Re: [Rdkit-discuss] Request for Assistance: Understanding InChI to Mol Conversion Issue in RDKit
You can also cross-check with standard InChI to see if this is an RDKit issue or a more general InChI issue. To convert InChI strings (and optionally AuxInfo) to SDF format with the standard inchi-1 executable, put the InChI string and AuxInfo into a text file and convert it like this. P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>*type test.txt* InChI=1/Ca.2H AuxInfo=1/0/N:1;2;3/rA:3Ca0H0H0/rB:;;/rC:;;; P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>*inchi-1.exe /InChI2Struct /OutputSDF test.txt* InChI version 1, Software v. 1.06 (inchi-1 executable) Windows 32-bit Build (MS VS 2015) of Dec 18 2020 20:45:14 Opened log file 'test.txt.log' Opened input file 'test.txt' Opened output file 'test.txt.txt' Opened problem file 'test.txt.prb' The command line used: "inchi-1.exe /InChI2Struct /OutputSDF test.txt" Converting InChI(s) to structure(s) in MOL format Output SDfile only without stereochemical information and atom coordinates Input format: InChI (plain identifier) Output format: SDfile only (without stereochemical info and atom coordinates) Timeout per structure: 6 msec Up to 1024 atoms per structure Finished processing 1 structure: 0 errors, processing time 0:00:00.00 Elapsed walltime: 15 msec. P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit>type test.txt.txt Structure #1. InChIV10 3 0 0 0 0 0 0 0 0 0 1 V2000 0. 0. 0. Ca 0 0 0 0 15 0 0 0 0 0. 0. 0. H 0 0 0 0 15 0 0 0 0 0. 0. 0. H 0 0 0 0 15 0 0 0 0 M END P:\Projects\RInChI\INCHI-1-BIN__V1.06\windows\32bit> Cheers -- Jan On 2023-12-12 07:59, S Joshua Swamidass wrote: Perhaps provide some examples were this failure happens. Sent from Gmail Mobile On Tue, Nov 28, 2023 at 7:35 PM 李大舟 wrote: Dear RDKit Developers and Maintainers, I hope this email finds you well. My name is Dr. Dazhou Li, and I am a researcher working on the development of a tool for extracting chemical compound structures recognized by OCR (Optical Character Recognition) technology. I have been using the RDKit library for a crucial step in this process, specifically the rdkit.Chem.inchi.MolFromInchi() function, to convert InChI-format strings into Mol format representations. Firstly, I would like to express my gratitude for the excellent work you have done in developing and maintaining the RDKit library, which has been an invaluable resource in my research. The library has consistently delivered high-quality results in various aspects of chemical informatics, and I appreciate your dedication to its development. However, I have encountered a specific issue with the rdkit.Chem.inchi.MolFromInchi() function that I hope you can help me understand and resolve. When attempting to convert InChI-format strings generated by my tool, some of them fail with an error message reporting "NaN." Since the rdkit.Chem.inchi.MolFromInchi() function calls C++ code, I am unable to directly inspect its execution or source code to diagnose the issue. My primary request is for assistance in understanding the internal workings of the rdkit.Chem.inchi.MolFromInchi() function, specifically the checking process or generation step that leads to the "NaN" error when certain InChI-format strings are processed. It is crucial for my research to determine at which point in the execution of this function my generated InChI-formatted strings are considered unreasonable, as this information will help me refine my tool's output to be compatible with RDKit. I understand that the RDKit library is a complex and comprehensive toolkit, and I appreciate the complexity involved in diagnosing such issues. However, any insights or guidance you can provide regarding the problematic cases and the internal processes of the rdkit.Chem.inchi.MolFromInchi() function would be immensely valuable to me and would help me ensure the compatibility of my tool with RDKit. If possible, I would be grateful for access to relevant documentation or insights into the specific error conditions that may lead to the "NaN" result. Additionally, any suggestions or best practices for generating InChI-format strings that are more likely to be successfully processed by RDKit would be greatly appreciated. Thank you for your time and consideration. I look forward to your response and hope that we can collaborate to resolve this issue and enhance the compatibility of my tool with the RDKit library. Please feel free to reach out to me if you require any additional information or if there are specific details about my tool or the InChI-format strings that would aid in diagnosing the issue. Best regards, Dr. Dazhou Li Shenyang University of Chemical Technology
Re: [Rdkit-discuss] SDMolSupplier warning 2023.9.2
> I could not figure out how Rdkit is guessing it as 2D structure, as there is no such information in SDF. Ah, but there is, just a little hidden :-). The source-and-timestamp line of each molfile in the SDF contains that information. The line is the second line of the molfile and you can find the 2D/3D tag as the last two characters of that line. An example: :MOLFILE_BEGINS: Mol2Comp0618061807*2D* 1 0 0 0 0 0 0 0 0 0999 V2000 10.2967 -1.5283 0. Ar 0 0 0 0 0 0 0 0 0 0 0 0 M END :MOLFILE_ENDS: Cheers -- Jan On 2023-12-13 03:39, Mandar Kulkarni wrote: Hello, I am using RDKit 2023.9.2's SDMolSupplier to read docked SDF files (V2000 formats, suppl = Chem.SDMolSupplier(sdf_file);) and getting a warning as: Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. I could not figure out how Rdkit is guessing it as 2D structure, as there is no such information in SDF. Is there any more information need to provide SDMolSupplier to make it understand it's a 3D molecule? I kindly look forward to hearing to suggestions. TIhanks in advance, Mandar Kulkarni smime.p7s Description: S/MIME Cryptographic Signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] mol_from_ctab doesn't preserve coordinates
Hi Sharang (adding the list as I missed reply-all previously),
Glad to hear that RDKit does what it is supposed to.
I am unfortunately not familiar with how Datawarrior processes
molecules, so I don't know if it does its own layout. To remove RDKit
from the equation - if you can feed Datawarrior a molfile directly from
disk, you can see if Datawarrior preserves the layout of the molfile or not.
Cheers
-- Jan
On 2020-05-09 16:32, Sharang Phatak wrote:
Hi Jan,
Thank you for your message. I did go back and check with mol_to_ctab
and found out the coordinates are indeed identical. I am using
Datawarrior to visualize these structures using Datawarrior's native
SQL integration tool. The structures then are displayed a bit
differently, flipped / rotated within this tool. Perhaps it's a
different issue unrelated to RDKit. If you've experienced such issues
and share what you did to overcome them, it would be much appreciated.
Cheers,
Sharang
On Thu, May 7, 2020 at 3:22 AM Jan Holst Jensen <mailto:j...@biochemfusion.com>> wrote:
Hi Sharang,
A very old version of RDKit ?
When I use your form of calling mol_to_ctab() it does preserve
coordinates for me.
select mol_to_ctab(mol_from_ctab('
4 3 0 0 0 0 0 0 1 0999 V2000
5. 5. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
5. 4. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
6. 3. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
4. 3. 0. O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
M END
'::cstring, true));
RDKit 3D
4 3 0 0 0 0 0 0 0 0999 V2000
5. 5. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
5. 4. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
6. 3. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
4. 3. 0. O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1
2 3 1 0
2 4 1 0
M END
If I leave out the second optional boolean parameter, which
defaults to
false, the coordinates are re-generated by RDKit.
select mol_to_ctab(mol_from_ctab('
4 3 0 0 0 0 0 0 1 0999 V2000
5. 5. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
5. 4. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
6. 3. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
4. 3. 0. O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
M END
'::cstring));
RDKit 2D
4 3 0 0 0 0 0 0 0 0999 V2000
0. 0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0. C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 2.2500 0. O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 6
2 3 1 0
2 4 1 0
M END
This is on a fairly old RDKit 2016_09_4 on Postgres 9.6. Earlier
versions would ignore the second parameter - that was fixed around
the
2016_09 release if I recall correctly.
Cheers
-- Jan Holst Jensen
On 2020-05-07 00:21, Sharang Phatak wrote:
> Hi,
>
> I am following the documentation for postgres / rdkit. I have a
table
> with valid molfiles as confirmed from is_valid_ctab(). I am then
> trying to insert into a table 'mols' using
> mol_from_ctab(molfile::cstring,true).
>
> However, the coordinates are not preserved. Is there something I am
> missing?
>
> Thank you,
> Sharang
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Re: [Rdkit-discuss] Different InChI: RDKit Knime Vs RDKit Python
Hi Christos, The differences are as far as I can see all in the /b layer of the InChI (/b = stereo parity of double bonds), so my guess is that differing 2D coordinates is the cause. Do you also see the difference if you run the output SDF back through KNIME (that is: Are the coordinates generated by SDF production different than earlier conformations used to calculate InChI ?) ? I don't know if subtle RDKit version differences between KNIME and conda could cause it - I am not familiar enough with the KNIME nodes to be able to judge that. Cheers -- Jan Holst Jensen On 2019-11-12 13:14, Christos Kannas wrote: Dear RDKiters, I'm having the following problem. I have a workflow that standardises compounds and as part of the process it generates standard InChI and InChIkey for the compound. The output is stored in an SDF. If I parse the SDF to a dataframe in jupyter notebook, then use the mol object to generate standard inchi, for a small number of compounds the new standard InChI is slightly different than the one generated in Knime environment. Environments Details: - RDKit Knime Nodes: 3.8.0v201906261723 - RDKit Python (conda): 2018.09.3, 2019.03.4, 2019.09.1 See image: https://imgur.com/a/EnYoHWG Best, Christos Christos Kannas Scientific Software Developer (Cheminformatics) smime.p7s Description: S/MIME Cryptographic Signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Question on chirality
Hi Navid,
I am not familiar with the paper you mention, but I believe that the
problem is caused by non-isomeric input SMILES.
Below is an Alanine read in from molfile, with coordinates. It has a
chiral center with "S" configuration. When you output it as non-isomeric
SMILES and read it back in, the chiral information is lost because the
molecule no longer has a conformation:
>>> mol = Chem.MolFromMolBlock("""
... BIOCHEMF09131911262D
...
... 7 6 0 0 1 0 0 0 0 0999 V2000
... 0. 0. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
... 0.7145 0.4125 0. C 0 0 0 0 0 0 0 0 0 0 0 0
... 1.4290 0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
... 1.4209 -0.8208 0. O 0 0 0 0 0 0 0 0 0 0 0 0
... 0.7084 1.2417 0. C 0 0 0 0 0 0 0 0 0 0 0 0
... -1. 0. 0. H 0 0 0 0 0 0 0 0 0 0 0 0
... 2.4290 0. 0. O 0 0 0 0 0 0 0 0 0 0 0 0
... 2 3 1 0 0 0 0
... 1 2 1 0 0 0 0
... 3 4 2 0 0 0 0
... 2 5 1 1 0 0 0
... 1 6 1 0 0 0 0
... 3 7 1 0 0 0 0
... M END
... """)
>>> Chem.AssignAtomChiralTagsFromStructure(mol)
>>> Chem.FindMolChiralCenters(mol)
[(1, 'S')]
>>> Chem.MolToSmiles(mol)
'CC(N)C(=O)O'
>>> mol = Chem.MolFromSmiles("CC(N)C(=O)O")
>>> Chem.AssignAtomChiralTagsFromStructure(mol)
>>> Chem.FindMolChiralCenters(mol)
[]
>>>
You can generate a conformation that produces chiral information by 3D
embedding the molecule.
>>> from rdkit.Chem import AllChem
>>> AllChem.EmbedMolecule(mol)
0
>>> Chem.AssignAtomChiralTagsFromStructure(mol)
>>> Chem.FindMolChiralCenters(mol)
[(1, 'S')]
>>>
Another way would be if you can get isomeric SMILES as input. Then the
chiral information is right there.
>>> Chem.MolToSmiles(mol, isomericSmiles = True)
'C[C*@*H](N)C(=O)O'
>>> mol = Chem.MolFromSmiles("C[C@H](N)C(=O)O")
>>> Chem.FindMolChiralCenters(mol)
[(1, 'S')]
>>>
Cheers
-- Jan Holst Jensen
On 2019-09-12 04:44, Navid Shervani-Tabar wrote:
Hello,
In the paper: "Graph Networks as a Universal Machine Learning
Framework for Molecules and Crystals", authors introduce chirality as
an atom feature input to analyze QM9 dataset. I was trying to recreate
this atom feature as following
> Chirality: (categorical) R, S, or not a Chiral center (one-hot encoded).
The code I used is:
from chainer_chemistry import datasets
from chainer_chemistry.dataset.preprocessors.ggnn_preprocessor
import GGNNPreprocessor
from rdkit import Chem
import numpy as np
dataset, dataset_smiles = datasets.get_qm9(GGNNPreprocessor(),
return_smiles=True)
for i in range(len(dataset_smiles)):
mol = Chem.MolFromSmiles(dataset_smiles[i])
Chem.AssignAtomChiralTagsFromStructure(mol)
chiral_cc = Chem.FindMolChiralCenters(mol)
if not len(chiral_cc) == 0:
print(chiral_cc)
The output shows no Chiral centers for this dataset. When I use
`includeUnassigned=True`, code gives a list of tuples, but instead of
"R/S", I get "?". I was wondering if there is a mistake in my
implementation. If this is expected, any thoughts on how chirality was
assigned in the above paper? Thanks.
Sincerely,
Navid
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Re: [Rdkit-discuss] Generating .rxn and/or .rdf fiiles from reaction smiles
Hi Markus,
You can generate the RXN file output from the rxn object via
ReactionToRxnBlock, like this Python code:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> rxn = AllChem.ReactionFromSmarts('CC(=O)O.OCC>>CC(=O)OCC')
>>> AllChem.ReactionToRxnBlock(rxn)
'$RXN\n\n RDKit\n\n 2 1\n$MOL\n\n RDKit \n\n 4 3 0 0
0 0 0 0 0 0999 V2000\n 0. 0. 0. C 0 0 0
0 0 0 0 0 0 0 0 0\n 0. 0. 0. C 0 0 0
0 0 0 0 0 0 0 0 0\n 0. 0. 0. O 0 0
0 0 0 0 0 0 0 0 0 0\n 0. 0. 0. O 0
0 0 0 0 0 0 0 0 0 0 0\n 1 2 6 0\n 2 3 2 0\n 2 4
6 0\nM END\n$MOL\n\n RDKit \n\n 3 2 0 0 0 0 0
0 0 0999 V2000\n 0. 0. 0. O 0 0 0 0 0
0 0 0 0 0 0 0\n 0. 0. 0. C 0 0 0 0
0 0 0 0 0 0 0 0\n 0. 0. 0. C 0 0 0 0
0 0 0 0 0 0 0 0\n 1 2 6 0\n 2 3 6 0\nM
END\n$MOL\n\n RDKit \n\n 6 5 0 0 0 0 0 0 0 0999
V2000\n 0. 0. 0. C 0 0 0 0 0 0 0 0 0 0
0 0\n 0. 0. 0. C 0 0 0 0 0 0 0 0 0 0
0 0\n 0. 0. 0. O 0 0 0 0 0 0 0 0 0
0 0 0\n 0. 0. 0. O 0 0 0 0 0 0 0 0
0 0 0 0\n 0. 0. 0. C 0 0 0 0 0 0 0
0 0 0 0 0\n 0. 0. 0. C 0 0 0 0 0 0 0
0 0 0 0 0\n 1 2 6 0\n 2 3 2 0\n 2 4 6 0\n 4 5 6
0\n 5 6 6 0\nM END\n'
>>>
Writing an RDF file is quite like writing an SD file, except that the
molfile entry is replaced with an RXN file entry. The syntax for data
fields is a bit different too. Data fields can be used to describe
agents, conditions, etc. but there is no fixed vocabulary (that I know
of) for e.g. specifying "this is an agent". Hence, exchanging and
parsing RDF files can be ... interesting.
Cheers
-- Jan Holst Jensen
On 2019-09-03 11:59, Markus Grimm via Rdkit-discuss wrote:
Dear all,
I'm trying to generate .rxn files or one single .rdf file from a csv
file where I have a bunch of reactions smiles stored.
I know how to instantiate a rxn object but I no idea how to safe this
to several .rxn files or a RDF file.
I already asked this question last Friday but unfortunately I did not
receive any answer. So I'm wondering is it even possible?
Thank you very much for your support.
Best regards,
Markus
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Re: [Rdkit-discuss] The RDKit database cartridge install problem
On 2019-02-05 20:38, tech tech wrote: Hi, all, I tried to install the cartridge for Postgres. I am using ubuntu 18.04 and postgres 9.6 However, when I typed this commond: /home/hat/anaconda3/envs/my-rdkit-env/bin/initdb -D /var/www/rdkit I saw following errors. I don't know how to fix it. Does anyone have a correct input file to init the database? Thanks Tom The files belonging to this database system will be owned by user "hat". [...] performing post-bootstrap initialization ... FATAL: column pol.polpermissive does not exist at character 169 STATEMENT: CREATE VIEW pg_policies AS SELECT N.nspname AS schemaname, C.relname AS tablename, [...] FROM pg_catalog.pg_policy pol JOIN pg_catalog.pg_class C ON (C.oid = pol.polrelid) LEFT JOIN pg_catalog.pg_namespace N ON (N.oid = C.relnamespace); child process exited with exit code 1 initdb: removing contents of data directory "/var/www/rdkit" Hi Tom, The polpermissive column is not available in Postgres 9.6. On a Postgres 9.6 database the pg_catalog.pg_policies table has the columns polname polrelid polcmd polroles polqual polwithcheck and on a Postgres 11.1 database the table has these columns: polname polrelid polcmd *polpermissive* polroles polqual polwithcheck Don't know if you have the option of using a newer version of Postgres ? Cheers -- Jan smime.p7s Description: S/MIME Cryptographic Signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] C++ - how do I create a copy of an RWMol ?
Hi,
I have an issue with the cartridge - mol_to_svg() changes the input
molecule so I want to make MolGetSVG() to work on a copy of the input
molecule instead.
In Code/PgSQL/rdkit/adapter.cpp:
extern "C" char *MolGetSVG(CROMol i, unsigned int w, unsigned int h,
const char *legend, const char *params) {
// This is the original code that makes a read-write
// "im" that is passed to the drawing routines where
// it gets changed.
RWMol *im = (RWMol *)i;
// SVG routines need an RWMol since they change the
// molecule as they prepare it for drawing. We don't
// want a plain SQL function (mol_to_svg) to have
// unexpected side effects, so take a copy and render
// (and change) that instead.
RWMol *input_mol = (RWMol *)i;
RWMol input_copy = *input_mol;
RWMol *im = _copy;
...
My construction of the "input_copy" object is obviously wrong, 'cause
the database crashes. What is the correct way of copying an RWMol object ?
Cheers
-- Jan
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Re: [Rdkit-discuss] number of significant digits in molblock?
Hi Michal,
V2000 format is restricted by its specification to fixed format with 4
decimals. V3000 output is not restricted to a fixed format, but the
current code still rounds it in practice as seen below.
To get extra precision you could change the formatting of x, y, and z
coordinate output in Code/GraphMol/FileParsers/MolFileWriter.cpp,
function GetV3000MolFileAtomLine(), look for the
ss << " " << x << " " << y << " " << z;
line. Adding extra digits to the X, Y, and Z coordinates *should* not
cause issues for compliant V3000 readers.
Cheers
-- Jan
>>> import rdkit
>>> from rdkit import Chem
>>> from Chem import AllChem
>>> m = Chem.MolFromSmiles('CC')
>>> AllChem.Compute2DCoords(m)
0
>>> m.GetConformer(0).SetAtomPosition(0,
rdkit.Geometry.Point3D(0.123456789, 0.2, 0.3))
>>> print(Chem.MolToMolBlock(m))
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.1235 0.2000 0.3000 C 0 0 0 0 0 0 0 0 0 0 0 0
<== 4 decimal digits
0.7500 -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
>>> print(Chem.MolToMolBlock(m, forceV3000=True))
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 2 1 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.123457 0.2 0.3 0 <== 6 decimal digits
M V30 2 C 0.75 -5.55112e-17 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 END BOND
M V30 END CTAB
M END
>>>
On 2018-10-05 11:42, Michal Krompiec wrote:
Hello,
Is it possible to control the number of significant digits of XYZ
coordinates? I am modifying coordinates of my molecules
using SetAtomPosition but when I save them into an SDF it seems that
the precision is limited to 4 digits after the decimal point (I'd like
10 instead...).
Best wishes,
Michal
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Re: [Rdkit-discuss] Strange behaviour of the substructure search
On 2017-11-30 11:45, Lionel Colliandre wrote: 1- for polymers (brackets with n label) , the ctab is not considered as valid and the mol_from_ctab function is not working (example of a ctab at the end of the email). I think that it is the "M STY 1 1 SRU" block that is problematic. To the best of my knowledge no cartridge is able to search directly a polymer but I would like simply to be able to search the monomeric motif. Even with big warning, is there a way to read and search such polymeric molecules with RDKit? Hi Lionel, I have the exact same challenge in a molecule database. We decided to go with a convention that end users will register polymers with exactly 3 repeats so you can do sensible SSS searches. In the registered polymers we use MUL (multiple-group) S-group brackets instead of the SRU bracket type which RDKit (most sensibly) refuses to process. We have various checks in place that ensure that polymers get registered this way. The checks are implemented through regexp expressions - I know, processing molfiles via regexp parsing is crazy :-) but it works OK. If you want a simple dirty hack you can try to process the polymers this way: 1) Replace "SRU" S-group types with "MUL". 2) Change the "n" label to "1". That will change your example molfile into: " Mrv1718011301710072D 4 3 0 0 0 0 999 V2000 -6.3839 2.3661 0. O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7428 1.8469 0. C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9726 2.1425 0. O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3314 1.6233 0. H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 M STY 1 1 *MUL* M SCN 1 1 HT M SAL 1 2 2 3 M SDI 1 4 -4.3971 2.3134 -5.0201 1.5441 M SDI 1 4 -6.3183 1.6760 -5.6953 2.4454 M SBL 1 2 1 3 M SMT 1 *1* M END " which RDKit will process and you get the single monomer unit. Cheers -- Jan Holst Jensen -- 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] Masking groups as atoms in RDKit
Hi Kovas,
Greg has precisely pointed out the major problem of collapsing fragments
into single atoms: Searching and comparing structures.
With that warning in mind: I use pseudo atoms (e.g. "Ala", "Arg",...) to
good effect to represent amino acids in peptides and proteins. My
colleague Esben Bjerrum has done custom builds of RDKit where the
atomic_data.cpp file was changed to add the 22 natural amino acids.
The rest of RDKit handles the new atoms surprisingly well. The new atoms
can also be used in SMARTS queries as long as you reference them by
atomic number (and Greg's caution about searching applies doubly in that
case).
So, yes, that's one way of doing it. Just don't expect anyone else to be
able to interpret your molfiles reliably :-).
You write that you want to mask away the macromolecule part since you
are not going to interact with it. In that case it sounds like it is OK
to throw away the underlying chemistry of the macromolecule and
substitute a label for depiction. I would then go with Greg's suggestion
to use dummy atoms and labels, e.g.
import rdkit
from rdkit import Chem
from rdkit.Chem import Draw
m = Chem.MolFromSmiles('CC[*:1]')
# Put a molfile label on the star atom.
m.GetAtoms()[2].SetProp("molFileAlias", "Macromol-section")
print(Chem.MolToMolBlock(m))
PRINT OUTPUT:
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0. 0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
0. 0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
0. 0. 0. R 0 0 0 0 0 1 0 0 0 1 0 0
1 2 1 0
2 3 1 0
A 3
Macromol-section
M END
If you paste that molfile into MarvinSketch you see this (different
tools will show labels in different ways):
I am very much a molfile guy, so I don't know if labels can be carried
over to RDKit SMILES strings.
Cheers
-- Jan
On 2017-09-28 08:00, Kovas Palunas wrote:
The way i was thinking about it, the smarts of OCC would not match the
O[but] because [but] is a totally new atom that is not related to
carbon at all. This doesn't really make sense in this example, but it
does (i think) for most of my purposes (where i want to mask away a
biological macromolecule that i do not want to interact with).
There are probably still edge cases i'm not seeing... but maybe it's
still worth a try? I saw there was a periodic table module in RDKit.
Is it possible to add these atoms there?
- Kovas
From: Greg Landrum
Sent: Wednesday, September 27, 10:13 PM
Subject: Re: [Rdkit-discuss] Masking groups as atoms in RDKit
To: Kovas Palunas
Cc: rdkit-discuss@lists.sourceforge.net
I'm afraid that there's likely to be rather a lot of devil hiding in
the details (as is so often the case).
A simple example of one problem: let's take your [But]O case. Suppose
you do a substructure search for the molecule defined by the SMARTS
"OCC". Does that match "[But]O"? What does it return when I ask for
the substructure matches (this function, if you aren't familiar with
it, returns the indices of the matching atoms)? What about the SMARTS
"CC"?
One solution to this that works with substructure searching is to have
the molecule contain all the atoms - "O" in your example - but to
have the four C atoms marked as a group so that drawings of the
molecule display "[But]O". Supporting this type of functionality is on
the To Do list (it's part of supporting S Groups from Mol files).
If you just want to indicate that there is a [But] group there but not
really do anything with the group's structure, there's are probably
already ways to handle this using dummy atoms and custom labels.
-greg
On Wed, Sep 27, 2017 at 9:26 PM, Kovas Palunas
> wrote:
Ideally, I'd like to treat these pseudoatoms as similarly to normal
atoms as possible. I would mostly want to use them for substructure
matching, running reactions, and also display purposes. Also, basic
atom queries, such as getting a mapping number or a atom symbol.
I was thinking that maybe this could be done by just defining the CoA
atom type (for example) just as the carbon or oxygen atom types are
defined (setting atomic weight, valences, etc.).
Does this make sense?
- Kovas
*From:*Greg Landrum>
*Sent:*Wednesday, September 27, 2017 2:27:04 AM
*To:*Kovas Palunas
*Cc:*rdkit
-disc...@lists.sourceforge.net
*Subject:*Re: [Rdkit-discuss] Masking groups as atoms in RDKit
Where would you want to use this?
Is it for depiction (i.e. drawing molecules) or something else?
-greg
On Tue, Sep 26, 2017 at 10:12 PM, Kovas Palunas
> wrote:
Hi all,
Has anyone tried implementing or using a group to atom
[Rdkit-discuss] RDKit for Excel - Python3-ready.
Hi RDKitters, I was able to use the RDKit Hackathon to work on getting RDKit for Excel ready for Python 3. The current version now supports both Python 2 and 3. The documentation has also been extended so I hope that it is now relatively straightforward to get it up and running. https://github.com/janholstjensen/rdkit4excel <https://github.com/janholstjensen/rdkit4excel> Cheers -- Jan Holst Jensen -- 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] Announce: RDKit for Excel.
Hi Curt, The add-in is based on COM automation services, so it is Windows-only to the best of my knowledge. We chose to implement it as a COM service since the Python code was then extremely simple and very easy to extend. I don't have access to a Mac so I am having a hard time figuring out if MS Office on Mac implements enough of the COM subsystem to support COM automation servers. It might be that both Mac and Windows could be supported if the add-in was written in C++ as an XLL. My gut feeling is that it would then be harder to extend dynamically, but I could be wrong. One thing I do know is that it would be more complex to write. To support both Windows and Mac you can also take the approach that xlwings has taken where a DLL is loaded by VBA code and talks to the Python code: https://www.xlwings.org/ We initially tried to base our add-in on xlwings but got into trouble sharing Excel worksheets with User Defined Functions. The UDFs in xlwings are made available to Excel through VBA auto-generated from the Python code. Smart concept, but gets us into trouble using UDFs in sheets that are passed around or copied. Python 3 - yes, we should go there. If the COM support that the add-in relies on is available in Python 3 it should be straightforward (famous last words :-) ). Hopefully I will have some time to check this out over the summer. Cheers -- Jan On 2017-06-19 18:40, Curt Fischer wrote: This is great! Thanks Jan. I haven't tried it yet, but based on the GitHub README it looks like this is only for Excel on a Windows box. Is that right, or can Mac versions of Excel also work? And since it's come up on the mailing list recently, is there a plan to expand to/move to Python 3 at any point soon? Curt On Sun, Jun 18, 2017 at 11:06 AM, Jan Holst Jensen <j...@biochemfusion.com <mailto:j...@biochemfusion.com>> wrote: Hi RDKitters, I am happy to announce an open source Excel add-in that gives easy access to the RDKit Python API. The add-in is BSD-licensed like RDKit. https://github.com/janholstjensen/rdkit4excel <https://github.com/janholstjensen/rdkit4excel> Screenshot of the add-in running in Excel 2016 (note: molecule rendering requires additional 3rd party software): The add-in is easily extendable via pure Python scripting. A new Excel function is added by adding a function to the CRDKitXL Python class and annotating the new function's input/output parameter types through structured comments. For example, adding an "rdkit_SmilesToMolBlock()" function that has a single "smiles" string input parameter: #RDKITXL: in:smiles:str, out:str def rdkit_SmilesToMolBlock(self, smiles): # Python function implementation follows here... Many thanks to Esben Jannik Bjerrum who did the implementation of this first version. Cheers -- Jan Holst Jensen -- 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 <mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss <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
[Rdkit-discuss] Announce: RDKit for Excel.
Hi RDKitters, I am happy to announce an open source Excel add-in that gives easy access to the RDKit Python API. The add-in is BSD-licensed like RDKit. https://github.com/janholstjensen/rdkit4excel Screenshot of the add-in running in Excel 2016 (note: molecule rendering requires additional 3rd party software): The add-in is easily extendable via pure Python scripting. A new Excel function is added by adding a function to the CRDKitXL Python class and annotating the new function's input/output parameter types through structured comments. For example, adding an "rdkit_SmilesToMolBlock()" function that has a single "smiles" string input parameter: #RDKITXL: in:smiles:str, out:str def rdkit_SmilesToMolBlock(self, smiles): # Python function implementation follows here... Many thanks to Esben Jannik Bjerrum who did the implementation of this first version. Cheers -- Jan Holst Jensen -- 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] RDKit Windows binaries - exists ? Where ?
Hi Greg, > Using conda makes the installation a lot simpler and saves me a fair amount of time while doing the builds. Sounds like a good deal. > Is using the anaconda python distribution a problem for you? Actually not. I was concerned about its support for other packages, but it comes with pywin32 built-in so we can create COM services (think Excel...) and it does indeed make it much easier to install RDKit. Thanks for the help. Cheers -- Jan On 2017-05-05 04:48, Greg Landrum wrote: Hi Jan, I've stopped creating standalone windows binaries now that the conda packages are available. Using conda makes the installation a lot simpler and saves me a fair amount of time while doing the builds. Is using the anaconda python distribution a problem for you? On Thu, May 4, 2017 at 5:41 PM, Jan Holst Jensen <j...@biochemfusion.com <mailto:j...@biochemfusion.com>> wrote: Hi, I was trying to find Python Windows binaries for the latest RDKit release. I could find them for the older 2016_03_1 release on SourceForge but had no luck finding anything newer on SourceForge or Github. According to GitHub they should be there: https://github.com/rdkit/rdkit/tree/Release_2017_03_1 <https://github.com/rdkit/rdkit/tree/Release_2017_03_1> Under "Installation": "Windows binaries are available with each release." - but where :-) ? Cheers -- Jan -- 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
[Rdkit-discuss] RDKit Windows binaries - exists ? Where ?
Hi, I was trying to find Python Windows binaries for the latest RDKit release. I could find them for the older 2016_03_1 release on SourceForge but had no luck finding anything newer on SourceForge or Github. According to GitHub they should be there: https://github.com/rdkit/rdkit/tree/Release_2017_03_1 Under "Installation": "Windows binaries are available with each release." - but where :-) ? Cheers -- Jan -- 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] SD file read error
rceforge.net/p/rdkit/mailman/message/30036309/ In principle it should be possible to fix these errors on the fly by loading the molecules without sanitization, detect the valence issues and somehow automagically correct them, then sanitize and calculate mol weights. In this case it looks like it would be easier and faster to locate the relatively few molecules with valence errors and fix them manually. Cheers -- Jan Holst Jensen, Biochemfusion -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI support PostgreSQL cartridge
On 2016-03-03 15:23, Max Kretzschmar wrote:
Dear all,
I have a problem regarding the postgres cartridge. Everything is
working fine except the Inchi functions:
select * from mol_inchi('c1c1'::mol);
mol_inchi
-
InChI not available
(1 Zeile)
The RDKit was build from source with InChI support and they are
available within my python environment. The RDKit version I use is
2014_03_01, the cartridge version is 0.72.0. Did I miss something
here? Is there a parameter to set when building the cartridge?
I appreciate any help you can provide.
Max
Hi Max,
Indeed there is a parameter. You need to modify
Code/PgSQL/rdkit/Makefile. It starts with
# -
# Variables used and default values:
# USE_INCHI enables InChI functions; requires rdkit built with inchi support:
#USE_INCHI=0
# USE_AVALON enables the avalon fingerprint; requires rdkit built with avalon
support:
#USE_AVALON=0
# USE_THREADS links against boost.system; required with non-ancient boost
versions if inchi is enabled or the rdkit is built with threadsafe SSS:
#USE_THREADS=0
# STATIC_LINK links against the static RDKit libraries:
#STATIC_LINK=1
# -
Uncomment the #USE_INCHI=0 line and change it so it reads:
USE_INCHI=1
and then rebuild and reinstall the cartridge. That should do it :-).
Cheers
-- Jan Holst Jensen
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Re: [Rdkit-discuss] RDKit Valences
On 2016-01-29 17:02, Rich Lewis wrote:
Dear all,
I tried to load a periodate from its smiles (I think these are
correct), but it failed as according to rdkit, Iodine cannot have a
valence of 7. However, it can when stabilised with oxygens (at least
from what I recall from my undergraduate course!).
In [*2**3*]: Chem.MolFromSmiles('[O-]I(=O)(=O)=O')
[15:29:04] Explicit valence for atom # 1 I, 7, is greater than permitted
In [*24*]: Chem.MolFromSmiles('OI(=O)(=O)=O')
[15:24:21] Explicit valence for atom # 1 I, 7, is greater than permitted
In [*25*]: Chem.MolFromSmiles('[H]OI(=O)(=O)=O')
[15:24:26] Explicit valence for atom # 1 I, 7, is greater than permitted
I don’t know if the file rdkit/Code/GraphMol/atomic_data.cpp is where
the valences are configured for rdkit, but in the file, I saw that the
allowed valence states are +1, +2(?) and +5 but not +7. A few of the
other elements are also similarly conservative, such as Br only
allowing +1. Should these be expanded, or is this deliberate?
Hi Rich,
The file rdkit/Code/GraphMol/atomic_data.cpp is indeed where the
valences are configured. There was a similar discussion in 2015 that
resulted in additional valence data being added to P.
http://sourceforge.net/p/rdkit/mailman/message/34131420/
You can try out the valence change locally by adding it to
atomic_data.cpp (TAB-delimited format) and rebuilding RDKit.
Cheers
-- Jan Holst Jensen
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Re: [Rdkit-discuss] molecule standardization in cartridge search
Hi Tim,
Soren (cc:ed) wrote me and asked about molvs. Thanks to Soren for
reminding that the original question was about standardization more than
calling Python code from Postgres :-).
http://molvs.readthedocs.org/en/latest/
Take a look at molvs - it's got lots of functionality that you will
need. We also use molvs as the backbone for much of our standardization.
Cheers
-- Jan
Hi Tim,
A simple getting-started example is:
CREATE FUNCTION smiles2molfile(smiles text) RETURNS text
LANGUAGE plpythonu AS $$
import rdkit
from rdkit import Chem
mol = Chem.MolFromSmiles(smiles)
return Chem.MolToMolBlock(mol)
$$;
and you can then
select smiles2molfile('CC');
and get back a molfile.
For more advanced usage it is worth taking a look at the rdchord project
that TJ has sent links to.
Cheers
-- Jan
On 2015-09-25 15:54, Tim Dudgeon wrote:
Jan,
thanks for that. I'll give it a try.
Are there any examples of writing RDKit functions and procedures for
postgres in python?
I see this general postgres docs:
http://www.postgresql.org/docs/9.4/static/plpython.html
but wondered if there are any RDKit specific examples anywhere?
Tim
On 25/09/2015 08:30, Jan Holst Jensen wrote:
On 2015-09-24 16:22, Tim Dudgeon wrote:
I'm trying to get to grips with using the RDKit cartridge, and so far
its going well.
One thing I'm concerned about is molecule standardization, along the
lines of the ChemAxon Standardizer that allows substructure searches to
be done is a way that is largely independent of the quirks of structure
representation. The classic example would be how nitro groups are
represented, so that it didn't matter which nitro representation was in
the query or target structures, because both were converted to a
canonical form.
My initial thoughts are that this would be done by:
1. loading the "raw" structures into a source column that would never be
changed
2. defining a function that performed the necessary transform to
generate the canonical form of a molecule.
3. generating a "canonical" structure column that was the result of
passing the raw structures through that function
4. building the SSS index on that canonical column
5. executing queries using that function to canonicalize the query
structure
The problem I'm finding is that there do not seem to be postgres
functions defined for doing molecular transforms (essentially a reaction
transform) and doing things like removing explicit hydrogens. At least
not in the functions listed on this page:
http://rdkit.org/docs/Cartridge.html#functions
Am I missing something here, or might I be barking up completely the
wrong tree?
Tim
Hi Tim,
We have about the same situation and we're adding standardization
(beyond what RDKit implicitly does when it sanitizes the molecule)
through Python stored procedures. You will need to build and maintain
a normal Python-enabled RDKit installation in parallel to the
cartridge. The Python stored procedures can access the normal RDKit
installation and then run whatever Python code is necessary to do
additional molecule cleanup.
You will need to tweak your Postgres environment so the Python stored
procedures can load RDKit. This is what I have defined in an
environment file on CentOS:
RDBASE=/opt/rdkit
LD_LIBRARY_PATH=/opt/rdkit/lib
PYTHONPATH=/opt/rdkit
On Ubuntu this would go into /etc/postgresql/9.x/main/environment (in
a slightly different format where the values have to be single-quoted).
Cheers
-- Jan, Biochemfusion
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Re: [Rdkit-discuss] molecule standardization in cartridge search
On 2015-09-24 16:22, Tim Dudgeon wrote: > I'm trying to get to grips with using the RDKit cartridge, and so far > its going well. > One thing I'm concerned about is molecule standardization, along the > lines of the ChemAxon Standardizer that allows substructure searches to > be done is a way that is largely independent of the quirks of structure > representation. The classic example would be how nitro groups are > represented, so that it didn't matter which nitro representation was in > the query or target structures, because both were converted to a > canonical form. > > My initial thoughts are that this would be done by: > 1. loading the "raw" structures into a source column that would never be > changed > 2. defining a function that performed the necessary transform to > generate the canonical form of a molecule. > 3. generating a "canonical" structure column that was the result of > passing the raw structures through that function > 4. building the SSS index on that canonical column > 5. executing queries using that function to canonicalize the query structure > > The problem I'm finding is that there do not seem to be postgres > functions defined for doing molecular transforms (essentially a reaction > transform) and doing things like removing explicit hydrogens. At least > not in the functions listed on this page: > http://rdkit.org/docs/Cartridge.html#functions > > Am I missing something here, or might I be barking up completely the > wrong tree? > > Tim Hi Tim, We have about the same situation and we're adding standardization (beyond what RDKit implicitly does when it sanitizes the molecule) through Python stored procedures. You will need to build and maintain a normal Python-enabled RDKit installation in parallel to the cartridge. The Python stored procedures can access the normal RDKit installation and then run whatever Python code is necessary to do additional molecule cleanup. You will need to tweak your Postgres environment so the Python stored procedures can load RDKit. This is what I have defined in an environment file on CentOS: RDBASE=/opt/rdkit LD_LIBRARY_PATH=/opt/rdkit/lib PYTHONPATH=/opt/rdkit On Ubuntu this would go into /etc/postgresql/9.x/main/environment (in a slightly different format where the values have to be single-quoted). Cheers -- Jan, Biochemfusion -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Save files with new atom properties and read again
Hi Hitesh,
Great to hear, and glad that it worked for you out-of-the-box :-).
Cheers
-- Jan
On 2015-07-06 15:57, Hitesh Patel wrote:
Hi Jan and Greg,
I have tried the way you explained. It works fine for me. I am also
using 2015.03.1 version So, additional function was not required.
Thanks.
On Sun, Jul 5, 2015 at 11:30 PM Hitesh Patel hiteshpatel...@gmail.com
mailto:hiteshpatel...@gmail.com wrote:
Hi Jan and Greg,
Thanks for nice suggestion. I think that will serve the purpose. I
will do it tomorrow asap and let you know.
Regards,
Dr. Hitesh Patel
Post-Doctoral Fellow,
Technische Universität Dortmund,
Chemische Biologie,
Otto-Hahn-Straße 6,
44227, Dortmund,
Germany
Room: C1-05-181
Work: 0231 755-4740
Mob.: +49 (0)176 5544 6467
Email: hitesh.pa...@tu-dortmund.de
mailto:hitesh.pa...@tu-dortmund.de
On Sun, Jul 5, 2015 at 10:49 AM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi Greg,
I was running with both RDKit 2014.09.2 and 2013.09.1. V lines
accepted and read in input, but no V lines produced in mol
block output.
I downloaded 2015.03.1 and that produces V lines in mol block
output. Another good reason to upgrade :-).
2014.09.2:
from rdkit import rdBase
rdBase.rdkitVersion
'2014.09.2'
from rdkit import Chem
m = Chem.MolFromSmiles('CO')
m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
print Chem.MolToMolBlock(m)
RDKit
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0
0 0 0
0.0.0. O 0 0 0 0 0 0 0 0 0
0 0 0
1 2 1 0
M END
2015.03.1:
from rdkit import rdBase
rdBase.rdkitVersion
'2015.03.1'
from rdkit import Chem
m = Chem.MolFromSmiles('CO')
m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
print Chem.MolToMolBlock(m)
RDKit
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0
0 0 0
0.0.0. O 0 0 0 0 0 0 0 0 0
0 0 0
1 2 1 0
V1 a1
M END
Cheers
-- Jan
On 2015-07-05 04:59, Greg Landrum wrote:
Hmm, that's strange. Unless that atom also has a query
associated with
it, the atom values definitely should be written. It
certainly works
at least some of the time:
In [5]: m = Chem.MolFromSmiles('CO')
In [6]: m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
In [7]: mb = Chem.MolToMolBlock(m)
In [8]: print(mb)
RDKit
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0
0 0 0
0.0.0. O 0 0 0 0 0 0 0 0 0
0 0 0
1 2 1 0
V1 a1
M END
Jan: what version of the RDKit are you using?
-greg
On Sat, Jul 4, 2015 at 8:08 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com
mailto:j...@biochemfusion.com mailto:j...@biochemfusion.com
wrote:
Hi Hitesh,
The V2000 molfile format has a feature that can be used
to set a
simple text value for an atom by adding V lines to the
molfile. The RDKit molfile *reader* supports this
feature as seen
below (I have seen this feature used to e.g. tag
reactive centers
in a molecule when doing RDKit reaction-based enumeration).
from rdkit import Chem molfile_with_values =
.join(open(C:/temp/cns-with-values.mol).readlines()) print
molfile_with_values
-ISIS- 07041519212D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0958 -2.68330. C 0 0 0 0 0 0 0 0
0 0 0 0
0.8083 -2.27080. N 0 0 0 0 0 0 0 0
0 0 0 0
1.5208 -2.6792 0.
tel:2.6792%20%20%20%200. S 0
0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
V1 Carbs
V3 Sulfuric
M END
m = Chem.MolFromMolBlock(molfile_with_values)
m.GetAtoms()[0].GetProp('molFileValue')
'Carbs
Re: [Rdkit-discuss] Save files with new atom properties and read again
Hi Greg,
I was running with both RDKit 2014.09.2 and 2013.09.1. V lines
accepted and read in input, but no V lines produced in mol block output.
I downloaded 2015.03.1 and that produces V lines in mol block
output. Another good reason to upgrade :-).
2014.09.2:
from rdkit import rdBase
rdBase.rdkitVersion
'2014.09.2'
from rdkit import Chem
m = Chem.MolFromSmiles('CO')
m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
print Chem.MolToMolBlock(m)
RDKit
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
2015.03.1:
from rdkit import rdBase
rdBase.rdkitVersion
'2015.03.1'
from rdkit import Chem
m = Chem.MolFromSmiles('CO')
m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
print Chem.MolToMolBlock(m)
RDKit
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
V1 a1
M END
Cheers
-- Jan
On 2015-07-05 04:59, Greg Landrum wrote:
Hmm, that's strange. Unless that atom also has a query associated with
it, the atom values definitely should be written. It certainly works
at least some of the time:
In [5]: m = Chem.MolFromSmiles('CO')
In [6]: m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
In [7]: mb = Chem.MolToMolBlock(m)
In [8]: print(mb)
RDKit
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
V1 a1
M END
Jan: what version of the RDKit are you using?
-greg
On Sat, Jul 4, 2015 at 8:08 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi Hitesh,
The V2000 molfile format has a feature that can be used to set a
simple text value for an atom by adding V lines to the
molfile. The RDKit molfile *reader* supports this feature as seen
below (I have seen this feature used to e.g. tag reactive centers
in a molecule when doing RDKit reaction-based enumeration).
from rdkit import Chem molfile_with_values =
.join(open(C:/temp/cns-with-values.mol).readlines()) print
molfile_with_values
-ISIS- 07041519212D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0958 -2.68330. C 0 0 0 0 0 0 0 0 0 0 0 0
0.8083 -2.27080. N 0 0 0 0 0 0 0 0 0 0 0 0
1.5208 -2.6792 0. tel:2.6792%20%20%20%200. S 0
0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
V1 Carbs
V3 Sulfuric
M END
m = Chem.MolFromMolBlock(molfile_with_values)
m.GetAtoms()[0].GetProp('molFileValue')
'Carbs'
m.GetAtoms()[1].GetProp('molFileValue')
Traceback (most recent call last):
File stdin, line 1, in module
KeyError: 'molFileValue'
m.GetAtoms()[2].GetProp('molFileValue')
'Sulfuric'
As you can see, the V lines in the molfile are put into RDKit
atom molFileValue properties.
Unfortunately, the atom values are not written when RDKit outputs
a molfile:
print Chem.MolToMolBlock(m)
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0958 -2.68330. C 0 0 0 0 0 0 0 0 0 0 0 0
0.8083 -2.27080. N 0 0 0 0 0 0 0 0 0 0 0 0
1.5208 -2.6792 0. tel:2.6792%20%20%20%200. S 0
0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
But, it is fairly easy to add them with this function:
def MolToMolBlock_WithAtomValues(mol):
mol_block = Chem.MolToMolBlock(mol).split(\n)
# Delete the M END line.
mol_block = mol_block[:-2]
# Add appropriate V lines.
for atom in mol.GetAtoms():
if atom.HasProp(molFileValue):
mol_block.append(V %3d %s % (atom.GetIdx() + 1,
atom.GetProp(molFileValue)))
mol_block.append(M END)
return \n.join(mol_block)
This lets you persist atom text values. Disclaimer: I have no idea
if this will break in the presence of other property lines, e.g.
M CHG etc., but ... it's a start.
As an example, let's first create the CNS molecule without atom
values.
m = Chem.MolFromSmiles(CNS) print
MolToMolBlock_WithAtomValues(m)
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. N 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. S 0 0 0 0 0 0 0 0 0
Re: [Rdkit-discuss] Save files with new atom properties and read again
Hi Hitesh,
The V2000 molfile format has a feature that can be used to set a simple
text value for an atom by adding V lines to the molfile. The RDKit
molfile *reader* supports this feature as seen below (I have seen this
feature used to e.g. tag reactive centers in a molecule when doing RDKit
reaction-based enumeration).
from rdkit import Chem molfile_with_values =
.join(open(C:/temp/cns-with-values.mol).readlines()) print
molfile_with_values
-ISIS- 07041519212D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0958 -2.68330. C 0 0 0 0 0 0 0 0 0 0 0 0
0.8083 -2.27080. N 0 0 0 0 0 0 0 0 0 0 0 0
1.5208 -2.67920. S 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
V1 Carbs
V3 Sulfuric
M END
m = Chem.MolFromMolBlock(molfile_with_values)
m.GetAtoms()[0].GetProp('molFileValue')
'Carbs'
m.GetAtoms()[1].GetProp('molFileValue')
Traceback (most recent call last):
File stdin, line 1, in module
KeyError: 'molFileValue'
m.GetAtoms()[2].GetProp('molFileValue')
'Sulfuric'
As you can see, the V lines in the molfile are put into RDKit atom
molFileValue properties.
Unfortunately, the atom values are not written when RDKit outputs a molfile:
print Chem.MolToMolBlock(m)
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0958 -2.68330. C 0 0 0 0 0 0 0 0 0 0 0 0
0.8083 -2.27080. N 0 0 0 0 0 0 0 0 0 0 0 0
1.5208 -2.67920. S 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
But, it is fairly easy to add them with this function:
def MolToMolBlock_WithAtomValues(mol):
mol_block = Chem.MolToMolBlock(mol).split(\n)
# Delete the M END line.
mol_block = mol_block[:-2]
# Add appropriate V lines.
for atom in mol.GetAtoms():
if atom.HasProp(molFileValue):
mol_block.append(V %3d %s % (atom.GetIdx() + 1,
atom.GetProp(molFileValue)))
mol_block.append(M END)
return \n.join(mol_block)
This lets you persist atom text values. Disclaimer: I have no idea if
this will break in the presence of other property lines, e.g. M CHG
etc., but ... it's a start.
As an example, let's first create the CNS molecule without atom values.
m = Chem.MolFromSmiles(CNS) print
MolToMolBlock_WithAtomValues(m)
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. N 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. S 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
Add two atom values and use the new function to persist the atom values
to the V2000 molfile output:
m.GetAtoms()[0].SetProp(molFileValue, C-atom)
m.GetAtoms()[2].SetProp(molFileValue, Here is an S-atom)
print MolToMolBlock_WithAtomValues(m)
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. N 0 0 0 0 0 0 0 0 0 0 0 0
0.0.0. S 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
V1 C-atom
V3 Here is an S-atom
M END
Check that the output can be read back in:
molblock_test = MolToMolBlock_WithAtomValues(m) m_test =
Chem.MolFromMolBlock(molblock_test)
m_test.GetAtoms()[0].GetProp(molFileValue)
'C-atom'
m_test.GetAtoms()[1].GetProp(molFileValue)
Traceback (most recent call last):
File stdin, line 1, in module
KeyError: 'molFileValue'
m_test.GetAtoms()[2].GetProp(molFileValue)
'Here is an S-atom'
If you have multiple properties they would have to be encoded into the
text value as e.g. key-value pairs. The text values are in principle
limited to max. 70-80 characters (72 ?) by the MDL molfile
specification, but RDKit probably accepts longer strings (I would guess,
but have not tried).
A more generic solution would be to map RDKit atom and bond properties
to molfile S-group data - but that's a bit more involved and is not
supported at the moment.
Cheers
-- Jan Holst Jensen
On 2015-07-04 18:28, Greg Landrum wrote:
Hi,
On Friday, July 3, 2015, Hitesh Patel hiteshpatel...@gmail.com
mailto:hiteshpatel...@gmail.com wrote:
Hi Greg,
At first priority, I will use mol2 format. A s shown in mol2 format
explanation, we can set user specified atom attributes. I copied the
text below for your convenience. See the bold text.
The rdkit does not yet have a mol2 writer, so that isn't an option.
For second priority, I can use mol files. There I have to set
Properties block:
* |M ALS| - atom list and exclusive list * |M APO| - Rgroup
attachment point * |M CHG| - charge * .
But, I am not sure, whether the user defined property block is
allowed or not.
M CHG and M ALS are already used by the rdkit when atoms have charges
Re: [Rdkit-discuss] @= operator doesn't work as expected with the latest RDKit
Hi Michael, I don't know what's wrong, but I can confirm the behavior on an RDKit build based on 2013_09_2: select id, molecule from parents$calc_props where molecule operator(rdkit.@) 'CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' limit 10 id molecule 56 CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21 select id, molecule from parents$calc_props where molecule operator(rdkit.@) 'CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' limit 10 same result as above - record with ID = 56 select id, molecule from parents$calc_props where molecule operator(rdkit.@=) 'CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' limit 10 no results The operator should work according to docs http://www.rdkit.org/docs/Cartridge.html Substructure and exact structure search * @ : substructure search operator. Returns whether or not the mol or qmol on the right is a substructure of the mol on the left. * @ : substructure search operator. Returns whether or not the mol or qmol on the left is a substructure of the mol on the right. * @= : returns whether or not two molecules are the same. A workaround is this: select id, molecule from parents$calc_props where molecule operator(rdkit.@) 'CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' and molecule operator(rdkit.@) 'CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' limit 10 which returns the molecule as intended. It was suggested by Greg in an ancient post from 2010: http://sourceforge.net/p/rdkit/mailman/message/26662092/ Cheers -- Jan On 2015-06-18 18:01, Michał Nowotka wrote: Hi, I'm working on mychembl_20 and I have latest stable RDKit version (Release_2015_03_1) installed and compiled as postgres cartridge. Some facts: 1. All tests went fine, including tests for postgres extension. 2. Substructure (@) and similarity (tanimoto_sml) searches are working fine. Now I'm trying to execute this SQL statement: SELECT COUNT(*) FROM mols_rdkit WHERE (m@='C'); This runs without errors but returns 0. It returns 0 for any SMILES string, even if I know that the structure exists in the database. Table mold_rdkit exists, is not empty and has column m (as I said, substructure and similarity are working fine). Am I doing something wrong? Is there anything I can do to verify if the problem is related to RDKit or something else? Kind regards, Michał Nowotka -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SDF tags and -
Actually, you want to send your loving thoughts to MDL (now: Biovia).
They defined the SDF format :-).
Cheers
-- Jan
On 2015-04-29 13:26, Nicholas Firth wrote:
Ahh ok… Interesting way to format a file! Got to love ChemAxon...
Best,
Nick
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On 29 Apr 2015, at 12:23, Paolo Tosco paolo.to...@unito.it
mailto:paolo.to...@unito.it wrote:
Hi Nick,
newlines in data properties are fine, but they should not include
blank lines (i.e., multiple newlines).
For example, in:
my_property1
1
2
3
4
my_property2
1234
my_property3
5678
my_property1 will be truncated to just 1. Based on the
specifications, if you want to include a blank line, it should
actually be either a or a \t, rather than being completely blank.
Cheers,
Paolo
On 04/29/15 12:16, Nicholas Firth wrote:
I use SD files with new lines in the properties quite frequently
(inherited from Pipeline Pilot's merge function) and I've never had a
problem reading them. I've attached an SD file that works fine for me.
In [2]: suppl = Chem.SDMolSupplier('/Volumes/nfirth/tempf.sdf')
In [3]: m = suppl[0]
In [4]: t = m.GetProp('genNum')
In [5]: print t
1
2
3
4
In [6]: print t.split('\n')
['1', '2', '3', '4']
So I guess the problem is in the writer?
Best,
Nick
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Re: [Rdkit-discuss] XAMPP server No module named RDkit
I dont have python and RDkit path in my XAMPP environment variable path. but python and RDkit path is set on my system (windows server 2003) coluld you please suggest how to add python and RDkit path in XAMPP environment variable . Hi Sujit, An issue that could cause this behavior, is that services (and I assume that XAMPP is running as a service on your Windows system) do not inherit the environment of the process that starts the service. The only way to get services to see the new environment on a Windows 2003 server is to reboot the server. Unless you can find a way to set the environment for the XAMMP service via a file as JP can on Linux, then you need to reboot the server. And... I guess you have done this, but don't forget to set the environment variables as SYSTEM variables so the service can see them. Cheers -- Jan Holst Jensen On 2015-03-05 11:13, JP wrote: I don't have access to a Windows OS to play with this. Sorry I cannot be of more help. On my system (Apache2 and Ubuntu) - you hardcore the env variables in a file called envvars in /etc/apache2. You should be able to use the SetEnv directive in the the apache conf file or in the sites conf files. This is explained here: http://httpd.apache.org/docs/current/mod/mod_env.html A really terrible way to do this would be directly in PHP before your shell_exec call (http://php.net/manual/en/function.putenv.php). This is bound to bite you later. - Jean-Paul Ebejer Early Stage Researcher On 5 March 2015 at 10:25, Sujit Tangadpalliwar sujit.tangadpalli...@gmail.com mailto:sujit.tangadpalli...@gmail.com wrote: Dear Ebejer, Thanks for your reply. I dont have python and RDkit path in my XAMPP environment variable path. but python and RDkit path is set on my system (windows server 2003) coluld you please suggest how to add python and RDkit path in XAMPP environment variable . Thanks in advance Regards Sujit -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Inchi installation in postgresql database driving me mad
On 2015-02-12 17:50, JP wrote: My Makefile now looks: # - # Variables used and default values: USE_INCHI=1 # enables InChI functions; requires rdkit built with inchi support # USE_AVALON=0 # enables avalon fingerprint; requires rdkit built with avalon support USE_POPCOUNT=1 # enables use of the CPU's popcount instruction # USE_THREADS=0# links against boost.system; required with non-ancient boost versions if inchi is enabled or the rdkit is built with threadsafe SSS # STATIC_LINK=1# link against the static RDKit libraries # Hi JP, You were almost there. I had this problem too. The USE_INCHI line should read USE_INCHI=1 and not USE_INCHI=1 # enables InChI functions; requires rdkit built with inchi support I guess the comment gets included into the USE_INCHI variable and then the check for is USE_INCHI == 1 in the makefile fails. Cheers -- Jan -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Building RDKit with static runtime on Windows.
Hi,
I have a couple of plugins (DLLs) that are based on RDKit. To minimize
deployment issues I build the DLLs with /MT instead of the default /MD
so the MSVC runtime libraries will be linked statically into the DLL.
And so I won't have to worry about the presence or absence of MSVC
runtime DLLs on the target system.
I had to hack a little to get RDKit to build with a static runtime and
link it correctly to boost. I am fine with hacking it, as I might be the
only one building it this way. But if there is already a way to make
cmake build RDKit with a static runtime I'd love to hear about it.
RDKit source files in C:\RDKit_2014_09_1\. InChI sources downloaded.
Using boost binaries from
http://sourceforge.net/projects/boost/files/boost-binaries/. Doing a
32-bit build.
set RDBASE=C:\RDKit_2014_09_1
set PATH=%PATH%;%RDBASE%\lib;c:\local\boost_1_57_0\lib32-msvc-10.0
cd C:\RDKit_2014_09_1\build
*# Add to cmake command line: -DBoost_USE_STATIC_LIBS=ON and
-DBoost_USE_STATIC_RUNTIME=ON**
*cmake -DBOOST_ROOT=C:/local/boost_1_57_0/
*-DBoost_USE_STATIC_LIBS=ON -DBoost_USE_STATIC_RUNTIME=ON*
-DRDK_BUILD_PYTHON_WRAPPERS= -DRDK_BUILD_INCHI_SUPPORT=ON -GVisual
Studio 10 ..
# Switch to a Cygwin prompt.
cd /cygdrive/C/RDKit_2014_09_1/build/
*# Force compiler to compile with /MT instead of /MD in Release builds.
*find . -name *.vcxproj -type f -exec sed -i
s/RuntimeLibraryMultiThreadedDLL/RuntimeLibraryMultiThreaded/
'{}' \;
*# Remove the BOOST_ALL_DYN_LINK define which will otherwise cause a
link error in boost's auto_link.hpp.
*find . -name *.vcxproj -type f -exec sed -i
s/BOOST_ALL_DYN_LINK;// '{}' \;
# Switch back to DOS prompt to build.
c:/Windows/Microsoft.NET/Framework64/v4.0.30319/MSBuild.exe /m:4
/p:Configuration=Release INSTALL.vcxproj
Cheers
-- Jan Holst Jensen
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Re: [Rdkit-discuss] portable PostgreSQL + RDKit cartridge?
On 2014-08-28 14:34, Michal Krompiec wrote: Hello, has anybody tried to compile a portable Windows binary of PostgreSQL with RDKit cartridge? There is a portable PostreSQL at http://sourceforge.net/projects/postgresqlportable/ and I wonder if it is possible to use it with the cartridge. Best regards, Michal Hi Michal, I got through building a Windows version of the RDKit cartridge a while back, but I didn't end up using it for real. I would think that the instructions still mostly apply: http://sourceforge.net/p/rdkit/mailman/message/30127487/ If the resulting DLL and the extension control files are put in the right place in the portable image, I guess you should be able to get it working. Cheers -- Jan -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] cartridge build fail
On 2014-08-26 17:34, Andrew Pannifer wrote: Hi, I have just installed rdkit on a RHEL machine (from source) together with postgresql 9.0 (from the repo on the website). rdkit is doing fine on the ctest results and modules import fine while postgresql is also OK. In contrast, attempts to build the cartridge are not so good (results below). I wasn't sure if the devel package was in there so installed again via yum and no errors there but still get the same result. Any help here to solve this would be appreciated. make make install make installcheck make: pg_config: Command not found /bin/sh: pg_config: command not found make: Nothing to be done for `all'. make: pg_config: Command not found /bin/sh: pg_config: command not found make: *** No rule to make target `install'. Stop. thanks, Andrew Hi Andrew, Red Hat is a bit peculiar about how it packages PostgreSQL - well, at least it differs from Debian/Ubuntu. Even when you have installed the devel package, pg_config may not be on your standard PATH. I am on CentOS 6.5 with PostgreSQL 9.3 at the moment and to build the RDKit cartridge I do this first: export PATH=$PATH:/usr/pgsql-9.3/bin/ and then it builds for me. So something similar may apply to your setup ? When you can run 'pg_config' from the command line before you build, you should be good to go. Cheers -- Jan -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] getting stereo info from bonds
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
This is very good question so I will begin with answering this. I'm
writing a module, which converts *mrv files to molfiles, both ways. In
my case, the original mrv file looks like this:
[...] and down so '1' and '6' ('W' and 'H' in marvin terms). So what about
other values which this field can have, If for example I have this
molfile:
[...] So 4 instead of 1, how I will get this information from RDKit?
Hi Michal,
If you don't already have it you should grab a copy of the molfile
specification, ctfile.pdf - you can get it here:
https://community.accelrys.com/docs/DOC-3451
Valid values for bond type are:
bond type
1 = Single, 2 = Double,
3 = Triple, 4 = Aromatic,
5 = Single or Double,
6 = Single or Aromatic,
7 = Double or Aromatic, 8 = Any
[Query] Values 4 through 8
are for SSS queries only.
So a 4 is a query bond feature. I don't know the corresponding RDKit
property, but I would expect it to be query-related.
Cheers
-- Jan
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Re: [Rdkit-discuss] getting stereo info from bonds
Hi Michal,
Apologies.
Cheers
-- Jan
On 2014-08-22 14:43, Michał Nowotka wrote:
Hi Jan,
First of all, please note, that in my message you are citing I'm
referring to the same document you are suggesting me to read.
Secondly, after reading my message carefully, you will probably find
out that '4' value in my question refers to the 'bond stereo'
property, not 'bond type'.
On Fri, Aug 22, 2014 at 1:32 PM, Jan Holst Jensen j...@biochemfusion.com
wrote:
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
This is very good question so I will begin with answering this. I'm
writing a module, which converts *mrv files to molfiles, both ways. In
my case, the original mrv file looks like this:
[...] and down so '1' and '6' ('W' and 'H' in marvin terms). So what about
other values which this field can have, If for example I have this
molfile:
[...] So 4 instead of 1, how I will get this information from RDKit?
Hi Michal,
If you don't already have it you should grab a copy of the molfile
specification, ctfile.pdf - you can get it here:
https://community.accelrys.com/docs/DOC-3451
Valid values for bond type are:
bond type
1 = Single, 2 = Double,
3 = Triple, 4 = Aromatic,
5 = Single or Double,
6 = Single or Aromatic,
7 = Double or Aromatic, 8 = Any
[Query] Values 4 through 8
are for SSS queries only.
So a 4 is a query bond feature. I don't know the corresponding RDKit
property, but I would expect it to be query-related.
Cheers
-- Jan
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Re: [Rdkit-discuss] getting stereo info from bonds
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
[...] Now imagine I only have this molfile and I want to convert it back to
*mrv. I don't want to write my own parser for molfiles when I know
that RDKit can already parse it. But I need to extract this 'bond
stereo' information from within RDKit somehow.
Now when you say that this '1' or 'W' value corresponds to bond
direction, I'm guessing that 'direction' can store only two values: up
and down so '1' and '6' ('W' and 'H' in marvin terms). So what about
other values which this field can have, If for example I have this
molfile:
10 10 0 0 0 0 0 0 0 0999 V2000
-1.6741 -0.26870. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3885 -0.68120. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3885 -1.50630. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6741 -1.91880. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9596 -1.50630. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9596 -0.68120. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2451 -0.26860. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.24510.55630. O 0 0 0 0 0 0 0 0 0 0 0 0
0.4692 -0.68110. C 0 0 0 0 0 0 0 0 0 0 0 0
0.4692 -1.50610. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 0 0
7 9 1 0 0 0 0
9 10 1 0 0 0 0
7 8 1 4 0 0 0
M END
So 4 instead of 1, how I will get this information from RDKit?
Hi Michal,
I took a look at the C++ code in GraphMol/FileParsers/MolFileParser.cpp.
ParseMolFileBondLine() for parsing V2000 molfiles sets the BondDir to
UNKNOWN (case 4, bond stereo type = 4):
stereo = FileParserUtils::toInt(text.substr(9,3));
switch(stereo){
case 0:
res-setBondDir(Bond::NONE);
break;
case 1:
res-setBondDir(Bond::BEGINWEDGE);
break;
case 6:
res-setBondDir(Bond::BEGINDASH);
break;
case 3: // either double bond
res-setBondDir(Bond::EITHERDOUBLE);
res-setStereo(Bond::STEREOANY);
break;
case 4: // either single bond
res-setBondDir(Bond::UNKNOWN);
break;
}
In ParseV3000BondBlock() for V3000 molfiles the same thing happens, so
they agree (case 2, CFG=2, bond type = single (1)):
if(prop==CFG){
unsigned int cfg=atoi(val.c_str());
switch(cfg){
case 0: break;
case 1:
bond-setBondDir(Bond::BEGINWEDGE);
chiralityPossible=true;
break;
case 2:
if(bType==1) bond-setBondDir(Bond::UNKNOWN);
else if(bType==2){
bond-setBondDir(Bond::EITHERDOUBLE);
bond-setStereo(Bond::STEREOANY);
}
break;
case 3:
bond-setBondDir(Bond::BEGINDASH);
chiralityPossible=true;
break;
default:
errout bad bond CFG val' on line line;
throw FileParseException(errout.str()) ;
}
} else if(prop==TOPO){
The bonds will therefore be assigned a BondDir value of Bond::UNKNOWN
for single either bonds and BOND::EITHERDOUBLE for double either bonds.
I read in a V2000 molfile where the second bond is a single either bond
(stereo bond type of 4) and the third bond is a double either bond
(stereo bond type of 3).
from rdkit import Chem
m = Chem.MolFromMolFile(C:/temp/either.mol, sanitize=False,
removeHs=False)
for b in m.GetBonds(): print b.GetBondDir()
...
NONE
UNKNOWN
5
NONE
NONE
NONE
Only slight surprise is that Python returns a 5 instead of an
EITHERDOUBLE string.
Chem.rdchem.BondDir.values
{0: rdkit.Chem.rdchem.BondDir.NONE, 1:
rdkit.Chem.rdchem.BondDir.BEGINWEDGE, 2:
rdkit.Chem.rdchem.BondDir.BEGINDASH, 3: rdkit.Chem.rdchem.BondDir.ENDDOWNRI
GHT, 4: rdkit.Chem.rdchem.BondDir.ENDUPRIGHT, 6:
rdkit.Chem.rdchem.BondDir.UNKNOWN}
For some reason Python does not map the BondDir value 5 to a name. But
the value does match EITHERDOUBLE's implicit ordinal value defined in
GraphMol/Bond.h, so it matches what I expect from reading the parser code:
//! the bond's direction (for chirality)
typedef enum {
NONE=0, //! no special style
BEGINWEDGE, //! wedged: narrow at begin
BEGINDASH, //! dashed: narrow at begin
// FIX: this may not really be adequate
ENDDOWNRIGHT, //! for cis/trans
ENDUPRIGHT, //! ditto
EITHERDOUBLE, //! a crossed double bond
UNKNOWN,//! intentionally unspecified stereochemistry
} BondDir;
So the information is
Re: [Rdkit-discuss] RDKit database cartridge question
On 2014-07-29 12:17, acanada wrote:
Hello,
I have a postgres table with compound names and other info. I want to save also
.mol or .sdf information associated to this compounds. I'm getting the
structure information from the chebi web service and I assume that I have to
save this info in some way in order to enable the substructural search and
other searching options
I have searched for information in The RDKit database cartridge but I cannot find an
explanation for my purposes. I'm searching a type for saving structures, and the way to
tell the table some options (tautomers, repeated molecules...etc) when saving the data.
Can anybody tell me where to find information, how-to or tutorial for what I'm
trying to do?
My apologizes if this is a too simple question.
Thank you very much,
Andrés
Hi Andrés,
The type you are looking for is mol - an RDKit molecule type column
which can be indexed for substructure searches.
To convert a molfile to the mol type, use the cartridge
mol_from_ctab() function.
So e.g. create a table like this:
create table mols (
id serial,
molecule mol
);
and to insert molecules into it:
insert into mols (molecule) values ('CCN');
SMILES text will be automatically converted to mol type. Assuming that
you have a variable molfile that holds a molfile as text do this:
insert into mols (molecule) values (mol_from_ctab(molfile::cstring));
Note that the molfile string has to be cast to cstring. You probably
also want to register it like this:
insert into mols (molecule) values (mol_from_ctab(molfile::cstring,
true));
The additional boolean parameter controls whether the coordinates of the
original molfile are retained in the database. The default is false
meaning that molfile coordinates are not retained. If you want to be
able to export the structures as-they-were you want to set the parameter
to true.
To get back the molfiles, use the mol_to_ctab() function:
select id, mol_to_ctab(molecule) from mols;
Hope this gets you started.
Cheers
-- Jan
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Re: [Rdkit-discuss] Fw: how can I test if a molecule already has 2D coordinates?
On 2014-05-07 17:26, chemis...@gmx.de wrote:
*Gesendet:* Mittwoch, 07. Mai 2014 um 15:56 Uhr
*Von:* chemis...@gmx.de
*An:* rdkit-discuss@lists.sourceforge.net
*Betreff:* how can I test if a molecule already has 2D coordinates?
for a given molecule, how can I test if it already has 2D coordinates?
I would like to calculate these coordinates only for molecules that do
not yet have them.
Many thanks in advance.
Kind regards,
Axel
I think I found a way: if I call
mol.GetConformer()
I get a ValueError, if no 2D coordinates are present. This error I can
catch.
Kind regards,
Axel
Hi Axel,
And even more straightforward: mol.GetNumConformers().
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('CCF')
mol.GetNumConformers()
0
AllChem.Compute2DCoords(mol)
0
mol.GetNumConformers()
1
Cheers
-- Jan
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[Rdkit-discuss] ReducedGraphs - now, where is this code ?
Hi Rdkitters, A colleague of mine has stumbled upon this page: http://www.rdkit.org/Python_Docs/rdkit.Chem.rdReducedGraphs-module.html And so he asked me how to use it, because he couldn't find it. Neither can I, not even in the latest git version. Is this a special secret feature :-) ? Cheers -- Jan -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Inconsistency between Cartridge and Python
On 2014-04-23 16:01, Daniel Moser wrote:
Hi all,
I think I found some inconsistent behaviour between the cartridge and
python. At least for NCO the cartridge function mol_hbd returns a
different value than Descriptors.NumHDonors.
[...]
I'm seeing this behaviour both with the 2013.09.2 as well as the
2012.12.1 cartridge version. Can anyone confirm this?
I can confirm this difference between Python and the cartridge using a
fairly recent git version.
The cartrige mol_hbd() function calls calcLipinskiHBD:
MOLDESCR(HBD,RDKit::Descriptors::calcLipinskiHBD,int)
which is
unsigned int calcLipinskiHBD(const ROMol mol){
unsigned int res=0;
for(ROMol::ConstAtomIterator iter=mol.beginAtoms();
iter!=mol.endAtoms();++iter){
if( ((*iter)-getAtomicNum()==7 || (*iter)-getAtomicNum()==8) ) {
res += (*iter)-getTotalNumHs(true);
}
}
return res;
}
while the Python NumHDonors() is using a SMARTS-based approach as far as
I can tell.
The function that the cartridge uses can be accessed via AllChem and
then I can also demonstrate the difference in Python:
from rdkit import Chem
m = Chem.MolFromSmiles('NCO')
from rdkit.Chem import Descriptors
print Descriptors.NumHDonors(m)
2
from rdkit.Chem import AllChem
print AllChem.CalcNumLipinskiHBD(m)
3
Cheers
-- Jan
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Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?
I have added a comment to the Wiki that describes how I built RDKit on a CentOS 5.3 server, in case others also suddenly find themselves on an old OS. https://code.google.com/p/rdkit/wiki/BuildingWithCmake Thanks again to Gianluca and Greg - the EPEL repository does save the day. Cheers -- Jan On 2014-02-26 11:26, Jan Holst Jensen wrote: On 2014-02-26 11:04, Greg Landrum wrote: On Wed, Feb 26, 2014 at 10:56 AM, Gianluca Sforna gia...@gmail.com mailto:gia...@gmail.com wrote: On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: I am testing if rdkit can be used from Oracle on a customer (test!) database. And said database runs on a CentOS 5.3 server - no OS upgrade in the near future. First step is to get rdkit working in Python 2.4 on that server. For a start, you can make your life easier by adding the EPEL repository and pulling python26 package from there. Yeah, I am pretty sure that there is python code that is not going to work with 2.4 IIRC the only real blocker that prevented me from building RDKit against CentOS5 + EPEL was flex Fortunately, flex is no longer required, so that one is gone. -greg Thanks, Gianluca and Greg. The EPEL repository looks like it could save the day, giving me a tool chain so I can build rdkit. I'll give it a try! Cheers -- Jan -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Three tests failing on CentOS 5.3 - important ?
On 2014-03-19 05:54, Greg Landrum wrote: On Tue, Mar 18, 2014 at 4:59 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: Hi RDKitters, I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a short recipe later. Wow; that's an ancient version. Yup. Approaching archaeology-region here. Right now, I am still left with three tests that fail, but I think (hope) that I can live with that ? Failing tests are: 72:pythonTestDbCLI 73:pythonTestDirML 78:pythonTestDirChem The test log shows that test 72 won't run because of missing SQLite support. 72/78 Testing: pythonTestDbCLI 72/78 Test: pythonTestDbCLI Command: /usr/bin/python26 /u01/software/RDKit_2013_09_2/Projects/test_list.py --testDir /u01/software/RDKit_2013_09_2/Projects Directory: /u01/software/RDKit_2013_09_2/build/Projects pythonTestDbCLI start time: Mar 05 11:07 CET Output: -- Traceback (most recent call last): File TestDbCLI.py, line 9, in ? from rdkit.Dbase.DbConnection import DbConnect File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbConnection.py, line 21, in ? from rdkit.Dbase import DbUtils,DbInfo File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbUtils.py, line 17, in ? from rdkit.Dbase.DbResultSet import DbResultSet,RandomAccessDbResultSet File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbResultSet.py, line 12, in ? from rdkit.Dbase import DbInfo File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbInfo.py, line 12, in ? import DbModule File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbModule.py, line 61, in ? raise ImportError,Neither sqlite nor PgSQL support found. ImportError: Neither sqlite nor PgSQL support found. A bit puzzling, since I can import sqlite3 just fine from Python when run interactively. As far as I can understand RDConfig.py a successful import of sqlite3 should make it report that SQLite support is availabe ? For my purposes, failing this test is probably fine - I don't expect I need sqlite support on this machine. It's probably not important unless you are planning on using the DbCLI code. If you want to try and track it down: can you do from rdkit.Dbase import DbModule? Goes just fine interactively. [oracle@localhost ~]$ python26 Python 2.6.8 (unknown, Nov 7 2012, 14:47:45) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 Type help, copyright, credits or license for more information. from rdkit.Dbase import DbModule quit() [oracle@localhost ~]$ Well, let's leave it at that. Since I am not planning to use the DbCLI code at the moment I am OK with it. Tests 73 has this in the log: Traceback (most recent call last): File UnitTestBuildComposite.py, line 16, in ? from rdkit.ML import BuildComposite File /u01/software/RDKit_2013_09_2/rdkit/ML/BuildComposite.py, line 203, in ? from rdkit.ML.Composite import Composite,BayesComposite File /u01/software/RDKit_2013_09_2/rdkit/ML/Composite/Composite.py, line 25, in ? from rdkit.ML.Data import DataUtils File /u01/software/RDKit_2013_09_2/rdkit/ML/Data/DataUtils.py, line 57, in ? from rdkit.ML.Data import MLData File /u01/software/RDKit_2013_09_2/rdkit/ML/Data/MLData.py, line 8, in ? import numpy ImportError: No module named numpy ... and test 78: Output: -- File UnitTestInchi.py, line 187 except InchiReadWriteError as inst: ^ SyntaxError: invalid syntax File PandasTools.py, line 100 except Exception as e: ^ SyntaxError: invalid syntax Traceback (most recent call last): File UnitTestEState.py, line 17, in ? import numpy ImportError: No module named numpy Traceback (most recent call last): File UnitTestFingerprints.py, line 17, in ? import numpy ImportError: No module named numpy ... The numpy module loads fine when run interactively. So maybe it is something else that is wrong - just that the error reported from Python is a bit misleading (?). That's a strange one, but if you can import numpy and rdkit.Chem, then I wouldn't be concerned about it. Again, if you're interested in trying to track it down, there are some experiments we can do. I haven't run into stuff that doesn't
Re: [Rdkit-discuss] Three tests failing on CentOS 5.3 - important ?
Hi Markus, It is Python 2.6.8. Old, but apparently not *that* old :-) : [oracle@localhost ~]$ cat test.py try: raise Exception, Hello, I am an error except Exception as e: print An exception was raised: + str(e) + . [oracle@localhost ~]$ python26 test.py An exception was raised: Hello, I am an error. [oracle@localhost ~]$ Cheers -- Jan On 2014-03-19 09:35, Markus Sitzmann wrote: I think the syntax except Exception as e: did't exist before python 2.6 ... are you running this on an older version? :-) Cheers, Markus On Wed, Mar 19, 2014 at 7:54 AM, Jan Holst Jensen j...@biochemfusion.com wrote: On 2014-03-19 05:54, Greg Landrum wrote: On Tue, Mar 18, 2014 at 4:59 PM, Jan Holst Jensen j...@biochemfusion.com wrote: Hi RDKitters, I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a short recipe later. Wow; that's an ancient version. Yup. Approaching archaeology-region here. Right now, I am still left with three tests that fail, but I think (hope) that I can live with that ? Failing tests are: 72:pythonTestDbCLI 73:pythonTestDirML 78:pythonTestDirChem The test log shows that test 72 won't run because of missing SQLite support. 72/78 Testing: pythonTestDbCLI 72/78 Test: pythonTestDbCLI Command: /usr/bin/python26 /u01/software/RDKit_2013_09_2/Projects/test_list.py --testDir /u01/software/RDKit_2013_09_2/Projects Directory: /u01/software/RDKit_2013_09_2/build/Projects pythonTestDbCLI start time: Mar 05 11:07 CET Output: -- Traceback (most recent call last): File TestDbCLI.py, line 9, in ? from rdkit.Dbase.DbConnection import DbConnect File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbConnection.py, line 21, in ? from rdkit.Dbase import DbUtils,DbInfo File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbUtils.py, line 17, in ? from rdkit.Dbase.DbResultSet import DbResultSet,RandomAccessDbResultSet File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbResultSet.py, line 12, in ? from rdkit.Dbase import DbInfo File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbInfo.py, line 12, in ? import DbModule File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbModule.py, line 61, in ? raise ImportError,Neither sqlite nor PgSQL support found. ImportError: Neither sqlite nor PgSQL support found. A bit puzzling, since I can import sqlite3 just fine from Python when run interactively. As far as I can understand RDConfig.py a successful import of sqlite3 should make it report that SQLite support is availabe ? For my purposes, failing this test is probably fine - I don't expect I need sqlite support on this machine. It's probably not important unless you are planning on using the DbCLI code. If you want to try and track it down: can you do from rdkit.Dbase import DbModule? Goes just fine interactively. [oracle@localhost ~]$ python26 Python 2.6.8 (unknown, Nov 7 2012, 14:47:45) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 Type help, copyright, credits or license for more information. from rdkit.Dbase import DbModule quit() [oracle@localhost ~]$ Well, let's leave it at that. Since I am not planning to use the DbCLI code at the moment I am OK with it. Tests 73 has this in the log: Traceback (most recent call last): File UnitTestBuildComposite.py, line 16, in ? from rdkit.ML import BuildComposite File /u01/software/RDKit_2013_09_2/rdkit/ML/BuildComposite.py, line 203, in ? from rdkit.ML.Composite import Composite,BayesComposite File /u01/software/RDKit_2013_09_2/rdkit/ML/Composite/Composite.py, line 25, in ? from rdkit.ML.Data import DataUtils File /u01/software/RDKit_2013_09_2/rdkit/ML/Data/DataUtils.py, line 57, in ? from rdkit.ML.Data import MLData File /u01/software/RDKit_2013_09_2/rdkit/ML/Data/MLData.py, line 8, in ? import numpy ImportError: No module named numpy ... and test 78: Output: -- File UnitTestInchi.py, line 187 except InchiReadWriteError as inst: ^ SyntaxError: invalid syntax File PandasTools.py, line 100 except Exception as e: ^ SyntaxError: invalid syntax Traceback (most recent call last): File UnitTestEState.py, line 17, in ? import numpy ImportError: No module named numpy Traceback (most recent call last): File UnitTestFingerprints.py, line 17, in ? import numpy ImportError: No module named numpy ... The numpy module loads fine when run interactively. So maybe it is something else that is wrong - just that the error reported from Python is a bit misleading (?). That's a strange one, but if you can import numpy and rdkit.Chem, then I wouldn't be concerned about it. Again, if you're interested in trying to track it down, there are some experiments we can do. I haven't run into stuff that doesn't work yet because of these test
[Rdkit-discuss] Three tests failing on CentOS 5.3 - important ?
Hi RDKitters, I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a short recipe later. Right now, I am still left with three tests that fail, but I think (hope) that I can live with that ? Failing tests are: 72:pythonTestDbCLI 73:pythonTestDirML 78:pythonTestDirChem The test log shows that test 72 won't run because of missing SQLite support. 72/78 Testing: pythonTestDbCLI 72/78 Test: pythonTestDbCLI Command: /usr/bin/python26 /u01/software/RDKit_2013_09_2/Projects/test_list.py --testDir /u01/software/RDKit_2013_09_2/Projects Directory: /u01/software/RDKit_2013_09_2/build/Projects pythonTestDbCLI start time: Mar 05 11:07 CET Output: -- Traceback (most recent call last): File TestDbCLI.py, line 9, in ? from rdkit.Dbase.DbConnection import DbConnect File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbConnection.py, line 21, in ? from rdkit.Dbase import DbUtils,DbInfo File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbUtils.py, line 17, in ? from rdkit.Dbase.DbResultSet import DbResultSet,RandomAccessDbResultSet File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbResultSet.py, line 12, in ? from rdkit.Dbase import DbInfo File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbInfo.py, line 12, in ? import DbModule File /u01/software/RDKit_2013_09_2/rdkit/Dbase/DbModule.py, line 61, in ? raise ImportError,Neither sqlite nor PgSQL support found. ImportError: Neither sqlite nor PgSQL support found. A bit puzzling, since I can import sqlite3 just fine from Python when run interactively. As far as I can understand RDConfig.py a successful import of sqlite3 should make it report that SQLite support is availabe ? For my purposes, failing this test is probably fine - I don't expect I need sqlite support on this machine. Tests 73 has this in the log: Traceback (most recent call last): File UnitTestBuildComposite.py, line 16, in ? from rdkit.ML import BuildComposite File /u01/software/RDKit_2013_09_2/rdkit/ML/BuildComposite.py, line 203, in ? from rdkit.ML.Composite import Composite,BayesComposite File /u01/software/RDKit_2013_09_2/rdkit/ML/Composite/Composite.py, line 25, in ? from rdkit.ML.Data import DataUtils File /u01/software/RDKit_2013_09_2/rdkit/ML/Data/DataUtils.py, line 57, in ? from rdkit.ML.Data import MLData File /u01/software/RDKit_2013_09_2/rdkit/ML/Data/MLData.py, line 8, in ? import numpy ImportError: No module named numpy ... and test 78: Output: -- File UnitTestInchi.py, line 187 except InchiReadWriteError as inst: ^ SyntaxError: invalid syntax File PandasTools.py, line 100 except Exception as e: ^ SyntaxError: invalid syntax Traceback (most recent call last): File UnitTestEState.py, line 17, in ? import numpy ImportError: No module named numpy Traceback (most recent call last): File UnitTestFingerprints.py, line 17, in ? import numpy ImportError: No module named numpy ... The numpy module loads fine when run interactively. So maybe it is something else that is wrong - just that the error reported from Python is a bit misleading (?). I haven't run into stuff that doesn't work yet because of these test failures, so I think that I can get by without them passing. But it would be nice to know if it is potentially critical or not. Cheers -- Jan -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Pg cartridge - mol_to_ctab() and trouble with conformers.
Hi,
About ready to push a changeset for implementing mol_to_ctab(), but I
would like it to play nice and preserve input depictions.
Ideally I would like the following
select mol_to_ctab(mol_from_ctab(input-molfile));
to output a molfile where the coordinates of input-molfile are preserved.
If I do that in Python it works:
from rdkit import Chem
m = Chem.MolFromMolBlock(chiral1.mol
... ChemDraw04200416412D
...
... 5 4 0 0 0 0 0 0 0 0999 V2000
...-0.01410.05530. C 0 0 0 0 0 0 0 0 0 0 0 0
... 0.81090.05530. F 0 0 0 0 0 0 0 0 0 0 0 0
...-0.42660.76970. Br 0 0 0 0 0 0 0 0 0 0 0 0
...-0.0141 -0.76970. Cl 0 0 0 0 0 0 0 0 0 0 0 0
...-0.8109 -0.15830. C 0 0 0 0 0 0 0 0 0 0 0 0
... 1 2 1 0
... 1 3 1 0
... 1 4 1 1
... 1 5 1 0
... M END)
m
rdkit.Chem.rdchem.Mol object at 0x1240980
* m.GetNumConformers()**
**1*
Chem.MolToMolBlock(m)
'chiral1.mol\n RDKit 2D\n\n 5 4 0 0 0 0 0 0 0
0999 V2000\n -0.01410.05530. C 0 0 0 0 0 0 0
0 0 0 0 0\n0.81090.05530. F 0 0 0 0 0 0
0 0 0 0 0 0\n -0.42660.76970. Br 0 0 0 0 0
0 0 0 0 0 0 0\n -0.0141 -0.7697 0. Cl 0 0 0 0 0
0 0 0 0 0 0 0\n -0.8109 -0.15830. C 0 0 0 0 0
0 0 0 0 0 0 0\n 1 2 1 6\n 1 3 1 0\n 1 4 1 0\n 1
5 1 0\nM END\n'
quit()
In the PG cartridge I lose the conformer of the input. My implementation
looks like this:
rdkit_io.c:
PG_FUNCTION_INFO_V1(mol_to_ctab);
Datum mol_to_ctab(PG_FUNCTION_ARGS);
Datum
mol_to_ctab(PG_FUNCTION_ARGS) {
CROMol mol;
char*str;
int len;
fcinfo-flinfo-fn_extra = SearchMolCache(
fcinfo-flinfo-fn_extra,
fcinfo-flinfo-fn_mcxt,
PG_GETARG_DATUM(0),
NULL, mol, NULL);
bool createDepictionIfMissing = PG_GETARG_BOOL(1);
str = makeCtabText(mol, len, createDepictionIfMissing);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
adapter.cpp:
extern C char *
makeCtabText(CROMol data, int *len, bool createDepictionIfMissing) {
ROMol *mol = (ROMol*)data;
try {
ereport(NOTICE,
(errcode(ERRCODE_SUCCESSFUL_COMPLETION),
errmsg(mol conformer count = %d,
mol-getNumConformers(;
if (createDepictionIfMissing mol-getNumConformers() == 0) {
RDDepict::compute2DCoords(*mol);
}
StringData = MolToMolBlock(*mol);
} catch (...) {
ereport(WARNING,
(errcode(ERRCODE_WARNING),
errmsg(makeCtabText: problems converting molecule to
CTAB)));
StringData=;
}
*len = StringData.size();
return (char*)StringData.c_str();
}
If I run the Python example equivalent from psql:
postgres=# select mol_to_ctab(mol_from_ctab('chiral1.mol
ChemDraw04200416412D
5 4 0 0 0 0 0 0 0 0999 V2000
-0.01410.05530. C 0 0 0 0 0 0 0 0 0 0 0 0
0.81090.05530. F 0 0 0 0 0 0 0 0 0 0 0 0
-0.42660.76970. Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.0141 -0.76970. Cl 0 0 0 0 0 0 0 0 0 0 0 0
-0.8109 -0.15830. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 1
1 5 1 0
M END', false));
*NOTICE: mol conformer count = 0*
mol_to_ctab
---
+
RDKit 2D +
+
5 4 0 0 0 0 0 0 0 0999 V2000 +
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0+
-1.50000.0. F 0 0 0 0 0 0 0 0 0 0 0 0+
-0. -1.50000. Br 0 0 0 0 0 0 0 0 0 0 0 0+
0.1.50000. Cl 0 0 0 0 0 0 0 0 0 0 0 0+
1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0+
1 2 1 6 +
1 3 1 0 +
1 4 1 0 +
1 5 1 0 +
M END +
(1 row)
postgres=#
Something I missed about querying a mol for conformers ? As of now I
lose the input conformer and the code will always output a
calculated-from-scratch depiction.
Cheers
-- Jan
--
Subversion Kills Productivity. Get off Subversion Make the Move to
Re: [Rdkit-discuss] Pg cartridge - mol_to_ctab() and trouble with conformers.
Hi Greg,
Thanks for the explanation.
I added this to rdkit_io.c in mol_from_ctab():
+ bool keepConformer = PG_GETARG_BOOL(1);
- mol = parseMolCTAB(data,false,true);
+ mol = parseMolCTAB(data,keepConformer,true);
and then I can get the expected behavior and have my tests complete
successfully. Yes :-).
I will go ahead and create a pull request for mol_to_ctab(). The tests
for mol_to_ctab() will assume that mol_from_ctab() uses the optional
parameter to keep the conformer.
Cheers
-- Jan
On 2014-03-05 13:25, Greg Landrum wrote:
Hi Jan,
The below behavior is the result of a bug
(https://github.com/rdkit/rdkit/issues/229).
mol_from_ctab() takes an (undocumented) optional argument that is
supposed to determine whether or not the molecule's conformation is
stored in the database. The default is to not store the conformation;
this reduces the size of the database and the speed at which molecules
are depickled. The bug is that even if you try to keep the
conformation the argument is ignored and the conformation is discarded.
I'll get this fixed tomorrow morning. Alternatively, if you want to
fix it now, the change just needs to be made in the definition of
mol_from_ctab() in rdkit_io.c
-greg
On Wed, Mar 5, 2014 at 10:27 AM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi,
About ready to push a changeset for implementing mol_to_ctab(),
but I would like it to play nice and preserve input depictions.
Ideally I would like the following
select mol_to_ctab(mol_from_ctab(input-molfile));
to output a molfile where the coordinates of input-molfile are
preserved.
If I do that in Python it works:
from rdkit import Chem
m = Chem.MolFromMolBlock(chiral1.mol
... ChemDraw04200416412D
...
... 5 4 0 0 0 0 0 0 0 0999 V2000
...-0.01410.05530. C 0 0 0 0 0 0 0 0
0 0 0 0
... 0.81090.05530. F 0 0 0 0 0 0 0 0
0 0 0 0
...-0.42660.76970. Br 0 0 0 0 0 0 0 0
0 0 0 0
...-0.0141 -0.76970. Cl 0 0 0 0 0 0 0 0
0 0 0 0
...-0.8109 -0.15830. C 0 0 0 0 0 0 0 0
0 0 0 0
... 1 2 1 0
... 1 3 1 0
... 1 4 1 1
... 1 5 1 0
... M END)
m
rdkit.Chem.rdchem.Mol object at 0x1240980
* m.GetNumConformers()**
**1*
Chem.MolToMolBlock(m)
'chiral1.mol\n RDKit 2D\n\n 5 4 0 0 0 0 0
0 0 0999 V2000\n -0.01410.0553 0. C 0 0 0 0
0 0 0 0 0 0 0 0\n 0.81090.05530. F 0 0
0 0 0 0 0 0 0 0 0 0\n -0.42660.76970.
Br 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0141 -0.7697
0. Cl 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8109
-0.15830. C 0 0 0 0 0 0 0 0 0 0 0 0\n 1
2 1 6\n 1 3 1 0\n 1 4 1 0\n 1 5 1 0\nM END\n'
quit()
In the PG cartridge I lose the conformer of the input. My
implementation looks like this:
rdkit_io.c:
PG_FUNCTION_INFO_V1(mol_to_ctab);
Datum mol_to_ctab(PG_FUNCTION_ARGS);
Datum
mol_to_ctab(PG_FUNCTION_ARGS) {
CROMol mol;
char*str;
int len;
fcinfo-flinfo-fn_extra = SearchMolCache(
fcinfo-flinfo-fn_extra,
fcinfo-flinfo-fn_mcxt,
PG_GETARG_DATUM(0),
NULL, mol, NULL);
bool createDepictionIfMissing = PG_GETARG_BOOL(1);
str = makeCtabText(mol, len, createDepictionIfMissing);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
adapter.cpp:
extern C char *
makeCtabText(CROMol data, int *len, bool
createDepictionIfMissing) {
ROMol *mol = (ROMol*)data;
try {
ereport(NOTICE,
(errcode(ERRCODE_SUCCESSFUL_COMPLETION),
errmsg(mol conformer count = %d,
mol-getNumConformers(;
if (createDepictionIfMissing mol-getNumConformers() ==
0) {
RDDepict::compute2DCoords(*mol);
}
StringData = MolToMolBlock(*mol);
} catch (...) {
ereport(WARNING,
(errcode(ERRCODE_WARNING),
errmsg(makeCtabText: problems converting
molecule to CTAB)));
StringData=;
}
*len = StringData.size();
return (char*)StringData.c_str();
}
If I run the Python example equivalent from psql:
postgres=# select mol_to_ctab(mol_from_ctab('chiral1.mol
ChemDraw04200416412D
5 4 0 0 0 0 0 0 0 0999 V2000
-0.0141
[Rdkit-discuss] Announce: RDKit in Oracle - via pypl cartridge.
Hi RDKitters, I have dabbled with calling RDKit from Oracle and have succeeded. It is done via an Oracle cartridge that makes it possible to call Python scripts from Oracle. The cartridge is not nearly as sophisticated as Postgres' support for Python, but it gets the job done. The cartridge is open source, BSD-licensed, and can be downloaded from here: http://biochemfusion.com/downloads/pypl_2014-02-27.zip - Yes, it's only an 8.3 KB download. The cartridge was created on a Linux machine with CentOS 6.2 and Oracle 11g. It shouldn't be too hard to make it compile on Windows too, but I haven't had the need yet. With the cartridge we can create Oracle functions like below that operate on MDL molfiles, returning SMILES and LogP values: create function mol_to_smiles(molfile in clob) return varchar2 is begin return pypl.run_script( 'from rdkit import Chem' || Chr(10) || 'from rdkit.Chem import Descriptors' || Chr(10) || 'molfile = ' || molfile || '' || Chr(10) || 'result = Chem.MolToSmiles(Chem.MolFromMolBlock(molfile))', 'result'); end; / create function mol_logp(molfile in clob) return number is begin return to_number(pypl.run_script( 'from rdkit import Chem' || Chr(10) || 'from rdkit.Chem import Descriptors' || Chr(10) || 'molfile = ' || molfile || '' || Chr(10) || 'result = str(Descriptors.MolLogP(Chem.MolFromMolBlock(molfile)))', 'result')); end; / If we have a COMPOUNDS table where the STRUCTURE column has the molecule stored in Accelrys Direct format, we can then do the following select: select id, mol_to_smiles(molfile(structure)) as smiles, mol_logp(molfile(structure)) as logp from compounds where id = 3; *ID**SMILES**LOGP* 1 O=C(O)c1c1 1.3848 2 CCC(=O)OCCOc1c1 2.0186 3 CC1=CC(=O)C=CC1=O 0.6407 [The molfile() function is an Accelrys Direct function that produces a molfile CLOB from the STUCTURE BLOB column.] There you have it - RDKit functionality directly in an Oracle database. Hope that you will find this useful. Cheers -- Jan -- Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?
On 2014-02-26 11:04, Greg Landrum wrote: On Wed, Feb 26, 2014 at 10:56 AM, Gianluca Sforna gia...@gmail.com wrote: On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst Jensen j...@biochemfusion.com wrote: I am testing if rdkit can be used from Oracle on a customer (test!) database. And said database runs on a CentOS 5.3 server - no OS upgrade in the near future. First step is to get rdkit working in Python 2.4 on that server. For a start, you can make your life easier by adding the EPEL repository and pulling python26 package from there. Yeah, I am pretty sure that there is python code that is not going to work with 2.4 IIRC the only real blocker that prevented me from building RDKit against CentOS5 + EPEL was flex Fortunately, flex is no longer required, so that one is gone. -greg Thanks, Gianluca and Greg. The EPEL repository looks like it could save the day, giving me a tool chain so I can build rdkit. I'll give it a try! Cheers -- Jan -- Biochemfusion ApS CVR(VAT) No. DK 32 05 74 46 by Jan Holst Jensen e-mail: j...@biochemfusion.com Lindegrdsvej 44, 2. TV Web: http://biochemfusion.com DK-2920 Charlottenlund, Copenhagen Phone: +45 30 48 00 50 . -- Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit cartridge - opposite of mol_from_ctab() would be nice.
Hi TJ, Interesting approach. I have also used plpython to get to rdkit functionality that were not in the postgres cartridge. Very useful. Cheers -- Jan On 2014-02-24 21:41, TJ O'Donnell wrote: Hi All I would like to announce the availability of a somewhat different rdkit-based postgresql extension. This uses rdkit for all the basic cheminformatics functions (canonical smiles, molfile handling, smarts matching, fingerprints, etc.) but is based on the use of postgres' plpython language. This does not use the existing rdkit postgres cartridge, although I have demonstrated that the two can be used side-by-side (via the use of rdkit pickled mol objects). I hope this use of python might make it easier to extend postgres even further with additional functions based on rdkit. The code can be checked out from sourceforge using this: svn checkout svn://svn.code.sf.net/p/sci3d/code/trunk/openchord/src/rdkit http://svn.code.sf.net/p/sci3d/code/trunk/openchord/src/rdkit chord This is a work in progress, so I would appreciate any feedback. There are still some wrinkles that need to be ironed out. I plan to document the installation and useage better, probably using github. TJ O'Donnell On Sat, Feb 22, 2014 at 10:53 PM, Greg Landrum greg.land...@gmail.com mailto:greg.land...@gmail.com wrote: On Fri, Feb 21, 2014 at 5:45 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: Hi Greg, It would be great to gain the experience. I am working on a registration project where we will likely need to surface additional functions in the cartridge, just to try them out. So, knowing how to do that in a way where things that turn out useful can be contributed back cleanly would be great. Sounds good. if structures don't have conformers Ah, yes; good question. Decisions, decisions... I'll dodge the question :-) and say it sounds like a perfect fit for an optional parameter, e.g. mol_to_ctab(m mol, add_depiction_if_missing bool default true) I would go for default true because I believe that is the general preference. Having the optional argument that defaults to true make sense to me. Here's an attempt to briefly summarize what needs to be changed in order to add the new functionality: - Add mol_to_ctab to rdkit_io.c - Add molToCtabText (or some such thing) to adapter.cpp and rdkit.h - Add mol_to_ctab() definitions to rdkit.sql91.in http://rdkit.sql91.in and, if you want to support older versions of postgres, rdkit.sql.in http://rdkit.sql.in - Update link dependencies in Makefile if necessary (will be necessary if you add depictions) - Add tests to one of the files in sql/ (the most logical place is probably rdkit-91.sql and rdkit-pre91.sql if you are supporting older versions) and the corresponding output file in expected/ I think that's it. -greg Cheers -- Jan On 2014-02-21 16:47, Greg Landrum wrote: Hi Jan, Great idea. I'd be happy to add it, but I can also talk you through it if you want to gain the experience. One important question: if structures don't have conformers (if they are loaded from SMILES, for example), should ctabs with all zero coordinates be generated or should depictions be generated? -greg On Fri, Feb 21, 2014 at 2:23 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: Hi Greg, Are there any plans for a mol_*to*_ctab() function in the PG cartridge ? Would make SD file export from the database a bit easier. If there are no immediate plans, I can take a stab at adding it myself. * Looks like rdkit_io.c is the place to add it ? * Should I manually define the new SQL function in rdkit.sql.in http://rdkit.sql.in, or is there some higher-level place I should add it instead ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Managing the Performance of Cloud-Based Applications Take
[Rdkit-discuss] rdkit RPM for CentOS 5.3 ?
Hi RDKitters, OK - CentOS 5.3 is getting ancient, but: Does anyone have an rdkit RPM or just a binary build for CentOS 5.3 that works with its standard Python 2.4 ? The build process doesn't look so fun on such an old OS. I am testing if rdkit can be used from Oracle on a customer (test!) database. And said database runs on a CentOS 5.3 server - no OS upgrade in the near future. First step is to get rdkit working in Python 2.4 on that server. Cheers -- Jan -- Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Pg cartridge: Linking issue when adding depiction functionality.
Hi Greg,
I now have a working version of mol_to_ctab() - except when I add in
depiction generation. There is a linking issue I don't understand.
In adapter.cpp I have added this function that implements the C++ part
of mol_to_ctab():
extern C char *
makeCtabText(CROMol data, int *len, bool createDepictionIfMissing) {
ROMol *mol = (ROMol*)data;
try {
if (createDepictionIfMissing mol-getNumConformers() == 0) {
RDDepict::compute2DCoords(*mol);
}
StringData = MolToMolBlock(*mol);
} catch (...) {
ereport(WARNING,
(errcode(ERRCODE_WARNING),
errmsg(makeCtabText: problems converting molecule to
CTAB)));
StringData=;
}
*len = StringData.size();
return (char*)StringData.c_str();
}
But, postgres then won't start (I preload the 'rdkit' library) and in
the postgres startup log I see a complaint about unresolved symbols.
Those are caused by the RDDepict::compute2DCoords() call. If I compile
without the RDDepict::... line, all is well, and the cartridge loads.
I check the built rdkit.so (with the depiction call):
[jhje@bcfregbuild rdkit]$ nm -D rdkit.so | grep U |grep RD
U
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DES3_S3_S3_
U
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DEd
U
_ZNK6RDGeom11Transform2D14TransformPointERNS_7Point2DE
[jhje@bcfregbuild rdkit]$
So I do a naive search for those unresolved symbols in rdkit's lib
directory to see what libs are needed:
[jhje@bcfregbuild lib]$ grep
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DES3_S3_S3_ *.a
Binary file libDepictor_static.a matches
Binary file libRDGeometryLib_static.a matches
[jhje@bcfregbuild lib]$ grep
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DEd *.a
Binary file libDepictor_static.a matches
Binary file libRDGeometryLib_static.a matches
[jhje@bcfregbuild lib]$ grep
_ZNK6RDGeom11Transform2D14TransformPointERNS_7Point2DE *.a
Binary file libDepictor_static.a matches
Binary file libRDGeometryLib_static.a matches
[jhje@bcfregbuild lib]$
I have added Depictor to the RDKLIBS in the Makefile - RDGeometryLib was
already there:
RDKLIBS = ${INCHILIBS} [...] -lDataStructs -lRDGeometryLib
-lRDGeneral *-lDepictor*
So I would have thought that all was well. But I still have these three
unlinked symbols after adding the Depictor lib and rebuilding. Some
secondary dependencies ... ? I hope that I can slap my forehead and say
DUH when I am told the reason why...
Cheers
-- Jan
--
Managing the Performance of Cloud-Based Applications
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Re: [Rdkit-discuss] Pg cartridge: Linking issue when adding depiction functionality.
RDKLIBS changed:
- ... -lRDGeometryLib -lRDGeneral -lDepictor
+ ... -lDepictor -lRDGeometryLib -lRDGeneral
And lo, there was much rejoicing and slapping of foreheads - that did
it. Thanks!
Cheers
-- Jan
On 2014-02-23 12:56, Greg Landrum wrote:
Jan,
It is probably the order of the libraries (static linking can
introduce that).
Try moving the depiction lib to the beginning of the libs list
-greg
On Sunday, February 23, 2014, Jan Holst Jensen j...@biochemfusion.com
mailto:j...@biochemfusion.com wrote:
Hi Greg,
I now have a working version of mol_to_ctab() - except when I add
in depiction generation. There is a linking issue I don't understand.
In adapter.cpp I have added this function that implements the C++
part of mol_to_ctab():
extern C char *
makeCtabText(CROMol data, int *len, bool
createDepictionIfMissing) {
ROMol *mol = (ROMol*)data;
try {
if (createDepictionIfMissing mol-getNumConformers() ==
0) {
RDDepict::compute2DCoords(*mol);
}
StringData = MolToMolBlock(*mol);
} catch (...) {
ereport(WARNING,
(errcode(ERRCODE_WARNING),
errmsg(makeCtabText: problems converting
molecule to CTAB)));
StringData=;
}
*len = StringData.size();
return (char*)StringData.c_str();
}
But, postgres then won't start (I preload the 'rdkit' library) and
in the postgres startup log I see a complaint about unresolved
symbols. Those are caused by the RDDepict::compute2DCoords() call.
If I compile without the RDDepict::... line, all is well, and the
cartridge loads.
I check the built rdkit.so (with the depiction call):
[jhje@bcfregbuild rdkit]$ nm -D rdkit.so | grep U |grep RD
U
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DES3_S3_S3_
U
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DEd
U
_ZNK6RDGeom11Transform2D14TransformPointERNS_7Point2DE
[jhje@bcfregbuild rdkit]$
So I do a naive search for those unresolved symbols in rdkit's lib
directory to see what libs are needed:
[jhje@bcfregbuild lib]$ grep
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DES3_S3_S3_ *.a
Binary file libDepictor_static.a matches
Binary file libRDGeometryLib_static.a matches
[jhje@bcfregbuild lib]$ grep
_ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DEd *.a
Binary file libDepictor_static.a matches
Binary file libRDGeometryLib_static.a matches
[jhje@bcfregbuild lib]$ grep
_ZNK6RDGeom11Transform2D14TransformPointERNS_7Point2DE *.a
Binary file libDepictor_static.a matches
Binary file libRDGeometryLib_static.a matches
[jhje@bcfregbuild lib]$
I have added Depictor to the RDKLIBS in the Makefile -
RDGeometryLib was already there:
RDKLIBS = ${INCHILIBS} [...] -lDataStructs
-lRDGeometryLib -lRDGeneral *-lDepictor*
So I would have thought that all was well. But I still have these
three unlinked symbols after adding the Depictor lib and
rebuilding. Some secondary dependencies ... ? I hope that I can
slap my forehead and say DUH when I am told the reason why...
Cheers
-- Jan
--
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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Re: [Rdkit-discuss] RDKit nodes in KNIME stopped working suddenly
On 2014-02-21 11:04, Michal Krompiec wrote: Hello, We've been using the RDKit nodes in KNIME for quite a while without any problems. But suddenly they ceased to work on some computers, while still working on other ones. Tried with a fresh KNIME installation with latest RDKit nodes - same problem. What could be wrong? I pasted the warning/error messages below: WARNRDKitTypesPluginActivator Library file GraphMolWrap.dll found: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\GraphMolWrap.dll ERROR RDKitTypesPluginActivator Loading of library GraphMolWrap.dll failed (possibly a subsequent error): C:\Temp\knime_2.9.1\configuration\org.eclipse.osgi\bundles\libtemp\224_0\GraphMolWrap.dll: Can't find dependent libraries ERROR RDKitTypesPluginActivator The library GraphMolWrap.dll has dependency issues. Please run a dependency walker on this file to find out what is missing. ERROR RDKitTypesPluginActivator Suggestion for fix: Please correct your system libraries based on the outcome of the dependency walker. WARNHistogram 2 columns without a valid domain will be ignored. In order to calculate the domain use the Nominal Values or Domain Calculator node. WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries Thanks in advance, Michal Hello Michal, Could it be missing VC++ runtime DLLs on those machines ? Do you have MSVCP100.DLL and MSVCR100.DLL in your path ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit cartridge - opposite of mol_from_ctab() would be nice.
Hi Greg, Are there any plans for a mol_*to*_ctab() function in the PG cartridge ? Would make SD file export from the database a bit easier. If there are no immediate plans, I can take a stab at adding it myself. * Looks like rdkit_io.c is the place to add it ? * Should I manually define the new SQL function in rdkit.sql.in, or is there some higher-level place I should add it instead ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit cartridge - opposite of mol_from_ctab() would be nice.
Hi Greg, It would be great to gain the experience. I am working on a registration project where we will likely need to surface additional functions in the cartridge, just to try them out. So, knowing how to do that in a way where things that turn out useful can be contributed back cleanly would be great. if structures don't have conformers Ah, yes; good question. Decisions, decisions... I'll dodge the question :-) and say it sounds like a perfect fit for an optional parameter, e.g. mol_to_ctab(m mol, add_depiction_if_missing bool default true) I would go for default true because I believe that is the general preference. Cheers -- Jan On 2014-02-21 16:47, Greg Landrum wrote: Hi Jan, Great idea. I'd be happy to add it, but I can also talk you through it if you want to gain the experience. One important question: if structures don't have conformers (if they are loaded from SMILES, for example), should ctabs with all zero coordinates be generated or should depictions be generated? -greg On Fri, Feb 21, 2014 at 2:23 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: Hi Greg, Are there any plans for a mol_*to*_ctab() function in the PG cartridge ? Would make SD file export from the database a bit easier. If there are no immediate plans, I can take a stab at adding it myself. * Looks like rdkit_io.c is the place to add it ? * Should I manually define the new SQL function in rdkit.sql.in http://rdkit.sql.in, or is there some higher-level place I should add it instead ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] flexmatch in RDKit cartridge?
Hi George et al,
flexmatch(... 'all') is the most strict exact match that the
Symyx/Accelrys cartridge has. You can relax the matching behavior to
varying degrees by passing it different options, e.g. using 'tau'
instead of 'all' will make the identity check tautomer-agnostic (to the
extent that the cartridge will perceive tautomers correctly - an
interesting discussion topic in itself).
The various options to flexmatch() are well documented in the Accelrys
documentation for the cartridge, but I don't know if that is publicly
available.
The short answer in my opinion: Yes, @= should be the equivalent of
flexmatch(m1, m2, 'all'). To emulate flexmatch(..., 'all') with rdkit, I
find a small gotcha with regards to chiral matching:
-- Clearly not identical.
postgres=# select mol('CCC') @= mol('CCF');
?column?
--
f
(1 row)
-- Clearly identical.
postgres=# select mol('CCC') @= mol('CCC');
?column?
--
t
(1 row)
-- Ala versus dAla - should *not* be identical ?
postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@@H](N)C(=O)O');
?column?
--
t
(1 row)
To get the expected behavior of @= you need to turn on chiral matching.
Even though the parameter says that is controls SSS behavior it
apparently also has an effect on exact matching:
postgres=# set rdkit.do_chiral_sss=true;
SET
-- Ala versus dAla - no longer identical.
postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@@H](N)C(=O)O');
?column?
--
f
(1 row)
-- Ala versus Ala - phew, identical.
postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@H](N)C(=O)O');
?column?
--
t
(1 row)
Cheers
-- Jan
On 2014-02-20 13:46, George Papadatos wrote:
Hi there,
Wouldn't that be (at least partly) possible with an exact structure
search?
* @= : returns whether or not two molecules are the same.
Cheers,
George
On 20 February 2014 11:59, Greg Landrum greg.land...@gmail.com
mailto:greg.land...@gmail.com wrote:
Sounds interesting. Can anyone provide a pointer to a doc with
more specific info about what this actually does?
On Thursday, February 20, 2014, Micha? Nowotka mmm...@gmail.com
mailto:mmm...@gmail.com wrote:
Hi,
Symix cartridge defines something called flexmatch - Finds
records that are an exact match of the 2D or 3D structure that
you specify in the query.
Is there anything similar in RDKit cartridge? I looked into
documentation and couldn't find this feature.
Regards,
Michal Nowotka
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Re: [Rdkit-discuss] Chem.MolToMolBlock() does not switch to V3000 format as expected, when number of atoms or bonds 999.
On 2013-12-20 04:57, Greg Landrum wrote: Hi Jan On Thu, Dec 19, 2013 at 11:32 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: The first lines of C:/temp/big.mol are: HERCEPTIN FAB (ANTIBODY) - LIGHT CHAIN RDKit 3D 78908023 0 0 0 0 0 0 0 0999 V2000 34.5390 88.7520 88.2980 N 0 0 0 0 0 0 0 0 0 0 0 0 34.7910 87.4610 89.0350 C 0 0 2 0 0 0 0 0 0 0 0 0 35.9070 86.7790 88.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 which is unreadable since there are 7890 atoms and 8023 bonds and V2000 format supports max. 999 atoms/bonds. I would have expected RDKit to switch to V3000 format automatically (?). I don't see any parameter in MolToMolBlock() that can force V3000 output ? That's a perfectly reasonable expectation, but, unfortunately, the RDKit has a small hole in the functionality it provides: there is no V3000 mol block writer. I just added the feature request in github and will try to get it in for the next release. Sorry for the inconvenience. -greg Ah, OK. No worries; sounds like I am the only one who has run into it this far. I'll just use a different output format for now. Cheers -- Jan -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] install error
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 $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't be found. Please note that I have turned on the flag of inchi. Thanks. Yingfeng -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] install error
OK, that looks fine. And I assume you build directly in /opt/RDKit_latest/latest/, so 'make install' puts files in /opt/RDKit_latest/latest/lib/. The only other thing that comes to my mind is if your boost libraries are included in LD_LIBRARY_PATH. Cheers -- Jan On 2013-06-05 16:55, Yingfeng Wang wrote: Yes, I did. export RDBASE=/opt/RDKit_latest/latest export LD_LIBRARY_PATH=$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 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI strings from molfiles - stereo perception.
Dear Greg,
On 2013-05-01 09:58, Greg Landrum wrote:
Dear Jan,
On Mon, Apr 29, 2013 at 8:03 AM, Jan Holst Jensen j...@biochemfusion.com
wrote:
Hi RDKitters,
I wonder why the InChI strings generated by RDKit differ from the ones
generated by the standard IUPAC inchi-1 executable.
At least some were due to an RDKit bug that has been fixed for a while
(it's in the 2013.03 release). The fix isn't reflected in the knime
nodes because we haven't done an update of the knime binaries in a
while; that's coming in the next day or so.
Ah - sounds wonderful. Thanks.
Out of sheer laziness my Python-enabled RDKit builds have been without
InChI support so I couldn't compare with the KNIME nodes - just assumed
that they behaved identically. Well... as they say Assumption is the
mother of all sc***-ups :-).
OK, now those InChI samples look like they are heavy on fringe cases and
perhaps thus likely to really stress toolkits.
These are the best kind. :-)
Indeed :-).
So I took something more peaceful and ran a peptide from PubChem through
(pubchem_71296070.mol - attached).
In [4]: Chem.MolToInchi(Chem.MolFromMolFile('pubchem_71296070.mol'))
Out[4]:
'InChI=1S/C33H55N9O10/c1-18(43)26(37)31(49)40-23(16-20-10-4-3-5-11-20)30(48)39-21(12-6-8-14-34)28(46)38-22(13-7-9-15-35)29(47)42-27(19(2)44)32(50)41-24(33(51)52)17-25(36)45/h3-5,10-11,18-19,21-24,26-27,43-44H,6-9,12-17,34-35,37H2,1-2H3,(H2,36,45)(H,38,46)(H,39,48)(H,40,49)(H,41,50)(H,42,47)(H,51,52)/t18-,19-,21+,22+,23+,24+,26+,27+/m1/s1'
also looks fine.
Yep. Everything should be in order then.
Cheers
-- Jan
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[Rdkit-discuss] InChI strings from molfiles - stereo perception.
Hi RDKitters, I wonder why the InChI strings generated by RDKit differ from the ones generated by the standard IUPAC inchi-1 executable. I have used the IUPAC inchi-1 executable from a command line to generate IUPAC InChI strings (the executable that comes pre-built with the InChI 1.04 binary download). RDKit InChI strings were generated with the RDKit KNIME nodes, this version: RDKit KNIME integration2.1.0.201302211506 I constructed a KNIME workflow that reads in an SD-file, uses the Molecule to RDKit node and then the RDKit To InChI node with default options to generate RDKit InChI strings. I ran the standard InChI example file Samples.sdf through the KNIME workflow and compared with the InChIs generated from the IUPAC executable. A number of InChI strings are different; it seems to be almost all stereo-related. For example: InChI strings generated for spiro.mol (spiro.mol - attached): IUPAC: InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3/t2*7-,8-,9-/m10/s1 RDKit: InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3 and stertaut.mol (stertaut.mol - attached): IUPAC: InChI=1S/C6H6O5/c7-1-2-3(5(8)9)4(2)6(10)11/h1,3-4,7H,(H,8,9)(H,10,11)/b2-1-/t3-,4+/m0/s1 RDKit: InChI=1S/C6H6O5/c7-1-2-3(5(8)9)4(2)6(10)11/h1,3-4,7H,(H,8,9)(H,10,11)/t3-,4-/m1/s1 OK, now those InChI samples look like they are heavy on fringe cases and perhaps thus likely to really stress toolkits. So I took something more peaceful and ran a peptide from PubChem through (pubchem_71296070.mol - attached). IUPAC: InChI=1S/C33H55N9O10/c1-18(43)26(37)31(49)40-23(16-20-10-4-3-5-11-20)30(48)39-21(12-6-8-14-34)28(46)38-22(13-7-9-15-35)29(47)42-27(19(2)44)32(50)41-24(33(51)52)17-25(36)45/h3-5,10-11,18-19,21-24,26-27,43-44H,6-9,12-17,34-35,37H2,1-2H3,(H2,36,45)(H,38,46)(H,39,48)(H,40,49)(H,41,50)(H,42,47)(H,51,52)/t18-,19-,21+,22+,23+,24+,26+,27+/m1/s1 RDKit: InChI=1S/C33H55N9O10/c1-18(43)26(37)31(49)40-23(16-20-10-4-3-5-11-20)30(48)39-21(12-6-8-14-34)28(46)38-22(13-7-9-15-35)29(47)42-27(19(2)44)32(50)41-24(33(51)52)17-25(36)45/h3-5,10-11,18-19,21-24,26-27,43-44H,6-9,12-17,34-35,37H2,1-2H3,(H2,36,45)(H,38,46)(H,39,48)(H,40,49)(H,41,50)(H,42,47)(H,51,52)/t18-,19-,21+,22+,23+,24+,26+,27+/m0/s1 The only difference in this case is that IUPAC outputs an InChI string with /m0 and RDKit an InChI with /m1. As far as I can understand from the InChI FAQ the /m0 /m1 difference indicates that these are different enantiomers. I converted the InChIs back to molecule with the InChI to RDKit KNIME node. The molecule generated from the IUPAC InChI (from-iupac-inchi.mol - attached) faithfully reconstructs the original PubChem molecule. When I construct a molecule from the RDKit InChI (from-rdkit-inchi.mol - attached), all the stereo centers have been inverted (as expected - different enantiomer). Is there a good explanation for this ? Cheers -- Jan 71296070 -OEChem-04201305312D 107107 0 1 0 0 0 0 0999 V2000 8.06221.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 10.6603 -1.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 13.2583 -1.75000. O 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -1.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 13.25831.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 2.86601.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 2.86604.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 16.72240.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 15.8564 -1.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 16.72241.25000. O 0 0 0 0 0 0 0 0 0 0 0 0 8.9282 -0.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 6.33010.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 11.52630.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 4.59811.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 14.1244 -0.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 11.52634.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 8.9282 -4.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 4.59813.25000. N 0 0 0 0 0 0 0 0 0 0 0 0 15.85642.75000. N 0 0 0 0 0 0 0 0 0 0 0 0 7.1962 -0.25000. C 0 0 1 0 0 0 0 0 0 0 0 0 9.79420.25000. C 0 0 1 0 0 0 0 0 0 0 0 0 7.1962 -1.25000. C 0 0 0 0 0 0 0 0 0 0 0 0 9.79421.25000. C 0 0 0 0 0 0 0 0 0 0 0 0 8.0622 -1.75000. C 0 0 0 0 0 0 0 0 0 0 0 0 10.66031.75000. C 0 0 0 0 0 0 0 0 0 0 0 0 8.06220.25000. C 0 0 0 0 0 0 0 0 0 0 0 0 10.6603 -0.25000. C 0 0 0 0 0 0 0 0 0 0 0 0 4.59810.25000. C 0 0 2 0 0 0 0 0 0 0 0 0 10.66032.75000. C 0
[Rdkit-discuss] PG cartridge - Strange SearchMolCache() usage in rdkit_op.c
Hi RDKitters, I now have the Postgres cartridge code compiling on 64-bit Windows. I had to add a few explicit casts to dodge C2440 compiler errors but nothing strange there. What puzzles me are the compile errors I saw when compiling rdkit_op.c. rdkit.h defines SearchMolCache() like this: void* SearchMolCache( void *cache, struct MemoryContextData * ctx, Datum a, Mol **m, CROMol *mol, bytea **sign); and it is called with 6 parameters all over the place - except in rdkit_op.c where an extra seventh NULL parameter is consistently added. That results in a: rdkit_op.c(75) : error C2660: 'SearchMolCache' : function does not take 7 arguments which makes good sense to me. Why don't I see this error when compiling on Linux ? I first though that it was because I am compiling in C++ mode (C mode is pretty limited when using MSVC) but compiling rdkit_op.c in C mode still gives me: rdkit_op.c(75) : warning C4020: 'SearchMolCache' : too many actual parameters Is it because gcc is more laid-back than MSVC and thinks that hey, an extra parameter on the stack - no worries, or what's happening here ? Disclaimer: I don't have much C experience, only a couple of years programming C++. Anyway, I removed the extra NULL parameter and now it compiles. I will post patches when I get the linking sorted out and the cartridge runs. Cheers -- Jan -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit pgSQL cartridge on 64-bit Windows, anyone ?
On 2012-11-14 10:30, paul.czodrow...@merckgroup.com wrote:
Dear Jan,
nope - but this reminds me on one UGM topic:
Could anyone provide a 64bit Win7 build?
Well, a couple of notes along the way to building the PostgreSQL
cartridge for Windows. This one is for building 64-bit RDKit on Windows.
I am building on a Windows Server 2008 R2 x64 machine with Visual Studio
2010, cygwin, boost 1.51 (both x86 and x64 present), and cmake. Note
that I have built without Python wrappers and without Java wrappers.
I downloaded RDKit 2012_09_1 and generated a VS solution file with
cmake. Started Visual Studio and changed the build configuraton to
Release/x64.
Only half of the projects build, the others fail with a linker error. I
found three reasons for this:
1) cmake is apparently a little too smart when it locates boost
libraries. I had changed my PATH to include the x64 boost libs instead
of the x86 libs but still cmake was clever enough to find the x86 libs
(perhaps because they were installed in the default installation path).
I renamed the directory name of the x86 boost libs and set BOOST_ROOT to
point to the x64 boost libs - not sure which one did the trick but it
helped.
2) cmake generates project files that link EXEs with a /machine:X86
flag. If you look in $RDBASE/build/CMakeCache.txt you can find this line
which must be the one responsible:
CMAKE_EXE_LINKER_FLAGS:STRING=' /STACK:1000 /machine:X86 '
I could not really figure out where this came from. Perhaps cmake just
adds it per default when no machine type is explicity specified (?). But
I had cygwin installed, so I did this (my $RDBASE is C:\RDKit_2012_09_1\):
cd /cygdrive/C/RDKit_2012_09_1/build/
find . -name *.vcxproj -type f -exec sed -i
s/machine:X86/machine:X64/ '{}' \;
3) After the above changes an ALL_BUILD build still gives me 50
succeeded, 31 failed. The failed ones have the linker error LNK2001:
unresolved external symbol class boost::system::error_category. I did
apply the patches Greg sent for the boost::thread_resource_error build
problem 2012-11-18, but it needs a couple of additional fixes.
In $RDBASE/Code/GraphMol/CMakeLists.txt all the rdkit_test()
expressions - 8 in total - need to link in ${Boost_SYSTEM_LIBRARY}, so e.g.
rdkit_test(graphmolTest1 test1.cpp LINK_LIBRARIES GraphMol
RDGeometryLib RDGeneral)
becomes
rdkit_test(graphmolTest1 test1.cpp LINK_LIBRARIES
${Boost_SYSTEM_LIBRARY} GraphMol RDGeometryLib RDGeneral)
And that also needs to be fixed in all the CMakeLists.txt files in the
following subdirectories of GraphMol/ :
ChemReactions
ChemTransforms
Depictor
DistGeomHelpers
FileParsers
Fingerprints
ForceFieldHelpers
FragCatalog
MolAlign
MolCatalog
MolChemicalFeatures
MolTransforms
ShapeHelpers
SLNParse
SmilesParse
SubGraphs
Substruct
Once those things were fixed I got a 64-bit build of RDKit. And all 44
tests pass :-).
The build generates tons of warnings, but they are mostly harmless ones
about conversion from 'size_t' to 'unsigned int', possible loss of data.
Next: Cartridge building. Stay tuned...
Cheers
-- Jan
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Re: [Rdkit-discuss] Yet another build question - boost::thread_resource_error not found when building 2012_09_1.
Hi Riccardo,
On 2012-11-16 13:29, Riccardo Vianello wrote:
Hi Jan,
On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
[...]
../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to
`boost::thread_resource_error::~thread_resource_error()'
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/graphmolIterTest] Error 1
make[1]: *** [Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all] Error 2
make: *** [all] Error 2
I encontered a similar link problem in building rdkit on an oldish
linux x86_64 machine with boost 1.39 (that, according to the cmake
build files, is the minimum required version), but I couldn't yet find
the time to investigate the details. For the time being I worked
around it with the addition of
find_package(Boost 1.39.0 COMPONENTS thread REQUIRED)
in $RDBASE/CMakeLists.txt (after the assignment of
Boost_ADDITIONAL_VERSIONS and before if(RDK_BUILD_PYTHON_WRAPPERS))
and with the addition of ${Boost_THREAD_LIBRARY} to the GraphMol's
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt
Excellent! I added such a line to $RDBASE/CMakeLists.txt:
if(MSVC)
SET(Boost_ADDITIONAL_VERSIONS 1.481.48.0 1.45 1.45.0
1.44 1.44.0 1.43 1.43.0 1.42 1.42.0 1.41 1.41.0 1.40
1.40.0)
endif(MSVC)
+ find_package(Boost 1.40.0 COMPONENTS thread REQUIRED)
if(RDK_BUILD_PYTHON_WRAPPERS)
#---
and added ${Boost_THREAD_LIBRARY} after each occurrence of
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt. I now have a
build of 2012_09_1 that passes all tests. Thanks :-) !!
Cheers
-- Jan
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Re: [Rdkit-discuss] Yet another build question - boost::thread_resource_error not found when building 2012_09_1.
Quick follow-up:
For the postgres cartridge I also needed to add this line to the Makefile:
SHLIB_LINK += -pthread
+ SHLIB_LINK += -lboost_thread
ifndef BOOSTHOME
BOOSTHOME=/usr/local/include
endif
Don't know if it is more appropriate to link boost_thread statically for
the cartridge, but this works OK for me - on that machine at least.
Cheers
-- Jan
__
Hi Riccardo,
On 2012-11-16 13:29, Riccardo Vianello wrote:
Hi Jan,
On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
[...]
../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to
`boost::thread_resource_error::~thread_resource_error()'
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/graphmolIterTest] Error 1
make[1]: *** [Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all] Error 2
make: *** [all] Error 2
I encontered a similar link problem in building rdkit on an oldish
linux x86_64 machine with boost 1.39 (that, according to the cmake
build files, is the minimum required version), but I couldn't yet find
the time to investigate the details. For the time being I worked
around it with the addition of
find_package(Boost 1.39.0 COMPONENTS thread REQUIRED)
in $RDBASE/CMakeLists.txt (after the assignment of
Boost_ADDITIONAL_VERSIONS and before if(RDK_BUILD_PYTHON_WRAPPERS))
and with the addition of ${Boost_THREAD_LIBRARY} to the GraphMol's
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt
Excellent! I added such a line to $RDBASE/CMakeLists.txt:
if(MSVC)
SET(Boost_ADDITIONAL_VERSIONS 1.481.48.0 1.45 1.45.0
1.44 1.44.0 1.43 1.43.0 1.42 1.42.0 1.41 1.41.0 1.40
1.40.0)
endif(MSVC)
+ find_package(Boost 1.40.0 COMPONENTS thread REQUIRED)
if(RDK_BUILD_PYTHON_WRAPPERS)
#---
and added ${Boost_THREAD_LIBRARY} after each occurrence of
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt. I now have a
build of 2012_09_1 that passes all tests. Thanks :-) !!
Cheers
-- Jan
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[Rdkit-discuss] RDKit pgSQL cartridge on 64-bit Windows, anyone ?
Hi RDKitters, Before I embark on this journey - has anyone else attempted compiling and running the RDKit pgSQL cartridge on 64-bit Windows ? Gotchas, success stories, and fiaskos/war stories would be equally appreciated :-). Cheers -- Jan Holst Jensen -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] [Rdkit-devel] 2012.09 (Q3 2012) RDKit release
On 2012-10-21 21:15, Gianluca Sforna wrote: On Sun, Oct 21, 2012 at 5:12 AM, Greg Landrum greg.land...@gmail.com wrote: I'm very happy to announce that the next version of the RDKit -- 2012.09 (a.k.a Q3 2012) -- is released. Hi Greg, sorry, I didn't it before but trying to rebuild the RPMs I'm getting a test error: 76/76 Test #76: pythonTestDirChem ***Failed 29.80 sec 99% tests passed, 1 tests failed out of 76 Total Test time (real) = 106.14 sec The following tests FAILED: 76 - pythonTestDirChem (Failed) Errors while running CTest make: *** [test] Error 8 How do I find which of the tests in there is failing? Some expect a failure so I can't readily tell from the log which ones are problematic. Hi Gianluca, ctest --output-on-failure should give you a lot more information so you can pinpoint the cause. At least it has helped me in the past. Cheers -- Jan -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] C++ - Strange error message thrown by MolDataStreamToMol.
On 2012-09-15 05:40, Greg Landrum wrote:
Hi Jan,
On Sat, Sep 15, 2012 at 12:47 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
I have now managed to produce a nice little self-contained DLL that uses
RDKit to do substructure mapping. It receives a query and a target molecule
as two MDL molfile strings. When the inputs are valid it behaves well and
returns the atom mapping to me. Yes :-).
Excellent!
However, when I give it an invalid MDL molfile as input, e.g. a text file
with regular prose, MolDataStreamToMol() throws a highly unexpected error
message.
This piece of my test code:
ifstream query_file (C:\\SubstructData\\results.txt);
auto_ptrRWMol query (NULL);
unsigned int line = 0;
try {
query.reset( MolDataStreamToMol(query_file, line, false, false,
false) );
} catch (std::exception e) {
cout STD-ERROR: e.what() endl;
return 1;
} catch (...) {
cout UNK-ERROR: Unknown exception. endl;
return 1;
}
produces this output:
[00:13:24] CTAB version string invalid at line 4
STD-ERROR: Unknown exception
In MolFileParser.cpp line 1881 I can locate the reported error message:
std::ostringstream errout;
erroutCTAB version string invalid at line line;
if(strictParsing){
if(res) delete res;
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) errout.str() std::endl;
}
Since I run with strictParsing==false the BOOST_LOG(rdWarningLog) call must
be the one that emits the first line of output, and I assume that the boost
warning log does not throw an exception. I haven't been able to figure out
where the exception gets thrown, but that must be later in the code.
If I switch to strict parsing (last parameter in MolDataStreamToMol() set to
true) I don't see the boost log message anymore, only the single line
STD-ERROR: Unknown exception. So strict parsing actually yields less error
message context.
I hope the exception error message can be changed to something more
meaningful ?
I would guess that the exception being thrown is a FileParseException.
These don't do anything to override the what() method, so you get the
unknown exception text. I will fix that.
Here's the code from the python wrapper for constructing a molecule
from a mol block
($RDBASE/Code/GraphMol/Wrap/rdmolfiles.cpp:MolFromMolFile()). It
catches the exceptions that are likely to arise and returns a NULL if
something fails. This might be useful:
RWMol *newM=0;
try {
newM = MolFileToMol(molFilename, sanitize,removeHs,strictParsing);
} catch (RDKit::BadFileException e) {
PyErr_SetString(PyExc_IOError,e.message());
throw python::error_already_set();
} catch (RDKit::FileParseException e) {
BOOST_LOG(rdWarningLog) e.message() std::endl;
} catch (...) {
}
return static_castROMol *(newM);
-greg
Hi Greg,
Ah, so the actual message is in .message() instead of .what() - that
explains it. I changed my test code to:
try {
query.reset( MolDataStreamToMol(query_file, line, false,
false, true) );
*} catch (RDKit::BadFileException e) {**
**cout RDK-ERROR: e.message() endl;**
**return 1;**
**} catch (RDKit::FileParseException e) {**
**cout RDK-ERROR: e.message() endl;**
**return 1;*
} catch (std::exception e) {
cout STD-ERROR: e.what() endl;
return 1;
} catch (...) {
cout UNK-ERROR: Unknown exception. endl;
return 1;
}
and now I get this output:
RDK-ERROR: CTAB version string invalid at line 4
Problem solved for now - thanks :-). Having the actual message available
in .what() as well in future will be nice though.
Cheers
-- Jan
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[Rdkit-discuss] C++ - Strange error message thrown by MolDataStreamToMol.
Hi,
I have now managed to produce a nice little self-contained DLL that uses
RDKit to do substructure mapping. It receives a query and a target
molecule as two MDL molfile strings. When the inputs are valid it
behaves well and returns the atom mapping to me. Yes :-).
However, when I give it an invalid MDL molfile as input, e.g. a text
file with regular prose, MolDataStreamToMol() throws a highly unexpected
error message.
This piece of my test code:
ifstream query_file (C:\\SubstructData\\results.txt);
auto_ptrRWMol query (NULL);
unsigned int line = 0;
try {
query.reset( MolDataStreamToMol(query_file, line, false, false,
false) );
} catch (std::exception e) {
cout STD-ERROR: e.what() endl;
return 1;
} catch (...) {
cout UNK-ERROR: Unknown exception. endl;
return 1;
}
produces this output:
[00:13:24] CTAB version string invalid at line 4
STD-ERROR: *Unknown exception*
In MolFileParser.cpp line 1881 I can locate the reported error message:
std::ostringstream errout;
errout*CTAB version string invalid at line* line;
if(strictParsing){
if(res) delete res;
throw FileParseException(errout.str());
} else {
* BOOST_LOG(rdWarningLog) errout.str() std::endl;*
}
Since I run with strictParsing==false the BOOST_LOG(rdWarningLog) call
must be the one that emits the first line of output, and I assume that
the boost warning log does not throw an exception. I haven't been able
to figure out where the exception gets thrown, but that must be later in
the code.
If I switch to strict parsing (last parameter in MolDataStreamToMol()
set to true) I don't see the boost log message anymore, only the single
line STD-ERROR: Unknown exception. So strict parsing actually yields
less error message context.
I hope the exception error message can be changed to something more
meaningful ?
Cheers
-- Jan
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[Rdkit-discuss] Windows build - build succeeds, half the tests fail with SEGFAULT.
Hi, I have attempted a build of RDKit_2012_06_1 on Windows. The build seems to go fine, but I get a SEGFAULT in half the tests when I run the test suite. Below follows what I have done. Any clues appreciated. Followed http://code.google.com/p/rdkit/wiki/BuildingOnWindows on a Windows 2008 R2 x64 server with VS2010 installed. Note: This will be a C++-only build, no Python installed. Install binary boost 1.51 - for VS2010 only, select all library types, install into C:\boost\ (delete the Program Files (x86) path bit). Install cmake - all defaults chosen (does not add cmake to PATH). Install Cygwin - add 'flex' and 'bison' to package selection, otherwise use defaults. Create a user env. var; PATH=C:\RDKit_2012_06_1\lib;C:\boost\boost_1_51\lib;C:\cygwin\bin Start cmake GUI. Point it to C:\RDKit_2012_06_1\ for source code location and C:\RDKit_2012_06_1\build\ for output location. Click Configure Select your compiler - Visual Studio 10, Use default native compilers. This will produce a handful of red error entries. Uncheck RDK_BUILD_PYTHON_WRAPPERS. Click Configure again. Still red entries, but apparently this is some caching done by cmake ? Click Configure again. We now have all-white entries shown. OK. Click Generate. Close cmake GUI. Start Visual Studio 2010. Open the RDKit.sln solution in C:\RDKit_2012_06_1\build\. Use the Configuration Manager to change the build to a Release Win32 build. It will be set per default to Debug Win32 by cmake. Build the ALL_BUILD target. Takes a while and generates warnings, but no errors. OK. Build the INSTALL target. OK - no issues. Test the build: Open a command prompt. cd to C:\RDKit_2012_06_1\build\ and run ctest C:\RDKit_2012_06_1\buildpath PATH=C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32 \WindowsPowerShell\v1.0\;C:\RDKit_2012_06_1\lib;C:\boost\boost_1_51\lib;C:\cygwi n\bin C:\RDKit_2012_06_1\buildc:\Program Files (x86)\CMake 2.8\bin\ctest.exe * 50% tests passed, 22 tests failed out of 44 Total Test time (real) = 31.89 sec The following tests FAILED: 2 - testDataStructs (SEGFAULT) 4 - testGrid (SEGFAULT) 13 - graphmolMolOpsTest (SEGFAULT) 15 - graphmoltestChirality (SEGFAULT) 16 - graphmoltestPickler (SEGFAULT) 18 - testDepictor (SEGFAULT) 21 - fileParsersTest1 (SEGFAULT) 22 - testMolSupplier (SEGFAULT) 23 - testMolWriter (SEGFAULT) 24 - testTplParser (SEGFAULT) 25 - testMol2ToMol (SEGFAULT) 27 - testReaction (SEGFAULT) 28 - testChemTransforms (SEGFAULT) 31 - testFragCatalog (SEGFAULT) 32 - testDescriptors (SEGFAULT) 33 - testFingerprints (SEGFAULT) 34 - testMolTransforms (SEGFAULT) 35 - testForceFieldHelpers (SEGFAULT) 36 - testDistGeomHelpers (SEGFAULT) 37 - testMolAlign (SEGFAULT) 38 - testFeatures (SEGFAULT) 39 - testShapeHelpers (SEGFAULT) Errors while running CTest _ Any clues as to a common denominator for these failures ? I did check that the boost DLLs I have installed in C:\boost\boost_1_51\lib\ are x86 (32-bit). Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] C-interface to RDKit libraries on Windows ?
Hi all, I would like to use RDKit from a Pascal (Delphi) program on Windows and for that a DLL with a C-style interface would be easiest to work with. At least that is an approach that always works. I downloaded RDKit_2012_06_1.win32.py27.zip but that only contains Python-specific binaries - am I correct here ? And there is no standard C-style interface to RDKit functionality ? The option that seems most likely to succeed is then that I program what I need in C++; build that as a DLL, and expose my own API for the subset of functionality I want as C-functions. Not a problem at all, but I would like to avoid setting up the Windows build process if I can - unless a talk or tutorial at the upcoming UGM will show me that it is quite easy :-). Any smarter alternatives to this ? Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] C-interface to RDKit libraries on Windows ?
On 2012-09-11 16:13, Greg Landrum wrote: Hi, On Tue, Sep 11, 2012 at 2:50 PM, Jan Holst Jensen j...@biochemfusion.com wrote: Hi all, I would like to use RDKit from a Pascal (Delphi) program on Windows and for that a DLL with a C-style interface would be easiest to work with. At least that is an approach that always works. I downloaded RDKit_2012_06_1.win32.py27.zip but that only contains Python-specific binaries - am I correct here ? And there is no standard C-style interface to RDKit functionality ? Correct: there's no standard C-style interface. The windows binaries really just include enough to use the python wrappers; they don't include DLLs. The option that seems most likely to succeed is then that I program what I need in C++; build that as a DLL, and expose my own API for the subset of functionality I want as C-functions. Not a problem at all, but I would like to avoid setting up the Windows build process if I can - unless a talk or tutorial at the upcoming UGM will show me that it is quite easy :-). There's nothing along those lines planned, but it's still pretty easy. :-) This wiki page has instructions for doing a windows build: http://code.google.com/p/rdkit/wiki/BuildingOnWindows Since you aren't interested in doing a Python build, you can ignore everything python-related. When you run the cmake GUI, just uncheck the RDK_BUILD_PYTHON_WRAPPERS variable after you run configure for the first time, then re-run configure. -greg Hi Greg, Thanks for the info. I'll give the Windows build a try :-). Cheers -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] windows binary install
On 2012-08-09 00:13, stanley5101 wrote: Hi, I'm trying to install the Windows binary of RDKit but having a problem. After from rdkit import Chem I get Traceback (most recent call last): File pyshell#1, line 1, in module from rdkit import Chem File C:\RDKit_2012_03_1\rdkit\Chem\__init__.py, line 18, in module from rdkit import rdBase ImportError: DLL load failed: %1 is not a valid Win32 application. I am using the Enthought Python distribution (EPD 7.0-2 32 bit python 2.7.1) on Windows 7 64 bit. I have the following environment variables: PYTHONPATH %RDBASE% RDBASE C:/RDKit_2012_03_1 Path ;%RDBASE%/lib; (amongst other things) I'd be grateful for any suggestions as to what is going wrong and a fix. Is the 64 bit OS an issue? thanks, Alan Hi Alan, It sounds like you are trying to load a 64-bit RDKit library in a 32-bit Python environment. Is that the case ? The RDKit bitness must be the same as the Python version you are using, which is 32-bit (EPD 7.0-2 *32 bit python* 2.7.1). Kind regards -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] cartridge problems
On 2012-05-31 07:52, Greg Landrum wrote: On Wed, May 30, 2012 at 4:50 PM, Greg Landrumgreg.land...@gmail.com wrote: On Wed, May 30, 2012 at 4:13 PM, Jan Holst Jensenj...@biochemfusion.com wrote: My failing Linux Mint is 32-bit like George's 12.04. Don't know if it is significant but it could be that the problem only occurs on 32-bit. Greg mentioned that he has successfully built and tested on Ubuntu 12.04 - was that 64-bit or 32-bit ? 64bit. I'll try it on a 32bit VM tonight. This morning I installed the rdkit on a clean 32bit Ubuntu 12.04 VM. While installing the cartridge, I was able to reproduce the problems you guys observed. I was also able to find the problem and a provisional fix for it. If you edit guc.c and replace the calls to DefineCustomRealVariable() with the following: Hi Greg, Did the changes to guc.c on my previously-failing Linux Mint VM. Did a make clean; make; sudo make install and lo and behold: postgres=# create extension rdkit; CREATE EXTENSION postgres=# And there was much joy in 32-bit land :-). Many thanks :-). I think we can then remove the Linux Mint behaves badly with rdkit observation from the books. Cheers -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] cartridge problems
On 2012-05-30 11:28, George Papadatos wrote: Hi Jan, I followed your advice and I added the new repo, however the problem still persists: [...] Again, _all_ the tests fail as do the create extension attempts. I even tried explicit postgresql-9.1 and postgresql-9.2 (beta version) but with the same sad results. Do I do something wrong here, like still installing the default postgresql packages and not the good ones? Hi George, Sorry for leading you on a wild goose chase here, but I wasn't sure whether you were using custom postgres packages or the standard Ubuntu package. As Adrian Schreyer has pointed out, if you are using the Ubuntu-supplied packages then you are already using Martin Pitt's build so it actually shouldn't make a difference. On 12.04 you do not need to add the PPA, PostgreSQL 9.1 is the official package there. In addition, the official packages are also provided by Martin Pitt, so the packages in the PPA and in the distro are actually the same. It only make sense on 10.04 (and those that do not ship with 9.1). I would go with Adrian's suggestion to check if the PG_VERSION_NUM is somehow mis-reported on your system. In fact, I will see if I still have the Linux Mint VM (that also has this behavior) somewhere and check it on that system too. Cheers -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] cartridge problems
On 2012-05-30 13:24, George Papadatos wrote:
Thanks to both of you.
I do not know how to check for the PG_VERSION_NUM.
Hi George,
I think the snippets below should do it. It shows what my Linux Mint
machine thinks. It seems to be reporting the correct version though,
even though it fails to load the cartridge (I have postgresql 9.1.3
installed from the standard Ubuntu 11.10 repository).
jhje@linux-dev-x86 ~ $ cat test.c
#include postgres.h
int main() {
int version_no = PG_VERSION_NUM;
printf(%d\n, version_no);
return 0;
}
jhje@linux-dev-x86 ~ $ cat make.sh
PG_INCLUDE_DIR=`pg_config | grep INCLUDEDIR-SERVER = | sed
s/INCLUDEDIR-SERVER = //`
echo Include dir found via 'pg_config' = $PG_INCLUDE_DIR
gcc test.c -I$PG_INCLUDE_DIR
jhje@linux-dev-x86 ~ $ . make.sh; ./a.out
Include dir found via 'pg_config' = /usr/include/postgresql/9.1/server
90103
jhje@linux-dev-x86 ~ $
Cheers
-- Jan
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Re: [Rdkit-discuss] cartridge problems
On 2012-05-30 13:24, George Papadatos wrote:
Thanks to both of you.
I do not know how to check for the PG_VERSION_NUM. I tried to edit to
guc.c by removing the conditional check of the PG_VERSION but with the
same results:
Adrian, is this what you meant?
DefineCustomRealVariable(
rdkit.tanimoto_threshold,
Lower threshold of Tanimoto similarity,
Molecules with similarity lower than
threshold are not similar by % operation,
rdkit_tanimoto_smlar_limit,
0.5,
0.0,
1.0,
PGC_USERSET,
0,
(GucRealCheckHook)TanimotoLimitAssign,
NULL,
NULL
);
DefineCustomRealVariable(
rdkit.dice_threshold,
Lower threshold of Dice similarity,
Molecules with similarity lower than
threshold are not similar by # operation,
rdkit_dice_smlar_limit,
0.5,
0.0,
1.0,
PGC_USERSET,
0,
(GucRealCheckHook)DiceLimitAssign,
NULL,
NULL
);
Regards,
George
Hi George,
I just tried the same on my VM, with no change for the better either. My
version of guc.c now looks like this:
static void
initRDKitGUC()
{
if (rdkit_guc_inited)
return;
DefineCustomRealVariable(
rdkit.tanimoto_threshold,
Lower threshold of Tanimoto similarity,
Molecules with similarity lower than
threshold are not similar by % operation,
rdkit_tanimoto_smlar_limit,
0.5,
0.0,
1.0,
PGC_USERSET,
0,
//if PG_VERSION_NUM = 90100
(GucRealCheckHook)TanimotoLimitAssign,
NULL,
//else
// TanimotoLimitAssign,
//endif
NULL
);
DefineCustomRealVariable(
rdkit.dice_threshold,
Lower threshold of Dice similarity,
Molecules with similarity lower than
threshold are not similar by # operation,
rdkit_dice_smlar_limit,
0.5,
0.0,
1.0,
PGC_USERSET,
0,
//if PG_VERSION_NUM = 90100
(GucRealCheckHook)DiceLimitAssign,
NULL,
//else
// DiceLimitAssign,
//endif
NULL
);
rdkit_guc_inited = true;
}
Did a cartridge make clean, make, sudo make install, and it still
fails for me with
postgres=# create extension rdkit;
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
The connection to the server was lost. Attempting reset: Succeeded.
postgres=#
Cheers
-- Jan
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Re: [Rdkit-discuss] cartridge problems
How odd. Adrian, are you using a 32-bit or 64-bit version of Ubuntu 12.04 ? Cheers -- Jan On 2012-05-30 15:26, Adrian Schreyer wrote: Yes, I could build and install the cartridge without problems (Release_2012.03.1) on 12.04. On Wed, May 30, 2012 at 2:23 PM, George Papadatosgpapada...@gmail.com wrote: Hi Jan, Mine is exactly the same: gcc test.c -I/usr/include/postgresql/9.1/server;./a.out 90103 So, I am back to square 1! I am starting to get a bit desperate here, has anyone ever successfully built the cartridge from the trunk on a plain Ubuntu 12.04? Many thanks for your help, George -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] cartridge problems
My failing Linux Mint is 32-bit like George's 12.04. Don't know if it is significant but it could be that the problem only occurs on 32-bit. Greg mentioned that he has successfully built and tested on Ubuntu 12.04 - was that 64-bit or 32-bit ? Cheers -- Jan On 2012-05-30 15:49, Adrian Schreyer wrote: 64-bit, PostgreSQL packages are from the official archive. I simply do 'make' followed by 'sudo make install' and then create schema rdkit; create extension rdkit with schema rdkit; and that's it. $ make installcheck /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=. --psqldir='/usr/lib/postgresql/9.1/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps (using postmaster on Unix socket, default port) == dropping database contrib_regression == DROP DATABASE == creating database contrib_regression == CREATE DATABASE ALTER DATABASE == running regression test queries== test rdkit-91 ... ok test props... ok test btree... ok test molgist ... ok test bfpgist-91 ... ok test sfpgist ... ok test slfpgist ... ok test fps ... ok = All 8 tests passed. = On Wed, May 30, 2012 at 2:43 PM, Jan Holst Jensenj...@biochemfusion.com wrote: How odd. Adrian, are you using a 32-bit or 64-bit version of Ubuntu 12.04 ? Cheers -- Jan On 2012-05-30 15:26, Adrian Schreyer wrote: Yes, I could build and install the cartridge without problems (Release_2012.03.1) on 12.04. On Wed, May 30, 2012 at 2:23 PM, George Papadatosgpapada...@gmail.com wrote: Hi Jan, Mine is exactly the same: gcc test.c -I/usr/include/postgresql/9.1/server;./a.out 90103 So, I am back to square 1! I am starting to get a bit desperate here, has anyone ever successfully built the cartridge from the trunk on a plain Ubuntu 12.04? Many thanks for your help, George -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Molecule with no atoms, so is it valid?
On 2012-04-30 13:41, Paul Emsley wrote: On 30/04/12 01:03, Eddie Cao wrote: Hi Andrew, I also prefer #2. #1 is not quite sensible because many readers like MolFromSmiles will return None on failure and it will be hard to distinguish bad input from an empty one if we choose to do #1. Semantically, in many RDKit use cases, None and Empty Mol are as different as a webpage not found (HTTP 404) and a blank web page. FWIW, I agree to #2 too. Paul. My humble opinion would also be that #2 is the best option. In line with the analogy given by Eddie, treating an empty molecule as an error is equivalent to saying that a blank string is equal to NULL - which would be unfortunate, since there is a big semantic difference. Also, imagine that you delete all atoms and bonds in a molecule in order to replace them. Enforcing the semantics of empty molecules are invalid should then cause your code to break half-way through the process ? Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
On 2012-04-26 05:32, Greg Landrum wrote:
I continue to be unable to reproduce these problems.
Running on a 64bit Ubuntu 11.10 VM I installed the following packages
using apt-get:
sudo apt-get install postgresql
sudo apt-get install postgresql-contrib postgresql-server-dev-all
I build the cartridge:
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make
Install it (notice the sudo):
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo make install
Create a postgresql account for my user:
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su postgres
postgres@ubuntu:/home/glandrum/RDKit_2012_03_1/Code/PgSQL/rdkit$
createuser glandrum
Shall the new role be a superuser? (y/n) y
And then run the tests:
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck
/usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=. --psqldir='/usr/lib/postgresql/9.1/bin'
--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91
sfpgist slfpgist fps
(using postmaster on Unix socket, default port)
== dropping database contrib_regression ==
NOTICE: database contrib_regression does not exist, skipping
DROP DATABASE
== creating database contrib_regression ==
CREATE DATABASE
ALTER DATABASE
== running regression test queries==
test rdkit-91 ... ok
test props... ok
test btree... ok
test molgist ... ok
test bfpgist-91 ... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
=
All 8 tests passed.
=
Can you please check your configuration to make sure that the packages
are all installed and the appropriate accounts are there?
-greg
Dear Greg,
On my Ubuntu 10.04 I can build against and install into Postgres 9.0
without any issues. I did a createuser jhje as postgres and then ran
the test suite.
jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck
/opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=. --psqldir=/opt/postgres/9.0/bin --dbname=contrib_regression
rdkit-pre91 props btree molgist bfpgist-pre91 sfpgist slfpgist fps
(using postmaster on Unix socket, port 5432)
== dropping database contrib_regression ==
DROP DATABASE
== creating database contrib_regression ==
CREATE DATABASE
ALTER DATABASE
== running regression test queries==
test rdkit-pre91 ... ok
test props... ok
test btree... ok
test molgist ... ok
test bfpgist-pre91... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
=
All 8 tests passed.
=
jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$
After having installed the cartridge as the postgres user with psql
/opt/postgres/9.0/share/postgresql/contrib/rdkit.sql:
postgres@ubuntu-lynet-test:~$ psql
Password:
psql (9.0.4)
Type help for help.
postgres=# select mol_amw('');
mol_amw
-
58.124
(1 row)
postgres=# show rdkit.tanimoto_threshold;
rdkit.tanimoto_threshold
--
0.5
(1 row)
postgres=#
But against postgres 9.1 both the test suite and the attempt to do
create extension rdkit fails with
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
On the Linux Mint VM I found that I didn't have the postgresql-contrib
package installed. I added it but it didn't make a difference.
Both of the VMs I have used are 32-bit and you are using a 64-bit VM. I
wonder if that is significant. I don't have a 64-bit Linux VM ready for
test building at the moment but let me see if I can establish one.
Kind regards
-- Jan Holst Jensen
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Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
On 2012-04-26 08:37, Gianluca Sforna wrote: On Thu, Apr 26, 2012 at 8:26 AM, Jan Holst Jensenj...@biochemfusion.com wrote: jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ After having installed the cartridge as the postgres user with psql /opt/postgres/9.0/share/postgresql/contrib/rdkit.sql: I am not able to dig details now, but IIRC there are two different cartridges, one for 8.x and another one for 9.x. Just to be sure, I'd double check you are installing the right one in there. Dear Gianluca, The cartridge is indeed postgres-version specifc. Which one is built depends on your postgres environment when you run make. On one machine I have both postgres 9.0 and 9.1 installed and so if I setup the 9.0 environment and run make, it will build the 9.0 cartridge. And vice versa. Like this (the third line in each block sources the version-specific postgres environment): jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export RDBASE=/home/jhje/RDKit_2012_03_1 jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export LD_LIBRARY_PATH=/home/jhje/RDKit_2012_03_1/lib/ jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . /opt/postgres/9.1/pg91-openscg.env jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make clean rm -f rdkit.so librdkit.a rm -f rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o rm -f rdkit--3.1.sql rm -rf results/ regression.diffs regression.out tmp_check/ log/ jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make cp rdkit.sql91.in rdkit--3.1.sql gcc -I/usr/local/include -I/home/jhje/RDKit_2012_03_1/Code -DRDKITVER='004100' -I. -I. -I/opt/postgres/9.1/include/postgresql/server -I/opt/postgres/9.1/include/postgresql/internal -D_GNU_SOURCE -I/usr/local/include/libxml2 -I/usr/local/openssl/include -I/usr/local/ldap-2.4.23/include -I/usr/local/include -fPIC -c -o rdkit_io.o rdkit_io.c ... jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export RDBASE=/home/jhje/RDKit_2012_03_1 jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export LD_LIBRARY_PATH=/home/jhje/RDKit_2012_03_1/lib/ jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . /opt/postgres/9.0/pg90-openscg.env jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make clean rm -f rdkit.so librdkit.a rm -f rdkit.sql rm -f rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o rm -rf results tmp_check log rm -f regression.diffs regression.out regress.out run_check.out jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make sed 's,MODULE_PATHNAME,$libdir/rdkit,g' rdkit.sql.in rdkit.sql gcc -I/usr/local/include -I/home/jhje/RDKit_2012_03_1/Code -DRDKITVER='004100' -I. -I. -I/opt/postgres/9.0/include/postgresql/server -I/opt/postgres/9.0/include/postgresql/internal -D_GNU_SOURCE -I/usr/local/include/libxml2 -I/usr/local/include -fPIC -c -o rdkit_io.o rdkit_io.c ... And you also have to take care that when you do make install as root that the environment is setup to point to your correct postgres version. You can verify that is the case by checking the output of make install and see what directories the library and SQL scripts are installed into, e.g. here I am installing into postgres 9.0: root@ubuntu-lynet-test:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/ root@ubuntu-lynet-test:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# . /opt/postgres/9.0/pg90-openscg.env root@ubuntu-lynet-test:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make install /bin/mkdir -p '/opt/postgres/9.0/lib/postgresql' /bin/mkdir -p '/opt/postgres/9.0/share/postgresql/contrib' /bin/sh /opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/opt/postgres/9.0/lib/postgresql/rdkit.so' /bin/sh /opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./uninstall_rdkit.sql '/opt/postgres/9.0/share/postgresql/contrib' /bin/sh /opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 rdkit.sql '/opt/postgres/9.0/share/postgresql/contrib' root@ubuntu-lynet-test:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# So yes, it can certainly get mixed up, but if you only have a single postgres version installed and you build and test on that same machine this should not be an issue. I haven't seen any differences in behavior between the 8.4 and 9.0 series. I think the build script only changes when you go to 9.1 (?). I have the cartridge running fine in postgres 9.0 for a while now and I also recently got it installed on a postgres 8.4.5 in an emulated Raspberry Pi (ARM architecture) without any issues. Kind regards -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond.
[Rdkit-discuss] Trouble installing 2012_03_1's PgSQL cartridge in Postgres 9.1. [Follow-up #2- on 64-bit Ubuntu 10.04.2]
Dear Greg, I can again reproduce the Postgres 9.1 issue, this time in a brand new 64-bit VM. Ubuntu 10.04.2 x86_64 server installed from scratch. gnome-desktop-environment installed, VMware tools installed. jhje@ubuntu-x64-build:~$ cat /etc/issue Ubuntu 10.04.2 LTS \n \l jhje@ubuntu-x64-build:~$ uname -a Linux ubuntu-x64-build 2.6.32-28-server #55-Ubuntu SMP Mon Jan 10 23:57:16 UTC 2011 x86_64 GNU/Linux jhje@ubuntu-x64-build:~$ Packages build-essential, bison, flex, boost libraries, numpy, cmake installed. RDKit_2012_03_1 builds (after the needed one-line patch to Wrap.h) and all tests pass. Installed OpenSCG postgresql 9.1.3 package (latest postgres for Ubuntu 10.04.2 is Pg 8.5, so not interesting). Set trust authentication for local connections in pg_hba.conf so rdkit postgres test suite can run without prompting for password. postgres@ubuntu-x64-build:~$ createuser jhje Shall the new role be a superuser? (y/n) y postgres@ubuntu-x64-build:~$ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . /opt/postgres/9.1/pg91-openscg.env jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make ... builds with the usual 3-4 warnings ... jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su - [sudo] password for jhje: root@ubuntu-x64-build:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/ root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# . /opt/postgres/9.1/pg91-openscg.env root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make install /bin/mkdir -p '/opt/postgres/9.1/lib/postgresql' /bin/mkdir -p '/opt/postgres/9.1/share/postgresql/extension' /bin/sh /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/opt/postgres/9.1/lib/postgresql/rdkit.so' /bin/sh /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/opt/postgres/9.1/share/postgresql/extension/' /bin/sh /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/opt/postgres/9.1/share/postgresql/extension/' root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=. --psqldir='/opt/postgres/9.1/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps (using postmaster on Unix socket, port 5432) == dropping database contrib_regression == NOTICE: database contrib_regression does not exist, skipping DROP DATABASE == creating database contrib_regression == CREATE DATABASE ALTER DATABASE == running regression test queries== test rdkit-91 ... FAILED (test process exited with exit code 2) test props... FAILED test btree... FAILED test molgist ... FAILED test bfpgist-91 ... FAILED test sfpgist ... FAILED test slfpgist ... FAILED test fps ... FAILED == 8 of 8 tests failed. == The differences that caused some tests to fail can be viewed in the file /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.diffs. A copy of the test summary that you see above is saved in the file /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.out. make: *** [installcheck] Error 1 jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ less regression.diffs [... ...] --- 4,9 -- SET client_min_messages = warning; \set ECHO none ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 ! connection to server was lost OK, this time around it is the dice_threshold instead of the tanimoto_threshold that cannot be initialized, but still... Hmmm... 'less' is reporting a linking issue, but only when the postgres environment has been loaded: jhje@ubuntu-x64-build:~$ less Missing filename (less --help for help) jhje@ubuntu-x64-build:~$ . /opt/postgres/9.1/pg91-openscg.env jhje@ubuntu-x64-build:~$ less less: Symbol `ospeed' has different size in shared object, consider re-linking Missing filename (less --help for help) jhje@ubuntu-x64-build:~$ echo $LD_LIBRARY_PATH /opt/postgres/9.1/lib: jhje@ubuntu-x64-build:~$ Could a library conflict be what causes rdkit to abort ? Kind regards -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Dear Greg, The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# This is an error message that's been reported before, but we never really did find a root cause. I will start from scratch on my VM with Ubuntu 11.10 and take careful notes as I'm doing the installation, then post those on the wiki. I don't have time to do it this morning, but I'll try and get to it tonight or tomorrow a.m. Best, -greg Thanks. Meanwhile, I got RDKit_2012_03_1 running fine in Postgres 9.0.4 (the OpenSCG version) on an Ubuntu 10.04 build server. I will try to install Postgres 9.1 on that server and see if the error can be reproduced with that setup. Kind regards -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] One-line patch for 2012_03_1 when compiling with boost 1.40.0 on Ubuntu 10.04.2.
Dear Greg, When compiling 2012_03_1 on Ubuntu 10.04.2 with boost 1.40.0 I get the following make error: [ 4%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o In file included from /home/jhje/RDKit_2012_03_1/Code/RDBoost/Wrap.cpp:16: /home/jhje/RDKit_2012_03_1/Code/RDBoost/Wrap.h: In function \u2018std::vectorT, std::allocator_CharT * pythonObjectToVect(boost::python::api::object, T)\u2019: /home/jhje/RDKit_2012_03_1/Code/RDBoost/Wrap.h:108: error: \u2018uint32_t\u2019 is not a member of \u2018boost\u2019 /home/jhje/RDKit_2012_03_1/Code/RDBoost/Wrap.h:108: error: expected \u2018;\u2019 before \u2018v\u2019 /home/jhje/RDKit_2012_03_1/Code/RDBoost/Wrap.h:109: error: \u2018v\u2019 was not declared in this scope /home/jhje/RDKit_2012_03_1/Code/RDBoost/Wrap.h:112: error: \u2018v\u2019 was not declared in this scope make[2]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o] Error 1 make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2 make: *** [all] Error 2 I found that this change to line 44 of Code/RDBoost/Wrap.h fixes the issue: #ifndef RDKIT_WRAP_DECL #define RDKIT_WRAP_DECL #endif #include boost/python/suite/indexing/vector_indexing_suite.hpp + #include boost/cstdint.hpp #include list_indexing_suite.hpp #include vector 'make test' subsequently pass OK - all 76 tests. I guess the change should be harmless to implement in general ? Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1. [Follow-up - testing on Ubuntu 10.04]
Meanwhile, I got RDKit_2012_03_1 running fine in Postgres 9.0.4 (the OpenSCG version) on an Ubuntu 10.04 build server. I will try to install Postgres 9.1 on that server and see if the error can be reproduced with that setup. Dear Greg, I have now installed Postgres 9.1 on the mentioned build server. Postgres 9.1 was installed via the DEB package from http://www.openscg.com/se/postgresql/packages.jsp I got RDKit_2012_03_1 compiled after implementing the one-line patch I sent a little earlier. The Postgres install error seems reproducible as I also get it here, which is a configuration quite different from the Linux Mint 12 developer VM I originally saw the issue on. postgres@ubuntu-lynet-test:~$ cat /etc/issue Ubuntu 10.04.2 LTS \n \l postgres@ubuntu-lynet-test:~$ uname -a Linux ubuntu-lynet-test 2.6.32-28-generic-pae #55-Ubuntu SMP Mon Jan 10 22:34:08 UTC 2011 i686 GNU/Linux postgres@ubuntu-lynet-test:~$ psql Password: psql.bin (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# Cheers -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Hi, I am having problems install the Postgres cartridge in Postgres 9.1 on Linux Mint 12 (which is based on Ubuntu 11.10). RDKit 2012_03_1 builds without any issues and all tests pass. The PgSQL cartridge builds fine too, and installs fine as seen below. jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ sudo make install /bin/mkdir -p '/usr/lib/postgresql/9.1/lib' /bin/mkdir -p '/usr/share/postgresql/9.1/extension' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/usr/lib/postgresql/9.1/lib/rdkit.so' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/usr/share/postgresql/9.1/extension/' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/usr/share/postgresql/9.1/extension/' jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ However, the make installcheck step fails. In the regression.diffs I see: [... tons of lines ...] --- 4,9 -- SET client_min_messages = warning; \set ECHO none ! FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 ! FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 ! connection to server was lost The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# /var/log/postgresql/postgres-9.1-main-log doesn't tell me anything extra: 2012-04-24 18:23:32 CEST LOG: invalid value for parameter rdkit.tanimoto_threshold: 0.5 2012-04-24 18:23:32 CEST STATEMENT: create extension rdkit; 2012-04-24 18:23:32 CEST FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 2012-04-24 18:23:32 CEST STATEMENT: create extension rdkit; Being in Denmark, I suspected regional settings, but apparently it is not the issue (?): postgres=# select 7.0/3; ?column? 2. (1 row) postgres=# \q The decimal separator used in Postgres is a period, not a comma as I feared. Any help appreciated :-). Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
