Hi,
after installation of latest nodes (Indigo KNIME integration
1.1.0.201201291733) I could not load my sample any more. It always
terminates with a Visual C++ runtime error and takes knime with it
(either molecule to indigo and query molecule to indigo).
Best, Hinnerk
PS: Many thx for the C example of the transformation.
> Hi,
> after installation of latest nodes (Indigo KNIME integration
> 1.1.0.201201291733) I could not load my sample any more. It always
> terminates with a Visual C++ runtime error and takes knime with it
> (either molecule to indigo and query molecule to indigo).
> Best, Hinnerk
> PS: Many thx for the C example of the transformation.
nevertheless. murcko and scaffold finder are not stable and results in
either crash (Vusial C++ runtime error) or lots of errors in log (both
nodes with write tables to disc, 32bit, win7). I try to figure out at
least one problematic structure.
On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> Sorry, my fault. It was again the "write tables to disc" issue. I have
> forgotten this.
> On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > Hi,
> > after installation of latest nodes (Indigo KNIME integration
> > 1.1.0.201201291733) I could not load my sample any more. It always
> > terminates with a Visual C++ runtime error and takes knime with it
> > (either molecule to indigo and query molecule to indigo).
> > Best, Hinnerk
> > PS: Many thx for the C example of the transformation.
Thank you for informing us that the nodes has some instability
problem! We should fix them before releasing the stable version. It
would be great if you could provide us some example. Also could you
tell how much RAM do you have on your computer, and how many molecules
are being proceeded?
Mikhail
On Jan 31, 1:36 am, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> nevertheless. murcko and scaffold finder are not stable and results in
> either crash (Vusial C++ runtime error) or lots of errors in log (both
> nodes with write tables to disc, 32bit, win7). I try to figure out at
> least one problematic structure.
> On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > Sorry, my fault. It was again the "write tables to disc" issue. I have
> > forgotten this.
> > On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > Hi,
> > > after installation of latest nodes (Indigo KNIME integration
> > > 1.1.0.201201291733) I could not load my sample any more. It always
> > > terminates with a Visual C++ runtime error and takes knime with it
> > > (either molecule to indigo and query molecule to indigo).
> > > Best, Hinnerk
> > > PS: Many thx for the C example of the transformation.
> Thank you for informing us that the nodes has some instability
> problem! We should fix them before releasing the stable version. It
> would be great if you could provide us some example. Also could you
> tell how much RAM do you have on your computer, and how many molecules
> are being proceeded?
> Mikhail
> On Jan 31, 1:36 am, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > nevertheless. murcko and scaffold finder are not stable and results in
> > either crash (Vusial C++ runtime error) or lots of errors in log (both
> > nodes with write tables to disc, 32bit, win7). I try to figure out at
> > least one problematic structure.
> > On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > Sorry, my fault. It was again the "write tables to disc" issue. I have
> > > forgotten this.
> > > On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > Hi,
> > > > after installation of latest nodes (Indigo KNIME integration
> > > > 1.1.0.201201291733) I could not load my sample any more. It always
> > > > terminates with a Visual C++ runtime error and takes knime with it
> > > > (either molecule to indigo and query molecule to indigo).
> > > > Best, Hinnerk
> > > > PS: Many thx for the C example of the transformation.
These error messages are really not expected, and something has gone
wrong. Could you update the Indigo nodes: I have added an addional
diagnostics, by printing rowid for the row that caused this error. In
particular, I would like to know what molecule caused "cis-trans:
can't sort restored substituents" and "pool: access to unused element"
messages.
And are you using 32-bit or 64-bit KNIME?
Best,
Mikhail
On 31 янв, 09:02, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> Hi,
> I have 8gb ram and this sample is ~100k compounds. But i get the
> errors quite early. Here is the log:
> **************************************************************************
> ERROR Murcko Scaffold Execute failed: pool: access to unused element
> 1
> ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> trans: can't sort restored substituents
> ERROR BufferFromFileIteratorVersion20 Errors while reading row 2152
> from file "knime_container_20120131_919338784171118525.bin.gz": cis-
> trans: can't sort restored substituents; Suppressing further warnings.
> WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> cells: ignoring
> ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> trans: can't sort restored substituents
> WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> cells: ignoring
> ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> trans: can't sort restored substituents
> WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> cells: ignoring
> ERROR Scaffold Finder Execute failed: array: reserve(): no memory
> ERROR SyncExecQueueDispatcher Uncaught exception while queuing
> events into main thread
> Row 2152 is empty.
> Best, Hinnerk
> On Jan 30, 10:47 pm, Mikhail Rybalkin <rybal...@ggasoftware.com>
> wrote:
> > Hello Hinnerk,
> > Thank you for informing us that the nodes has some instability
> > problem! We should fix them before releasing the stable version. It
> > would be great if you could provide us some example. Also could you
> > tell how much RAM do you have on your computer, and how many molecules
> > are being proceeded?
> > Mikhail
> > On Jan 31, 1:36 am, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > nevertheless. murcko and scaffold finder are not stable and results in
> > > either crash (Vusial C++ runtime error) or lots of errors in log (both
> > > nodes with write tables to disc, 32bit, win7). I try to figure out at
> > > least one problematic structure.
> > > On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > Sorry, my fault. It was again the "write tables to disc" issue. I have
> > > > forgotten this.
> > > > On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > Hi,
> > > > > after installation of latest nodes (Indigo KNIME integration
> > > > > 1.1.0.201201291733) I could not load my sample any more. It always
> > > > > terminates with a Visual C++ runtime error and takes knime with it
> > > > > (either molecule to indigo and query molecule to indigo).
> > > > > Best, Hinnerk
> > > > > PS: Many thx for the C example of the transformation.
Hi Mikhail,
I use 32bit with the latest updates / nodes (Indigo KNIME integration
1.1.0.201201312226). Knime is freshly started without any other nodes
(only SDFile Reader and Indigo-Nodes).
I still get the same error (row 2152 has a missing cell in the MOL-
Block). My 64bit installation with an old version (how do i determine,
what is installed) works OK.
> These error messages are really not expected, and something has gone
> wrong. Could you update the Indigo nodes: I have added an addional
> diagnostics, by printing rowid for the row that caused this error. In
> particular, I would like to know what molecule caused "cis-trans:
> can't sort restored substituents" and "pool: access to unused element"
> messages.
> And are you using 32-bit or 64-bit KNIME?
> Best,
> Mikhail
> On 31 янв, 09:02, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > Hi,
> > I have 8gb ram and this sample is ~100k compounds. But i get the
> > errors quite early. Here is the log:
> > **************************************************************************
> > ERROR Murcko Scaffold Execute failed: pool: access to unused element
> > 1
> > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > trans: can't sort restored substituents
> > ERROR BufferFromFileIteratorVersion20 Errors while reading row 2152
> > from file "knime_container_20120131_919338784171118525.bin.gz": cis-
> > trans: can't sort restored substituents; Suppressing further warnings.
> > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > cells: ignoring
> > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > trans: can't sort restored substituents
> > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > cells: ignoring
> > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > trans: can't sort restored substituents
> > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > cells: ignoring
> > ERROR Scaffold Finder Execute failed: array: reserve(): no memory
> > ERROR SyncExecQueueDispatcher Uncaught exception while queuing
> > events into main thread
> > Row 2152 is empty.
> > Best, Hinnerk
> > On Jan 30, 10:47 pm, Mikhail Rybalkin <rybal...@ggasoftware.com>
> > wrote:
> > > Hello Hinnerk,
> > > Thank you for informing us that the nodes has some instability
> > > problem! We should fix them before releasing the stable version. It
> > > would be great if you could provide us some example. Also could you
> > > tell how much RAM do you have on your computer, and how many molecules
> > > are being proceeded?
> > > Mikhail
> > > On Jan 31, 1:36 am, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > nevertheless. murcko and scaffold finder are not stable and results in
> > > > either crash (Vusial C++ runtime error) or lots of errors in log (both
> > > > nodes with write tables to disc, 32bit, win7). I try to figure out at
> > > > least one problematic structure.
> > > > On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > Sorry, my fault. It was again the "write tables to disc" issue. I have
> > > > > forgotten this.
> > > > > On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > Hi,
> > > > > > after installation of latest nodes (Indigo KNIME integration
> > > > > > 1.1.0.201201291733) I could not load my sample any more. It always
> > > > > > terminates with a Visual C++ runtime error and takes knime with it
> > > > > > (either molecule to indigo and query molecule to indigo).
> > > > > > Best, Hinnerk
> > > > > > PS: Many thx for the C example of the transformation.
As you have the errors only in the 32-bit version, I think that the
problem is with the memory management inside our nodes in Knime. We
will try to fix it after returning from the 5th KNIME Users Group
Meeting and Workshop.
Just to ensure that the 64-bit version works fine, could you check the
same workflow with the 64-bit Knime with the latest indigo nodes?
Best regards,
Mikhail
On 1 фев, 22:59, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> Hi Mikhail,
> I use 32bit with the latest updates / nodes (Indigo KNIME integration
> 1.1.0.201201312226). Knime is freshly started without any other nodes
> (only SDFile Reader and Indigo-Nodes).
> I still get the same error (row 2152 has a missing cell in the MOL-
> Block). My 64bit installation with an old version (how do i determine,
> what is installed) works OK.
> On Feb 1, 2:39 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> > Hello Hinnerk,
> > These error messages are really not expected, and something has gone
> > wrong. Could you update the Indigo nodes: I have added an addional
> > diagnostics, by printing rowid for the row that caused this error. In
> > particular, I would like to know what molecule caused "cis-trans:
> > can't sort restored substituents" and "pool: access to unused element"
> > messages.
> > And are you using 32-bit or 64-bit KNIME?
> > Best,
> > Mikhail
> > On 31 янв, 09:02, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > Hi,
> > > I have 8gb ram and this sample is ~100k compounds. But i get the
> > > errors quite early. Here is the log:
> > > **************************************************************************
> > > ERROR Murcko Scaffold Execute failed: pool: access to unused element
> > > 1
> > > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > > trans: can't sort restored substituents
> > > ERROR BufferFromFileIteratorVersion20 Errors while reading row 2152
> > > from file "knime_container_20120131_919338784171118525.bin.gz": cis-
> > > trans: can't sort restored substituents; Suppressing further warnings.
> > > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > > cells: ignoring
> > > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > > trans: can't sort restored substituents
> > > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > > cells: ignoring
> > > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > > trans: can't sort restored substituents
> > > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > > cells: ignoring
> > > ERROR Scaffold Finder Execute failed: array: reserve(): no memory
> > > ERROR SyncExecQueueDispatcher Uncaught exception while queuing
> > > events into main thread
> > > Row 2152 is empty.
> > > Best, Hinnerk
> > > On Jan 30, 10:47 pm, Mikhail Rybalkin <rybal...@ggasoftware.com>
> > > wrote:
> > > > Hello Hinnerk,
> > > > Thank you for informing us that the nodes has some instability
> > > > problem! We should fix them before releasing the stable version. It
> > > > would be great if you could provide us some example. Also could you
> > > > tell how much RAM do you have on your computer, and how many molecules
> > > > are being proceeded?
> > > > Mikhail
> > > > On Jan 31, 1:36 am, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > nevertheless. murcko and scaffold finder are not stable and results in
> > > > > either crash (Vusial C++ runtime error) or lots of errors in log (both
> > > > > nodes with write tables to disc, 32bit, win7). I try to figure out at
> > > > > least one problematic structure.
> > > > > On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > Sorry, my fault. It was again the "write tables to disc" issue. I have
> > > > > > forgotten this.
> > > > > > On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > > Hi,
> > > > > > > after installation of latest nodes (Indigo KNIME integration
> > > > > > > 1.1.0.201201291733) I could not load my sample any more. It always
> > > > > > > terminates with a Visual C++ runtime error and takes knime with it
> > > > > > > (either molecule to indigo and query molecule to indigo).
> > > > > > > Best, Hinnerk
> > > > > > > PS: Many thx for the C example of the transformation.
Hi Mikhail,
with 64bit and the latest nodes i also get:
ERROR Murcko Scaffold Execute failed: pool: access to unused element
2
WARN IndigoScaffoldFinderNodeModel exact method has reached
iteration limit: trying to search approximate
ERROR Scaffold Finder Execute failed: element: bad valence on B
having 5 drawn bonds, charge -2, and 0 radical electrons
Best, Hinnerk
PS: Have fun on the UGM
On Feb 2, 10:05 am, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> As you have the errors only in the 32-bit version, I think that the
> problem is with the memory management inside our nodes in Knime. We
> will try to fix it after returning from the 5th KNIME Users Group
> Meeting and Workshop.
> Just to ensure that the 64-bit version works fine, could you check the
> same workflow with the 64-bit Knime with the latest indigo nodes?
> Best regards,
> Mikhail
> On 1 фев, 22:59, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > Hi Mikhail,
> > I use 32bit with the latest updates / nodes (Indigo KNIME integration
> > 1.1.0.201201312226). Knime is freshly started without any other nodes
> > (only SDFile Reader and Indigo-Nodes).
> > I still get the same error (row 2152 has a missing cell in the MOL-
> > Block). My 64bit installation with an old version (how do i determine,
> > what is installed) works OK.
> > On Feb 1, 2:39 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> > > Hello Hinnerk,
> > > These error messages are really not expected, and something has gone
> > > wrong. Could you update the Indigo nodes: I have added an addional
> > > diagnostics, by printing rowid for the row that caused this error. In
> > > particular, I would like to know what molecule caused "cis-trans:
> > > can't sort restored substituents" and "pool: access to unused element"
> > > messages.
> > > And are you using 32-bit or 64-bit KNIME?
> > > Best,
> > > Mikhail
> > > On 31 янв, 09:02, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > Hi,
> > > > I have 8gb ram and this sample is ~100k compounds. But i get the
> > > > errors quite early. Here is the log:
> > > > **************************************************************************
> > > > ERROR Murcko Scaffold Execute failed: pool: access to unused element
> > > > 1
> > > > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > > > trans: can't sort restored substituents
> > > > ERROR BufferFromFileIteratorVersion20 Errors while reading row 2152
> > > > from file "knime_container_20120131_919338784171118525.bin.gz": cis-
> > > > trans: can't sort restored substituents; Suppressing further warnings.
> > > > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > > > cells: ignoring
> > > > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > > > trans: can't sort restored substituents
> > > > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > > > cells: ignoring
> > > > ERROR IndigoMolCell Error while unserializing Indigo object: cis-
> > > > trans: can't sort restored substituents
> > > > WARN IndigoScaffoldFinderNodeModel Molecule table contains missing
> > > > cells: ignoring
> > > > ERROR Scaffold Finder Execute failed: array: reserve(): no memory
> > > > ERROR SyncExecQueueDispatcher Uncaught exception while queuing
> > > > events into main thread
> > > > Row 2152 is empty.
> > > > Best, Hinnerk
> > > > On Jan 30, 10:47 pm, Mikhail Rybalkin <rybal...@ggasoftware.com>
> > > > wrote:
> > > > > Hello Hinnerk,
> > > > > Thank you for informing us that the nodes has some instability
> > > > > problem! We should fix them before releasing the stable version. It
> > > > > would be great if you could provide us some example. Also could you
> > > > > tell how much RAM do you have on your computer, and how many molecules
> > > > > are being proceeded?
> > > > > Mikhail
> > > > > On Jan 31, 1:36 am, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > nevertheless. murcko and scaffold finder are not stable and results in
> > > > > > either crash (Vusial C++ runtime error) or lots of errors in log (both
> > > > > > nodes with write tables to disc, 32bit, win7). I try to figure out at
> > > > > > least one problematic structure.
> > > > > > On Jan 30, 10:21 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > > Sorry, my fault. It was again the "write tables to disc" issue. I have
> > > > > > > forgotten this.
> > > > > > > On Jan 30, 10:14 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > > > Hi,
> > > > > > > > after installation of latest nodes (Indigo KNIME integration
> > > > > > > > 1.1.0.201201291733) I could not load my sample any more. It always
> > > > > > > > terminates with a Visual C++ runtime error and takes knime with it
> > > > > > > > (either molecule to indigo and query molecule to indigo).
> > > > > > > > Best, Hinnerk
> > > > > > > > PS: Many thx for the C example of the transformation.
We have uploaded a new KNIME nodes version. The new version is much
more stable to huge data sets. Also, some runtime crashes were fixed.
Could you download the new version from the nightly builds. It would
be very helpful for us to know about the new behaviour with huge data
inputs. Please let us know if any exceptions are raised.
Hi
I can isolated the problem. There are 2. First, the node "molecule to
indigo" does not work correct with moil-files any more. With "Indigo
KNIME integration 1.1.0.201111071836" (knime 64bit, 2.5.0, win7) I can
import rows with a molfile. Now with the latest version, I always get
"missing cell", although the renderer can render the rows (I see a
picture in SDFreader). Furthermore with the mentioned version I can
process attached entry. This means, the entry shows up in invalid
molecules, which is not the best behavior, but OK. Now the entry leads
to a crash of the node, that means no processing of any row is
possible. Furthermore any processing of a missing cell with an indigo
node can have strange side effects.
I hope, this helps to identify some of the problems.
Best, Hinnerk
> We have uploaded a new KNIME nodes version. The new version is much
> more stable to huge data sets. Also, some runtime crashes were fixed.
> Could you download the new version from the nightly builds. It would
> be very helpful for us to know about the new behaviour with huge data
> inputs. Please let us know if any exceptions are raised.
Thank you for your attention. I have reproduced the bug. It seems like
changes have not been so painless, as we would like to. Now the
serialization errors reveal. I think the issue was not noticed in the
old version, because cells were saved only if memory ended (or if the
"write tables to disc" flag is specified). Anyway, I have fixed the
crashes. Now, a verification for input structures is applied. We have
uploaded the new version, and it will be available soon in nightly
builds.
Could you also specify the nodes, where missing cells lead to the
"strange side effects".
Hi Alexander,
reading mol files with Molecule to Indigo is now OK. When I try to
detect Murcko scaffolds, I immediately get "ERROR Murcko Scaffold
Execute failed: pool: access to unused element 1".
When I convert the mol files to smiles with ChemAxon MolConvert-Node,
import the smiles to Indigo, and detect Murcko, it works.
If i try to convert mol to smiles wit Indigo via import / export i get
a runtime exception.
Trying the MCS-node with smiles as sources leads to "ERROR
IndigoScaffoldFinderNodeModel internal error while launching extract
scaffold: array: reserve(): no memory
"
Best, Hinnerk
On Feb 21, 4:08 pm, Savelyev Alexander <asavel...@ggasoftware.com>
wrote:
> Thank you for your attention. I have reproduced the bug. It seems like
> changes have not been so painless, as we would like to. Now the
> serialization errors reveal. I think the issue was not noticed in the
> old version, because cells were saved only if memory ended (or if the
> "write tables to disc" flag is specified). Anyway, I have fixed the
> crashes. Now, a verification for input structures is applied. We have
> uploaded the new version, and it will be available soon in nightly
> builds.
> Could you also specify the nodes, where missing cells lead to the
> "strange side effects".
Dear Hinnerk,
Many thanks for the given examples. We have fixed the molecule loading
errors. New features were added to the KNIME nodes and to the internal
format for avoiding such crashes. The new version is available in the
nightly builds (1.1.0.201202272004)
As for the last issues
- Murcko scaffold: could you give an example molecules?
- MCS: how many molecules are processed?. Could you also specify the
memory parameters (JVM settings and nodes memory policy)
Hi Alexander,
many thx for the quick fix of the valence problem. This seems to work
now (I do not get any analog errors any more).
Here is a mol, which causes the problem with murcko in the worklfow,
sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko Scaffold
Execute failed: pool: access to unused element 1).
With MCS. Maybe my set was to large. :-) I will check this later.
Best, Hinnerk
--------------------
test
19 19 0 0 0 0 0 0 0 0999 V2000
4.0950 2.2596 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
3.2858 2.8467 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7859 1.3083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5951 3.1258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9242 1.7004 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
2.4766 2.2596 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
2.7857 1.3083 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.0950 3.9920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.5954 3.1258 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.5981 0.7552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8384 1.2943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9765 3.1258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5644 1.8525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1975 0.4991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5951 4.8582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4766 3.9920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.9772 3.1258 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9775 4.8582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4093 2.5746 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 6 0 0 0
1 5 1 0 0 0 0
2 6 1 0 0 0 0
3 7 1 0 0 0 0
4 8 1 0 0 0 0
4 9 2 0 0 0 0
5 10 1 0 0 0 0
5 11 1 0 0 0 0
5 19 1 1 0 0 0
6 7 1 0 0 0 0
6 12 1 0 0 0 0
6 13 1 1 0 0 0
7 14 1 1 0 0 0
8 15 1 0 0 0 0
12 16 1 0 0 0 0
12 17 2 0 0 0 0
16 18 1 0 0 0 0
M STY 3 1 DAT 2 DAT 3 DAT
M SAL 1 1 1
M SDT 1 MDLBG_STEREO_KEY F
M SDD 1 3.5950 1.7996 DA ALL 1 5
M SED 1 R
M SAL 2 1 5
M SDT 2 MDLBG_STEREO_KEY F
M SDD 2 4.4242 1.2404 DA ALL 1 5
M SED 2 S
M SAL 3 1 6
M SDT 3 MDLBG_STEREO_KEY F
M SDD 3 1.9766 1.7996 DA ALL 1 5
M SED 3 R
M END
$$$$
--------------------------
On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com>
wrote:
> Dear Hinnerk,
> Many thanks for the given examples. We have fixed the molecule loading
> errors. New features were added to the KNIME nodes and to the internal
> format for avoiding such crashes. The new version is available in the
> nightly builds (1.1.0.201202272004)
> As for the last issues
> - Murcko scaffold: could you give an example molecules?
> - MCS: how many molecules are processed?. Could you also specify the
> memory parameters (JVM settings and nodes memory policy)
Hi,
here the next problem. :-)
When i open a file (ReadFile node) with 10k entries
(B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and can
import them to Indigo. While exporting these structures to InChIKey,
Knime vanishes (crash wihout any error, etc). I do not know, whether
this is a Indigo problem and / or Knime problem.
Best, Hinnerk
> Hi Alexander,
> many thx for the quick fix of the valence problem. This seems to work
> now (I do not get any analog errors any more).
> Here is a mol, which causes the problem with murcko in the worklfow,
> sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko Scaffold
> Execute failed: pool: access to unused element 1).
> With MCS. Maybe my set was to large. :-) I will check this later.
> Best, Hinnerk
> On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com>
> wrote:
> > Dear Hinnerk,
> > Many thanks for the given examples. We have fixed the molecule loading
> > errors. New features were added to the KNIME nodes and to the internal
> > format for avoiding such crashes. The new version is available in the
> > nightly builds (1.1.0.201202272004)
> > As for the last issues
> > - Murcko scaffold: could you give an example molecules?
> > - MCS: how many molecules are processed?. Could you also specify the
> > memory parameters (JVM settings and nodes memory policy)
On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> Hi, > here the next problem. :-) > When i open a file (ReadFile node) with 10k entries > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and can > import them to Indigo. While exporting these structures to InChIKey, > Knime vanishes (crash wihout any error, etc). I do not know, whether > this is a Indigo problem and / or Knime problem. > Best, Hinnerk
> On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote: > > Hi Alexander, > > many thx for the quick fix of the valence problem. This seems to work > > now (I do not get any analog errors any more). > > Here is a mol, which causes the problem with murcko in the worklfow, > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko Scaffold > > Execute failed: pool: access to unused element 1). > > With MCS. Maybe my set was to large. :-) I will check this later. > > Best, Hinnerk
> > On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com> > > wrote:
> > > Dear Hinnerk, > > > Many thanks for the given examples. We have fixed the molecule loading > > > errors. New features were added to the KNIME nodes and to the internal > > > format for avoiding such crashes. The new version is available in the > > > nightly builds (1.1.0.201202272004) > > > As for the last issues > > > - Murcko scaffold: could you give an example molecules? > > > - MCS: how many molecules are processed?. Could you also specify the > > > memory parameters (JVM settings and nodes memory policy)
Hi Mikhail,
I can confirm, that with latest nodes, the smile-inchi problem does
not further crash knime. Nevertheless, the result is not as expected
(Could not convert structure with RowId='Row1': core: Indigo-InChI:
InChI generation failed: (null). Code: 2.). If this problem is somehow
caused by InChI-sources, let me know. Next week we have a meeting.
And do you have a solution for the reported murcko-problem?
Best, Hinnerk
On Mar 12, 1:27 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> We have fixed this issue in the latest nightly build. Thank you for the bug
> report!
> Best regards,
> Mikhail
> On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > Hi,
> > here the next problem. :-)
> > When i open a file (ReadFile node) with 10k entries
> > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and can
> > import them to Indigo. While exporting these structures to InChIKey,
> > Knime vanishes (crash wihout any error, etc). I do not know, whether
> > this is a Indigo problem and / or Knime problem.
> > Best, Hinnerk
> > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > Hi Alexander,
> > > many thx for the quick fix of the valence problem. This seems to work
> > > now (I do not get any analog errors any more).
> > > Here is a mol, which causes the problem with murcko in the worklfow,
> > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko Scaffold
> > > Execute failed: pool: access to unused element 1).
> > > With MCS. Maybe my set was to large. :-) I will check this later.
> > > Best, Hinnerk
> > > On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com>
> > > wrote:
> > > > Dear Hinnerk,
> > > > Many thanks for the given examples. We have fixed the molecule loading
> > > > errors. New features were added to the KNIME nodes and to the internal
> > > > format for avoiding such crashes. The new version is available in the
> > > > nightly builds (1.1.0.201202272004)
> > > > As for the last issues
> > > > - Murcko scaffold: could you give an example molecules?
> > > > - MCS: how many molecules are processed?. Could you also specify the
> > > > memory parameters (JVM settings and nodes memory policy)
I have fixed an issue with murcko problem. You can check this in the latest Indigo Knime nodes 1.1.3.
And also I have restored the error message notification as in the previous version there was a "(null)" instead of an error message. For the molecule provided it gives "Accepted unusual valence(s): C(3); Cannot process aromatic bonds. Code: 2." I will check why it is so.
Just to make clear I want to say that we do not compute a stereocenter layout in the InChI yet, but this is planned to be done soon. How is it important for your application?
On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> Hi Mikhail, > I can confirm, that with latest nodes, the smile-inchi problem does > not further crash knime. Nevertheless, the result is not as expected > (Could not convert structure with RowId='Row1': core: Indigo-InChI: > InChI generation failed: (null). Code: 2.). If this problem is somehow > caused by InChI-sources, let me know. Next week we have a meeting. > And do you have a solution for the reported murcko-problem? > Best, Hinnerk
> On Mar 12, 1:27 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote: > > Hello Hinnerk,
> > We have fixed this issue in the latest nightly build. Thank you for the > bug > > report!
> > Best regards, > > Mikhail
> > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > Hi, > > > here the next problem. :-) > > > When i open a file (ReadFile node) with 10k entries > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and can > > > import them to Indigo. While exporting these structures to InChIKey, > > > Knime vanishes (crash wihout any error, etc). I do not know, whether > > > this is a Indigo problem and / or Knime problem. > > > Best, Hinnerk
> > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote: > > > > Hi Alexander, > > > > many thx for the quick fix of the valence problem. This seems to > work > > > > now (I do not get any analog errors any more). > > > > Here is a mol, which causes the problem with murcko in the worklfow, > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko > Scaffold > > > > Execute failed: pool: access to unused element 1). > > > > With MCS. Maybe my set was to large. :-) I will check this later. > > > > Best, Hinnerk
> > > > On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com> > > > > wrote:
> > > > > Dear Hinnerk, > > > > > Many thanks for the given examples. We have fixed the molecule > loading > > > > > errors. New features were added to the KNIME nodes and to the > internal > > > > > format for avoiding such crashes. The new version is available in > the > > > > > nightly builds (1.1.0.201202272004) > > > > > As for the last issues > > > > > - Murcko scaffold: could you give an example molecules? > > > > > - MCS: how many molecules are processed?. Could you also specify > the > > > > > memory parameters (JVM settings and nodes memory policy)
Hi Mikhail,
InChI is for me not that important, since in an productive environment
I rely on the InChI binaries (comparison with other databases). I
combination with indigo (via c or knime) it is an easy way for me to
use InChI in an early stage of development. I know your limitation
with stereo and the general InChI limits (inorganic /
organometallics).
Best, Hinnerk
PS: Is the InChI dll / so OK for you, or would you prefer a java
interfaces directly provided by InChI?
On Mar 14, 8:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> I have fixed an issue with murcko problem. You can check this in the latest
> Indigo Knime nodes 1.1.3.
> And also I have restored the error message notification as in the previous
> version there was a "(null)" instead of an error message. For the molecule
> provided it gives "Accepted unusual valence(s): C(3); Cannot process
> aromatic bonds. Code: 2." I will check why it is so.
> Just to make clear I want to say that we do not compute a stereocenter
> layout in the InChI yet, but this is planned to be done soon. How is it
> important for your application?
> Best regards,
> Mikhail
> On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > Hi Mikhail,
> > I can confirm, that with latest nodes, the smile-inchi problem does
> > not further crash knime. Nevertheless, the result is not as expected
> > (Could not convert structure with RowId='Row1': core: Indigo-InChI:
> > InChI generation failed: (null). Code: 2.). If this problem is somehow
> > caused by InChI-sources, let me know. Next week we have a meeting.
> > And do you have a solution for the reported murcko-problem?
> > Best, Hinnerk
> > On Mar 12, 1:27 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> > > Hello Hinnerk,
> > > We have fixed this issue in the latest nightly build. Thank you for the
> > bug
> > > report!
> > > Best regards,
> > > Mikhail
> > > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > > Hi,
> > > > here the next problem. :-)
> > > > When i open a file (ReadFile node) with 10k entries
> > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and can
> > > > import them to Indigo. While exporting these structures to InChIKey,
> > > > Knime vanishes (crash wihout any error, etc). I do not know, whether
> > > > this is a Indigo problem and / or Knime problem.
> > > > Best, Hinnerk
> > > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > Hi Alexander,
> > > > > many thx for the quick fix of the valence problem. This seems to
> > work
> > > > > now (I do not get any analog errors any more).
> > > > > Here is a mol, which causes the problem with murcko in the worklfow,
> > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko
> > Scaffold
> > > > > Execute failed: pool: access to unused element 1).
> > > > > With MCS. Maybe my set was to large. :-) I will check this later.
> > > > > Best, Hinnerk
> > > > > On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com>
> > > > > wrote:
> > > > > > Dear Hinnerk,
> > > > > > Many thanks for the given examples. We have fixed the molecule
> > loading
> > > > > > errors. New features were added to the KNIME nodes and to the
> > internal
> > > > > > format for avoiding such crashes. The new version is available in
> > the
> > > > > > nightly builds (1.1.0.201202272004)
> > > > > > As for the last issues
> > > > > > - Murcko scaffold: could you give an example molecules?
> > > > > > - MCS: how many molecules are processed?. Could you also specify
> > the
> > > > > > memory parameters (JVM settings and nodes memory policy)
> > > > > > With best regards,
> > > > > > Alexander
> I have fixed an issue with murcko problem. You can check this in the latest
> Indigo Knime nodes 1.1.3.
> And also I have restored the error message notification as in the previous
> version there was a "(null)" instead of an error message. For the molecule
> provided it gives "Accepted unusual valence(s): C(3); Cannot process
> aromatic bonds. Code: 2." I will check why it is so.
> Just to make clear I want to say that we do not compute a stereocenter
> layout in the InChI yet, but this is planned to be done soon. How is it
> important for your application?
> Best regards,
> Mikhail
> On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > Hi Mikhail,
> > I can confirm, that with latest nodes, the smile-inchi problem does
> > not further crash knime. Nevertheless, the result is not as expected
> > (Could not convert structure with RowId='Row1': core: Indigo-InChI:
> > InChI generation failed: (null). Code: 2.). If this problem is somehow
> > caused by InChI-sources, let me know. Next week we have a meeting.
> > And do you have a solution for the reported murcko-problem?
> > Best, Hinnerk
> > On Mar 12, 1:27 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> > > Hello Hinnerk,
> > > We have fixed this issue in the latest nightly build. Thank you for the
> > bug
> > > report!
> > > Best regards,
> > > Mikhail
> > > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > > Hi,
> > > > here the next problem. :-)
> > > > When i open a file (ReadFile node) with 10k entries
> > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and can
> > > > import them to Indigo. While exporting these structures to InChIKey,
> > > > Knime vanishes (crash wihout any error, etc). I do not know, whether
> > > > this is a Indigo problem and / or Knime problem.
> > > > Best, Hinnerk
> > > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > Hi Alexander,
> > > > > many thx for the quick fix of the valence problem. This seems to
> > work
> > > > > now (I do not get any analog errors any more).
> > > > > Here is a mol, which causes the problem with murcko in the worklfow,
> > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko
> > Scaffold
> > > > > Execute failed: pool: access to unused element 1).
> > > > > With MCS. Maybe my set was to large. :-) I will check this later.
> > > > > Best, Hinnerk
> > > > > On Feb 28, 11:25 am, Savelyev Alexander <asavel...@ggasoftware.com>
> > > > > wrote:
> > > > > > Dear Hinnerk,
> > > > > > Many thanks for the given examples. We have fixed the molecule
> > loading
> > > > > > errors. New features were added to the KNIME nodes and to the
> > internal
> > > > > > format for avoiding such crashes. The new version is available in
> > the
> > > > > > nightly builds (1.1.0.201202272004)
> > > > > > As for the last issues
> > > > > > - Murcko scaffold: could you give an example molecules?
> > > > > > - MCS: how many molecules are processed?. Could you also specify
> > the
> > > > > > memory parameters (JVM settings and nodes memory policy)
> > > > > > With best regards,
> > > > > > Alexander
> PS: Is the InChI dll / so OK for you, or would you prefer a java
interfaces directly provided by InChI? We are using InChI source code to create a indigo-inchi.dll/so/dylib for all platforms, and this Indigo InChI plugin used not only in Knime via Java interface, but also it can be used in Python or C#. So we are not using dynamic libraries provided by InChI because we need to support different platforms and programming interfaces via single Indigo InChI plugin for Indigo. Am I right, that you are asking as a developer how to make InChI programming interface better? Because only now I have found that you are a member of InChI subcommittee.
On Wednesday, March 14, 2012 1:35:53 PM UTC+4, Hinnerk Rey wrote:
> Hi Mikhail, > InChI is for me not that important, since in an productive environment > I rely on the InChI binaries (comparison with other databases). I > combination with indigo (via c or knime) it is an easy way for me to > use InChI in an early stage of development. I know your limitation > with stereo and the general InChI limits (inorganic / > organometallics). > Best, Hinnerk
> PS: Is the InChI dll / so OK for you, or would you prefer a java > interfaces directly provided by InChI?
> On Mar 14, 8:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote: > > Hi Hinnerk,
> > I have fixed an issue with murcko problem. You can check this in the > latest > > Indigo Knime nodes 1.1.3.
> > And also I have restored the error message notification as in the > previous > > version there was a "(null)" instead of an error message. For the > molecule > > provided it gives "Accepted unusual valence(s): C(3); Cannot process > > aromatic bonds. Code: 2." I will check why it is so.
> > Just to make clear I want to say that we do not compute a stereocenter > > layout in the InChI yet, but this is planned to be done soon. How is it > > important for your application?
> > Best regards, > > Mikhail
> > On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > > Hi Mikhail, > > > I can confirm, that with latest nodes, the smile-inchi problem does > > > not further crash knime. Nevertheless, the result is not as expected > > > (Could not convert structure with RowId='Row1': core: Indigo-InChI: > > > InChI generation failed: (null). Code: 2.). If this problem is somehow > > > caused by InChI-sources, let me know. Next week we have a meeting. > > > And do you have a solution for the reported murcko-problem? > > > Best, Hinnerk
> > > On Mar 12, 1:27 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> > wrote: > > > > Hello Hinnerk,
> > > > We have fixed this issue in the latest nightly build. Thank you for > the > > > bug > > > > report!
> > > > Best regards, > > > > Mikhail
> > > > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > > > Hi, > > > > > here the next problem. :-) > > > > > When i open a file (ReadFile node) with 10k entries > > > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and > can > > > > > import them to Indigo. While exporting these structures to > InChIKey, > > > > > Knime vanishes (crash wihout any error, etc). I do not know, > whether > > > > > this is a Indigo problem and / or Knime problem. > > > > > Best, Hinnerk
> > > > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote: > > > > > > Hi Alexander, > > > > > > many thx for the quick fix of the valence problem. This seems to > > > work > > > > > > now (I do not get any analog errors any more). > > > > > > Here is a mol, which causes the problem with murcko in the > worklfow, > > > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko > > > Scaffold > > > > > > Execute failed: pool: access to unused element 1). > > > > > > With MCS. Maybe my set was to large. :-) I will check this > later. > > > > > > Best, Hinnerk
> > > > > > On Feb 28, 11:25 am, Savelyev Alexander < > asavel...@ggasoftware.com> > > > > > > wrote:
> > > > > > > Dear Hinnerk, > > > > > > > Many thanks for the given examples. We have fixed the molecule > > > loading > > > > > > > errors. New features were added to the KNIME nodes and to the > > > internal > > > > > > > format for avoiding such crashes. The new version is available > in > > > the > > > > > > > nightly builds (1.1.0.201202272004) > > > > > > > As for the last issues > > > > > > > - Murcko scaffold: could you give an example molecules? > > > > > > > - MCS: how many molecules are processed?. Could you also > specify > > > the > > > > > > > memory parameters (JVM settings and nodes memory policy)
> > > > > > > With best regards, > > > > > > > Alexander On Wednesday, March 14, 2012 1:35:53 PM UTC+4, Hinnerk Rey wrote:
> Hi Mikhail, > InChI is for me not that important, since in an productive environment > I rely on the InChI binaries (comparison with other databases). I > combination with indigo (via c or knime) it is an easy way for me to > use InChI in an early stage of development. I know your limitation > with stereo and the general InChI limits (inorganic / > organometallics). > Best, Hinnerk
> PS: Is the InChI dll / so OK for you, or would you prefer a java > interfaces directly provided by InChI?
> On Mar 14, 8:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote: > > Hi Hinnerk,
> > I have fixed an issue with murcko problem. You can check this in the > latest > > Indigo Knime nodes 1.1.3.
> > And also I have restored the error message notification as in the > previous > > version there was a "(null)" instead of an error message. For the > molecule > > provided it gives "Accepted unusual valence(s): C(3); Cannot process > > aromatic bonds. Code: 2." I will check why it is so.
> > Just to make clear I want to say that we do not compute a stereocenter > > layout in the InChI yet, but this is planned to be done soon. How is it > > important for your application?
> > Best regards, > > Mikhail
> > On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > > Hi Mikhail, > > > I can confirm, that with latest nodes, the smile-inchi problem does > > > not further crash knime. Nevertheless, the result is not as expected > > > (Could not convert structure with RowId='Row1': core: Indigo-InChI: > > > InChI generation failed: (null). Code: 2.). If this problem is somehow > > > caused by InChI-sources, let me know. Next week we have a
Also I have checked the SMILES B1=CB=c2cc3B=CC=c3cc12 converted into molfile with the winchi-1.exe InChI utility and it works fine. I think that there might be some problem in providing correction information about valencies from Indigo into InChI library, and I will check this.
On Wednesday, March 14, 2012 1:59:05 PM UTC+4, Hinnerk Rey wrote:
> Hi Mikhail, > just for info. Murcko is now OK. > Best, Hinnerk
> On Mar 14, 8:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote: > > Hi Hinnerk,
> > I have fixed an issue with murcko problem. You can check this in the > latest > > Indigo Knime nodes 1.1.3.
> > And also I have restored the error message notification as in the > previous > > version there was a "(null)" instead of an error message. For the > molecule > > provided it gives "Accepted unusual valence(s): C(3); Cannot process > > aromatic bonds. Code: 2." I will check why it is so.
> > Just to make clear I want to say that we do not compute a stereocenter > > layout in the InChI yet, but this is planned to be done soon. How is it > > important for your application?
> > Best regards, > > Mikhail
> > On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > > Hi Mikhail, > > > I can confirm, that with latest nodes, the smile-inchi problem does > > > not further crash knime. Nevertheless, the result is not as expected > > > (Could not convert structure with RowId='Row1': core: Indigo-InChI: > > > InChI generation failed: (null). Code: 2.). If this problem is somehow > > > caused by InChI-sources, let me know. Next week we have a meeting. > > > And do you have a solution for the reported murcko-problem? > > > Best, Hinnerk
> > > On Mar 12, 1:27 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> > wrote: > > > > Hello Hinnerk,
> > > > We have fixed this issue in the latest nightly build. Thank you for > the > > > bug > > > > report!
> > > > Best regards, > > > > Mikhail
> > > > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > > > Hi, > > > > > here the next problem. :-) > > > > > When i open a file (ReadFile node) with 10k entries > > > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and > can > > > > > import them to Indigo. While exporting these structures to > InChIKey, > > > > > Knime vanishes (crash wihout any error, etc). I do not know, > whether > > > > > this is a Indigo problem and / or Knime problem. > > > > > Best, Hinnerk
> > > > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote: > > > > > > Hi Alexander, > > > > > > many thx for the quick fix of the valence problem. This seems to > > > work > > > > > > now (I do not get any analog errors any more). > > > > > > Here is a mol, which causes the problem with murcko in the > worklfow, > > > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko > > > Scaffold > > > > > > Execute failed: pool: access to unused element 1). > > > > > > With MCS. Maybe my set was to large. :-) I will check this > later. > > > > > > Best, Hinnerk
> > > > > > On Feb 28, 11:25 am, Savelyev Alexander < > asavel...@ggasoftware.com> > > > > > > wrote:
> > > > > > > Dear Hinnerk, > > > > > > > Many thanks for the given examples. We have fixed the molecule > > > loading > > > > > > > errors. New features were added to the KNIME nodes and to the > > > internal > > > > > > > format for avoiding such crashes. The new version is available > in > > > the > > > > > > > nightly builds (1.1.0.201202272004) > > > > > > > As for the last issues > > > > > > > - Murcko scaffold: could you give an example molecules? > > > > > > > - MCS: how many molecules are processed?. Could you also > specify > > > the > > > > > > > memory parameters (JVM settings and nodes memory policy)
> > > > > > > With best regards, > > > > > > > Alexander
> Am I right, that you are asking as a developer how to make InChI
> programming interface better?
That was my question. I know, that you can access inchi via c and
languages, which support a c interface (python, .net, etc.). But in
the past, there have been the demand to support a java interface,
since various chemical information tools only support java. I know,
that there is a (slow?) inchi-jni solution, a chemaxon solution, etc.
They all have the disadvantage of not being officially supported.
Therefore the question, if you would also prefer a java interface or
if you are fine with the existing libraries.
On Mar 14, 11:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com>
wrote:
> > PS: Is the InChI dll / so OK for you, or would you prefer a java
> interfaces directly provided by InChI?
> We are using InChI source code to create a indigo-inchi.dll/so/dylib for
> all platforms, and this Indigo InChI plugin used not only in Knime via Java
> interface, but also it can be used in Python or C#. So we are not using
> dynamic libraries provided by InChI because we need to support different
> platforms and programming interfaces via single Indigo InChI plugin for
> Indigo. Am I right, that you are asking as a developer how to make InChI
> programming interface better? Because only now I have found that you are a
> member of InChI subcommittee.
> Best regards,
> Mikhail
> On Wednesday, March 14, 2012 1:35:53 PM UTC+4, Hinnerk Rey wrote:
> > Hi Mikhail,
> > InChI is for me not that important, since in an productive environment
> > I rely on the InChI binaries (comparison with other databases). I
> > combination with indigo (via c or knime) it is an easy way for me to
> > use InChI in an early stage of development. I know your limitation
> > with stereo and the general InChI limits (inorganic /
> > organometallics).
> > Best, Hinnerk
> > PS: Is the InChI dll / so OK for you, or would you prefer a java
> > interfaces directly provided by InChI?
> > On Mar 14, 8:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:
> > > Hi Hinnerk,
> > > I have fixed an issue with murcko problem. You can check this in the
> > latest
> > > Indigo Knime nodes 1.1.3.
> > > And also I have restored the error message notification as in the
> > previous
> > > version there was a "(null)" instead of an error message. For the
> > molecule
> > > provided it gives "Accepted unusual valence(s): C(3); Cannot process
> > > aromatic bonds. Code: 2." I will check why it is so.
> > > Just to make clear I want to say that we do not compute a stereocenter
> > > layout in the InChI yet, but this is planned to be done soon. How is it
> > > important for your application?
> > > Best regards,
> > > Mikhail
> > > On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > > > Hi Mikhail,
> > > > I can confirm, that with latest nodes, the smile-inchi problem does
> > > > not further crash knime. Nevertheless, the result is not as expected
> > > > (Could not convert structure with RowId='Row1': core: Indigo-InChI:
> > > > InChI generation failed: (null). Code: 2.). If this problem is somehow
> > > > caused by InChI-sources, let me know. Next week we have a meeting.
> > > > And do you have a solution for the reported murcko-problem?
> > > > Best, Hinnerk
> > > > > We have fixed this issue in the latest nightly build. Thank you for
> > the
> > > > bug
> > > > > report!
> > > > > Best regards,
> > > > > Mikhail
> > > > > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > > > > Hi,
> > > > > > here the next problem. :-)
> > > > > > When i open a file (ReadFile node) with 10k entries
> > > > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles and
> > can
> > > > > > import them to Indigo. While exporting these structures to
> > InChIKey,
> > > > > > Knime vanishes (crash wihout any error, etc). I do not know,
> > whether
> > > > > > this is a Indigo problem and / or Knime problem.
> > > > > > Best, Hinnerk
> > > > > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> wrote:
> > > > > > > Hi Alexander,
> > > > > > > many thx for the quick fix of the valence problem. This seems to
> > > > work
> > > > > > > now (I do not get any analog errors any more).
> > > > > > > Here is a mol, which causes the problem with murcko in the
> > worklfow,
> > > > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR Murcko
> > > > Scaffold
> > > > > > > Execute failed: pool: access to unused element 1).
> > > > > > > With MCS. Maybe my set was to large. :-) I will check this
> > later.
> > > > > > > Best, Hinnerk
> > > > > > > On Feb 28, 11:25 am, Savelyev Alexander <
> > asavel...@ggasoftware.com>
> > > > > > > wrote:
> > > > > > > > Dear Hinnerk,
> > > > > > > > Many thanks for the given examples. We have fixed the molecule
> > > > loading
> > > > > > > > errors. New features were added to the KNIME nodes and to the
> > > > internal
> > > > > > > > format for avoiding such crashes. The new version is available
> > in
> > > > the
> > > > > > > > nightly builds (1.1.0.201202272004)
> > > > > > > > As for the last issues
> > > > > > > > - Murcko scaffold: could you give an example molecules?
> > > > > > > > - MCS: how many molecules are processed?. Could you also
> > specify
> > > > the
> > > > > > > > memory parameters (JVM settings and nodes memory policy)
> > > > > > > > With best regards,
> > > > > > > > Alexander
> On Wednesday, March 14, 2012 1:35:53 PM UTC+4, Hinnerk Rey wrote:
> > Hi Mikhail,
> > InChI is for me not that important, since in an productive environment
> > I rely on
We are providing common interface for Indigo functionality in different languages, and so we do not need InChI Java interface. Even more it will bring to us more problems, because we cannot use InChI Java library for .NET or Python. So the short answer is that for our purpose we can use only the InChI source code. But if someone developing an application in Java then the official InChI Java library will be very helpful.
On Wednesday, March 14, 2012 3:48:01 PM UTC+4, Hinnerk Rey wrote:
> > Am I right, that you are asking as a developer how to make InChI > > programming interface better? > That was my question. I know, that you can access inchi via c and > languages, which support a c interface (python, .net, etc.). But in > the past, there have been the demand to support a java interface, > since various chemical information tools only support java. I know, > that there is a (slow?) inchi-jni solution, a chemaxon solution, etc. > They all have the disadvantage of not being officially supported. > Therefore the question, if you would also prefer a java interface or > if you are fine with the existing libraries.
> On Mar 14, 11:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> > wrote: > > Hi Hinnerk,
> > > PS: Is the InChI dll / so OK for you, or would you prefer a java
> > interfaces directly provided by InChI? > > We are using InChI source code to create a indigo-inchi.dll/so/dylib for > > all platforms, and this Indigo InChI plugin used not only in Knime via > Java > > interface, but also it can be used in Python or C#. So we are not using > > dynamic libraries provided by InChI because we need to support different > > platforms and programming interfaces via single Indigo InChI plugin for > > Indigo. Am I right, that you are asking as a developer how to make InChI > > programming interface better? Because only now I have found that you are > a > > member of InChI subcommittee.
> > Best regards, > > Mikhail
> > On Wednesday, March 14, 2012 1:35:53 PM UTC+4, Hinnerk Rey wrote:
> > > Hi Mikhail, > > > InChI is for me not that important, since in an productive environment > > > I rely on the InChI binaries (comparison with other databases). I > > > combination with indigo (via c or knime) it is an easy way for me to > > > use InChI in an early stage of development. I know your limitation > > > with stereo and the general InChI limits (inorganic / > > > organometallics). > > > Best, Hinnerk
> > > PS: Is the InChI dll / so OK for you, or would you prefer a java > > > interfaces directly provided by InChI?
> > > On Mar 14, 8:00 am, Mikhail Rybalkin <rybal...@ggasoftware.com> > wrote: > > > > Hi Hinnerk,
> > > > I have fixed an issue with murcko problem. You can check this in the > > > latest > > > > Indigo Knime nodes 1.1.3.
> > > > And also I have restored the error message notification as in the > > > previous > > > > version there was a "(null)" instead of an error message. For the > > > molecule > > > > provided it gives "Accepted unusual valence(s): C(3); Cannot process > > > > aromatic bonds. Code: 2." I will check why it is so.
> > > > Just to make clear I want to say that we do not compute a > stereocenter > > > > layout in the InChI yet, but this is planned to be done soon. How is > it > > > > important for your application?
> > > > Best regards, > > > > Mikhail
> > > > On Tuesday, March 13, 2012 7:59:48 PM UTC+4, Hinnerk Rey wrote:
> > > > > Hi Mikhail, > > > > > I can confirm, that with latest nodes, the smile-inchi problem > does > > > > > not further crash knime. Nevertheless, the result is not as > expected > > > > > (Could not convert structure with RowId='Row1': core: > Indigo-InChI: > > > > > InChI generation failed: (null). Code: 2.). If this problem is > somehow > > > > > caused by InChI-sources, let me know. Next week we have a meeting. > > > > > And do you have a solution for the reported murcko-problem? > > > > > Best, Hinnerk
> > > > > > We have fixed this issue in the latest nightly build. Thank you > for > > > the > > > > > bug > > > > > > report!
> > > > > > Best regards, > > > > > > Mikhail
> > > > > > On Friday, March 2, 2012 8:10:58 PM UTC+4, Hinnerk Rey wrote:
> > > > > > > Hi, > > > > > > > here the next problem. :-) > > > > > > > When i open a file (ReadFile node) with 10k entries > > > > > > > (B1=CB=c2cc3B=CC=c3cc12 each line), i can cast them to smiles > and > > > can > > > > > > > import them to Indigo. While exporting these structures to > > > InChIKey, > > > > > > > Knime vanishes (crash wihout any error, etc). I do not know, > > > whether > > > > > > > this is a Indigo problem and / or Knime problem. > > > > > > > Best, Hinnerk
> > > > > > > On Feb 28, 10:46 pm, Hinnerk Rey <hrey2...@googlemail.com> > wrote: > > > > > > > > Hi Alexander, > > > > > > > > many thx for the quick fix of the valence problem. This > seems to > > > > > work > > > > > > > > now (I do not get any analog errors any more). > > > > > > > > Here is a mol, which causes the problem with murcko in the > > > worklfow, > > > > > > > > sdfreader, indigo2molecule, indigo-murcko (ERROR > Murcko > > > > > Scaffold > > > > > > > > Execute failed: pool: access to unused element 1). > > > > > > > > With MCS. Maybe my set was to large. :-) I will check this > > > later. > > > > > > > > Best, Hinnerk
