold/Total/totalscaffold.sdf.sdf)
writer = Chem.SDWriter(C:\Data\scaffold/Eval/evalcount.sdf)
z = 0
for mol in reader1:
h = Chem.MolToSmiles(mol)
suppl = open('C:\Data\scaffold/Total/total.txt','r')
for a in suppl:
r = 0
r+=1
**
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the extent that it relates to their official business.
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Re: [Rdkit-discuss] read 2 SDF files in the loop
On Thu, Jul 1, 2010 at 9:01 PM, Noel O'Boyle baoille...@gmail.com wrote:
I think what you want is something like the following:
suppl1 = Chem.SDMolSupplier('file1.sdf')
suppl2 = Chem.SDMolSupplier('file2.sdf')
for mol1 in suppl1:
mol2 = suppl2.next()
# do something with the two molecules
Maybe for mol1, mol2 in zip(suppl1, suppl2): ?
That's a really nice and clean way of spelling it, but a bit of a
disaster when the files are large: zip(a,b) creates the whole joined
list at once, it's not a generator (at least with python 2.5).
What this means to those of you who don't get excited about these
things is that Noel's form reads all the molecules from both suppliers
into memory and then loops over them. The form I originally proposed
only has two molecules in memory at a time.
Best Regards,
-greg
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Re: [Rdkit-discuss] read 2 SDF files in the loop
On Thu, Jul 1, 2010 at 9:26 PM, Noel O'Boyle baoille...@gmail.com wrote: Two molecules in memory, eh? I raise you the complicated itertools module: import itertools for mol1, mol2, in itertools.izip(suppl1, suppl2): This is the cleanest of the approaches yet; thanks Noel! -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
