date:20130605

Re: [Rdkit-discuss] install error

2013-06-05 Thread Yingfeng Wang

Yes. I tried again. This time,

after run download-inchi.sh

I
mkdir build
cd build
sudo cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
sudo make
sudo make install

by far, no error reported.

but, when I run sudo ctest

I got

The following tests FAILED:
  1 - testInchi (OTHER_FAULT)
  3 - testDataStructs (OTHER_FAULT)
  4 - pyBV (Failed)
  5 - pyDiscreteValueVect (Failed)
  6 - pySparseIntVect (Failed)
  8 - testGrid (OTHER_FAULT)
  9 - testPyGeometry (Failed)
 12 - pyAlignment (Failed)
 16 - pyDistGeom (Failed)
 20 - graphmolMolOpsTest (SEGFAULT)
 22 - graphmoltestChirality (OTHER_FAULT)
 23 - graphmoltestPickler (OTHER_FAULT)
 25 - testDepictor (OTHER_FAULT)
 26 - pyDepictor (Failed)
 29 - fileParsersTest1 (OTHER_FAULT)
 30 - testMolSupplier (OTHER_FAULT)
 31 - testMolWriter (OTHER_FAULT)
 32 - testTplParser (OTHER_FAULT)
 33 - testMol2ToMol (OTHER_FAULT)
 35 - testReaction (OTHER_FAULT)
 36 - pyChemReactions (Failed)
 37 - testChemTransforms (OTHER_FAULT)
 40 - testFragCatalog (OTHER_FAULT)
 41 - pyFragCatalog (Failed)
 42 - testDescriptors (OTHER_FAULT)
 43 - pyMolDescriptors (Failed)
 44 - testFingerprints (OTHER_FAULT)
 45 - pyPartialCharges (Failed)
 46 - testMolTransforms (OTHER_FAULT)
 47 - pyMolTransforms (Failed)
 48 - testForceFieldHelpers (OTHER_FAULT)
 49 - pyForceFieldHelpers (Failed)
 50 - testDistGeomHelpers (OTHER_FAULT)
 51 - pyDistGeom (Failed)
 52 - testMolAlign (OTHER_FAULT)
 53 - pyMolAlign (Failed)
 54 - testFeatures (OTHER_FAULT)
 55 - pyChemicalFeatures (Failed)
 56 - testShapeHelpers (OTHER_FAULT)
 57 - pyShapeHelpers (Failed)
 59 - pyMolCatalog (Failed)
 61 - pySLNParse (Failed)
 62 - pyGraphMolWrap (Failed)
 63 - pyTestConformerWrap (Failed)
 66 - pyMatCalc (Failed)
 67 - pyCMIM (Failed)
 68 - pyRanker (Failed)
 70 - pyFeatures (Failed)
 71 - pythonTestDbCLI (Failed)
 72 - pythonTestDirML (Failed)
 77 - pythonTestDirChem (Failed)
Errors while running CTest

Thanks.



On Wed, Jun 5, 2013 at 5:54 AM, JP jeanpaul.ebe...@inhibox.com wrote:

 ,

 Before running cmake - have you run ./External/INCHI-API/download-inchi.sh
 ?




 On 5 June 2013 04:13, Yingfeng Wang ywang...@gmail.com wrote:

 After getting the latest code by git, I install RDKit on my ubuntu 12.04.

 In the step of make install, I got

 CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE):

 It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't be
 found. Please note that I have turned on the flag of inchi.

 Thanks.

 Yingfeng


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 Rdkit-discuss@lists.sourceforge.net
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Re: [Rdkit-discuss] install error

2013-06-05 Thread Jan Holst Jensen


Hi Yingfeng,

Looks like what happened to me, when I had forgotten to set the 
environment. Did you set LD_LIBRARY_PATH to $RDBASE/lib before running 
the tests ?


Kind regards
-- Jan Holst Jensen

On 2013-06-05 16:09, Yingfeng Wang wrote:

Yes. I tried again. This time,

after run download-inchi.sh

I
mkdir build
cd build
sudo cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
sudo make
sudo make install

by far, no error reported.

but, when I run sudo ctest

I got

The following tests FAILED:
 1 - testInchi (OTHER_FAULT)
 3 - testDataStructs (OTHER_FAULT)
 4 - pyBV (Failed)
 5 - pyDiscreteValueVect (Failed)
 6 - pySparseIntVect (Failed)
 8 - testGrid (OTHER_FAULT)
 9 - testPyGeometry (Failed)
12 - pyAlignment (Failed)
16 - pyDistGeom (Failed)
20 - graphmolMolOpsTest (SEGFAULT)
22 - graphmoltestChirality (OTHER_FAULT)
23 - graphmoltestPickler (OTHER_FAULT)
25 - testDepictor (OTHER_FAULT)
26 - pyDepictor (Failed)
29 - fileParsersTest1 (OTHER_FAULT)
30 - testMolSupplier (OTHER_FAULT)
31 - testMolWriter (OTHER_FAULT)
32 - testTplParser (OTHER_FAULT)
33 - testMol2ToMol (OTHER_FAULT)
35 - testReaction (OTHER_FAULT)
36 - pyChemReactions (Failed)
37 - testChemTransforms (OTHER_FAULT)
40 - testFragCatalog (OTHER_FAULT)
41 - pyFragCatalog (Failed)
42 - testDescriptors (OTHER_FAULT)
43 - pyMolDescriptors (Failed)
44 - testFingerprints (OTHER_FAULT)
45 - pyPartialCharges (Failed)
46 - testMolTransforms (OTHER_FAULT)
47 - pyMolTransforms (Failed)
48 - testForceFieldHelpers (OTHER_FAULT)
49 - pyForceFieldHelpers (Failed)
50 - testDistGeomHelpers (OTHER_FAULT)
51 - pyDistGeom (Failed)
52 - testMolAlign (OTHER_FAULT)
53 - pyMolAlign (Failed)
54 - testFeatures (OTHER_FAULT)
55 - pyChemicalFeatures (Failed)
56 - testShapeHelpers (OTHER_FAULT)
57 - pyShapeHelpers (Failed)
59 - pyMolCatalog (Failed)
61 - pySLNParse (Failed)
62 - pyGraphMolWrap (Failed)
63 - pyTestConformerWrap (Failed)
66 - pyMatCalc (Failed)
67 - pyCMIM (Failed)
68 - pyRanker (Failed)
70 - pyFeatures (Failed)
71 - pythonTestDbCLI (Failed)
72 - pythonTestDirML (Failed)
77 - pythonTestDirChem (Failed)
Errors while running CTest

Thanks.



On Wed, Jun 5, 2013 at 5:54 AM, JP jeanpaul.ebe...@inhibox.com 
mailto:jeanpaul.ebe...@inhibox.com wrote:


,

Before running cmake - have you
run ./External/INCHI-API/download-inchi.sh ?




On 5 June 2013 04:13, Yingfeng Wang ywang...@gmail.com
mailto:ywang...@gmail.com wrote:

After getting the latest code by git, I install RDKit on my
ubuntu 12.04.

In the step of make install, I got

CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE):

It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre
can't be found. Please note that I have turned on the flag of
inchi.

Thanks.

Yingfeng



--
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1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
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Re: [Rdkit-discuss] install error

2013-06-05 Thread Jan Holst Jensen

OK, that looks fine. And I assume you build directly in 
/opt/RDKit_latest/latest/, so 'make install' puts files in 
/opt/RDKit_latest/latest/lib/.


The only other thing that comes to my mind is if your boost libraries 
are included in LD_LIBRARY_PATH.


Cheers
-- Jan

On 2013-06-05 16:55, Yingfeng Wang wrote:

Yes, I did.

export RDBASE=/opt/RDKit_latest/latest
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH

I put them on ~/.bashrc


On Wed, Jun 5, 2013 at 10:53 AM, Jan Holst Jensen 
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:


Hi Yingfeng,

Looks like what happened to me, when I had forgotten to set the
environment. Did you set LD_LIBRARY_PATH to $RDBASE/lib before
running the tests ?

Kind regards
-- Jan Holst Jensen


On 2013-06-05 16:09, Yingfeng Wang wrote:

Yes. I tried again. This time,

after run download-inchi.sh

I
mkdir build
cd build
sudo cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
sudo make
sudo make install

by far, no error reported.

but, when I run sudo ctest

I got

The following tests FAILED:
 1 - testInchi (OTHER_FAULT)
 3 - testDataStructs (OTHER_FAULT)
 4 - pyBV (Failed)
 5 - pyDiscreteValueVect (Failed)
 6 - pySparseIntVect (Failed)
 8 - testGrid (OTHER_FAULT)
 9 - testPyGeometry (Failed)
12 - pyAlignment (Failed)
16 - pyDistGeom (Failed)
20 - graphmolMolOpsTest (SEGFAULT)
22 - graphmoltestChirality (OTHER_FAULT)
23 - graphmoltestPickler (OTHER_FAULT)
25 - testDepictor (OTHER_FAULT)
26 - pyDepictor (Failed)
29 - fileParsersTest1 (OTHER_FAULT)
30 - testMolSupplier (OTHER_FAULT)
31 - testMolWriter (OTHER_FAULT)
32 - testTplParser (OTHER_FAULT)
33 - testMol2ToMol (OTHER_FAULT)
35 - testReaction (OTHER_FAULT)
36 - pyChemReactions (Failed)
37 - testChemTransforms (OTHER_FAULT)
40 - testFragCatalog (OTHER_FAULT)
41 - pyFragCatalog (Failed)
42 - testDescriptors (OTHER_FAULT)
43 - pyMolDescriptors (Failed)
44 - testFingerprints (OTHER_FAULT)
45 - pyPartialCharges (Failed)
46 - testMolTransforms (OTHER_FAULT)
47 - pyMolTransforms (Failed)
48 - testForceFieldHelpers (OTHER_FAULT)
49 - pyForceFieldHelpers (Failed)
50 - testDistGeomHelpers (OTHER_FAULT)
51 - pyDistGeom (Failed)
52 - testMolAlign (OTHER_FAULT)
53 - pyMolAlign (Failed)
54 - testFeatures (OTHER_FAULT)
55 - pyChemicalFeatures (Failed)
56 - testShapeHelpers (OTHER_FAULT)
57 - pyShapeHelpers (Failed)
59 - pyMolCatalog (Failed)
61 - pySLNParse (Failed)
62 - pyGraphMolWrap (Failed)
63 - pyTestConformerWrap (Failed)
66 - pyMatCalc (Failed)
67 - pyCMIM (Failed)
68 - pyRanker (Failed)
70 - pyFeatures (Failed)
71 - pythonTestDbCLI (Failed)
72 - pythonTestDirML (Failed)
77 - pythonTestDirChem (Failed)
Errors while running CTest

Thanks.



On Wed, Jun 5, 2013 at 5:54 AM, JP jeanpaul.ebe...@inhibox.com
mailto:jeanpaul.ebe...@inhibox.com wrote:

,

Before running cmake - have you
run ./External/INCHI-API/download-inchi.sh ?




On 5 June 2013 04:13, Yingfeng Wang ywang...@gmail.com
mailto:ywang...@gmail.com wrote:

After getting the latest code by git, I install RDKit on
my ubuntu 12.04.

In the step of make install, I got

CMake Error at External/INCHI-API/cmake_install.cmake:124
(FILE):

It seems the
file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't be
found. Please note that I have turned on the flag of inchi.

Thanks.

Yingfeng






--
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
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Re: [Rdkit-discuss] install error

2013-06-05 Thread Yingfeng Wang

Jan,

Thanks. I just found the problem. The environment setting is in .bashrc,
which is not for sudo.

Now, I install everything in a local directory, and don't need sudo. Then
it works now.

Sorry about my confusing mistake.

Yingfeng


On Wed, Jun 5, 2013 at 11:22 AM, Jan Holst Jensen j...@biochemfusion.comwrote:

  OK, that looks fine. And I assume you build directly in
 /opt/RDKit_latest/latest/, so 'make install' puts files in
 /opt/RDKit_latest/latest/lib/.

 The only other thing that comes to my mind is if your boost libraries are
 included in LD_LIBRARY_PATH.

 Cheers
 -- Jan


 On 2013-06-05 16:55, Yingfeng Wang wrote:

 Yes, I did.

  export RDBASE=/opt/RDKit_latest/latest
 export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
 export PYTHONPATH=$RDBASE:$PYTHONPATH

  I put them on ~/.bashrc


 On Wed, Jun 5, 2013 at 10:53 AM, Jan Holst Jensen 
 j...@biochemfusion.comwrote:

  Hi Yingfeng,

 Looks like what happened to me, when I had forgotten to set the
 environment. Did you set LD_LIBRARY_PATH to $RDBASE/lib before running the
 tests ?

 Kind regards
 -- Jan Holst Jensen


 On 2013-06-05 16:09, Yingfeng Wang wrote:

 Yes. I tried again. This time,

  after run download-inchi.sh

  I
  mkdir build
 cd build
 sudo cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
 sudo make
 sudo make install

  by far, no error reported.

  but, when I run sudo ctest

  I got

  The following tests FAILED:
   1 - testInchi (OTHER_FAULT)
   3 - testDataStructs (OTHER_FAULT)
   4 - pyBV (Failed)
   5 - pyDiscreteValueVect (Failed)
   6 - pySparseIntVect (Failed)
   8 - testGrid (OTHER_FAULT)
   9 - testPyGeometry (Failed)
  12 - pyAlignment (Failed)
  16 - pyDistGeom (Failed)
  20 - graphmolMolOpsTest (SEGFAULT)
  22 - graphmoltestChirality (OTHER_FAULT)
  23 - graphmoltestPickler (OTHER_FAULT)
  25 - testDepictor (OTHER_FAULT)
  26 - pyDepictor (Failed)
  29 - fileParsersTest1 (OTHER_FAULT)
  30 - testMolSupplier (OTHER_FAULT)
  31 - testMolWriter (OTHER_FAULT)
  32 - testTplParser (OTHER_FAULT)
  33 - testMol2ToMol (OTHER_FAULT)
  35 - testReaction (OTHER_FAULT)
  36 - pyChemReactions (Failed)
  37 - testChemTransforms (OTHER_FAULT)
  40 - testFragCatalog (OTHER_FAULT)
  41 - pyFragCatalog (Failed)
  42 - testDescriptors (OTHER_FAULT)
  43 - pyMolDescriptors (Failed)
  44 - testFingerprints (OTHER_FAULT)
  45 - pyPartialCharges (Failed)
  46 - testMolTransforms (OTHER_FAULT)
  47 - pyMolTransforms (Failed)
  48 - testForceFieldHelpers (OTHER_FAULT)
  49 - pyForceFieldHelpers (Failed)
  50 - testDistGeomHelpers (OTHER_FAULT)
  51 - pyDistGeom (Failed)
  52 - testMolAlign (OTHER_FAULT)
  53 - pyMolAlign (Failed)
  54 - testFeatures (OTHER_FAULT)
  55 - pyChemicalFeatures (Failed)
  56 - testShapeHelpers (OTHER_FAULT)
  57 - pyShapeHelpers (Failed)
  59 - pyMolCatalog (Failed)
  61 - pySLNParse (Failed)
  62 - pyGraphMolWrap (Failed)
  63 - pyTestConformerWrap (Failed)
  66 - pyMatCalc (Failed)
  67 - pyCMIM (Failed)
  68 - pyRanker (Failed)
  70 - pyFeatures (Failed)
  71 - pythonTestDbCLI (Failed)
  72 - pythonTestDirML (Failed)
  77 - pythonTestDirChem (Failed)
 Errors while running CTest

  Thanks.



 On Wed, Jun 5, 2013 at 5:54 AM, JP jeanpaul.ebe...@inhibox.com wrote:

 ,

  Before running cmake - have you
 run ./External/INCHI-API/download-inchi.sh ?




   On 5 June 2013 04:13, Yingfeng Wang ywang...@gmail.com wrote:

  After getting the latest code by git, I install RDKit on my ubuntu
 12.04.

  In the step of make install, I got

  CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE):

  It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't
 be found. Please note that I have turned on the flag of inchi.

  Thanks.

  Yingfeng





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1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
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Re: [Rdkit-discuss] separate module by breaking bonds

2013-06-05 Thread Yingfeng Wang

Dear Greg,

I update the version of RDKit by git. And it works as you described, like

 from rdkit import Chem
 from rdkit.Chem import Descriptors
 m
=Chem.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')
 em = Chem.EditableMol(m)
 em.RemoveBond(8,7)
 nm = em.GetMol()
 frags = Chem.GetMolFrags(nm,asMols=True,sanitizeFrags=False)
 from rdkit.Chem import AllChem
 [AllChem.CalcMolFormula(x) for x in frags]
['C4H4N3O', 'C6H5']
 [Descriptors.ExactMolWt(x) for x in frags]
[110.035436748, 77.03912516]

But with inchi format

 [Chem.MolToInchi(x) for x in frags]
['InChI=1S/C4H5N3O/c1-3-6-4(8)2-5-7-3/h2H,1H3,(H,6,7,8)',
'InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H']


it is still C6H6 not C6H5.

Actually, I need the 2D structure of fragments of C6H5 (not necessary
inchi format data). Is there a way to retrieve this information? Right now,
a solution in my mind could be to retrieve the 2D information of the
original compound (in my example, it's m) first. Then identify the removing
bonds (in my example, it's Bond(8,7)). Finally, I can get 2D information of
fragments. Could you please let me know whether there is a better solution
to get 2D information of fragments?

Thanks.

Yingfeng




On Sun, Jun 2, 2013 at 8:39 AM, Yingfeng Wang ywang...@gmail.com wrote:

 Dear Greg,

 Thank you very much! I think 'C6H5' is good enough to me.

 Yingfeng


 On Sun, Jun 2, 2013 at 12:25 AM, Greg Landrum greg.land...@gmail.comwrote:


 On Sat, Jun 1, 2013 at 6:46 AM, Yingfeng Wang ywang...@gmail.com wrote:

 Dear Greg,

 Thanks.

 As for
 In [19]: frags = Chem.GetMolFrags(nm,asMols=True)
 In [20]: [AllChem.CalcMolFormula(x) for x in frags]
 Out[20]: ['C4H5N3O', 'C6H6']

 Is it possible to directly get 'C6H5+' instead of 'C6H6'?


 You can't get C6H5+, because there's not really any way for the code to
 know here to assign charges if you just call break bonds, but as of this
 morning (I just committed it) you can tell the RDKit not to sanitize the
 fragments:

 In [10]: frags = Chem.GetMolFrags(nm,asMols=True,sanitizeFrags=False)

 In [11]: [AllChem.CalcMolFormula(x) for x in frags]
 Out[11]: ['C4H4N3O', 'C6H5']

 In [10]: frags = Chem.GetMolFrags(nm,asMols=True,sanitizeFrags=False)

 In [11]: [AllChem.CalcMolFormula(x) for x in frags]
 Out[11]: ['C4H4N3O', 'C6H5']




 As for the difference between ExactMolWt() and MolWt(). The confusion
 is from the following case:

 [Chem.MolToSmiles(x) for x in frags]
 ['Cc1nncc(O)n1', 'c1c1']

  Descriptors.MolWt(Chem.MolFromSmiles('Cc1nncc(O)n1'))
 111.103998
  Descriptors.MolWt(Chem.MolFromSmiles('c1c1'))
 78.113999
  [Descriptors.ExactMolWt(x) for x in frags]
 [111.04326178, 78.046950192]

 By far, every thing is perfect.

 But if I use

 [Descriptors.MolWt(x) for x in frags]
 [5.04, 6.048]

 It looks I can get correct mass by MolWt() if I transfer mol to Smiles
 format, and transfer Smiles format back to mol. However, if I directly
 apply MolWt() on the original mol, I got weird results.


 I can reproduce this and it looks like a bug. I'll get it fixed.

 -greg



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Re: [Rdkit-discuss] install error

Re: [Rdkit-discuss] install error

Re: [Rdkit-discuss] install error

Re: [Rdkit-discuss] install error

Re: [Rdkit-discuss] separate module by breaking bonds

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