Re: [Rdkit-discuss] Setting location of wedge/hashes
Great. And as regards what the bond direction means...? It tells you whether it's a wedge or dash but doesn't seem to specify which end of the bond is the thin end. Is the BeginAtom of the bond always the thin end, or is any attached chiral atom always the thin end? - Noel On 10 September 2015 at 15:03, Greg Landrum wrote: > Agreed. If you set the bond wedging explicitly it should be preserved. > > Here's the issue, which includes links to the commits with the fix (that's > now checked in): > https://github.com/rdkit/rdkit/issues/611 > > -greg > > > On Mon, Sep 7, 2015 at 1:10 PM, Noel O'Boyle wrote: >> >> Hey Greg, >> >> I hope you had a good meeting. >> >> I was wondering whether it is possible to set the location of depicted >> wedge/hashes in a MOL file output. >> >> Right now, it seems that I can call WedgeHashBonds and that tells me >> where the wedge or hashes are via GetBondDir() (although I am still a >> bit confused as to which direction they are supposed to be). And I can >> set the BondDir fine... >> >> However, when I subsequently write out a MOL file it seems that any >> changes to the location of the BondDirs are just ignored. >> >> This is not a biggie for me, but it would be nice to be able to always >> set the same bond as the stereobond in a set of amino acids, as this >> makes it obvious which are D- versus L-. >> >> Regards, >>Noel >> >> >> -- >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Using Chem.WrapLogs()
Hi all,
I'd like to capture error messages during SMILES parsing, but am having
trouble getting this to work.
The following code raises an AssertionError, for example. Is there
something here I'm missing? I'm using this from a Windows 7 conda
environment, Python 2.7 64-bit, RDKit 2017.03.3, but a similar conda
environment is also failing for me on Linux.
import sys
from rdkit import Chem
Chem.WrapLogs()
from StringIO import StringIO
old_stderr = sys.stderr
sio = sys.stderr = StringIO()
mol = Chem.MolFromSmiles("c1c")
sys.stderr = old_stderr
assert sio.read() != ""
Regards,
- Noel
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Re: [Rdkit-discuss] Using Chem.WrapLogs()
Thanks Maciek,
Both of those solutions works on Linux, which is fine for my purposes.
Neither works on Windows (let me know if you want me to file a bug).
Regards,
- Noel
On 8 September 2017 at 15:05, Maciek Wójcikowski
wrote:
> Hi Noel,
>
> sio.seek(0) before assert or sio.getvalue() instead read().
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-09-08 15:51 GMT+02:00 Noel O'Boyle :
>
>> Hi all,
>>
>> I'd like to capture error messages during SMILES parsing, but am having
>> trouble getting this to work.
>>
>> The following code raises an AssertionError, for example. Is there
>> something here I'm missing? I'm using this from a Windows 7 conda
>> environment, Python 2.7 64-bit, RDKit 2017.03.3, but a similar conda
>> environment is also failing for me on Linux.
>>
>> import sys
>> from rdkit import Chem
>> Chem.WrapLogs()
>> from StringIO import StringIO
>>
>> old_stderr = sys.stderr
>> sio = sys.stderr = StringIO()
>>
>> mol = Chem.MolFromSmiles("c1c")
>> sys.stderr = old_stderr
>>
>> assert sio.read() != ""
>>
>> Regards,
>> - Noel
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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[Rdkit-discuss] What is RDkit?
Any chance of more info on what RDkit contains? E.g. an API, or a website. Although Open Source projects are infamous for incomplete documentation, you seem to have taken this to an extreme :-) I'm involved in other open source cheminformatics packages (via the BlueObelisk, with varying degrees of documentation it must be admitted) so it would be good to know to what extent there is overlap, and whether we could share code, etc... Noel
Re: [Rdkit-discuss] What is RDkit?
On 12/09/2007, Greg Landrum wrote: > Hi Noel, > > Sorry for the very slow posting of your message and reply; I was on > vacation until yesterday and needed to approve your posting since you > aren't subscribed to the discuss list; that shouldn't be a problem > from now on. Don't worry about it. Hope you had a good holiday. > On 8/27/07, Noel O'Boyle wrote: > > Any chance of more info on what RDkit contains? E.g. an API, or a > > website. Although Open Source projects are infamous for incomplete > > documentation, you seem to have taken this to an extreme :-) > > ah hah! that's where you're wrong! :-) > We actually do have have some documentation, we just don't have any > obvious links to it from sourceforge. This is an oversight on my part > and something I will clear up. > > There are some useful links here: > http://www.rdkit.org/ > specifically to the overview PDF: > http://www.rdkit.org/RDKit_Overview.pdf > and some (automatically generated and somewhat out of date) API documentation: > http://www.rdkit.org/C++_Docs Just a note: you can point the SF home page to go to whatever website you want. > There's also an introduction to using the code from Python on > sourceforge that provides something of an overview of the > functionality: > http://downloads.sourceforge.net/rdkit/GettingStartedInPython.pdf Great! I'll read up on it. > > I'm involved in other open source cheminformatics packages (via the > > BlueObelisk, with varying degrees of documentation it must be > > admitted) so it would be good to know to what extent there is overlap, > > and whether we could share code, etc... > > My last look at blue obelisk was, admittedly, a while ago, but I > somehow got the impression at the time that it was pretty > Java-centric. Is this true? I can understand your impression. I'm not into Java though. The other side is the C++ code of OpenBabel, and Python code for various things (e.g. GaussSum, cclib for comp chem, and Python bindings for OpenBabel). Also, the BO is involved in sharing chemical data, e.g. names of elements, atomic weights and so on, so that we don't keep having to re-enter this information in different software. (Check out Blue Obelisk Data Repository on google). Interoperability is also one of our goals. In the end, the BO is a loosely coupled bunch of chemists/computer scientists with largely the same goals but lots of different ideas about getting there. In short, I recommend subscribing to the mailing list, or the RSS feed, checking out the wiki, and keeping an eye on things. There's a couple of very interesting blogs too, if I do say so myself.. Noel > Regards, > -greg >
Re: [Rdkit-discuss] What is RDkit?
On 13/09/2007, Greg Landrum wrote: > On 9/13/07, Noel O'Boyle wrote: > > So on to the questions: > > (1) Can I believe my eyes? Is this really open source? A lot of the > > Python code has a very restrictive copyright statement right at the > > start (see Windows release, AllChem.py for example) > > The "All rights reserved" is, in my opinion, superseded by the > license.txt file (which is BSD, except for the GUI components, which > are GPL due to Qt license restrictions). It's really open source and > it's as open as we could make it without going public domain (I > consider the BSD license to be far more open than the GPL, which is > quite restrictive IMO). I would definitely encourage you to replace the "All rights reserved" to be replaced with something more friendly. I'll check out some codes I'm involved with and suggest a change. > > (4) Why haven't you publicised RDKit, if you don't mind me asking? For > > example, there is an excellent (if I do say so myself) website called > > Linux4Chemistry which lists the excellent (if you do say so yourself) > > YaEHMOP. Also there's the CCL mailing list. I only found RDKit because > > of trawling through the SF software map. Is this, um, shyness, > > intentional? > > There are many components to the answer to this question. Some are: > 1) Promotion isn't something I enjoy or am particularly good at. > 2) I'm kind of afraid of having more users. I do a lot of this as a > free-time project and I'm afraid of spending all my time answering > questions. This is, of course, a bit stupid because if the whole open > source thing works then other people will pitch in and help with those > questions. For that to happen I need those other people as users, > which requires that I find them, which... it's a Catch 22 Well...don't worry about the publicisation...you can leave that to me (I feel a blog post coming on :-) ) As regards too much time answering questions, cheminformatics toolkits are a pretty niche interest. Also, I try to avoid answering any question twice; i.e. I update the documentation if someone doesn't know how to do something, and you can always send them over to OpenBabel if they don't behave. But it'd be wrong to think that people will pitch in to answer questions - they don't. They are more forthcoming finding bugs though, which is useful too. > > (5) You may/not be aware but Numeric is deprecrated to the extent that > > it is not available for Python 2.5 on Windows. I had to replace a > > couple of "import Numeric"s with "from numpy import oldnumeric as > > Numeric", but this is only a temporary solution. > > The Numeric thing is a definite problem (though it works fine for me > with Python2.5 under windows). I made an attempt a while ago to port > the code to use numpy, but was immediately frustrated by the lack of > documentation available (unless you buy the book) and the very > aggressive response of the community when I complained about this. I'll help if I can, but I'd be relying on the unittests to ensure correctness. > > (6) It'd be nice to have an installer for the Python stuff...I've done > > this for OpenBabel. It's pretty easy. > > If you care to share how you did this, I'd be happy to learn. It's a nice > idea. Will do. In fact, the one major flaw with promoting your toolkit is that it's not clear how it's installed on Windows or on Linux. You might want to consider writing this up. > > (12) Interested in easily converting a ROMol to an OBMol and vice > > versa? I am. It'd be trivial to do this at the Python level. We could > > coordinate a bit to make the methods somewhat symmetrical. It would > > make it easy to unittest shared algorithms against each other, e.g. > > LogP calculation, SMILES, or whatever. > > It would be an interesting exercise. I'm not convinced that it would > be trivial to get it right. There's a lot of devil in the details of > things like aromaticity handling and general sanitization problems > (the RDKit is *very* picky about molecules being "clean"). Well, as you can imagine, there are several levels of information in a chemical structure. I was initially thinking of just sharing coordinates, and allowing each program to work the rest out from there. Do you have bond perception? Well, anyway, we will sort this out later. Thanks for all the answers, Noel
Re: [Rdkit-discuss] What is RDkit?
> Well...don't worry about the publicisation...you can leave that to me > (I feel a blog post coming on :-) ) As promised, here's a blog post: http://baoilleach.blogspot.com/2007/09/rdkit-not-just-yet-another.html Noel
Re: [Rdkit-discuss] Changing build systems?
Several of the blue-obelisk projects are currently moving to CMake right about now... Noel
[Rdkit-discuss] Problem using SDMolSupplier
I am finding it difficult to read an SDF file. The following program
(on Windows):
for mol in Chem.SDMolSupplier("head.sdf"):
print mol
gives the following error:
runtime error R6025
- pure virtual function call
I'm using the Jan2008 release, with numpy instead of Numeric (if that
makes any difference).
Regards,
Noel
[Rdkit-discuss] Molecular weight
Does RDKit make the molecular weight available somewhere? - I just can't find it anywhere. Noel
[Rdkit-discuss] Depiction
I've been looking into depiction in RDKit. It uses sping, which unfortunately looks like it's not very up to date. I know that BKChem has moved from sping to pycairo. At the moment, is it actually possible to make a PNG with RDKit? Noel
Re: [Rdkit-discuss] Depiction
The good news is that the code you sent works, but the bad news is that I get a lot of PIL deprecation warnings: C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1>"c:\Program Fi les\Python25"\python draw.py C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:125: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead self._pen.setink(0) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:137: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead self._pen.setink( (int(c.red*255), int(c.green*255), int(c.blue*255)) ) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:331: DeprecationWarning: 'setfill' is deprecated; use keyword argum ents instead self._pen.setfill(1) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:334: DeprecationWarning: 'setfill' is deprecated; use keyword argum ents instead self._pen.setfill(0) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:388: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead temppen.setink( (255,255,255) ) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:414: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead temppen.setink( (int(color.red*255), int(color.green*255), int(color.blue*255) ) ) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:415: DeprecationWarning: 'setfill' is deprecated; use keyword argum ents instead temppen.setfill(1) If I use this in the API I'm writing (did I mention that?) I'll have users all over me complaining. So I'll be happy to see you move to using more up to date code, whether or not it looks better :-) Actually, I can't access the attachment as I'm not receiving mail from the list - you should probably cc me in future (I suffer from one-too-many mailing lists). Regards, Noel On 01/04/2008, Noel O'Boyle wrote: > I've been looking into depiction in RDKit. It uses sping, which > unfortunately looks like it's not very up to date. I know that BKChem > has moved from sping to pycairo. At the moment, is it actually > possible to make a PNG with RDKit? > > > Noel >
[Rdkit-discuss] Isomeric smiles and explicit hydrogens
I've been trying to get my head around what's happening when I read
and write isomeric smiles. As a user, I hope that the same molecule
will also have the same isomeric SMILES. However, look at the
following examples using cinfony which read a SMILES string and write
an isomeric SMILES string...
I'm trying to specify the chirality of the carbon in
chlorobromomethane, but RDKit is not picking up on the chirality:
>>> rdk.readstring("smi", "[C](Cl)Br").write("iso")
'ClCBr'
(No chirality, as expected)
>>> rdk.readstring("smi", "[C@@H](Cl)Br").write("iso")
'Cl[CH]Br'
>>> rdk.readstring("smi", "[...@](Cl)Br").write("iso")
'ClCBr'
>>> rdk.readstring("smi", "c...@]br").write("iso")
'ClCBr'
>>> rdk.readstring("smi", "Cl[C@@H]Br").write("iso")
'Cl[CH]Br'
(Expected chirality, but didn't get it)
Let's try 1-chloro,1-bromoethane:
>>> rdk.readstring("smi", "Cl[C@@](Br)C").write("iso")
'CC(Cl)Br'
(Expected chirality, but didn't get it)
>>> rdk.readstring("smi", "Cl[C@@H](Br)C").write("iso")
'C[C@@H](Cl)Br'
(Expected chirality, and got it)
Is the problem with me or with RDKit?
On a related note, I have found that RDKit, when reading SDF files,
turns all of the hydrogens into implicit hydrogens. However, when
reading SMILES strings, it retains any explicit hydrogens specified in
C@@H expressions. This doesn't seem to be consistent and requires the
user to remove hydrogens if he/she wants to create a canonical smiles
string.
Apologies in advance if my understanding of SMILES is shaky.
Regards,
Noel
Re: [Rdkit-discuss] Isomeric smiles and explicit hydrogens
I think I've been misunderstanding the square brackets. I need to
RTFM, I think, after which I'll post here again if still confused.
Noel
On 14/04/2008, Noel O'Boyle wrote:
> I've been trying to get my head around what's happening when I read
> and write isomeric smiles. As a user, I hope that the same molecule
> will also have the same isomeric SMILES. However, look at the
> following examples using cinfony which read a SMILES string and write
> an isomeric SMILES string...
>
> I'm trying to specify the chirality of the carbon in
> chlorobromomethane, but RDKit is not picking up on the chirality:
>
> >>> rdk.readstring("smi", "[C](Cl)Br").write("iso")
> 'ClCBr'
> (No chirality, as expected)
>
> >>> rdk.readstring("smi", "[C@@H](Cl)Br").write("iso")
> 'Cl[CH]Br'
> >>> rdk.readstring("smi", "[...@](Cl)Br").write("iso")
> 'ClCBr'
> >>> rdk.readstring("smi", "c...@]br").write("iso")
> 'ClCBr'
> >>> rdk.readstring("smi", "Cl[C@@H]Br").write("iso")
> 'Cl[CH]Br'
> (Expected chirality, but didn't get it)
>
> Let's try 1-chloro,1-bromoethane:
>
> >>> rdk.readstring("smi", "Cl[C@@](Br)C").write("iso")
> 'CC(Cl)Br'
> (Expected chirality, but didn't get it)
> >>> rdk.readstring("smi", "Cl[C@@H](Br)C").write("iso")
> 'C[C@@H](Cl)Br'
> (Expected chirality, and got it)
>
> Is the problem with me or with RDKit?
>
> On a related note, I have found that RDKit, when reading SDF files,
> turns all of the hydrogens into implicit hydrogens. However, when
> reading SMILES strings, it retains any explicit hydrogens specified in
> C@@H expressions. This doesn't seem to be consistent and requires the
> user to remove hydrogens if he/she wants to create a canonical smiles
> string.
>
> Apologies in advance if my understanding of SMILES is shaky.
>
> Regards,
>
> Noel
>
Re: [Rdkit-discuss] Isomeric smiles and explicit hydrogens
And (egg on face) chlorobromomethane isn't chiral in the first
place...what was I thinking?
On 14/04/2008, Noel O'Boyle wrote:
> I've been trying to get my head around what's happening when I read
> and write isomeric smiles. As a user, I hope that the same molecule
> will also have the same isomeric SMILES. However, look at the
> following examples using cinfony which read a SMILES string and write
> an isomeric SMILES string...
>
> I'm trying to specify the chirality of the carbon in
> chlorobromomethane, but RDKit is not picking up on the chirality:
>
> >>> rdk.readstring("smi", "[C](Cl)Br").write("iso")
> 'ClCBr'
> (No chirality, as expected)
>
> >>> rdk.readstring("smi", "[C@@H](Cl)Br").write("iso")
> 'Cl[CH]Br'
> >>> rdk.readstring("smi", "[...@](Cl)Br").write("iso")
> 'ClCBr'
> >>> rdk.readstring("smi", "c...@]br").write("iso")
> 'ClCBr'
> >>> rdk.readstring("smi", "Cl[C@@H]Br").write("iso")
> 'Cl[CH]Br'
> (Expected chirality, but didn't get it)
>
> Let's try 1-chloro,1-bromoethane:
>
> >>> rdk.readstring("smi", "Cl[C@@](Br)C").write("iso")
> 'CC(Cl)Br'
> (Expected chirality, but didn't get it)
> >>> rdk.readstring("smi", "Cl[C@@H](Br)C").write("iso")
> 'C[C@@H](Cl)Br'
> (Expected chirality, and got it)
>
> Is the problem with me or with RDKit?
>
> On a related note, I have found that RDKit, when reading SDF files,
> turns all of the hydrogens into implicit hydrogens. However, when
> reading SMILES strings, it retains any explicit hydrogens specified in
> C@@H expressions. This doesn't seem to be consistent and requires the
> user to remove hydrogens if he/she wants to create a canonical smiles
> string.
>
> Apologies in advance if my understanding of SMILES is shaky.
>
> Regards,
>
> Noel
>
Re: [Rdkit-discuss] Isomeric smiles and explicit hydrogens
If I found a bug earlier, it was completely by accident. The following
though I think is also a bug. I find that I can invert the
stereocenter by adding and removing Hs.
>>> mol = rdk.readstring("smi", "C[C@@H](O)(Cl)c1c1")
>>> mol.write("iso")
'C[C@@H](O)(Cl)c1c1'
>>> mol.addh()
>>> mol.write("iso")
'[h]...@](Cl)(C([H])([H])[H])([H])c1c([H])c([H])c([H])c([H])c1[H]'
>>> mol.removeh()
>>> mol.write("iso")
'c...@h](O)(Cl)c1c1'
Can you tell whether the problem is when I add the Hs, or when I
remove them? I might be able to workaround if the adding is working
okay.
Noel
Re: [Rdkit-discuss] Isomeric smiles and explicit hydrogens
Wait a second, that molecule has five substituents on the isomeric C.
But I think we share the blame again this time, Greg, because I took
that structure from the RDKit Python tutorial Section 2.3. :-)
Noel
On 14/04/2008, Noel O'Boyle wrote:
> If I found a bug earlier, it was completely by accident. The following
> though I think is also a bug. I find that I can invert the
> stereocenter by adding and removing Hs.
>
> >>> mol = rdk.readstring("smi", "C[C@@H](O)(Cl)c1c1")
> >>> mol.write("iso")
> 'C[C@@H](O)(Cl)c1c1'
> >>> mol.addh()
> >>> mol.write("iso")
> '[h]...@](Cl)(C([H])([H])[H])([H])c1c([H])c([H])c([H])c([H])c1[H]'
> >>> mol.removeh()
> >>> mol.write("iso")
> 'c...@h](O)(Cl)c1c1'
>
> Can you tell whether the problem is when I add the Hs, or when I
> remove them? I might be able to workaround if the adding is working
> okay.
>
>
> Noel
>
[Rdkit-discuss] Building a molecule from scratch
I am running into trouble building a molecule from scratch. Let's say
the molecule represented by "F/C=C/F" (taken from the Daylight SMILES
tutorial). Here's the code to build it (according to me):
import Chem
# Set some lookups
_bondtypes = {1: Chem.BondType.SINGLE,
2: Chem.BondType.DOUBLE,
3: Chem.BondType.TRIPLE}
_bondstereo = {0: Chem.rdchem.BondStereo.STEREONONE,
1: Chem.rdchem.BondStereo.STEREOE,
2: Chem.rdchem.BondStereo.STEREOZ}
# Build F/C=C/F
rdmol = Chem.Mol()
rdedmol = Chem.EditableMol(rdmol)
for atomnum in [9, 6, 6, 9]:
rdatom = Chem.Atom(atomnum)
rdedmol.AddAtom(rdatom)
for bond in [(0,1,1), (1,2,2), (2,3,1)]:
rdedmol.AddBond(bond[0],
bond[1],
_bondtypes[bond[2]])
rdmol = rdedmol.GetMol()
for stereoID, newbond in zip([0, 1, 0], rdmol.GetBonds()):
newbond.SetStereo(_bondstereo[stereoID])
Chem.SanitizeMol(rdmol)
# Gets here fine
# Print the result
print Chem.MolToSmiles(rdmol, isomericSmiles=True)
# RuntimeError: Pre-condition Violation
What am I missing? It works fine if I use [0, 0, 0] for stereoID, so
it's something to do with the way I handle the stereoisomer.
Noel
Re: [Rdkit-discuss] Building a molecule from scratch
On 15/04/2008, Greg Landrum wrote: > The problem is here. I shouldn't even have exposed SetStereo to > Python. To indicate bond stereochemistry, you need to set the > directionalities of the neighboring single bonds. So you'd do: > [13] >>> rdmol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.ENDUPRIGHT) > [15] >>> rdmol.GetBondWithIdx(2).SetBondDir(Chem.BondDir.ENDUPRIGHT) > > Notice that this does not set the stereochemistry of the double bond: > > [16] >>> rdmol.GetBondWithIdx(1).GetStereo() > Out[16]: Chem.rdchem.BondStereo.STEREONONE > > The RDKit is, at the moment, lazy about stereochemistry : it doesn't > do the perception until it's required. So if you ask for SMILES: > > [17] >>> Chem.MolToSmiles(rdmol,True) > Out[17]: 'F/C=C/F' > > you get stereochemistry calculated: > [18] >>> rdmol.GetBondWithIdx(1).GetStereo() > Out[18]: Chem.rdchem.BondStereo.STEREOE > > If you want the stereochem information earlier, you can call: > Chem.AssignBondStereoCodes(rdmol) I'm afraid that the chunks are still too big - you need to break it down a bit more... What exactly do UPRIGHT and DOWNRIGHT mean and how exactly do they indicate the stereochemistry of the double bond? Do they correspond to the SMILES usage of slashes? Noel
[Rdkit-discuss] RuntimeError creating MolBlock
I've done it again :-/
>>> print Chem.MolToMolBlock(Chem.MolFromSmiles(""))
Traceback (most recent call last):
File "", line 1, in
RuntimeError: Pre-condition Violation
Noel
Re: [Rdkit-discuss] RuntimeError creating MolBlock
Yes, I should have said - I'm using the latest release on Windows.
On 22/04/2008, Adrian Schreyer wrote:
> Works for me, you probably have to update to the latest svn version.
>
> In [8]: import Chem
>
> In [9]: print Chem.MolToMolBlock(Chem.MolFromSmiles(""))
>
> RDKit
>
> 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
> 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. C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> M END
>
>
> On Tue, Apr 22, 2008 at 1:25 PM, Noel O'Boyle wrote:
> > I've done it again :-/
> >
> > >>> print Chem.MolToMolBlock(Chem.MolFromSmiles(""))
> > Traceback (most recent call last):
> > File "", line 1, in
> > RuntimeError: Pre-condition Violation
> >
> > Noel
> >
>
> > -
> > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> > Don't miss this year's exciting event. There's still time to save $100.
> > Use priority code J8TL2D2.
> >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > ___
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
>
Re: [Rdkit-discuss] RuntimeError creating MolBlock
On 22/04/2008, Greg Landrum wrote:
> Hi Noel,
>
>
> On Tue, Apr 22, 2008 at 2:48 PM, Noel O'Boyle wrote:
> > Yes, I should have said - I'm using the latest release on Windows.
> >
> >
>
>
> By latest release do you mean the Jan2008 release or did you do a
> build of the svn version yourself?
"The most recent officially-blessed version". Jan2008. :-)
> I just tried this with the svn version on windows:
> [4] >>> print Chem.MolToMolBlock(Chem.MolFromSmiles(""))
>
>
> RDKit
>
> 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
> 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. C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> M END
>
>
> so that looks ok
>
> I can reproduce the error using the Jan2008 release though. The way to
> solve the problem with the Jan release is to add 2D coords to the
> molecule:
> [5] >>> from Chem import AllChem
> [6] >>> m = Chem.MolFromSmiles('')
> [7] >>> AllChem.Compute2DCoords(m)
> Out[7]: 0
> [8] >>> print Chem.MolToMolBlock(m)
>
>
>
>
> 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
>
> 1.29900.75000. C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.5981 -0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.89710.75000. C 0 0 0 0 0 0 0 0 0 0 0 0
>
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> M END
>
Thanks,
Noel
[Rdkit-discuss] Comparison of Crippen params (RDKit vs. OB)
I threw together a Python script to compare the data files of OB and RDKit to see whether they contained the same figures. I haven't yet looked at the paper to verify these, but here are the preliminary results: MR In OB, not in RDKit: set([-0.57542]) In RDKit, not in OB: set([5.75389998]) LOGP In OB, not in RDKit: set([0.083902, -1.95, 0.081297, 0.0 14999, 0.14411]) In RDKit, not in OB: set([0.081194, 0.1411, 0.010501, 0. 083799, -0.19501]) The 0.1411 vs. 0.1441 error (LogP) in RDKit was identified yesterday or so by Greg. Noel
[Rdkit-discuss] 2D depiction with RDKit
I'm a bit confused by how RDKit calculates the 2D coordinates. I use AllChem.Compute2DCoords(mol, clearConfs = False) to calculate the 2D coordinates. Given an SD file containing a 2D depiction, RDKit appears to use those coordinates rather than generating its own. Can you confirm that this is the case, as this is a bit unexpected? Noel
Re: [Rdkit-discuss] 2D depiction with RDKit
On 24/04/2008, Greg Landrum wrote:
> Hi Noel,
>
>
> On Thu, Apr 24, 2008 at 12:03 PM, Noel O'Boyle wrote:
> > I'm a bit confused by how RDKit calculates the 2D coordinates. I use
> > AllChem.Compute2DCoords(mol, clearConfs = False) to calculate the 2D
> > coordinates.
> >
> > Given an SD file containing a 2D depiction, RDKit appears to use those
> > coordinates rather than generating its own. Can you confirm that this
> > is the case, as this is a bit unexpected?
>
>
> Take a look at the documentation for AllChem.Compute2DCoords
> (accessible in Python via: "help AllChem.Compute2DCoords).
> By setting clearConfs=False you have told the code to keep the
> existing conformation (the one read from the SD file) and to add the
> 2D conformation as a new one. If you had left that argument in its
> default value (True), then the existing conformation(s) would have
> been replaced with the new 2D one.
>
> an example:
> [5]>>> m = Chem.MolFromMolFile('foo.mol')
> [6]>>> m.GetNumConformers()
> Out[6] 1
> [7]>>> AllChem.Compute2DCoords(m,clearConfs=False)
> Out[7] 1
> [8]>>> m.GetNumConformers()
> Out[8] 2
> [9]>>> AllChem.Compute2DCoords(m)
> Out[9] 0
> [10]>>> m.GetNumConformers()
> Out[10] 1
Right. In my initial testing I only used SMILES strings, which of
course don't have any conformers to begin with.
Re: [Rdkit-discuss] Comparison of Crippen params (RDKit vs. OB)
In my original email, in an effort to simplify the comparison I introduced some rounding errors. The correct output is: MR In OB, not in RDKit: set([-0.57542]) In RDKit, not in OB: set([5.7536]) LOGP In OB, not in RDKit: set([0.084506, 0.081297, 0.1441 1, 0.083902, -1.95, 0.01508]) In RDKit, not in OB: set([-0.19501, 0.08387, 0.081291, 0 .084518, 0.1411, 0.010581]) There's an error in the MR data in OB (Me1) - I've corrected this in SVN. There are three cases in OB where the LogP data has been shortened to 3 decimal places (instead of the 4 that are in the paper), leading to the disagreement with RDKit, but I don't think these are worth changing. Noel On 24/04/2008, Greg Landrum wrote: > Noel, > > Thanks for doing this; it's a nice way to catch typos. > > > On Thu, Apr 24, 2008 at 9:03 AM, Noel O'Boyle wrote: > > MR > > In OB, not in RDKit: set([-0.57542]) > > In RDKit, not in OB: set([5.75389998]) > > > This is Me1 and is correct in the RDKit. > > > > LOGP > > In OB, not in RDKit: set([0.083902, -1.95, > 0.081297, 0.0 > > 14999, 0.14411]) > > In RDKit, not in OB: set([0.081194, 0.1411, > 0.010501, 0. > > 083799, -0.19501]) > > > > The 0.1411 vs. 0.1441 error (LogP) in RDKit was identified yesterday > > or so by Greg. > > > I don't find 0.081199... in my parameter file. I do find 0.08129, > which is correct for CS > 0.1411 is the C1 typo (as you mention above) > 0.0105 I don't find, though I do see 0.010508 (N9), which should be 0.01508 > 0.08379... I don't find, it's probably 0.08387 (N5), which is correct. > -0.195 is N10, and should be -1.95(!!!) . this is the first of these > that will make a substantial difference. > > I will be fixing these in the RDKit for the next release. > > > -greg >
[Rdkit-discuss] Fwd: [Open Babel] Hydrogen adder error?
FYI - the bug below is also exhibited by RDKit. -- Forwarded message -- From: Steve Constable Date: 2008/5/1 Subject: [Open Babel] Hydrogen adder error? To: openbabel-disc...@lists.sourceforge.net Hello, I'm working with openbabel 2.1.1, and I'm having an issue with the OBMol::AddHydrogens function. I have the structure of guandinie ( N=C(N)N ). when I run babel with the -h option, everything looks good. However, if I change to the charged version, [N+]=C(N)N the additional hydrogen required is not added. Opening the structures in jmol shows that they look exactly the same. Is this something that has been fixed in SVN already? Thanks, Steve - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ OpenBabel-discuss mailing list openbabel-disc...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Rdkit-discuss] Fwd: [Open Babel] Hydrogen adder error?
I think I spoke too soon. Looks like it's not a bug... -- Forwarded message -- From: Tim Vandermeersch Date: 2008/5/1 Subject: Re: [Open Babel] Hydrogen adder error? To: Steve Constable Cc: openbabel-disc...@lists.sourceforge.net This doesn't work in trunk, when you place an atom bewteen [ ], the smiles format parser will call OBAtom::ForceNoH(). In other words, the atom doesn't get any implicit hydrogen atoms. >From mol.cpp: If NoImplicitH is true then the molecule has no implicit hydrogens. Individual atoms on which ForceNoH() has been called also have no implicit hydrogens. If NoImplicitH is false (the default), then if there are any explicit hydrogens on an atom then they constitute all the hydrogen on that atom. However, a hydrogen atom with its _isotope!=0 is not considered explicit hydrogen for this purpose. In addition, an atom which has had ForceImplH()called for it is never considered hydrogen deficient, e.g. unbracketed atoms in SMILES. Any discrepancy with the expected atom valency is interpreted as the atom being a radical of some sort and iits _spinMultiplicity is set to 2 when it is one hydrogen short and 3 when it is two hydrogens short and similarly for greater hydrogen deficiency. So SMILES C[CH] is interpreted as methyl carbene, CC[H][H] as ethane, and CC[2H] as CH3CH2D. So the correct smiles would be: [NH2+]=C(N)N After AddHydrogens(), the molecule will contain 6 hydrogens. Hope this helps. Tim On Thu, May 1, 2008 at 5:55 PM, Steve Constable wrote: > Hello again, > > I fixed my own problem. I added the line > > IMPVAL[$([N+r0]=C[Nr0])]3 > > to atomtyp.txt, right after line 71. Maybe this could be incorporated into > SVN? > > --Steve > > - > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > ___ > OpenBabel-discuss mailing list > openbabel-disc...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ OpenBabel-discuss mailing list openbabel-disc...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Rdkit-discuss] Python 2.4 version of RDKit
There are still a lot of people out there using Py2.4. It would be nice to see two versions of RDKit on Windows; one for Py2.4, one for Py2.5. Current download figures for openbabel-python indicate a 2:1 Py2.5:Py2.4 userbase. Noel
Re: [Rdkit-discuss] python2.5 and Numeric
I hope it's on Greg's to do list also, but there is a compiled version of Numeric for Py2.5 available from the following link: http://www.pygame.org/download.shtml 2008/5/22 TJ O'Donnell : > I'm new to RDKit and have had good success so far > building it under linux and installing it on windows. > Some of the tests fail (only tested under linux). > I can try to get that resolved later. > > The issue I am concerned about is Numeric. > It is not supported under python 2.5 > It was relatively easy to find Numeric for python2.5 > with Ubuntu (synaptics package manager found it) > but hard to find for windows. > Are there any plans to deliver Numeric for python 2.5 > with RDKit, or to move away from dependency on it? > > RDKit looks great so far and I'm anxious to try more > with it. > > TJ O'Donnell > > > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] python2.5 and Numeric
I've just tried to build on Linux and I've left some comments on your build under Linux page... 2008/5/22 Greg Landrum : > On Thu, May 22, 2008 at 9:19 PM, TJ O'Donnell wrote: >> I'm new to RDKit and have had good success so far >> building it under linux and installing it on windows. >> Some of the tests fail (only tested under linux). >> I can try to get that resolved later. > > I'm happy to help as you try and get the failures figured out. > >> The issue I am concerned about is Numeric. >> It is not supported under python 2.5 >> It was relatively easy to find Numeric for python2.5 >> with Ubuntu (synaptics package manager found it) >> but hard to find for windows. >> Are there any plans to deliver Numeric for python 2.5 >> with RDKit, or to move away from dependency on it? > > Indeed, it's on the ToDo list. I'd like to get it done for the next > (Q3) release, but I'm not going to make any guarantees. In the > meantime, Noel pointed to one source of a precompiled Numeric binary > for windows, another can be found here: > http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe > >> RDKit looks great so far and I'm anxious to try more >> with it. > > glad to hear it! > > -greg > > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
[Rdkit-discuss] Building on Linux
If I run bjam in /Code/GraphMol/Wrap, I get: ...found 4999 targets... ...updating 9 targets... gcc.link.dll ../bin/gcc-4.1.2/release/threading-multi/libGraphMol.so /usr/bin/ld: cannot find -lblas collect2: ld returned 1 exit status "g++"-o "../bin/gcc-4.1.2/release/threading-multi/libGraphMol.so" -Wl,-h -Wl,libGraphMol.so -shared -Wl,--start-group "../bin/gcc-4.1.2/release/threadin g-multi/Atom.o" "../bin/gcc-4.1.2/release/threading-multi/QueryAtom.o" "../bin/g cc-4.1.2/release/threading-multi/QueryBond.o" "../bin/gcc-4.1.2/release/threadin g-multi/Bond.o" "../bin/gcc-4.1.2/release/threading-multi/MolOps.o" "../bin/gcc- 4.1.2/release/threading-multi/FindRings.o" "../bin/gcc-4.1.2/release/threading-m ulti/ROMol.o" "../bin/gcc-4.1.2/release/threading-multi/RWMol.o" "../bin/gcc-4.1 .2/release/threading-multi/PeriodicTable.o" "../bin/gcc-4.1.2/release/threading- multi/atomic_data.o" "../bin/gcc-4.1.2/release/threading-multi/QueryOps.o" "../b in/gcc-4.1.2/release/threading-multi/MolPickler.o" "../bin/gcc-4.1.2/release/thr eading-multi/Canon.o" "../bin/gcc-4.1.2/release/threading-multi/AtomIterators.o" "../bin/gcc-4.1.2/release/threading-multi/BondIterators.o" "../bin/gcc-4.1.2/re lease/threading-multi/Aromaticity.o" "../bin/gcc-4.1.2/release/threading-multi/K ekulize.o" "../bin/gcc-4.1.2/release/threading-multi/MolDiscriminators.o" "../bi n/gcc-4.1.2/release/threading-multi/ConjugHybrid.o" "../bin/gcc-4.1.2/release/th reading-multi/AddHs.o" "../bin/gcc-4.1.2/release/threading-multi/RankAtoms.o" ". ./bin/gcc-4.1.2/release/threading-multi/Matrices.o" "../bin/gcc-4.1.2/release/th reading-multi/Chirality.o" "../bin/gcc-4.1.2/release/threading-multi/RingInfo.o" "../bin/gcc-4.1.2/release/threading-multi/Conformer.o" "../../RDGeneral/bin/gcc -4.1.2/release/optimization-off/threading-multi/Dict.o" "/home/oboyle/not-backed -up/Tools/RDKit_May2008_1RC2/bin/libDataStructs.so" "/home/oboyle/not-backed-up/ Tools/RDKit_May2008_1RC2/bin/libRDGeometry.so" "../../Geometry/bin/gcc-4.1.2/rel ease/threading-multi/libRDGeometry.so" "/home/oboyle/not-backed-up/Tools/RDKit_M ay2008_1RC2/bin/libRDGeneral.so" "../../RDGeneral/bin/gcc-4.1.2/release/threadin g-multi/libRDGeneral.so" "/home/oboyle/not-backed-up/Tools/RDKit_May2008_1RC2/Ex ternal/Lapack++/bin/gcc-4.1.2/release/link-static/threading-multi/liblapack++.a" "/home/oboyle/not-backed-up/Tools/RDKit_May2008_1RC2/External/Lapack++/bin/gcc- 4.1.2/release/link-static/threading-multi/libblas++.a" "/home/oboyle/not-backed- up/Tools/RDKit_May2008_1RC2/External/Lapack++/bin/gcc-4.1.2/release/link-static/ threading-multi/liblamatrix++.a" -lblas -llapack -lrt -Wl,--end-group -Wl,--st rip-all -pthread ...failed gcc.link.dll ../bin/gcc-4.1.2/release/threading-multi/libGraphMol.so.. etc. I thought that blas was included?
Re: [Rdkit-discuss] Building on Linux
It might be good also if the build system complained at this point by dying horribly... 2008/5/23 Greg Landrum : > Hi Noel, > > On Fri, May 23, 2008 at 2:50 PM, Noel O'Boyle wrote: >> If I run bjam in /Code/GraphMol/Wrap, I get: >> >> ...found 4999 targets... >> ...updating 9 targets... >> gcc.link.dll ../bin/gcc-4.1.2/release/threading-multi/libGraphMol.so >> /usr/bin/ld: cannot find -lblas >> collect2: ld returned 1 exit status >> etc. > > [snip] > >> >> I thought that blas was included? > > nope. You'll need to install lapack and blas (you should be able to > get these as a package for your linux distribution). > > This is now officially a FAQ, so I'll add some additional verbiage to > the build instructions. > > -greg >
Re: [Rdkit-discuss] Jet another compiling problem
2008/7/15 markus : > Hi there, > here's a compiling problem when trying to setup the latest trunk: > I wrote a small sh-script for (re-)installing RDKit on Ubuntu. This script > worked very well, until I tried to get the latest trunk on Friday. > For anti-spam-reasons I attached the script which should describe my > procedure > reasonably well: > I downloaded the trunk on Friday, > then removed the old /opt/RDKit and copied the new one in it's place > commented out the copy-related lines in the script (as they are not useful > here) > and ran the script. > > on my Laptop this worked very well, not so on my Desktop. > > i get a bunch of errors stating > failed gcc.compile.c++ ... > > even bjam invoked in the /usr/local/src/boost_1_34_1/boost directory > throws errors. > > I have to inform you that I had reinstalled my whole compiler suite > some weeks ago, but I think that all neccesary packages, the compilers as > well, > are installed in the first step of the script, aren't they? > > Thanks in advance for the help, > Markus > > > > # run this script as root! > # usage: install_RDkit > > apt-get install python-dev g++ gfortran lapack3-* flex bjam bison > boost-build libboost-* pyste python-yapgvb vflib2 vflib2-* vflib3 vflib3-* > python-imaging python-egenix-mx-base-dbg python-numpy-ext Correct me if I'm wrong, but won't the asterisk (*) get expanded to match files in the current directory...? You may have to do something like put quotation marks around it. I would just write out each name explicitly to be sure. > export RDBASE=/opt/RDKit > export BOOST=/usr/local/src/boost_1_34_1 > export BOOSTHOME=/usr/local/src/boost_1_34_1 > export BOOST_BUILD_PATH=$BOOSTHOME > export PYTHON_ROOT=/usr/lib/ > export PYTHON_VERSION=2.5 > export PYTHONPATH=/opt/RDKit/Python > export LD_LIBRARY_PATH=/opt/RDKit/bin > > #echo " > ##RDKit-Stuff > #export $RDBASE=/opt/RDKit/" > #export PYTHONPATH=/opt/RDKit/Python:$PYTHONPATH > #export LD_LIBRARY_PATH=/opt/RDKit/bin:$LD_LIBRARY_PATH" | tee -a > /etc/bash.bashrc > > echo " > RDBASE= $RDBASE > BOOST= $BOOST > BOOSTHOME= $BOOSTHOME > BOOST_BUILD_PATH= $BOOST_BUILD_PATH > PYTHON_ROOT= $PYTHON_ROOT > PYTHON_VERSION= $PYTHON_VERSION > PYTHONPATH= $PYTHONPATH > LD_LIBRARY_PATH= $LD_LIBRARY_PATH > " > > #cp -r /myshare/RDKit/RDKit /opt > #cp -r /myshare/RDKit/boost_1_34_1 /usr/local/src > > cd /usr/local/src/boost_1_34_1/boost > > echo " > ...running bjam --with-thread --with-python release install from $PWD > " > bjam --with-thread --with-python release install > > cd /opt/RDKit/Code > > echo " > ... running bjam from $PWD > " > > bjam > > > echo " > ...now running the tests: > " > cd $RDBASE/Code > > python $RDBASE/Python/TestRunner.py test_list.py > > #Here's what you need to uninstall > #bjam --clean > #cd /usr/local/src/boost_1_34_1/ > #bjam --clean > #rm -rf /usr/local/include/boost-1_34_1 /usr/local/src/boost /opt/RDKit > /usr/local/src/boost_1_34_1/ > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
Re: [Rdkit-discuss] Role of boost source?
I would be happy if you just concentrated on updating the documentation for the current supported builds so that they're self-contained and foolproof. I'm thinking here mainly of the Windows build - what boost stuff do I need to download exactly? Also, the Linux build tells me to read the boost documentation, but I don't want to do this. Noel 2008/7/16 Greg Landrum : > Dear all, > > On Mon, Jul 14, 2008 at 7:00 PM, Andrew Fant wrote: >> While we're on the topic of compiling, what is it from the boost sources >> that rdkit needs to compile that isn't in the various linux binary >> packages? On ubuntu, I've installed all the libboost-dev types, and I >> point BOOST_BUILD_PATH and BOOSTHOME to /usr/share/boost-build (which is >> where all the internal jam files and such are kept), but the compile >> bombs out complaining that jam can't find a jamfile in >> /usr/share/boost-build. I assume it's looking for the one that is used >> to actually build boost from source, but my boost-fu is weak. Does >> rdkit actually try and force a recompile of boost at build time, or are >> there just bits and pieces of the source that it wants to assimilate >> into its own tree? > > I did a bit of looking around and found a quite useful thread on this > topic here: > http://www.nabble.com/Using-boost-libraries-on-Ubuntu-through-Boost.Build-td15333685.html > > What I take from that thread and some other information I've found : > It would (at least theoretically) be possible to modify the existing > RDKit build files in order to allow the system to be built on machines > that have boost installed from packages instead of from source. In > order to do this, however, the location of the headers, libraries, and > boost.build itself will need to be provided. I guess this would be > done as environment variables. Additionally, some work would have to > be done to make sure that the correct libraries are linked (e.g. > debugging when you do a debug build). > > It seems to me like the gain from making these changes is pretty > minimal compared to how much additional complexity they would > introduce, but I'm open to discussion. > > -greg > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] new Building on Windows page
I think it's built fine, but initially it couldn't find find boost-build.jam. I needed to set a new environment variable BOOST_ROOT="%BOOSTHOME%" Note the quotation marks (I've got spaces in the path for BOOSTHOME). Here's the batch file I used to set the variables: @echo off set RDBASE=C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk set BOOSTHOME=C:\Documents and Settings\Noel\Desktop\Tools\RDKit\boost_1_35_0 set BOOST_ROOT="%BOOSTHOME%" set BOOST_BUILD_PATH=C:\Boost set PYTHONPATH=%RDBASE%\Python set PATH=%RDBASE%\bin;%BOOST_BUILD_PATH%\lib;%PATH% You also need to set PYTHONHOME to run the tests. Which I'm afraid still don't work for me. Seems to be due to spaces in the name again. It's a pretty crazy test suite so I wasn't able to dig too deep...here's an example error message: """ C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk\Code>set PYTHONHOME=C:\Program Files\Python25 C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk\Code>python ..\Python\TestRunner.py test_list.py C:\Program: can't open file 'Files\Python25\python.exe': [Errno 2] No such file or directory C:\Program: can't open file 'Files\Python25\python.exe': [Errno 2] No such file or directory """ If I put quotation marks around the PYTHONHOME directory, it fouls up Python itself, and won't start up properly (the error message is "cannot import os") Noel 2008/7/18 Greg Landrum : > Dear all, > > Since I made a new page for this, I'm doing one announcement here: > I put a first draft of a new, very explicit, "building on windows" > page up on the wiki: > http://code.google.com/p/rdkit/wiki/NewWindowsBuild > > Please send suggestions/comments/etc. > > -greg > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] new Building on Windows page
2008/7/21 Greg Landrum : > The problem with bjam not being able to find boost-build.jam is > because your BOOST_BUILD_PATH is set incorrectly; it should be set to > "%BOOSTHOME%"; then you won't need BOOST_ROOT. So, you're saying that I don't need anyt of the BOOST variables to point to the compiled boost stuff. They should just point to the source. >> You also need to set PYTHONHOME to run the tests. Which I'm afraid >> still don't work for me. > > Yes; the test suite assumes on windows that Python is in c:\python25 > or that you have PYTHONHOME set properly; I need to add this to the > wiki. > >> Seems to be due to spaces in the name again. >> It's a pretty crazy test suite so I wasn't able to dig too >> deep...here's an example error message: >> """ >> C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk\Code>set >> PYTHONHOME=C:\Program Files\Python25 >> >> C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk\Code>python >> ..\Python\TestRunner.py test_list.py >> C:\Program: can't open file 'Files\Python25\python.exe': [Errno 2] No such >> file >> or directory >> C:\Program: can't open file 'Files\Python25\python.exe': [Errno 2] No such >> file >> or directory >> """ >> If I put quotation marks around the PYTHONHOME directory, it fouls up >> Python itself, and won't start up properly (the error message is >> "cannot import os") > > hmm, that's irritating. It also looks to be at least partially a > python problem, not an RDKit problem. Maybe this is why the default > installation path for python is c:\python25? Just because they knew it'd be a problem for RDKit? :-) It's never been an issue before... BTW, it seems to import fine, so I think the compilation, etc. might have worked. > -greg >
[Rdkit-discuss] Looking for something that's slow
For purposes of timing comparison (C++ API vs. using Boost.Python), is there any operation available from the C++ API that takes about 0.5 seconds per molecule? I've tried to slow down the Forcefield Optimization by reducing the tolerances but it's much too fast still. Noel
[Rdkit-discuss] Timing of C++ versus Boost.Python
I'm getting some strange results when I compare the timing for using
cinfony to access RDKit, compared to writing the equivalent C++
program. Basically, for iteration over a very large SDF file, it's 50%
slower if you use cinfony (which simply calls SDMolSupplier and
'yields' the results).
I'm using an SDF file from ZINC that contains 25000 or so molecules
(the first subset of the drug-like molecules) for testing. I have C++
code like the following:
void ReadFromFile(){
ROMol* mol;
SDMolSupplier molfile = SDMolSupplier("3_p0.0.sdf");
while (!molfile.atEnd()) {
mol = molfile.next();
if (mol) delete mol;
}
}
Greg, when you have time (no pun intended), I'd appreciate if you
could compare the run time of this sort of C++ program versus the
equivalent Python script using SDMolSupplier. I'd just like
independent verification for the sort of figures I'm getting. The
thing is, while some overhead is expected, the web says that SWIG
should be worse than Boost.Python, but the SWIG overhead with
OpenBabel is of the order of 4%, not 50%.
Regards,
Noel
Re: [Rdkit-discuss] Timing of C++ versus Boost.Python
2008/8/6 Greg Landrum :
> On 8/6/08, Noel O'Boyle wrote:
>> I'm getting some strange results when I compare the timing for using
>> cinfony to access RDKit, compared to writing the equivalent C++
>> program. Basically, for iteration over a very large SDF file, it's 50%
>> slower if you use cinfony (which simply calls SDMolSupplier and
>> 'yields' the results).
>
> That doesn't sound right at all. I expect the python stuff to be a bit
> slower, but not dramatically so unless you are crossing the
> python<->c++ barrier frequently. An example of this slow case would be
> similarity searching using X molecules against a collection of Y
> molecules where Y (and possible X) is large. If you were to call the
> TanimotoSimilarity function X*Y times (e.g. once for each pair), that
> would be pretty slow in python relative to straight C++. If you use
> the BulkTanimotoSimilarity function from Python (so that you only have
> to cross over into C++ X times), the difference between Python and C++
> shrinks.
>
>> I'm using an SDF file from ZINC that contains 25000 or so molecules
>> (the first subset of the drug-like molecules) for testing. I have C++
>> code like the following:
>>
>> void ReadFromFile(){
>>ROMol* mol;
>>SDMolSupplier molfile = SDMolSupplier("3_p0.0.sdf");
>>while (!molfile.atEnd()) {
>>mol = molfile.next();
>>if (mol) delete mol;
>>}
>> }
>>
>> Greg, when you have time (no pun intended), I'd appreciate if you
>> could compare the run time of this sort of C++ program versus the
>> equivalent Python script using SDMolSupplier. I'd just like
>> independent verification for the sort of figures I'm getting. The
>> thing is, while some overhead is expected, the web says that SWIG
>> should be worse than Boost.Python, but the SWIG overhead with
>> OpenBabel is of the order of 4%, not 50%.
>
> I wasn't as patient as you, so I only used 2K molecules in my test:
>
>
> -bash-3.00$ cat sample.py
> import Chem
> for m in Chem.SDMolSupplier('pubchem_hts.2k.sdf'):
> pass
>
> -bash-3.00$ time python sample.py
>
> real0m4.097s
> user0m4.018s
> sys 0m0.079s
>
> -bash-3.00$ cat sample.cpp
> #include
> #include
> #include
>
> using namespace RDKit;
>
> int
> main(int argc, char *argv[])
> {
> RDLog::InitLogs();
> ROMol* mol;
> SDMolSupplier molfile("pubchem_hts.2k.sdf");
> while (!molfile.atEnd()) {
>mol = molfile.next();
>if (mol) delete mol;
> }
> }
>
> -bash-3.00$ time ./sample.exe
>
> real0m4.034s
> user0m4.003s
> sys 0m0.031s
>
>
> As you can see, there's little difference.
>
> So, why are you seeing such a huge difference? Are you sure that
> you're using the same C++ backend? i.e. Are the python wrappers you're
> using linked against the same C++ shared libraries as your sample C++
> program? The svn state of the code has some optimizations relative to
> the May2008 release that might explain what you're seeing.
>
> -greg
>
OK - there's some problem at my end. I'll track down the usual
suspects. Thanks for checking this...
Re: [Rdkit-discuss] Timing of C++ versus Boost.Python
Looks like I forgot to correct the PYTHONPATH. My figures are now in
agreement with yours...
2008/8/6 Noel O'Boyle :
> 2008/8/6 Greg Landrum :
>> On 8/6/08, Noel O'Boyle wrote:
>>> I'm getting some strange results when I compare the timing for using
>>> cinfony to access RDKit, compared to writing the equivalent C++
>>> program. Basically, for iteration over a very large SDF file, it's 50%
>>> slower if you use cinfony (which simply calls SDMolSupplier and
>>> 'yields' the results).
>>
>> That doesn't sound right at all. I expect the python stuff to be a bit
>> slower, but not dramatically so unless you are crossing the
>> python<->c++ barrier frequently. An example of this slow case would be
>> similarity searching using X molecules against a collection of Y
>> molecules where Y (and possible X) is large. If you were to call the
>> TanimotoSimilarity function X*Y times (e.g. once for each pair), that
>> would be pretty slow in python relative to straight C++. If you use
>> the BulkTanimotoSimilarity function from Python (so that you only have
>> to cross over into C++ X times), the difference between Python and C++
>> shrinks.
>>
>>> I'm using an SDF file from ZINC that contains 25000 or so molecules
>>> (the first subset of the drug-like molecules) for testing. I have C++
>>> code like the following:
>>>
>>> void ReadFromFile(){
>>>ROMol* mol;
>>>SDMolSupplier molfile = SDMolSupplier("3_p0.0.sdf");
>>>while (!molfile.atEnd()) {
>>>mol = molfile.next();
>>>if (mol) delete mol;
>>>}
>>> }
>>>
>>> Greg, when you have time (no pun intended), I'd appreciate if you
>>> could compare the run time of this sort of C++ program versus the
>>> equivalent Python script using SDMolSupplier. I'd just like
>>> independent verification for the sort of figures I'm getting. The
>>> thing is, while some overhead is expected, the web says that SWIG
>>> should be worse than Boost.Python, but the SWIG overhead with
>>> OpenBabel is of the order of 4%, not 50%.
>>
>> I wasn't as patient as you, so I only used 2K molecules in my test:
>>
>>
>> -bash-3.00$ cat sample.py
>> import Chem
>> for m in Chem.SDMolSupplier('pubchem_hts.2k.sdf'):
>> pass
>>
>> -bash-3.00$ time python sample.py
>>
>> real0m4.097s
>> user0m4.018s
>> sys 0m0.079s
>>
>> -bash-3.00$ cat sample.cpp
>> #include
>> #include
>> #include
>>
>> using namespace RDKit;
>>
>> int
>> main(int argc, char *argv[])
>> {
>> RDLog::InitLogs();
>> ROMol* mol;
>> SDMolSupplier molfile("pubchem_hts.2k.sdf");
>> while (!molfile.atEnd()) {
>>mol = molfile.next();
>>if (mol) delete mol;
>> }
>> }
>>
>> -bash-3.00$ time ./sample.exe
>>
>> real0m4.034s
>> user0m4.003s
>> sys 0m0.031s
>>
>>
>> As you can see, there's little difference.
>>
>> So, why are you seeing such a huge difference? Are you sure that
>> you're using the same C++ backend? i.e. Are the python wrappers you're
>> using linked against the same C++ shared libraries as your sample C++
>> program? The svn state of the code has some optimizations relative to
>> the May2008 release that might explain what you're seeing.
>>
>> -greg
>>
>
>
> OK - there's some problem at my end. I'll track down the usual
> suspects. Thanks for checking this...
>
Re: [Rdkit-discuss] SD File output
EmbedMolecule. I recommend you read the PDF supplied with RDKit. 2008/8/8 Evgueni Kolossov : > Thanks - this is kind of works. > Unfortunately there is no atomic coordinates generated - how we can do this? > Otherwise it will display just single dot. > > Regards, > Evgueni > > > 2008/8/8 Igor Filippov >> >> The following works for me: >> >>std::stringstream ss; >>SDWriter *writer = new SDWriter(&ss); >>writer->setProps(propNames); >>writer->write(*mol); >>writer->flush(); >>delete mol; >>delete writer; >>std::string sdf=ss.str(); >> >> Igor >> >> On Fri, 2008-08-08 at 12:05 +0100, Evgueni Kolossov wrote: >> > >> > Dear Greg, >> > >> > Can you please show how to extract text from stringstream (which in >> > your case actually ostream) into string? >> > ROMol *mol; >> > mol = SmilesToMol(strSmile); >> > ostream *ss = new stringstream(); >> > SDWriter *writer = new SDWriter(ss, false); >> > writer->write(*mol); >> > >> > string strMolStructure; >> > //Now we want to put MDLMol into the string. For stringstream >> > ss->str() will do the job but ss is ostream) >> > >> > Regards, >> > Evgueni >> > >> > >> > -Original Message- >> > From: rdkit-discuss-boun...@lists.sourceforge.net >> > [mailto:rdkit-discuss-boun...@lists.sourceforge.net] On Behalf Of Greg >> > Landrum >> > Sent: 05 August 2008 19:07 >> > To: Igor Filippov [Contr] >> > Cc: rdkit-discuss@lists.sourceforge.net >> > Subject: Re: [Rdkit-discuss] SD File output >> > >> > >> > Dear Igor, >> > >> > This is a good one for the mailing list, so I'm cross-posting my >> > reply. >> > >> > On Tue, Aug 5, 2008 at 6:47 PM, Igor Filippov [Contr] >> > wrote: >> > > >> > > Is there any way to convert a mol object into an SD file (i.e. CTAB >> > > plus user-defined properties) and have the result in a string? >> > > MolToMolBlock() only outputs CTAB portion without the properties. >> > >> > Indeed there is. You can construct an SDWriter (defined in >> > $RDBASE/GraphMol/FileParsers/MolWriters.h) using a pointer to a >> > stringstream, then use the SDWriter's write() method. It's probably >> > safest to call the flush() method before reading your text out of the >> > stringstream. >> > >> > An example for using this with a SmilesWriter is in the function >> > testSmilesWriter2() in testMolWriter.cpp. Using an SDWriter is exactly >> > equivalent. >> > >> > -greg >> > >> > >> > - >> > This SF.Net email is sponsored by the Moblin Your Move Developer's >> > challenge Build the coolest Linux based applications with Moblin SDK & >> > win great prizes Grand prize is a trip for two to an Open Source event >> > anywhere in the world >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > ___ >> > Rdkit-discuss mailing list >> > Rdkit-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > >> > >> > >> > - >> > This SF.Net email is sponsored by the Moblin Your Move Developer's >> > challenge >> > Build the coolest Linux based applications with Moblin SDK & win great >> > prizes >> > Grand prize is a trip for two to an Open Source event anywhere in the >> > world >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > ___ Rdkit-discuss mailing >> > list Rdkit-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> -- >> Igor Filippov >> > > > > -- > Dr. Evgueni Kolossov (PhD) > ekolos...@gmail.com > Tel. +44(0)1628 627168 > Mob. +44(0)7812070446 > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
Re: [Rdkit-discuss] Distance Matrix
Perhaps I misunderstand. Are you looking for a fast Python solution to creating a distance matrix? If so, you might want to use numpy (which uses C extensions), where the distance between two vectors x, y is simply sqrt(sum((x-y)**2)). See http://projects.scipy.org/pipermail/numpy-discussion/2007-April/027170.html for a procedure to generate a full distance matrix. Noel 2008/8/15 markus : > Dear all, > as there is so much Geometry functionality within the RDKit, I wonder if > it provides > a function that computes the DistanceMatrix of a list of Point3D Objects. > If RDKit does not have this functionality, can anyone give Ideas if the > Boost Libaries themselve > are capable of that? > At the moment I have my own compiled version of the C Clustering Library > (PyCluster) which I modified in order to get a distancematrix, > but this Libraries do not out of the box calculate the spatial Distance. > > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] PubChem Compount Info
Hmmm...sounds like something that is not specific to RDKit...I might think about adding this to cinfony. Especially if you send a patch :-) Noel 2008/8/17 markus : > Hi There, > I wonder if it could be possible to access the Pubchem Power User > Gateway directly via RDKit. > As there is already some XML based interfacing to Pymol and Pubmed, this > would be a nice additional tool. > I often have several compounds for which I have to know if there's any > Bioactivity documented at PubChem. > Until now I have to browse the Pubchem home, search for similar mols, > check out the assay-ids, IC50s :-( > Could that be done in a way like the Pubmed.PubmedUtils stuff? > > Cheers, Markus > > > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] PubChem Compount Info
Also see BioPython. It has some wrappers around NCBI's functionality already, but I haven't looked at using it with PubChem... 2008/10/18 Greg Landrum : > Hi Markus, > > I did a bit of exploring of the Pubchem Power User Gateway this > morning and discovered that they have a SOAP interface: > http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html > They even include a bit of help and some examples for using that > interface from Python: > http://pubchem.ncbi.nlm.nih.gov/pug_soap/examples/python_zsi/python_zsi.html > > This provides a pretty straightforward way of interacting with the PUG > from Python. > > I made some minor modifications to one of the sample scripts provided > in order to come up with the attached script. It shows how to convert > a list of pubchem CIDs into an RDKit SDMolSupplier. You will need to > have ZSI installed and to run wsdl2py as indicated on the above page. > > This is, perhaps, a place to start. > > -greg > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
[Rdkit-discuss] Compiling on MacOSX
Hello Greg, I was wondering whether RDKit has been successfully compiled on a Mac. Noel
Re: [Rdkit-discuss] New stuff in subversion
FYI, Stephan Nagy (of Tripos??) just said the following on FF (http://friendfeed.com/snagy/discussion): Tripos will be releasing some sln parsing and generation code for Java and C. There is a formal grammar that will also be made available with the release of those APIs. The current plan is to make them available under the Eclipse Public License, some time late in Q4 08 or early Q1 09. - Stephan Nagy Stephan, yes, heard some rumors about Tripos going into the chemistry workbench business... I assume Tripos aims at tight integration with KNIME? Of course, I'd be rather interested in seeing how it cooperates with Bioclipse and/or plugins... Cheers on planning to choose the EPL license for the SLN library! - Egon Willighagen Our new product offering, Pantheon, is an Eclipse based product that will be available in Q1 09. The first product that we've built that extends Pantheon is called Muse and will be available at the end of 08. As a result of our Pantheon activities we have created a tighter coupling to KNIME, and presumably our plugins should work with Bioclipse, and vice versa (although we haven't tried this). - Stephan Nagy Noel 2008/11/25 Greg Landrum : > Dear all, > > Yesterday I merged the contents of two branches in subversion into the trunk: > > The first includes some changes to the build system that allow the > RDKit to be built using the mingw system on windows. If you don't know > what this means, it's probably not important to you, so don't worry > about it. :-) > > The second change is more interesting (maybe): I've added two new > molecular input format parsers: Mol2 and SLN. > > Given the chaos that the poorly defined atom types in the mol2 format > make, we had to pick some "standard" definitions to use; we chose > Corina atom types. Nik Stiefl, who wrote the parser and dealt with the > mess that this format is, says it should also work reasonably well on > output from Tripos's dbtranslate program. > > The SLN parser supports a subset of SLN: all molecule features should > be supported, but only a subset of the query features are in place. I > will do a feature matrix for the parser some time in the next couple > of weeks so that it's clear what it can or cannot understand. > > Both parsers are relatively new, so I have no doubt that people will > find problems and areas where they could be improved. Please report > them in the bug tracker and, if possible, provide sample files that > demonstrate the problems. > > Thanks, > -greg > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
[Rdkit-discuss] Building on Mac
Hello Greg, To make life difficult, I've been trying to build RDKit on MacOSX 10.5 but using the Fink-installed python2.5 and numpy (note: I'm using Fink unstable): I'm a newbie to MacOSX. Fink is one of two options (also tried MacPorts - didn't work well enough) for package-managed installation of open source software. It's all installed into a new folder /sw and so doesn't interfere with anything already on the system. I'm trying to compile all components of cinfony on MacOSX; I can either figure out how to compile cairo and pycairo for the System Python, or I can install these with Fink (successfully!) and try to figure out how to compile RDKit for Fink's Python. In short, RDKit compiles fine but segfaults on "import Chem". I note that there's no need to compile boost-build, as a bjam executable for mac is included in the boost source distribution. There's one loose end I want to chase up (I want to make sure it's using the boost libs I compiled myself, rather than any Fink boost libs), but apart from that I'm all out of ideas. If it compiles fine, it should work, right? If I can get cairo compiled for the system python, I won't need to chase this up, but I just thought I let you know... Regards, Noel
Re: [Rdkit-discuss] Building on Mac
I now realise there is a third option for me. I could install cairo with Fink, and then try to compile pycairo for the System Python using the Fink installed libraries...hmmm... 2008/11/27 Noel O'Boyle : > Hello Greg, > > To make life difficult, I've been trying to build RDKit on MacOSX 10.5 > but using the Fink-installed python2.5 and numpy (note: I'm using Fink > unstable): > > I'm a newbie to MacOSX. Fink is one of two options (also tried > MacPorts - didn't work well enough) for package-managed installation > of open source software. It's all installed into a new folder /sw and > so doesn't interfere with anything already on the system. I'm trying > to compile all components of cinfony on MacOSX; I can either figure > out how to compile cairo and pycairo for the System Python, or I can > install these with Fink (successfully!) and try to figure out how to > compile RDKit for Fink's Python. > > In short, RDKit compiles fine but segfaults on "import Chem". I note > that there's no need to compile boost-build, as a bjam executable for > mac is included in the boost source distribution. There's one loose > end I want to chase up (I want to make sure it's using the boost libs > I compiled myself, rather than any Fink boost libs), but apart from > that I'm all out of ideas. If it compiles fine, it should work, right? > If I can get cairo compiled for the system python, I won't need to > chase this up, but I just thought I let you know... > > Regards, > Noel >
Re: [Rdkit-discuss] Building on Mac
Actually it builds pycairo and its dependencies on the spot, rather than installs them. The Sytem Python comes with PIL, Tkinter, wxPython, Numpy and Matplotlib. And that's it. There doesn't seem to be a package manager for Macs. So if you want any other extensions you're out of luck. And fink unstable is the only choice for pycairo for MacOSX on an Intel. Apparently it's a misnomer, but whatever, it's the only choice. It all compiles beautifully and works though. If I could just get RDKit working too... Noel 2008/11/27 Greg Landrum : > Noel, > > I'm not enough of a Mac person (yet?) to know what the compelling case > is for installing/using the fink python instead of the system version. > Aside from being able to install instead of build pycairo, what's the > argument for it? > > I'm pretty conservative when it comes to installing on unstable platforms. :-) > > -greg > > On Thu, Nov 27, 2008 at 10:10 AM, Noel O'Boyle wrote: >> >> To make life difficult, I've been trying to build RDKit on MacOSX 10.5 >> but using the Fink-installed python2.5 and numpy (note: I'm using Fink >> unstable): >> >> I'm a newbie to MacOSX. Fink is one of two options (also tried >> MacPorts - didn't work well enough) for package-managed installation >> of open source software. It's all installed into a new folder /sw and >> so doesn't interfere with anything already on the system. I'm trying >> to compile all components of cinfony on MacOSX; I can either figure >> out how to compile cairo and pycairo for the System Python, or I can >> install these with Fink (successfully!) and try to figure out how to >> compile RDKit for Fink's Python. >> >> In short, RDKit compiles fine but segfaults on "import Chem". I note >> that there's no need to compile boost-build, as a bjam executable for >> mac is included in the boost source distribution. There's one loose >> end I want to chase up (I want to make sure it's using the boost libs >> I compiled myself, rather than any Fink boost libs), but apart from >> that I'm all out of ideas. If it compiles fine, it should work, right? >> If I can get cairo compiled for the system python, I won't need to >> chase this up, but I just thought I let you know... >> >> Regards, >> Noel >> >> - >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
Re: [Rdkit-discuss] Building on Mac
2008/11/28 Greg Landrum : > On Thu, Nov 27, 2008 at 10:34 PM, Noel O'Boyle wrote: >> than installs them. The Sytem Python comes with PIL, Tkinter, >> wxPython, Numpy and Matplotlib. And that's it. There doesn't seem to >> be a package manager for Macs. So if you want any other extensions >> you're out of luck. > > For what it's worth, easy_install seems to work without problems using > the system python. That, of course, doesn't help you if a package > isn't available via easy_install. > >> And fink unstable is the only choice for pycairo >> for MacOSX on an Intel. > > hmm, I wonder: > ~ $ sudo easy_install pycairo > Password: > Searching for pycairo > Reading http://pypi.python.org/simple/pycairo/ > Reading http://www.cairographics.org/pycairo > Reading http://cairographics.org/releases/ > Best match: pycairo 1.6.4 > Downloading http://cairographics.org/releases/pycairo-1.6.4.tar.gz > Processing pycairo-1.6.4.tar.gz > Running pycairo-1.6.4/setup.py -q bdist_egg --dist-dir > /tmp/easy_install-sVFG8W/pycairo-1.6.4/egg-dist-tmp-XART3x > cairo >= 1.6.4 detected > creating pycairo.pc > zip_safe flag not set; analyzing archive contents... > Adding pycairo 1.6.4 to easy-install.pth file > > Installed > /Library/Python/2.5/site-packages/pycairo-1.6.4-py2.5-macosx-10.5-i386.egg > Processing dependencies for pycairo > Finished processing dependencies for pycairo > ~ $ python > Python 2.5.1 (r251:54863, Apr 15 2008, 22:57:26) > [GCC 4.0.1 (Apple Inc. build 5465)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import cairo >>>> > > Seems to work. But, but, but...where did cairo come from? Was it already there? If true, then it's problem solved. >> Apparently it's a misnomer, but whatever, it's >> the only choice. It all compiles beautifully and works though. If I >> could just get RDKit working too... > > Let's see if we can diagnose it. Is it just Chem that leads to the > crash, or do you see the same thing when you do the simplest possible > RDKit extension module import: "import rdBase" > If you do see a crash there, please send along the output of : 'otool > -L $RDBASE/Python/rdBase.so' > Otherwise, try running python -v and doing the Chem import, then at > least you will see which specific piece of Chem is causing the crash. Will do. It'll be late next week though before I see the Mac again. > -greg >
Re: [Rdkit-discuss] Packaging the RDKit : A warning and a query
Please make it all lowercase. It's very difficult to remember a mixture of upper and lower case. I think they've done with the standard libraries in Py3.0. Now Tkinter is tkinter, etc. But why pyrdkit? Why not rdkit? - Noel 2009/1/25 Greg Landrum : > As part of my effort to make the RDKit easier to install, a very > long-standing item on my ToDo list has come back up: setting the > python code up as a python package. > > In order to make this work, I need to change the way the code is > imported. Instead of: import Chem > the "correct" way of doing an import will become: from pyRDKit import Chem > > I put correct in quotes above because by setting your PYTHONPATH > appropriately, all of your existing code will continue to work. > > My question is what the name of that package should be. I've > temporarily selected pyRDKit, which isn't creative, but it is > descriptive. Please send me other suggestions if you have them. > > -greg > > -- > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
[Rdkit-discuss] RDKit descriptors
Hello Greg, Am I right in saying that there are no 3D descriptors in RDKit? That they're all either 1D or 2D? - Noel
Re: [Rdkit-discuss] Canonical SMILES
2009/2/13 George Oakman : > Hi, > > Thanks a lot for the speedy response. > > Yes, this is what I was suspecting - slightly different conventions (in this > case probably to do with which branch to deal with first) will lead to > different results. > > The book I was referring to is An Introduction to Chemoinformatics from A.R. > Leach and V.J. Gillet. Yes, they refer to the CANGEN algorithm and to the > Weininger paper you mentioned. > > It doesn't matter, as long as I'm aware of the scope of 'uniqueness'. > > Just out of interest, is the InChi representation more 'unique' across > different packages than canonical SMILES? I like that - "more unique". :-) You got it in one. With InChI, IUPAC provide the actual code and we (speaking for OpenBabel here) compile it. That said, you can pass various options to the InChI code to get different results and only recently have InChI provided a standard set of options. (I'm sure I'm glossing over some details here, but this is how I understand the general picture) So, in short, InChI's should be the same across different packages as they use the same code. > Thanks again, > > George. > > >> From: da...@dalkescientific.com >> Date: Fri, 13 Feb 2009 18:38:21 +0100 >> To: rdkit-discuss@lists.sourceforge.net >> Subject: Re: [Rdkit-discuss] Canonical SMILES >> >> On Feb 13, 2009, at 6:20 PM, George Oakman wrote: >> > One of the first example I have been playing with is the canonical >> > SMILES for Aspirin. >> .. >> > >> > This gave me the following result: >> > >> > CC(Oc1c1C(O)=O)=O >> > >> > But I was expecting >> > >> > CC(=O)Oc1c1C(=O)O) >> >> The canonical SMILES is canonical only on the context of an >> algorithm. The Daylight algorithm is different than the RDKit one is >> different from the OpenBabel one is different ... . In fact, the >> Daylight algorithm has changed over time to fix various problems. >> >> When that happens, the molecules need to be re-canonicalized. >> >> Even if you go back to the original Weininger paper, there are >> ambiguities in the description which make the result implementation- >> specific. >> >> Is the book you're using "Molecular Design" by Gisbert Schneider and >> Karl-Heinz Baringhaus? That came up when I searched for "canonical >> SMILES" and I see it has example of aspirin with your expected SMILES. >> >> >> Andrew >> da...@dalkescientific.com >> >> >> >> >> -- >> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, >> CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source code: >> SFAD >> http://p.sf.net/sfu/XcvMzF8H >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > Windows Live Hotmail just got better. Find out more! > -- > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
Re: [Rdkit-discuss] Canonical SMILES
2009/2/17 Andrew Dalke : > On Feb 17, 2009, at 9:18 AM, George Oakman wrote: >> Does someone know if I can assume that the canonical SMILES of >> RDKit are the same as the Open Babel ones? You can assume they are not the same. No attempt has been made to make them consistent. > I wouldn't assume that without a lot of testing. My assumption > is that canonical SMILES generation is so implementation > sensitive that it's very unlikely two systems would do it the > same way unless that was a deliberate goal. > > Which I know wasn't the case with those two implementations. > > I think also that RDKit pays more attention to handling > stereochemistry than OpenBabel. > >> Am I doing something wrong in responding to the mailing list, it >> looks like all my answers are logged as a separate message as >> oposed to being logged in the same thread - please let me know, I >> don't want to make it all untidy! > > I don't use a threaded mail reader so I can't tell. I use Gmail and everything is nicely threaded. >Andrew >da...@dalkescientific.com > > > > -- > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] packaging changes moved to trunk
Yes - I was wondering how you were going to pull off the Windows release. If you want someone to bounce ideas off, get in touch... 2009/2/27 Greg Landrum : > Dear all, > > I've merged the contents of the EasyInstall branch of the RDKit code > onto the trunk. This has some consequences for those using the code > from Python which are detailed in this repeat of some of the contents > of my previous message on this topic: > > > Build/installation instructions for linux: > http://code.google.com/p/rdkit/wiki/NewLinuxBuild > and for windows: > http://code.google.com/p/rdkit/wiki/NewWindowsBuild > > Adapting the linux build instructions for the Mac (things do work on > the Mac; I did most of the development work there) is left as an > exercise for the reader. :-) > > An important note about the new code layout, from ReleaseNotes.txt: > - The directory structure of the distribution has been changed in > order to make installation of the RDKit python modules more > straightforward. Specifically the directory $RDBASE/Python has been > renamed to $RDBASE/rdkit and the Python code now expects that > $RDBASE is in your PYTHONPATH. When importing RDKit Python modules, > one should now do: "from rdkit import Chem" instead of "import > Chem". Old code will continue to work if you also add $RDBASE/rdkit > to your PYTHONPATH, but it is strongly suggested that you update > your scripts to reflect the new organization. > > > I had hoped to be able to do a one click (or one line) binary > installer for the python modules, but that seems to be more difficult > than I had expected : things are fine on linux and the mac, but don't > seem to work the way I want on windows (which is probably where they > are most needed). I will try to do a bit more investigation of this > before the next release, but it's not high priority. > > Best regards, > -greg > > -- > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
Re: [Rdkit-discuss] packaging changes moved to trunk
You need a separate procedure for Windows (if sys.platform=="win32") with something along the lines of the Windows installer for OB 2.2.0 Python at: http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/tags/openbabel-2-2-0/windows-vc2005/OBPythonOBF/setup.py?revision=2698&view=markup The extension modules in this case are not built with distutils and yet it all works. It's also possible to set some environment variables at this time, if necessary. See the postinstall.py script in the same directory. - Noel 2009/2/27 Greg Landrum : > On Fri, Feb 27, 2009 at 10:08 AM, Noel O'Boyle wrote: >> Yes - I was wondering how you were going to pull off the Windows >> release. If you want someone to bounce ideas off, get in touch... > > Thanks for the offer. > What I tried is to use the python distutils to create either a tar > ball (linux and mac) or a clickable installer (windows). This would > take care of installing the RDKit in appropriate directories. The few > dependencies (numpy, pil, etc.) could be pretty easily installed using > other standard python tools (e.g. setuptools). > > The problem is that though distutils is quite good at installing > extension modules that are built using distutils, it seems to be much > weaker at installing extension modules that are built using some other > method (i.e. bjam, cmake, whatever). Essentially what happened is that > the windows installers that I'd get would end up putting the .py files > in the right place, but they'd screw up the location of the .pyd files > for the RDKit extension modules. This didn't happen on linux or the > mac. Unless I can find some time to look for work-arounds, I'm > probably just going to abandon the "simple windows installation" idea > and go back to a well-packaged zip archive (or tarball) that the user > can just extract in the appropriate place. > > Alternate suggestions are very welcome, > -greg >
[Rdkit-discuss] Moving to Python 2.6
Hello Greg, Hope you had a good holiday. Looking at the download figures from OB Python since Aug 09, the vast majority of users are now using Python 2.6 (on Windows at least!). Wearing my cinfony hat, is there any chance that the next windows release of RDKit will target 2.6 (or better still, both 2.5 and 2.6)? Also, it would be nice to have a .zip file instead of a .tgz file for Windows users (.tgz is heap powerful magic for many people). - Noel
[Rdkit-discuss] 2009 Q3 release for Windows
Hello Greg, In anticipation of the Spring ACS meeting, I'm updating cinfony. It's great to finally see an RDKit release with support for Python 2.6 on Windows. It's also a zip file, which is Windows-friendly. However, it's a 'zip bomb', which can cause some problems - you might want to fix that. All the best, - Noel -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2009 Q3 release for Windows
Just saw that you're preparing a new release. I guess you can ignore the comments below except for the praise. :-) I'll try the new version... - Noel 2010/1/24 Noel O'Boyle : > Hello Greg, > > In anticipation of the Spring ACS meeting, I'm updating cinfony. > > It's great to finally see an RDKit release with support for Python 2.6 > on Windows. It's also a zip file, which is Windows-friendly. However, > it's a 'zip bomb', which can cause some problems - you might want to > fix that. > > All the best, > - Noel > -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2009 Q3 release for Windows
2010/1/24 Greg Landrum : > aOn Sun, Jan 24, 2010 at 7:04 PM, Noel O'Boyle wrote: >> Just saw that you're preparing a new release. I guess you can ignore >> the comments below except for the praise. :-) I'll try the new >> version... >> > > Thanks for the praise. :-) > > Can you please clarify the "zip bomb" remark? Sorry - a quick google shows that "zip bomb" was the wrong term. I meant the zip version of a "tar bomb", where the expanded files fill the current directory instead of a creating just a single directory. The .tar.gz you provided previously were well-behaved, but the new zip file is not. > Thanks, > -greg > -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Q4 Release for Windows
Hello Greg, Just tried the Q4 .tar.gz for Windows. It seems to be missing several .pyd files. In particular, it is missing rdBase.pyd so that the following error occurs: >>> from rdkit import Chem Traceback (most recent call last): File "", line 1, in File "C:\Tools\cinfony\cinfony-0.9\cinfony\RDKit\rdkit\Chem\__init__.py", line 14, in from rdkit import rdBase ImportError: cannot import name rdBase >>> ^Z - Noel -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q4 Release for Windows
2010/1/25 Greg Landrum : > Hi Noel, > > On Sun, Jan 24, 2010 at 9:45 PM, Noel O'Boyle wrote: >> Hello Greg, >> >> Just tried the Q4 .tar.gz for Windows. It seems to be missing several >> .pyd files. In particular, it is missing rdBase.pyd so that the >> following error occurs: > > The .tar.gz file is a source release, so the lack of .pyd files is to > be expected. :-) > > I had forgotten to put up the windows binary of the beta for Q4 2009. Looks good to me. > I'm doing that now, but be forewarned it has the same path problem > (i.e. missing the RDKit_Q42009_1 base dir) as the old binaries. I'll > fix this for the actual release. > -greg > -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit and Cinfony
Hi Cedric, There will be a new version of cinfony released in the coming week (and a talk to follow at the ACS, the following week). This supports the latest version of RDKit. I also promise to set up a proper mailing list where enquiries of this sort can be sent (sorry Greg). - Noel Original message follows: On Fri, Mar 12, 2010 at 3:23 PM, Cedric MORETTI wrote: > Hello, > I would like to know if there is someone who uses utility Cinfony with > RDKit. > I use version 0.9 of Cinfony and an old version of RDKit (May 2008). > There is no problem when using both programs. But I cannot arrive to install > version Q2009P25, RDKit module is not found when I loaded. > > Although having only replace the contents of the directory rdkit "Cinfony". > I'm not a cinfony user, and it would be helpful to have the full traceback (as Andrew said), but I can make a guess about this: The package structure of the RDKit changed between the Q42008 and Q12009 release. If the older version of Cinfony is expecting the old RDKit structure, it's not going to work with newer versions. Maybe there's a newer version of cinfoy you can download? Best Regards, -greg -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] datamining with RDKIT and cinfony
On 19 March 2010 13:53, Cedric MORETTI wrote: > Hi > > I have a question with RDKIT… > > There are tools of dataminning in RDKIT?? > > I don’t find these tools… > > > > Other question > > When the news version to cinfony is available? > > The next week??? Cinfony 1.0a is available at http://cinfony.googlecode.com. You will also find a mailing list for cinfony at that website. Any questions should be sent there. > I’m really interested to use this version with the last version to OpenBabel > cdk and RDKIT.. > > Tks Noel and Greg for your job… > > Cedric > > > > > > ** > DISCLAIMER > This email and any files transmitted with it, including replies and > forwarded copies (which may contain alterations) subsequently > transmitted from Firmenich, are confidential and solely for the use > of the intended recipient. > The contents do not represent the opinion of Firmenich except > to the extent that it relates to their official business. > ** > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Compiling boost
Hello Greg, I'm trying to follow the instructions at http://code.google.com/p/rdkit/wiki/BuildingWithCmake on an Ubuntu 9.04 system. (1) I downloaded a boost source version. (http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz/download) (2) I extracted it and tried "bjam --with-python release install", but I don't have bjam. (3) I downloaded ../boost-jam-3.1.18. It said there was a precompiled version, but there wasn't so I compiled it. (4) I run "bjam --with-python release install", but got """u...@ubuntu904desktop:~/Tools/cinfony/boost_1_42_0$ ../boost-jam-3.1.18/bin.linuxx86/bjam Unable to load Boost.Build: could not find build system. - /home/user/Tools/cinfony/boost_1_42_0/boost-build.jam attempted to load the build system by invoking 'boost-build tools/build/v2 ;' but we were unable to find "bootstrap.jam" in the specified directory or in BOOST_BUILD_PATH (searching /home/user/Tools/cinfony/boost_1_42_0/tools/build/v2, /usr/share/boost-build). Please consult the documentation at 'http://www.boost.org'.""" What am I doing wrong? Were you using the same versions? - Noel -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling boost
Ok, I had to run the following after unzipping boost: ./bootstrap.sh --with-libraries=python --prefix=/home/user/Tools/cinfony/tree ./bjam install There was no need to download or install bjam separately. The RDKit build was then configured as follows: cmake .. -DCMAKE_INSTALL_PREFIX=/home/user/Tools/cinfony/tree -DBoost_INCLUDE_DIR=/home/user/Tools/cinfony/tree/include - Noel On 31 March 2010 17:16, Greg Landrum wrote: > Hi Noel, > > Looks like the problem with the build instructions is that I assume a > pre-built version of bjam; bad assumption. > > Your best bet is probably to follow the build instructions for boost > that are in the boost docs: > http://www.boost.org/doc/libs/1_42_0/more/getting_started/unix-variants.html#easy-build-and-install > > you only need the python library, so don't worry about building everything. > > Note: I haven't tested the RDKit with boost 1.42, but I don't > anticipate any major problems. > > -greg > > On Wed, Mar 31, 2010 at 8:46 AM, Noel O'Boyle wrote: >> Hello Greg, >> >> I'm trying to follow the instructions at >> http://code.google.com/p/rdkit/wiki/BuildingWithCmake on an Ubuntu >> 9.04 system. >> >> (1) I downloaded a boost source version. >> (http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz/download) >> (2) I extracted it and tried "bjam --with-python release install", but >> I don't have bjam. >> (3) I downloaded ../boost-jam-3.1.18. It said there was a precompiled >> version, but there wasn't so I compiled it. >> (4) I run "bjam --with-python release install", but got >> >> """u...@ubuntu904desktop:~/Tools/cinfony/boost_1_42_0$ >> ../boost-jam-3.1.18/bin.linuxx86/bjam >> >> Unable to load Boost.Build: could not find build system. >> - >> /home/user/Tools/cinfony/boost_1_42_0/boost-build.jam attempted to >> load the build system by invoking >> >> 'boost-build tools/build/v2 ;' >> >> but we were unable to find "bootstrap.jam" in the specified directory >> or in BOOST_BUILD_PATH (searching >> /home/user/Tools/cinfony/boost_1_42_0/tools/build/v2, >> /usr/share/boost-build). >> >> Please consult the documentation at 'http://www.boost.org'.""" >> >> What am I doing wrong? Were you using the same versions? >> >> - Noel >> >> -- >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling boost
On 1 April 2010 14:49, Greg Landrum wrote: > Dear Noel, > > On Thu, Apr 1, 2010 at 2:09 AM, Noel O'Boyle wrote: >> Ok, I had to run the following after unzipping boost: >> >> ./bootstrap.sh --with-libraries=python --prefix=/home/user/Tools/cinfony/tree >> ./bjam install >> >> There was no need to download or install bjam separately. The RDKit >> build was then configured as follows: >> >> cmake .. -DCMAKE_INSTALL_PREFIX=/home/user/Tools/cinfony/tree >> -DBoost_INCLUDE_DIR=/home/user/Tools/cinfony/tree/include > > Thanks for this. I will update the wiki. > One question: you didn't provide cmake with any information about > where the boost shared libraries are located. Are you sure that things > are linked against the correct version of boost? No they weren't. The truth is that I found it very difficult to convince cmake to use the new boost rather than the system one even after defining three boost related variables. In the end, I just uninstalled the system one. > -greg > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling boost
On 1 April 2010 14:53, Noel O'Boyle wrote: > On 1 April 2010 14:49, Greg Landrum wrote: >> Dear Noel, >> >> On Thu, Apr 1, 2010 at 2:09 AM, Noel O'Boyle wrote: >>> Ok, I had to run the following after unzipping boost: >>> >>> ./bootstrap.sh --with-libraries=python >>> --prefix=/home/user/Tools/cinfony/tree >>> ./bjam install >>> >>> There was no need to download or install bjam separately. The RDKit >>> build was then configured as follows: >>> >>> cmake .. -DCMAKE_INSTALL_PREFIX=/home/user/Tools/cinfony/tree >>> -DBoost_INCLUDE_DIR=/home/user/Tools/cinfony/tree/include >> >> Thanks for this. I will update the wiki. >> One question: you didn't provide cmake with any information about >> where the boost shared libraries are located. Are you sure that things >> are linked against the correct version of boost? > > No they weren't. The truth is that I found it very difficult to > convince cmake to use the new boost rather than the system one even > after defining three boost related variables. In the end, I just > uninstalled the system one. And I should say that the CMAKE_INSTALL_PREFIX is ignored by RDKit so there was no need to specify that. One of the core ideas behind CMake is to separate the source and build trees. However, RDKit insists on building around the source. It could be a good idea to change this in future. - Noel -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] beta of Q1 2010 release up
Since the world's attention has been drawn to this, maybe I'd better
sort this out now :-)
On 20 April 2010 19:04, Andrew Dalke wrote:
> On Apr 20, 2010, at 6:56 PM, Geoffrey Hutchison wrote:
>> Feel free to "steal" the CMake from Open Babel. See scripts/CMakeLists.txt.
>> A few weeks ago, we used CMake's SWIG support to compile and install the
>> Python bindings -- this was buggy.
>>
>> Now, we run distutils, e.g.:
>> install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE}
>> ${openbabel_SOURCE_DIR}/scripts/python/setup.py install
>> --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY
>> ${openbabel_BINARY_DIR}/scripts)")
>
> In trying to get OpenBabel to compile on my Mac last week, working with Noel
> on this, I found that this part of the OB configuration for the Mac doesn't
> work quite right.
>
> I expect the default installation to go into the standard Python
> site-packages directory, which for me is
>
> /Library/Python/2.6/site-packages
>
> However, cmake wants there to be a CMAKE_INSTALL_PREFIX, and uses the default
> "/usr/local". This caused OB to install the Python code into
> /usr/local/lib/python2.6/site-packages . It's the only package I have
> installed in that directory.
>
> I don't have a good feeling for how setting CMAKE_INSTALL_PREFIX should
> affect the install. Perhaps there should be a CMAKE_INSTALL_PYTHON_PREFIX or
> something like that. My observation here is only that when nothing is
> specified then the default Python installation directory should be the
> default determined by Python, and not by the cmake configuration.
>
> Noel knows about this.
>
> Andrew
> da...@dalkescientific.com
>
>
>
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Re: [Rdkit-discuss] beta of Q1 2010 release up
On 20 April 2010 19:20, Geoffrey Hutchison wrote:
>
> On Apr 20, 2010, at 2:04 PM, Andrew Dalke wrote:
>
>> In trying to get OpenBabel to compile on my Mac last week, working with Noel
>> on this, I found that this part of the OB configuration for the Mac doesn't
>> work quite right.
>> I expect the default installation to go into the standard Python
>> site-packages directory, which for me is
>>
>> /Library/Python/2.6/site-packages
>
> Yes, I need to fix Noel's CMakeLists -- it needs a special case for if(APPLE)
> here. That should show up in SVN in the next 15 minutes or so.
>
>> I don't have a good feeling for how setting CMAKE_INSTALL_PREFIX should
>> affect the install. Perhaps there should be a CMAKE_INSTALL_PYTHON_PREFIX or
>> something like that. My observation here is only that when nothing is
>> specified then the default Python installation directory should be the
>> default determined by Python, and not by the cmake configuration.
>
> Well, I haven't tried, it, but if you can give me a python script which gives
> the appropriate destination directory, I can hack the CMake code. e.g.
>
> EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c
> "import numpy; print numpy.get_include()"
> OUTPUT_VARIABLE NUMPY_INCLUDE_DIR)
>
> This particular bit gives CMake the location of the numpy headers. I'm sure
> there's some similar function call for distutils, right?
Please - don't edit this, right now. I'm sorting it out as we speak. I
will post the solution to openbabel-devel later today, and cc all
interested parties.
> Cheers,
> -Geoff
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Re: [Rdkit-discuss] Error depicting a smiles string
I'll look into this as soon as possible. On 30 April 2010 10:24, Cedric MORETTI wrote: > Tks you Greg for your answer. > > If my brain is good, I'm remember that Noel O'Boyle (the cinfony creator's) > subscribed to RDKIT mailing-list so maybe he could answer at my question. > Cedric > > -Original Message- > From: Greg Landrum [mailto:greg.land...@gmail.com] > Sent: vendredi, 30. avril 2010 11:14 > To: Cedric MORETTI > Cc: RDKit Discuss > Subject: Re: [Rdkit-discuss] Error depicting a smiles string > > Hi, > > On Fri, Apr 30, 2010 at 5:06 AM, Cedric MORETTI > wrote: >> I use a Q42009 with the package Cinfony. >> I am in windows system ( :( ) >> The picture made >> 300x300 >> Size 4.75kb > > I can't answer questions about cinfony since I don't know know how it > works. Please try using the RDKit without cinfony. > > Thanks, > -greg > ** > DISCLAIMER > This email and any files transmitted with it, including replies and forwarded > copies (which may contain alterations) subsequently transmitted from > Firmenich, are confidential and solely for the use of the intended recipient. > The contents do not represent the opinion of Firmenich except to the extent > that it relates to their official business. > ** > > > -- > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Having removed old libraries and compiled boost1.43 again
You should be able to accomplish the same with "cmake -DBoost_USE_STATIC_LIBS=OFF". On 25 June 2010 04:58, Kei Taneishi wrote: > Hi Christian, > > I'm using dynamic linking to libboost_regex. > At first, edit $RDBASE/Code/GraphMol/SLNParse/CMakeLists.txt as below. > > == > --- ../Code/GraphMol/SLNParse/CMakeLists.txt (revision 1440) > +++ ../Code/GraphMol/SLNParse/CMakeLists.txt (working copy) > @@ -1,7 +1,7 @@ > FIND_PACKAGE(BISON) > FIND_PACKAGE(FLEX) > > -set(Boost_USE_STATIC_LIBS ON) > +set(Boost_USE_STATIC_LIBS OFF) > find_package(Boost 1.39.0 COMPONENTS regex REQUIRED) > == > > and delete $RDBASE/build/CMakeCache.txt to forget the previous configs, > then in the $RDBASE/build directory, cmake .. && make. > > Regards, > Kei > > bouille wrote: >> Dear Greg >> >> Having removed old libraries and compiled boost1.43 again >> >> [ 80%] Built target MolCatalog >> [ 80%] Built target testMolCatalog >> [ 80%] Built target rdMolCatalog >> Linking CXX shared library libSLNParse.so >> /usr/bin/ld: /usr/local/lib/libboost_regex.a(instances.o): relocation >> R_X86_64_32 against >> `boost::object_cache, >> boost::re_detail::cpp_regex_traits_implementation >>> ::do_get(boost::re_detail::cpp_regex_traits_base const&, unsigned >> long)::s_data' can not be used when making a shared object; recompile >> with -fPIC >> /usr/local/lib/libboost_regex.a: could not read symbols: Bad value >> collect2: ld a retourné 1 code d'état d'exécution >> make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Erreur 1 >> make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Erreur >> 2 >> make: *** [all] Erreur 2 >> >> Best Regards >> Christian >> >> >> >> -- >> ThinkGeek and WIRED's GeekDad team up for the Ultimate >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the >> lucky parental unit. See the prize list and enter to win: >> http://p.sf.net/sfu/thinkgeek-promo >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > -- > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q2 2010 Release
On 1 July 2010 13:43, Evgueni Kolossov wrote: > Dear Greg, > > I was sure bison and flex are part of cygwin installation but cannot find > executables. > Can you suggest anything? Run cygwin setup, and type bison into the search box. > Regards, > Evgueni > > On 1 July 2010 13:06, Greg Landrum wrote: >> >> On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov >> wrote: >> > Greg, >> > looking like it cannot be done with cmake without python installed. >> > I have cygwin installed but cmake cannot find BISON and FLEX and >> > complaining >> > about python executable. Any suggestions? >> >> The python part should be easy: after you configure the first time, >> untick the "RDK_BUILD_PYTHON_WRAPPERS" box and then configure again. >> >> flex and bison should be found if they are in your PATH. Please check >> that they are. >> >> -greg > > > > -- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] read 2 SDF files in the loop
On 1 July 2010 19:52, Greg Landrum wrote:
> Dear Cedric,
>
> On Thu, Jul 1, 2010 at 10:52 AM, Cedric MORETTI
> wrote:
>> Hello all,
>>
>> I have a little question.
>>
>> I don’t arrive to read 2 SDF files with RDKIT when I use the for loop.
>>
>> I explain
>>
>> I have a first sdf files with 1 property and a second with another
>> properties.
>>
>> I put the second SDMolSupplier instead of “suppl” and load a sdf file ( look
>> exemple)
>
> I think what you want is something like the following:
>
> suppl1 = Chem.SDMolSupplier('file1.sdf')
> suppl2 = Chem.SDMolSupplier('file2.sdf')
>
> for mol1 in suppl1:
> mol2 = suppl2.next()
> # do something with the two molecules
Maybe "for mol1, mol2 in zip(suppl1, suppl2):" ?
>
> Best Regards,
> -greg
>
>
>
>>
>> If I replace the SDMolSupplier by a text file the program don’t have a
>> problem.
>>
>> I just search a writer to read 2 SDF ….
>>
>> Tks
>>
>> Cedric
>>
>>
>>
>>
>>
>> reader1 = Chem.SDMolSupplier("C:\Data\scaffold/Total/totalscaffold.sdf.sdf")
>>
>> writer = Chem.SDWriter("C:\Data\scaffold/Eval/evalcount.sdf")
>>
>> z = 0
>>
>> for mol in reader1:
>>
>> h = Chem.MolToSmiles(mol)
>>
>>
>>
>> suppl = open('C:\Data\scaffold/Total/total.txt','r')
>>
>>
>>
>> for a in suppl:
>>
>> r = 0
>>
>> r+=1
>>
>>
>>
>>
>>
>> **
>> DISCLAIMER
>> This email and any files transmitted with it, including replies and
>> forwarded copies (which may contain alterations) subsequently transmitted
>> from Firmenich, are confidential and solely for the use of the intended
>> recipient. The contents do not represent the opinion of Firmenich except to
>> the extent that it relates to their official business.
>> **
>>
>>
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Re: [Rdkit-discuss] read 2 SDF files in the loop
On 1 July 2010 20:15, Greg Landrum wrote:
> On Thu, Jul 1, 2010 at 9:01 PM, Noel O'Boyle wrote:
>>>
>>> I think what you want is something like the following:
>>>
>>> suppl1 = Chem.SDMolSupplier('file1.sdf')
>>> suppl2 = Chem.SDMolSupplier('file2.sdf')
>>>
>>> for mol1 in suppl1:
>>> mol2 = suppl2.next()
>>> # do something with the two molecules
>>
>> Maybe "for mol1, mol2 in zip(suppl1, suppl2):" ?
>>
>
> That's a really nice and clean way of spelling it, but a bit of a
> disaster when the files are large: zip(a,b) creates the whole joined
> list at once, it's not a generator (at least with python 2.5).
>
> What this means to those of you who don't get excited about these
> things is that Noel's form reads all the molecules from both suppliers
> into memory and then loops over them. The form I originally proposed
> only has two molecules in memory at a time.
Two molecules in memory, eh? I raise you the complicated itertools module:
import itertools
for mol1, mol2, in itertools.izip(suppl1, suppl2):
> Best Regards,
> -greg
>
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Re: [Rdkit-discuss] RDKit packaging issues
On 5 July 2010 21:33, Gianluca Sforna wrote:
> Hi all,
> after spending some time to prepare a Fedora package I have a couple
> remarks/suggestions I'd like to discuss with you in order to make the
> process easier for all the distributions around.
>
> Versioning - package manager programs (this is valid in all distros)
> handle updates by comparing versions to decide which one is newer.
> Having names like Q12010, Q22010 etc will break ordering next year
> (Q42010 > Q12011).
> I suggest you revise how you do name versions; one simple way to avoid
> the issue is to swap year with quarter, so 2010Q4 < 2011Q1. Avoiding
> non numeric versions would be a nice bonus, so you could use to the
> same effect something like ".MM" (so 2010.12 < 2011.04)
>
> Installation - files installed by the "make install" step should
> honour the "DESTDIR" environment variable; this is becasue packagers
> need to put files under a certain build directory to be picked up
> later by the packaging script; this is usually accomplished by setting
> the env variable DESTDIR or running "make install DESTDIR=xxx". I also
> need to mention this buildroot (xxx in the example) usually translates
> to "/" when the package is installed, so default installation
> subdirectories should be picked according to common standard naming.
AFAIK, with CMAKE you set -DCMAKE_INSTALL_PREFIX for a local install.
> For instance, libraries (lib*.so.*") are usually to be installed in
> /usr/lib{64}, binaries in /usr/bin, header files in /usr/include and
> so on; I believe cmake has all we need to use these these standard
> paths, but I'd need to dig manuals and/or other projects to find out
> the correct spell to cast...
>
> I think I could uncover more packaging issues as I proceed, but I
> wanted to kick off some discussions on these points early so we move
> on quicker toward good linux packages.
>
> Cheers
>
> G.
>
> --
> Gianluca Sforna
>
> http://morefedora.blogspot.com
> http://www.linkedin.com/in/gianlucasforna
>
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Re: [Rdkit-discuss] Build on Windows
On 28 July 2010 15:04, Evgueni Kolossov wrote: > Dear Greg, > > I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go > through the configuration stage with CMake: > > CMake Error at C:/Program Files/CMake > 2.8/share/cmake-2.8/Modules/FindBoost.cmake:910 (message): > Unable to find the requested Boost libraries. > > Boost version: 1.43.0 > > Boost include path: C:/boost/boost_1_43_0 > > The following Boost libraries could not be found: > > boost_regex > > No Boost libraries were found. You may need to set Boost_LIBRARYDIR to > the > directory containing Boost libraries or BOOST_ROOT to the location of > Boost. > Call Stack (most recent call first): > Code/GraphMol/SLNParse/CMakeLists.txt:4 (find_package) > > > CMake Error: The following variables are used in this project, but they are > set to NOTFOUND. > Please set them or make sure they are set and tested correctly in the CMake > files: > Boost_REGEX_LIBRARY (ADVANCED) > linked by target "testSLNParse" in directory > C:/RDKit/Code/GraphMol/SLNParse > > Configuring incomplete, errors occurred! > > I have tried to set environmental variable Boost_LIBRARYDIR to > .\boost_1_43_0\bin.v2\libs or to \boost_1_43_0\boost where regex directory > is but it still cannot find it. Run cmake with -DBoost_LIBRARYDIR=whatever > Please help. > > Regards, > Evgueni > > -- > > -- > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Build on Windows
Are you sure you installed regex? It needs to be compiled. On Windows I use the binary installer where you can tick the box for different boost components. On 28 July 2010 15:14, Evgueni Kolossov wrote: > Tried Run cmake with -DBoost_LIBRARYDIR=whatever > but it still cannot find regex > > On 28 July 2010 15:07, Noel O'Boyle wrote: >> >> On 28 July 2010 15:04, Evgueni Kolossov wrote: >> > Dear Greg, >> > >> > I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go >> > through the configuration stage with CMake: >> > >> > CMake Error at C:/Program Files/CMake >> > 2.8/share/cmake-2.8/Modules/FindBoost.cmake:910 (message): >> > Unable to find the requested Boost libraries. >> > >> > Boost version: 1.43.0 >> > >> > Boost include path: C:/boost/boost_1_43_0 >> > >> > The following Boost libraries could not be found: >> > >> > boost_regex >> > >> > No Boost libraries were found. You may need to set Boost_LIBRARYDIR >> > to >> > the >> > directory containing Boost libraries or BOOST_ROOT to the location of >> > Boost. >> > Call Stack (most recent call first): >> > Code/GraphMol/SLNParse/CMakeLists.txt:4 (find_package) >> > >> > >> > CMake Error: The following variables are used in this project, but they >> > are >> > set to NOTFOUND. >> > Please set them or make sure they are set and tested correctly in the >> > CMake >> > files: >> > Boost_REGEX_LIBRARY (ADVANCED) >> > linked by target "testSLNParse" in directory >> > C:/RDKit/Code/GraphMol/SLNParse >> > >> > Configuring incomplete, errors occurred! >> > >> > I have tried to set environmental variable Boost_LIBRARYDIR to >> > .\boost_1_43_0\bin.v2\libs or to \boost_1_43_0\boost where regex >> > directory >> > is but it still cannot find it. >> >> Run cmake with -DBoost_LIBRARYDIR=whatever >> >> > Please help. >> > >> > Regards, >> > Evgueni >> > >> > -- >> > >> > >> > -- >> > The Palm PDK Hot Apps Program offers developers who use the >> > Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> > of $1 Million in cash or HP Products. Visit us here for more details: >> > http://p.sf.net/sfu/dev2dev-palm >> > ___ >> > Rdkit-discuss mailing list >> > Rdkit-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > >> > > > > Mob. +44(0)7812070446 > -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problems importing rdkit on Windows
Hi all, I'm updating cinfony and using the latest RDKit Release (RDKit_2010_12_1, the binary Python 2.6 release), but "from rdkit import Chem" is causing Python to crash (on Windows 7) as below. I've tried with and without RDBASE defined. Can someone confirm that it works for them? - Noel C:\Tools\rdkit\RDKit_2010_12_1>echo %PATH% C:\Tools\rdkit\RDKit_2010_12_1\lib C:\Tools\rdkit\RDKit_2010_12_1>echo %PYTHONPATH% %PYTHONPATH% C:\Tools\rdkit\RDKit_2010_12_1>python 'python' is not recognized as an internal or external command, operable program or batch file. C:\Tools\rdkit\RDKit_2010_12_1>C:\Python26\python Python 2.6.4 (r264:75708, Oct 26 2009, 08:23:19) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> from rdkit import Chem CRASH!!! -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problems importing rdkit on Windows
On 31 March 2011 12:45, Greg Landrum wrote: > On Thu, Mar 31, 2011 at 8:51 AM, James Davidson > wrote: >> >> >> It then ocurred to me that it could have been an incompatibility with an >> earlier Numpy version(?) Would this be involved at the point of import? >> The version I reinstalled was 1.5.1rc1. >> >> Probably not going to be of help to you, but I thought I would share just on >> the off-chance! : ) > > The numpy thing could very well be it... In case it helps, I will > track down which numpy I built against tonight and post it. It looks like it is numpy (I have an old one, numpy 1.3.0, installed). I'm about to update it, and retry. > -greg > > -- > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problems importing rdkit on Windows
On 31 March 2011 13:13, Noel O'Boyle wrote: > On 31 March 2011 12:45, Greg Landrum wrote: >> On Thu, Mar 31, 2011 at 8:51 AM, James Davidson >> wrote: >>> >>> >>> It then ocurred to me that it could have been an incompatibility with an >>> earlier Numpy version(?) Would this be involved at the point of import? >>> The version I reinstalled was 1.5.1rc1. >>> >>> Probably not going to be of help to you, but I thought I would share just on >>> the off-chance! : ) >> >> The numpy thing could very well be it... In case it helps, I will >> track down which numpy I built against tonight and post it. > > It looks like it is numpy (I have an old one, numpy 1.3.0, installed). > I'm about to update it, and retry. Success! It works fine with numpy 1.5.1rc1. I didn't test the newer numpys. >> -greg >> >> -- >> Create and publish websites with WebMatrix >> Use the most popular FREE web apps or write code yourself; >> WebMatrix provides all the features you need to develop and >> publish your website. http://p.sf.net/sfu/ms-webmatrix-sf >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Getting the list of descriptors
Hi Greg, With the deprecation of the AvailDescriptors module, it seems that the only way to get the list of descriptors is: len(Descriptors._descList) I don't like accessing hidden attributes; is there some better way to do this? - Noel -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Getting the list of descriptors
I notice that _descList is missing at least the molecular formula and molecular weight. What I'm really looking for is a replacement for descDict in the original AvailDescriptors module. - Noel On 31 March 2011 18:28, Noel O'Boyle wrote: > Hi Greg, > > With the deprecation of the AvailDescriptors module, it seems that the > only way to get the list of descriptors is: > len(Descriptors._descList) > > I don't like accessing hidden attributes; is there some better way to do this? > > - Noel > -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Access RDKit from Java
Hi Greg, You mentioned that there is a Jar file and associated shared library for RDKit in the KNIME repository. Unfortunately, they don't provide access except on request (see http://tech.knime.org/node/20231 for example). Could you make these available somewhere or include them in a future release? - Noel -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Cinfony 1.1 released
Hello all, I've just released Cinfony 1.1 with support for RDKitl 2011.09. New in this release is support for Indigo and OPSIN. If you are interested in writing Python scripts that have access to several cheminformatics toolkits using the same API (CDK, Open Babel, Indigo, RDKit and OPSIN are all supported), check out http://cinfony.googlecode.com. All the best, Noel -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Smiles Atom order
Hi Greg, Is there any way to retrieve the SMILES atom order after generating a SMILES string, and if not, is this something that could easily be added (I might try a patch)? This is useful to store additional information relating to particular atoms in the comment field. Regards, Noel -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Smiles Atom order
Great. So if I understand you correctly, it is currently accessible from C++. - Noel On 11 June 2013 10:26, Greg Landrum wrote: > Noel, > > On Tue, Jun 11, 2013 at 10:49 AM, Noel O'Boyle wrote: >> >> >> Is there any way to retrieve the SMILES atom order after generating a >> SMILES string, and if not, is this something that could easily be >> added (I might try a patch)? This is useful to store additional >> information relating to particular atoms in the comment field. > > > There is a molecule property that is set called _smilesAtomOutputOrder that > contains the atom ordering. > It is unfortunately not currently accessible from python. Adding access to > it is probably pretty straightforward. I have to check if I can make > mol.GetProp work with this or if a special function (or optional argument to > MolToSmiles) is required. > > This is github issue #50: https://github.com/rdkit/rdkit/issues/50 > > -greg > -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Searching the Doxygen docs
Hi Greg, There's an option you can use when generating the Doxygen docs that creates a nice Javascript search function. I find this very useful with other docs (see top right of http://openbabel.org/api/2.3/ for example). Any chance you might use this in future? The option is SEARCHENGINE. Regards, - Noel -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Notes on building the latest RDKit
Hi Greg,
This isn't really a bug report, just an FYI that may be helpful. I've
been using Boost 1.49 until now to compile RDKit, but this is now too
old. Specifically, the FMCS code chokes on it.
Also, I've been compiling on Windows with mingw-w64 (the fork of
MinGW), and I needed to comment out the definition of struct timezone
in the FMCS code (DebugTrace.h) as it's already present in mingw-w64's
includes. I don't know if it's worth fixing but if so, maybe this link
will help:
http://quickgit.kde.org/?p=emerge.git&a=commitdiff&h=cffdf0eb0b8ed8f65c640ba33db03b8f7970a6f0&hp=a3f18e16cb9fffa406de70c84b855843e10e98a7
("check_type_size("timezone" HAVE_TIMEZONE_DEFINED)")
Regards,
Noel
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Re: [Rdkit-discuss] Notes on building the latest RDKit
Hi Greg,
It might be something at this end, but compiling the FMCS target with
MSVC 11.0 and Boost 1.49 I have:
C:\Boost\include\boost-1_49\boost/property_tree/detail/json_parser_read.hpp(105):
error C2664: 'boost::property_tree::basic_ptree::push_back'
: cannot convert parameter 1 from 'std::pair<_Ty1,_Ty2>' to 'const
std::pair<_Ty1,_Ty2> &'
This looks like an MSVC versus Boost issue rather than anything
related to RDKit.
Regards,
- Noel
On 21 May 2015 at 03:22, Greg Landrum wrote:
> Hi Noel,
>
> On Wed, May 20, 2015 at 10:54 AM, Noel O'Boyle wrote:
>>
>>
>> This isn't really a bug report, just an FYI that may be helpful. I've
>> been using Boost 1.49 until now to compile RDKit, but this is now too
>> old. Specifically, the FMCS code chokes on it.
>
>
> Though we likely will start requiring a reasonably up-to-date version of
> boost at some point in the not-too-distant future, that hasn't happened yet.
> I have built the current release using boost 1.48 and a recent version of
> the code using v1.42, so the problem isn't boost in general. If you send me
> the error messages you are seeing, I may be able to help diagnose this.
>
>
>> Also, I've been compiling on Windows with mingw-w64 (the fork of
>> MinGW), and I needed to comment out the definition of struct timezone
>> in the FMCS code (DebugTrace.h) as it's already present in mingw-w64's
>> includes. I don't know if it's worth fixing but if so, maybe this link
>> will help:
>>
>> http://quickgit.kde.org/?p=emerge.git&a=commitdiff&h=cffdf0eb0b8ed8f65c640ba33db03b8f7970a6f0&hp=a3f18e16cb9fffa406de70c84b855843e10e98a7
>> ("check_type_size("timezone" HAVE_TIMEZONE_DEFINED)")
>>
>
> Thanks for pointing that out. I'll take a look.
>
> Best,
> -greg
>
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[Rdkit-discuss] Setting location of wedge/hashes
Hey Greg, I hope you had a good meeting. I was wondering whether it is possible to set the location of depicted wedge/hashes in a MOL file output. Right now, it seems that I can call WedgeHashBonds and that tells me where the wedge or hashes are via GetBondDir() (although I am still a bit confused as to which direction they are supposed to be). And I can set the BondDir fine... However, when I subsequently write out a MOL file it seems that any changes to the location of the BondDirs are just ignored. This is not a biggie for me, but it would be nice to be able to always set the same bond as the stereobond in a set of amino acids, as this makes it obvious which are D- versus L-. Regards, Noel -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Possible stereo centers incorrectly assigned?
You are assuming that CHI_TETRAHEDRAL_CW means "R" and v.v. for "S". I
don't think that's correct.
On 8 September 2015 at 12:58, Michał Nowotka wrote:
> Hi,
>
> I'm comparing stereo centers assigned by ChemAxon JChem and RDKit.
>
> The code would be:
>
> #--
>
> from rdkit import Chem
>
> def getStereoInfo(smiles):
> ret = []
> mol = Chem.MolFromSmiles(smiles)
> Chem.AssignStereochemistry(mol, flagPossibleStereoCenters=True,
> force=True)
> for atom in mol.GetAtoms():
> stereo = str(atom.GetChiralTag())
> atomIndex = atom.GetIdx()
> if str(atom.GetChiralTag()) != "CHI_UNSPECIFIED":
> if stereo == "CHI_TETRAHEDRAL_CW":
> chirality = "R"
> elif stereo == "CHI_TETRAHEDRAL_CCW":
> chirality = "S"
> else:
> chirality = "R/S"
> ret.append({"atomIndex":atomIndex,"chirality":chirality})
> return ret
>
> #---
>
> Now for (1R,2S,3S)-1,2,3-trichlorocyclopentane
> (Cl[C@H]1CC[C@@H](Cl)[C@H]1Cl), both RDKit and JChem give the same
> results:
> https://dl.dropboxusercontent.com/u/10967207/a.png
>
> But for ephedrine (O[C@H](c1c1)[C@@H](NC)C) stereo centers are
> reversed. RDKit gives:
> https://dl.dropboxusercontent.com/u/10967207/b.png
>
> and JChem gives:
> https://dl.dropboxusercontent.com/u/10967207/c.png
>
> The same is shown by pseudo-ephedrine (O[C@@H](c1c1)[C@@H](NC)C)
> which returns both stereo centers as 'R'.
>
> Is that a bug or an expected behavior? Are there any parameters in
> RDKit that can be set to get results similar to JChem?
>
> Regards,
>
> Michał Nowotka
>
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[Rdkit-discuss] [Open position] Cheminformatician at Sosei Heptares, Cambridge, UK
Hi all, I'll keep it short: we're currently recruiting for a Cheminformatician at Sosei Heptares. We have no specific grade in mind - you could be just finishing your PhD, or be much more experienced. Here's the link for more details: https://cezanneondemand.intervieweb.it/heptares/jobs/cheminformatician-computational-chemistry-team-37704/en/ Happy to answer questions about the position - just email me off-list. Regards, Noel ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit PostgreSQL extension: Unexpected behaviour of substruct()
"Every valid SMILES is also a valid SMARTS": I think this is one of John
May's lines, which I was never keen on as it makes people think that if you
treat a SMILES as a SMARTS that it will match the original SMILES. It
mostly will, but I think you have found the difference between the SMILES
and SMARTS treatment of "[2H]" - one means deuterium, the other means an
isotope of mass 2 with a single implicit hydrogen attached. It doesn't
match because the deuterium doesn't have another hydrogen attached. [I
think??]
Regards,
Noel
On Thu, 27 Jun 2024 at 10:05, Wim Dehaen wrote:
> I would expect the problem here is kekulization. The SMARTS is pattern
> matching using the kekule structure (i.e. double and single bonds, non
> aromatic atoms) and is not sanitized whereas the SMILES after parsing and
> sanitization has aromatic bonds and aromatic atoms. Try what happens when
> you do a SMARTS match with the SMILES with aromatic atoms:
> `[2H]c1cc([3H])cc(C2=N[C@](C)([37Cl])CC2)c1`
>
> best wishes
> wim
>
> On Thu, Jun 27, 2024 at 10:56 AM pgchem pgchem
> wrote:
>
>> Hello all,
>>
>> if every valid SMILES is also a valid SMARTS, why does:
>>
>> select substruct('[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::mol,
>> '[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::mol)
>>
>> yield "True", but:
>>
>> select substruct('[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::mol,
>> '[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::qmol)
>>
>> is "False"? The same is observed when using the @> operator.
>>
>> RDKit 2024.03.3 built from source + PostgreSQL 16.3.
>>
>> best regards
>>
>> Ernst-Georg
>>
>>
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Re: [Rdkit-discuss] Atom aromatic, but not in a ring
There are other more subtle changes that can affect the aromaticity, e.g.
changing a bond order, the charge, or the atomic number of an atom. IMO,
the user needs to take responsibility for knowing if aromaticity might be
invalidated, and perform the appropriate actions. The alternative is for
the toolkit to take the responsibility, trigger a check on every edit and
take a performance hit in the general case. Indeed, atom deletion could be
treated specially, but slippery slope and confusion here we come! :-)
Regards,
Noel
On Tue, 27 Aug 2024 at 13:47, Ingvar Lagerstedt
wrote:
> Hello,
>
> When deleting an aromatic atom or bond, the ring information is removed,
> while any remaining atom in the broken aromatic ring is still labelled
> aromatic. When attempting to sanitize such a molecule I get an exception:
> "rdkit.Chem.rdchem.AtomKekulizeException:
> non-ring atom 0 marked aromatic"
>
> To recreate:
>
> >>> from rdkit import Chem
>
> >>> m = Chem.MolFromSmiles('c1c1')
>
> >>> mw = Chem.RWMol(m)
>
> >>> mw.RemoveAtom(0)
>
> >>> Chem.SanitizeMol(mw)
>
> [10:40:50] non-ring atom 0 marked aromatic
>
> Traceback (most recent call last):
>
> File "", line 1, in
>
> rdkit.Chem.rdchem.AtomKekulizeException: non-ring atom 0 marked aromatic
>
>
> The example is simplistic, but there are reactions where an aromatic
> system can be broken, such as Zincke-Koenig reaction or Djerassi-Rylander
> oxidation. The exception makes it harder to describe such reactions.
>
>
> I currently check if an atom/bond is aromatic before deleting it, and if
> so remove all aromatic flags in the molecule.
>
>
> To me it would make sense if RDKit removed the aromatic flags for any atom
> that is no longer in a ring when deleting an aromatic atom/bond.
>
> Alternatively remove the aromatic flag on any non-ring atom when
> attempting to kekulize the structure rather than throwing an exception.
>
>
> Compare with a Birch reduction where the ring stays intact, here the
> kekulization/the following aromatize step rightly fails to find an aromatic
> ring, no exception is thrown, and the atoms are marked as non-aromatic.
>
>
> Kind Regards,
>
> Ingvar
>
>
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