Re: [Rdkit-discuss] suggestions for comprehensive searchable database of natural products

2017-11-28 Thread Curt Fischer 
I'd also be interested in Juptyer notebooks for this.  Thanks Tyler!

Curt

On Tue, Nov 28, 2017 at 8:26 AM, Tyler Backman  wrote:

> Hi Jim,
>
> MiBIG is a useful database of natural product gene clusters and
> structures, which you can download in JSON format here, and use pretty
> easily from within Python:
> https://mibig.secondarymetabolites.org/repository.html This also
> includes pathway and organism information.
>
> Secondly, our ClusterCAD database is built with RDKit and Django, but
> only includes Type I modular PKSs imported from MiBIG. You can use it
> online at clustercad.jbei.org, or view the code and launch a docker
> install locally from https://github.com/JBEI/clusterCAD. Internally,
> it has a RDKit postgresql database, and includes predicted chemical
> intermediates at each step of biosynthesis in addition to final
> products. It is hand curated, to improve on the automatic AntiSMASH
> annotations in MiBIG. I will gradually expand this to support a
> greater diversity of natural products. I could send you an example
> Jupyter notebook for using it programatically.
>
> Sincerely,
> Tyler
>
> On Mon, Nov 27, 2017 at 1:30 PM, James T. Metz via Rdkit-discuss
>  wrote:
> > RDkit Discussion Group,
> >
> > My apologies in advance if my request is not appropriate for this
> > discussion group.
> >
> > Given a small molecule that might have some resemblance to natural
> > products,
> > can someone suggest a free, comprehensive, PYTHON/RDkit searchable
> database
> > of natural products that might be suitable for similarity and
> substructure
> > searching.
> >
> > I am aware of a few websites that permit searching on the website. If
> > possible,
> > I would like to programmatically search by running a PYTHON/RDkit script
> on
> > my
> > local machine and then return the structures of related molecules to my
> > local script.
> >
> > I would prefer not having to download and store a huge database.
> >
> > Also, if possible, it would be important to return the organism(s)
> that
> > creates
> > the natural product.  Pathway information would be also very, very
> helpful.
> >
> > I greatly welcome comments and suggestions.
> >
> > Thank you.
> >
> > Regards,
> > Jim Metz
> > Northwestern University
> >
> >
> >
> >
> >
> > 
> --
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> >
>
>
>
> --
> Tyler W. H. Backman
> Postdoctoral Fellow
> Lawrence Berkeley National Laboratory
> Joint BioEnergy Institute
>
> 
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Re: [Rdkit-discuss] suggestions for comprehensive searchable database of natural products

2017-11-28 Thread Tyler Backman 
Hi Jim,

MiBIG is a useful database of natural product gene clusters and
structures, which you can download in JSON format here, and use pretty
easily from within Python:
https://mibig.secondarymetabolites.org/repository.html This also
includes pathway and organism information.

Secondly, our ClusterCAD database is built with RDKit and Django, but
only includes Type I modular PKSs imported from MiBIG. You can use it
online at clustercad.jbei.org, or view the code and launch a docker
install locally from https://github.com/JBEI/clusterCAD. Internally,
it has a RDKit postgresql database, and includes predicted chemical
intermediates at each step of biosynthesis in addition to final
products. It is hand curated, to improve on the automatic AntiSMASH
annotations in MiBIG. I will gradually expand this to support a
greater diversity of natural products. I could send you an example
Jupyter notebook for using it programatically.

Sincerely,
Tyler

On Mon, Nov 27, 2017 at 1:30 PM, James T. Metz via Rdkit-discuss
 wrote:
> RDkit Discussion Group,
>
> My apologies in advance if my request is not appropriate for this
> discussion group.
>
> Given a small molecule that might have some resemblance to natural
> products,
> can someone suggest a free, comprehensive, PYTHON/RDkit searchable database
> of natural products that might be suitable for similarity and substructure
> searching.
>
> I am aware of a few websites that permit searching on the website. If
> possible,
> I would like to programmatically search by running a PYTHON/RDkit script on
> my
> local machine and then return the structures of related molecules to my
> local script.
>
> I would prefer not having to download and store a huge database.
>
> Also, if possible, it would be important to return the organism(s) that
> creates
> the natural product.  Pathway information would be also very, very helpful.
>
> I greatly welcome comments and suggestions.
>
> Thank you.
>
> Regards,
> Jim Metz
> Northwestern University
>
>
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>



-- 
Tyler W. H. Backman
Postdoctoral Fellow
Lawrence Berkeley National Laboratory
Joint BioEnergy Institute

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Re: [Rdkit-discuss] Problems with coordMap in EmbedMultipleConfs

2017-11-28 Thread Paolo Tosco 

Dear Jan,

I don't think you are doing anything wrong. I tried using coordMap 
myself a few weeks ago and it looked like the parameter was being 
ignored. I'll try and understand why that happens as soon as I have a 
bit of time.


Kind regards,
Paolo


On 11/28/17 10:16, Jan Halborg Jensen wrote:

The following code should produce 5 conformers of c1c1CCC” where the 
coordinates of the benzene ring is the same.  But it doesn’t.  What I am doing 
wrong?

Best regards, Jan


from rdkit import Chem
from rdkit.Chem import AllChem

template_smiles = "c1c1"
template = Chem.MolFromSmiles(template_smiles)
template = Chem.AddHs(template)

AllChem.EmbedMolecule(template)

prop = AllChem.MMFFGetMoleculeProperties(template, mmffVariant="MMFF94")
ff =AllChem.MMFFGetMoleculeForceField(template,prop)
ff.Minimize()

Chem.SDWriter("template.sdf").write(template)

mol_smiles = "c1c1CCC"
mol = Chem.MolFromSmiles(mol_smiles)
mol = Chem.AddHs(mol)

core = Chem.MolFromSmiles(template_smiles)

mol_match = mol.GetSubstructMatch(core)
template_match = template.GetSubstructMatch(core)

print mol_match, template_match

coordMap = {}
templateConf = template.GetConformer(-1)
for i_template, i_mol in zip(template_match,mol_match):
 corePtI = templateConf.GetAtomPosition(i_template)
 #print corePtI.x, corePtI.y, corePtI.z
 coordMap[i_mol] = corePtI

AllChem.EmbedMultipleConfs(mol,5,coordMap=coordMap)

w = Chem.SDWriter('conformers.sdf')
for conf in mol.GetConformers():
 tm = Chem.Mol(mol,False,conf.GetId())
 w.write(tm)
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[Rdkit-discuss] Problems with coordMap in EmbedMultipleConfs

2017-11-28 Thread Jan Halborg Jensen 
The following code should produce 5 conformers of c1c1CCC” where the 
coordinates of the benzene ring is the same.  But it doesn’t.  What I am doing 
wrong?

Best regards, Jan


from rdkit import Chem
from rdkit.Chem import AllChem

template_smiles = "c1c1"
template = Chem.MolFromSmiles(template_smiles)
template = Chem.AddHs(template)

AllChem.EmbedMolecule(template)

prop = AllChem.MMFFGetMoleculeProperties(template, mmffVariant="MMFF94")
ff =AllChem.MMFFGetMoleculeForceField(template,prop)
ff.Minimize()

Chem.SDWriter("template.sdf").write(template)

mol_smiles = "c1c1CCC"
mol = Chem.MolFromSmiles(mol_smiles)
mol = Chem.AddHs(mol)

core = Chem.MolFromSmiles(template_smiles)

mol_match = mol.GetSubstructMatch(core)
template_match = template.GetSubstructMatch(core)

print mol_match, template_match

coordMap = {}
templateConf = template.GetConformer(-1) 
for i_template, i_mol in zip(template_match,mol_match):
corePtI = templateConf.GetAtomPosition(i_template)
#print corePtI.x, corePtI.y, corePtI.z
coordMap[i_mol] = corePtI

AllChem.EmbedMultipleConfs(mol,5,coordMap=coordMap)

w = Chem.SDWriter('conformers.sdf') 
for conf in mol.GetConformers():
tm = Chem.Mol(mol,False,conf.GetId())
w.write(tm)
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Re: [Rdkit-discuss] RPM distros

2017-11-28 Thread Maciek Wójcikowski 
Hi Tim and Francois,

To fix missing dependencies use "sudo apt install -f" and use "yum install
rdkit_package_file.rpm" to install package to have all the dependencies.

On Debian (based systems) I prefer to install standalone packages via gdebi
which does this automatically.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-11-28 0:50 GMT+01:00 Francois BERENGER 
:

> On 11/28/2017 12:42 AM, Tim Dudgeon wrote:
> > I see exactly the same when I build with those cmake args.
>
> Maybe you are missing some of the dependencies.
> I don't think the packages we create have all the dependency information:
>
> fonts-freefont-ttf,
> libboost-python1.58.0,
> libboost-regex1.58.0,
> libboost-system1.58.0,
> libboost-thread1.58.0,
> libc6 (>= 2.14),
> libgcc1 (>= 1:4.1.1),
> libpython2.7 (>= 2.7),
> libstdc++6 (>= 5.2),
> python (<< 2.8),
> python (>= 2.7~)
>
> You should install the ones you are missing and test again.
>
> > On 27/11/2017 09:11, Francois BERENGER wrote:
> >> On 11/27/2017 06:01 PM, Tim Dudgeon wrote:
> >>> I did:
> >>>
> >>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF
> >>> -DCMAKE_INSTALL_PREFIX=/usr/ ..
> >> Try this instead, just for the cmake part:
> >>
> >> cmake -Wno-dev \
> >>  -DRDK_INSTALL_INTREE=OFF \
> >>  -DRDK_BUILD_INCHI_SUPPORT=ON \
> >>  -DRDK_BUILD_AVALON_SUPPORT=ON \
> >>  -DRDK_BUILD_PYTHON_WRAPPERS=ON \
> >>  -DCMAKE_INSTALL_PREFIX=/usr \
> >>  -DRDKit_VERSION=`date +%Y.%m` \
> >>  ../
> >>
> >> then do the rest (cpack ...) and test again
> >> after an install of the freshly created package.
> >>
> >> I advise to wipe out any prior rdkit install from your machine
> >> before installing the new packages (so that we test what we intend to
> >> test).
> >>
> >> On a Debian-like:
> >> sudo apt-get remove $(dpkg -l | grep rdkit | awk '{print $2}')
> >>
> >>> cpack -G DEB
> >>> cpack -G RPM
> >>>
> >>>
> >>> On 27/11/2017 00:05, Francois BERENGER wrote:
>  Hello,
> 
>  What are the exact commands you used to configure and compile rdkit?
> 
>  The script in there is my best attempt:
> 
>  https://github.com/rdkit/rdkit/pull/1655
> 
>  Regards,
>  F.
> 
>  On 11/25/2017 12:50 AM, Tim Dudgeon wrote:
> > I got round to testing the debs and rpms but without success.
> >
> > For the debs the following were built:
> >
> > RDKit-2018.03.1.dev1-Linux-Development.deb
> > RDKit-2018.03.1.dev1-Linux-Extras.deb
> > RDKit-2018.03.1.dev1-Linux-Python.deb
> > RDKit-2018.03.1.dev1-Linux-Runtime.deb
> >
> > On a clean Ubuntu Xenial system, with just python added (apt-get -y
> > install python) the packages installed fine:
> >
> > # dpkg -i *.deb
> > Selecting previously unselected package rdkit-development.
> > (Reading database ... 5666 files and directories currently
> installed.)
> > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ...
> > Unpacking rdkit-development (2018.03.1.dev1) ...
> > Selecting previously unselected package rdkit-extras.
> > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
> > Unpacking rdkit-extras (2018.03.1.dev1) ...
> > Selecting previously unselected package rdkit-python.
> > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
> > Unpacking rdkit-python (2018.03.1.dev1) ...
> > Selecting previously unselected package rdkit-runtime.
> > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ...
> > Unpacking rdkit-runtime (2018.03.1.dev1) ...
> > Setting up rdkit-development (2018.03.1.dev1) ...
> > Setting up rdkit-extras (2018.03.1.dev1) ...
> > Setting up rdkit-python (2018.03.1.dev1) ...
> > Setting up rdkit-runtime (2018.03.1.dev1) ...
> >
> > There seem to be header files in /usr/include/rdkit and the RDKit
> > installation (.py and .so files) in
> > /usr/lib/python2.7/dist-packages/rdkit
> >
> > But RDKit doesn't work from Python:
> >
> > # python
> > Python 2.7.12 (default, Nov 19 2016, 06:48:10)
> > [GCC 5.4.0 20160609] on linux2
> > Type "help", "copyright", "credits" or "license" for more
> information.
>  import rdkit
> > Traceback (most recent call last):
> > File "", line 1, in 
> > File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line
> > 2, in
> > 
> >   from .rdBase import rdkitVersion as __version__
> > ImportError: libpython2.7.so.1.0: cannot open shared object file: No
> > such file or directory
> >
> > For the rpms the story is similar. The same 4 files are built as
> rpms.
> > Installing them on a clean centos7 machine went fine and the files
> > seem
> > to get installed to the same places.
> > But RDKit again couldn't be used from Python, but with a different
> > error:
> >
> > # python
> >