[Rdkit-discuss] Check molecules
Hi, is there a function to check molecule structures, whether it actually is a possible structure. E.g. because of wrong assignment of aromaticity. And if not, to reassign aromaticity. regards -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generation of stereo-isomers
Hi all,
I opened an issue at rdkit-github for that matter.
https://github.com/rdkit/rdkit/issues/626
Thanks to your comments! If you want look at the code snippet I posted.
At the moment, simply all stereo-isomers are generated.
regards
Soren
On Fri, Sep 25, 2015 at 12:19 AM, Axel Pahl <axelp...@gmx.de> wrote:
> Hi Soren,
>
> maybe this function which enumerates racemates with one stereocenter into
> the corresponding enantiomers might help:
>
> def enum_racemates(sdf_list_or_file, find_only=True, mol_id="molid"):
> """returns: result_sdf::list, racemic_molids::list
> find_only==True: return new sdf as list which contains all the
> racemates of the input sdf.
> find_only==False: return new sdf as list with ALL input structures,
> where the racemates are
> replaced by their two enantiomers. The returned sdf
> is always
> equal in size or larger as the input sdf.
> Multiple stereo centers are not yet handled.
> In the new sdf the molids are no longer unique and should be reassigned
> (remove molid and run calc_props(sdf))."""
>
> result_sdf = Mol_List()
> racemic_molids = []
>
> if not isinstance(sdf_list_or_file, list) and
> sdf_list_or_file.atEnd(): # sdf is file
> print(" * file object is at end, please reload.")
> return None
>
> for mol in sdf_list_or_file:
> first_undefined = False
> chiral_centers = Chem.FindMolChiralCenters(mol,
> includeUnassigned=True)
>
> if chiral_centers:
> first_center= chiral_centers[0][0]
> first_undefined = chiral_centers[0][1] == "?"
>
> if first_undefined:
> racemic_molids.append(int(mol.GetProp(mol_id)))
> if find_only:
> result_sdf.append(mol)
> continue
>
> else:
> mol1 = Chem.Mol(mol)
> mol2 = Chem.Mol(mol)
>
> mol1.GetAtomWithIdx(first_center).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW)
>
> mol2.GetAtomWithIdx(first_center).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
> result_sdf.append(mol1)
> result_sdf.append(mol2)
>
> else:
> if not find_only: # return ALL mols
> result_sdf.append(mol)
>
> return result_sdf, racemic_molids
>
> Please also have a look at this post
> http://sourceforge.net/p/rdkit/mailman/message/32390126/ and Toby's
> answer which pointed me in the right direction.
>
> Kind regards,
> Axel
>
>
> On 24.09.2015 23:17, Soren Wacker wrote:
>
> Hi,
>
> is it possible with RDKit to generate all stereoisomers of a given
> compound?
>
> If not, is anyone working on it?
>
> If not, how difficult would it be / what would be the best way to
> implement such a function.
>
> best regards
>
> Soren
>
>
> --
>
>
>
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[Rdkit-discuss] Generation of stereo-isomers
Hi, is it possible with RDKit to generate all stereoisomers of a given compound? If not, is anyone working on it? If not, how difficult would it be / what would be the best way to implement such a function. best regards Soren -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Molecule objects conformation
Hi Greg,
thanks. Is the random conformation really randomly selected, or is it always
the same? I mean, if I generate a conformation from smiles without chiral
specifiaction, will I end up always with the same conformation?
So, I am using the Chem.Lipinski and Chem.Descriptors modules to calculate
properties of molecule objects that where generated by smiles strings. Are all
descriptors independent of the particular conformations? Or are you aware of
descriptors which definitely depend on a conformation?
I would like to generate descriptors that are reproducible for a given
compound, ideally independent of the conformation. One of the problem is that
sometimes smiles strings contain chiral specification, sometimes different
protonation states etc. I need to standardize it somehow.
kind regards
Soren
From: Greg Landrum [greg.land...@gmail.com]
Sent: Monday, March 30, 2015 10:00 PM
To: Soren Wacker
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Molecule objects conformation
Hi Soren,
On Mon, Mar 30, 2015 at 11:37 PM, Soren Wacker
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
I am wondering how RDKit handles molecule conformations and stereo-isomers.
E.G. when I generate a chiral molecule from a smiles string, where chirality is
not explicated.
Does RDKit generate a random conformation, or no specific conformation in the
first place?
By default no conformation is generated, but if you ask the RDKit to generate a
3D conformation (or conformations), it will attempt to generate one that
matches whatever stereochemistry is specified.
So if you specify the chirality it attempts to preserve it:
In [17]: m = Chem.AddHs(Chem.MolFromSmiles('Cl[C@H](F)CC[C@H](C)Br'))
In [18]: AllChem.EmbedMultipleConfs(m,10)
Out[18]: rdkit.rdBase._vecti at 0x7f6f9b3184d0
In [19]: _=AllChem.UFFOptimizeMoleculeConfs(m,maxIters=1000)
In [20]: for conf in m.GetConformers():
tm = Chem.Mol(m,False,conf.GetId())
Chem.AssignAtomChiralTagsFromStructure(tm)
print Chem.FindMolChiralCenters(tm)
:
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
But if you don't specify it, you get random stereoisomers:
In [21]: m = Chem.AddHs(Chem.MolFromSmiles('Cl[CH](F)CC[CH](C)Br'))
In [22]: AllChem.EmbedMultipleConfs(m,10)
Out[22]: rdkit.rdBase._vecti at 0x7f6f9b318350
In [23]: _=AllChem.UFFOptimizeMoleculeConfs(m,maxIters=1000)
In [24]: for conf in m.GetConformers():
tm = Chem.Mol(m,False,conf.GetId())
Chem.AssignAtomChiralTagsFromStructure(tm)
print Chem.FindMolChiralCenters(tm)
:
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'R')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'R')]
[(1, 'R'), (5, 'S')]
[(1, 'R'), (5, 'S')]
[(1, 'R'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'R'), (5, 'R')]
[(1, 'R'), (5, 'S')]
Does that answer your question?
-greg
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[Rdkit-discuss] Molecule objects conformation
Hi, I am wondering how RDKit handles molecule conformations and stereo-isomers. E.G. when I generate a chiral molecule from a smiles string, where chirality is not explicated. Does RDKit generate a random conformation, or no specific conformation in the first place? kind regards Soren -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] https://sourceforge.net
Hi, rdkit has moved to github, but there is still the repository on sourceforge.net. However, if you google 'rdkit bugs' the sourceforge page comes up first. I find that confusing. Is there a reason to keep the sourceforge.net stuff? If not, why don't you remove the sourceforge repository? kind regards Soren -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Wired dependencies.
Hi, OK, this issue is solved. Now, everything (anaconda, rdkit, ipython notebook jupiter) runs fine. I documented the installation process. In case anyone is interested here is my installation script. I did not run it a last time, but it should be at least a good start to install and run rdkit in a python notebook within an anaconda environment. regards Soren rdkit_anaconda_install.sh --- #!/bin/bash sourcedir=/tmp/install_modeling_env mkdir /tmp/install_modeling_env cd /tmp/install_modeling_env install_prefix=/path/to/target/dir #Check target exists if [ -d $install_prefix ] ;then echo Please create target directory first exit 1 fi export PATH=$PATH:$install_prefix/bin yum -y install wget tar bzip2 git gcc-c++ patch python-qt4 @development-tools boost\ boost-devel cmake bison python-devel tk-devel readline-devel\ zlib-devel bzip2-devel sqlite-devel wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh chmod +x Miniconda-latest-Linux-x86_64.sh $sourcedir/Miniconda-latest-Linux-x86_64.sh -b -p $install_prefix git clone https://github.com/rdkit/conda-rdkit.git conda-rdkit conda update conda conda update --all conda install --yes pip conda install --yes numpy conda install --yes scipy conda install --yes matplotlib conda install --yes ipython conda install --yes pil conda install --yes scikit-learn conda install --yes scikit-image conda install --yes pandas conda install --yes requests conda install --yes conda-build conda install --yes patchelf conda install --yes jinja2 conda install --yes pyzmq conda install --yes tornado conda install --yes jsonschema conda install --yes xwpython conda update --all cd $sourcedir/conda-rdkit conda build boost cd $sourcedir/conda-rdkit conda build rdkit cd $sourcedir conda create --use-local -n env rdkit ipython matplotlib requests pyzmq pyqt jinja2 tornado jsonschema pil scikit-learn pandas wxpython rm -r $sourcedir source activate env echo NOTE Remember to add 'export PATH=\$PATH:$install_prefix/bin' to you PATH echo NOTE Start the notebook with 'source activate env ; ipython notebook ; source deactivate ' -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Identify and repair broken molecules
Hi, when generating molecules from smiles and drawing them sometimes show little red squares around certain atoms. I guess, this means that the connectivity is wrong. Is there a way to identify and potentially repair these molecules in rdkit? Thanks Soren -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Wired dependencies.
Sorry, I mixed something up. I will try what you suggested, I think I actually did not do the installation in the environment. Please, add a corresponding comment here: https://github.com/rdkit/conda-rdkit It is not mentioned that you have to do conda install boost conda install rdkit in the environment. Thanks Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Soren Wacker [swac...@ucalgary.ca] Sent: Tuesday, March 17, 2015 11:33 AM To: Greg Landrum Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Wired dependencies. Yes, sorry, I did not mention that. But I did that, too. Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Greg Landrum [greg.land...@gmail.com] Sent: Monday, March 16, 2015 10:42 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Wired dependencies. Hi Soren, On Mon, Mar 16, 2015 at 11:58 PM, Soren Wacker swac...@ucalgary.camailto:swac...@ucalgary.ca wrote: Hi, I am using conda and rdkit, so installed https://github.com/rdkit/conda-rdkit with conda build boost conda build rdkit The installation seems to be successfull, at least in part, since I can import and use rdkit. Did you also do: conda install boost conda install rdkit in the environment you want to use? -greg However, I noticed some strange behaviour: When I activate a conda environment and import rdkit from ipython notebook, the kernel will crash. Apparently, I have to use the system python version at /usr/bin/python and import the packages installed with conda. Also upgrading the python packages with conda update --all will lead to a not working installation. Any ideas how to solve that? Or where it may come from? kind regards Soren -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Wired dependencies.
Yes, sorry, I did not mention that. But I did that, too. Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Greg Landrum [greg.land...@gmail.com] Sent: Monday, March 16, 2015 10:42 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Wired dependencies. Hi Soren, On Mon, Mar 16, 2015 at 11:58 PM, Soren Wacker swac...@ucalgary.camailto:swac...@ucalgary.ca wrote: Hi, I am using conda and rdkit, so installed https://github.com/rdkit/conda-rdkit with conda build boost conda build rdkit The installation seems to be successfull, at least in part, since I can import and use rdkit. Did you also do: conda install boost conda install rdkit in the environment you want to use? -greg However, I noticed some strange behaviour: When I activate a conda environment and import rdkit from ipython notebook, the kernel will crash. Apparently, I have to use the system python version at /usr/bin/python and import the packages installed with conda. Also upgrading the python packages with conda update --all will lead to a not working installation. Any ideas how to solve that? Or where it may come from? kind regards Soren -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Wired dependencies.
Hi, I am using conda and rdkit, so installed https://github.com/rdkit/conda-rdkit with conda build boost conda build rdkit The installation seems to be successfull, at least in part, since I can import and use rdkit. However, I noticed some strange behaviour: When I activate a conda environment and import rdkit from ipython notebook, the kernel will crash. Apparently, I have to use the system python version at /usr/bin/python and import the packages installed with conda. Also upgrading the python packages with conda update --all will lead to a not working installation. Any ideas how to solve that? Or where it may come from? kind regards Soren -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chem.Draw darker colors
but how? Soren From: Greg Landrum [greg.land...@gmail.com] Sent: Wednesday, February 11, 2015 10:27 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Chem.Draw darker colors My other answer about using the DrawingOptions object applies here too. Instead of setting elemDict to be a defaultDict, you would just change the colors for S and F to whatever you prefer. -greg On Thu, Feb 12, 2015 at 12:13 AM, Soren Wacker swac...@ucalgary.camailto:swac...@ucalgary.ca wrote: Hi, I printed some moecules with the Draw module of rdkit and generated some useful figures. I noticed that for some elements the contrast to white is very low. Therefore, I suggest to change the default colors to the darker versions. E.g. darkyellow instead of yellow for sulfur and darkcyan instead of cyan for fluorine kind regards Soren -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit YYDEBUG Redefined error
Hi, I printed some moecules with the Draw module of rdkit and generated some useful figures. I noticed that for some elements the contrast to white is very low. Therefore, I suggest to change the default colors to the darker versions. E.g. darkyellow instead of yellow for sulfur and darkcyan instead of cyan for fluorine kind regards Soren -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Draw molecules black and white.
Hi, I am looking for a keyword to draw molecules black and white or greyscale e.g. Draw.MolsToImage(...,keyword?) is there something like this? regards Soren -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Molecular descriptors / Fragments
--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4
Tel.: ++1 (403) 210 7860
Email: swac...@ucalgary.ca
From: Greg Landrum [greg.land...@gmail.com]
Sent: Friday, January 30, 2015 11:35 PM
To: Soren Wacker
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Molecular descriptors / Fragments
Hi Soren,
The functions should definitely still be there.
In [1]: from rdkit import rdBase
In [2]: rdBase.rdkitVersion
Out[2]: '2014.09.2'
In [3]: from rdkit import Chem
In [4]: from rdkit.Chem import Descriptors
In [5]: m = Chem.MolFromSmiles('c1c1NCOC')
In [6]: Descriptors.fr_Al_COO(m)
Out[6]: 0
Is this the same thing you are doing?
-greg
Yes. Using, iphython and the notebook:
INPUT:
from rdkit import rdBase
print rdBase.rdkitVersion
from rdkit import Chem
from rdkit.Chem import Descriptors
m = Chem.MolFromSmiles('c1c1NCOC')
Descriptors.fr_Al_COO(m)
OUTPUT:
2014.09.2
---
AttributeErrorTraceback (most recent call last)
ipython-input-6-737f81fc3bc6 in module()
5 from rdkit.Chem import Descriptors
6 m = Chem.MolFromSmiles('c1c1NCOC')
7 Descriptors.fr_Al_COO(m)
AttributeError: 'module' object has no attribute 'fr_Al_COO'
---
strange,hm?
Any ideas?
import rdkit
rdkit.__file__
.../anaconda/pkgs/rdkit-2014.09.2-np19py27_0/lib/python2.7/site-packages/rdkit/__init__.pyc'
regards
Sören
On Fri, Jan 30, 2015 at 11:40 PM, Soren Wacker
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
Hi,
I installed RDKit
python -c 'from rdkit import rdBase; print rdBase.rdkitVersion'
2014.09.2
with conda.
Before, I used molecular descriptors as explained here:
http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html
For example,
Descriptors.fr_Al_COO
However, in the current release I cannot find these functions anymore.
Can anyone point me to a documentation where it is explained what has happened
to this functions or which version of RDKit contains it?
Thanks
Sören
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[Rdkit-discuss] Molecular descriptors / Fragments
Hi, I installed RDKit python -c 'from rdkit import rdBase; print rdBase.rdkitVersion' 2014.09.2 with conda. Before, I used molecular descriptors as explained here: http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html For example, Descriptors.fr_Al_COO However, in the current release I cannot find these functions anymore. Can anyone point me to a documentation where it is explained what has happened to this functions or which version of RDKit contains it? Thanks Sören -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] rdkit.version()
Hi, I would like to find out the currently installed version on my System. However, I cannot find a version string in RDKit. Something like rdkit.version() would be nice. Is there something like this implemented?? kind regards Soren From: James Davidson [j.david...@vernalis.com] Sent: Wednesday, December 10, 2014 10:48 AM To: greg.land...@gmail.com Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Avalon test failing(?) Hi Greg, The new version of the test code is targeting the 1.2 avalon toolkit version. Here's the commit that did that. https://github.com/rdkit/rdkit/commit/42dab414ee6fbe5489078e5e52046608bbf785cb As an FYI, to make these tests pass on windows, you need to edit the code to fix a bug: you need to comment out line 1446 of reaccsio.c: //MyFree((char *)tempdir); Following your advice, I downloaded the 1.2 source from Sourceforge (http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/); commented-out the line in reaccsio.c; and then reconfigured in cmake and rebuilt in VS. The tests pass now – thanks! Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] [Rdkit-devel] 2014.03 (Q1 2014) RDKit release
I would appreciate RPMs for Fedora. best -- Dr. Soeren Wacker Centre For Molecular Simulation, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: GALLY Jose Manuel [jose.manuel.ga...@gmail.com] Sent: Monday, May 26, 2014 2:39 AM To: Gianluca Sforna Cc: RDKit Discuss; RDKit Developers List; Greg Landrum Subject: Re: [Rdkit-discuss] [Rdkit-devel] 2014.03 (Q1 2014) RDKit release Dear Gianluca, As a new user of RDKIT and Centos (6.5 x64), I would like to thank you for your RPMs which made my life much easier when I installed RDKIT! I would like to know if you are planning on building the RPMs for the last release of RDKIT? If it's the case I am very interested! Best regards, Jose Manuel 2014-05-12 11:40 GMT+02:00 Gianluca Sforna gia...@gmail.commailto:gia...@gmail.com: On Sun, May 11, 2014 at 9:50 AM, Greg Landrum greg.land...@gmail.commailto:greg.land...@gmail.com wrote: I have uploaded 32-bit and 64-bit Windows binaries for Python 2.7 and, in response to a couple of requests, 32-bit and 64-bit Windows binaries for Java. Talking about Java, I think I am not building the wrappers in the RPMs for Fedora/CentOS. If someone is interested I can try including them in my next build. -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/giallu -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- José-Manuel Gally PhD Student Structural Bioinformatics Chemoinformatics Institut de Chimie Organique et Analytique (ICOA) UMR CNRS-Université d'Orléans 7311 Université d'Orléans Rue de Chartres F-45067 Orléans phone: +33 238 494 577 -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] change behaviour of mailing list
Hi, I don't find a propties or options for the mailing list. Is it possible to get the mails forwarded and not combined in one email as attachments? best Soren -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
