Re: [Rdkit-discuss] Polar surface areas
Hi Josh You have TPSA (Topological Polar Surface Area) in Rdkit Descriptors http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html Check the list of all descriptors http://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors regards Adrian Jasiński 2016-08-17 16:17 GMT+02:00 Campbell J.E. : > Hi RDKitters, > > > > I’d like to be able to calculate polar surface areas on some molecules > using RDKit as a torsion changes. I’ve dug into the code and found the > MolSurf.py and some of the functions but as I understand it these are > mostly for a 2Dish representation of the molecule. So what’s the best way > to go about this? I can supply 3D coordinates for the conformations and > partial charges. Is there also a way to increase the accuracy of the > surface area calculated? > > > > Cheers, > > > > Josh Campbell > > > > > > > -- > > ___ > 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
[Rdkit-discuss] PgSQL / cartridge installation problem
I'm using Ubuntu 16.04 LTS, I successfully installed latest rdkit version 2016_03_03 from source, but when I tried to install Cartridge I found difficulties. Theres no good instruction in RDKit documentation how to install it. Only info is in README file but it is not valid. Possibly there should be some notes added to http://www.rdkit.org/docs/Install.html or in Cartridge tab: http://www.rdkit.org/docs/Cartridge.html First theres no file: pgsql_install.sh in: \Code\PgSQL\rdkit\pgsql_install.sh (It should be accroding README file in \Code\PgSQL\rdkit\README) Second when I tried run "make" command I got an error: gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/mit-krb5 -fPIC -pie -fno-omit-frame-pointer -fpic -I/usr/local/include -I/home/adrian/mm/apps/rdkit/current/Code -DRDKITVER='"007300"' -mpopcnt -I. -I./ -I/usr/include/postgresql/9.5/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/tcl8.6 -fPIC -c -o mol_op.o mol_op.c mol_op.c: In function ‘mol_substruct_count’: mol_op.c:137:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] bool uniquify = PG_GETARG_BOOL(2); ^ mol_op.c: In function ‘mol_formula’: mol_op.c:203:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] bool separateIsotopes = PG_GETARG_BOOL(1); ^ mol_op.c: In function ‘mol_inchi’: mol_op.c:222:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *res = pnstrdup(str, strlen(str)); ^ mol_op.c: In function ‘mol_inchikey’: mol_op.c:238:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *res = pnstrdup(str, strlen(str)); ^ mol_op.c: In function ‘mol_murckoscaffold’: mol_op.c:249:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] CROMol scaffold = MolMurckoScaffold(mol); ^ mol_op.c:251:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] Mol *res = deconstructROMol(scaffold); ^ In file included from mol_op.c:34:0: mol_op.c: In function ‘fmcs_mol2s_transition’: /usr/include/postgresql/9.5/server/fmgr.h:224:29: warning: initialization makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ mol_op.c:334:18: note: in expansion of macro ‘PG_GETARG_DATUM’ CROMol mol = PG_GETARG_DATUM(1); ^ In file included from /usr/include/postgresql/9.5/server/postgres.h:48:0, from rdkit.h:40, from mol_op.c:33: mol_op.c:339:19: error: format not a string literal and no format arguments [-Werror=format-security] elog(WARNING, t); ^ /usr/include/postgresql/9.5/server/utils/elog.h:212:23: note: in definition of macro ‘elog’ elog_finish(elevel, __VA_ARGS__); \ ^ mol_op.c:344:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *smiles = makeMolText(mol, &len, false); ^ In file included from mol_op.c:34:0: /usr/include/postgresql/9.5/server/fmgr.h:224:29: warning: initialization makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ mol_op.c:363:18: note: in expansion of macro ‘PG_GETARG_DATUM’ CROMol mol = PG_GETARG_DATUM(1); ^ In file included from /usr/include/postgresql/9.5/server/postgres.h:48:0, from rdkit.h:40, from mol_op.c:33: mol_op.c:368:19: error: format not a string literal and no format arguments [-Werror=format-security] elog(WARNING, t); ^ /usr/include/postgresql/9.5/server/utils/elog.h:212:23: note: in definition of macro ‘elog’ elog_finish(elevel, __VA_ARGS__); \ ^ mol_op.c:373:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *smiles = makeMolText(mol, &len, false); ^ mol_op.c: In function ‘fmcs_mols’: mol_op.c:411:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] int32 ts_size = VARHDRSZ + strlen(str); ^ In file included from mol_op.c:34:0: mol_op.c: In function ‘fmcs_mol_transition’: /usr/include/postgresql/9.5/server/fmgr.h:224:29: warning: initialization makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ mol_op.c:432:18: note: in expansion of macro ‘PG_GETARG_DATUM’ CROMol mol = PG_GETARG_DATUM(1); ^ In file included from rdkit.h:40:0, from mol
[Rdkit-discuss] next RDKit UGM?
Are there any plans for next RDKit UGM in 2016? I planning my conferences calendar for this year, for this reason it will be good to know. regards Adrian -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Latest version
The release and binary files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2015_09_2 regards Adrian 2015-12-10 11:12 GMT+01:00 David Cosgrove : > Hi All, > > I'm sorry to trouble you all with this one, as I feel I should be able to > do better. I'm trying to install the latest version, 2015.09.1, but I > can't find it on sourceforge. The latest one I can find there is > 2015.03.1. I've managed to get the ubuntu installation installed via > apt-get, and my python interpreter can find it. However, I can't find the > include files or object libraries for C++ development, which is what I'm > after. > > Can someone please point me in the right direction? Be as rude as you > like in the process, as I feel I must be being very dim! > > Thanks, > > Dave > > > > -- > > ___ > 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] Ridiculously easy problem - capture RDKit's error messages
see:
https://docs.python.org/2/tutorial/errors.html
import rdkit
from rdkit import Chem
try:
Chem.MolFromSmiles('XXX')
except Exception as msg:
(do something here e.g. pring msg)
pozdrawiam
Adrian
2015-01-23 14:58 GMT+01:00 JP :
>
> Yo RDKitters,
>
> I am stuck on something so basic, its embarrassing. But for the life of
> me I cannot figure it out on my own. This is probably more of a python
> question than an RDKit one.
>
> I want to capture the RDKit warning/error message from python. e.g.
>
> >>> import rdkit
> >>> from rdkit import Chem
> >>> Chem.MolFromSmiles('XXX')
> [14:51:32] SMILES Parse Error: syntax error for input: XXX
>
> I want to capture that error message (which in this case isn't very
> informative, but if you read in a mol2 you can get something like
> [14:25:46] 3ZGZ.A: warning - O.co2 with non C.2 or S.o2 neighbor. Which I
> am also interested in). The big picture is that I built a web up where you
> upload an sdf, mol, mol2 or smi file - and I want to show RDKit's error
> message if there something funny in the query file.
>
> I have tried the obvious (I think):
>
> #!/usr/bin/env python
> import sys
> import rdkit
> from rdkit import Chem
>
> f = open("err.log", "w")
> original_stderr = sys.stderr
> sys.stderr = f
> Chem.MolFromSmiles('XXX')
> sys.stderr = original_stderr
> f.close()
>
> This still shows the error message in the terminal and not in the file. I
> tried the same for stdout, still no cigar.
>
> Any ideas ?
>
> THANKS!
> JP
>
>
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[Rdkit-discuss] logD
Hi, Is there a way to calculate *distribution-coefficient* *(logD)* for a compound? I'm interested in calculation at PH 7.4 for some compounds. I haven't found it in the list of descriptors: http://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors If not it will be nice to have such a possibility. Regars Adrian -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] valence problem
Hi all
I have a problem with generating molecule from smiles.
from rdkit import Chem
template = Chem.MolFromSmiles('F[P-](F)(F)(F)(F)F.CN(C)C(F)=[N+](C)C')
I got an error:
Explicit valence for atom # 1 P, 7, is greater than permitted
But the SMILES for this structure should be valid.
I checked many web services and the structure is always the same
the CAS number for this structure is 164298-23-1
Can I skip checking the valence during generating mol from smiles?
regards
Adrian
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Re: [Rdkit-discuss] 2D Drawing in C++
If I can start a list of wishes for new function it will be nice to add a possibility for drawing the series of molecules with the same "core" in the same orientation (based on some alignment or something like that). pozdrawiam Adrian 2014-07-02 14:04 GMT+02:00 Greg Landrum : > Ah, what timing. > > I have just started thinking about updating the C++ drawing code (which I > agree is extremely basic) to improve the quality and make it more generally > useful. I agree that the abstract base class idea makes a lot of sense. > This is, in essence, what the Python code does already. > > There's definitely interest from my side. I think it would help a lot. > > If there's a way to do so, I would happy to help out as you proceed. I > certainly would be more than willing to add "refinements" like dealing with > chiral centers. > > -greg > > > > > On Wednesday, July 2, 2014, David Cosgrove > wrote: > >> >> Hi All, >> >> I am currently writing some code for which I needed a Qt widget with a 2D >> RDKit rendering that I could interact with. This needed >> $RDBASE/GraphMol/MolDrawing/MolDrawing.h, but I found it very difficult to >> find the drawing coordinates for all atoms in the RDKit drawing model and >> convert them to screen coordinates so I could add annotation to the >> drawing, find which atom users had picked, etc. So I have created new >> drawing classes using a design borrowed from the original OpenEye OEDepict >> toolkit written, I believe, by Roger Sayle. This uses an abstract base >> class that handles all the drawing in terms of pure virtual functions for >> drawing lines, writing text etc. The user derives a concrete class that >> implements these functions for his/her drawing library of choice. >> >> Currently I have something that's adequate for my purposes, but if >> there's enough interest from people on the list, I can tidy it up, provide >> some example code and submit it for inclusion. In the short term it would >> be an addition to the existing system so a non-breaking change, but in the >> longer term it could possibly be a route to unifying the python and C++ 2D >> drawing systems which seem at present to be quite separate. >> >> I mention this at this stage because it would be a non-trivial amount of >> work on my part to do this. To start with, I don't need to worry about >> drawing chiral centres in my current project, so I haven't done anything >> about that (MolDrawing.h doesn't either, for that matter!). The example >> codes would have to be written to do something useful that showed all the >> features, there might be a need for documentation, etc. Not insignificant >> is that I would have to bash this square peg through the round hole which >> is AstraZeneca's publication approval system that won't have seen anything >> like it before. There don't seem to be many of us C++ programmers posting >> to the list, so I'm really looking to gauge interest. I'm happy to put the >> work in to make this a useful submission to the project, but only if other >> people are likely to use it. >> >> Please let me know, either to this list or privately to >> david.cosgr...@astrazeneca.com. >> >> Thanks, >> Dave >> >> > > -- > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chemical formula
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolDescriptors-module.html#CalcMolFormula
from rdkit.Chem.rdMolDescriptors import CalcMolFormula
formula = CalcMolFormula(Chem.MolFromSmiles("CCCOC"))
pozdrawiam
Adrian
2014-06-13 10:20 GMT+02:00 Alexey Chernobrovkin :
> Hi all,
>
> Sorry for stupid question… But what is the simplest way to get chemical
> formula of a molecule using rdkit?
>
> Cheers,
> Alex
>
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Re: [Rdkit-discuss] SMARTS behaviour
you can allways visualise yours SMARTS by using http://www.smartsview.de/
pozdrawiam
Adrian
2014-03-27 17:44 GMT+01:00 Jameed Hussain :
> Try this:
>
> [*!H0;!$(*~[#0])]
>
>
>
> I don't think you can do what you want without a recursive SMARTS. It's
> well worth doing the Daylight exercises to get your head around recursive
> SMARTS - they are really useful.
>
>
>
> Cheers
>
> Jameed
>
>
>
> *From:* Nicholas Firth [mailto:nicholas.fi...@icr.ac.uk]
> *Sent:* 27 March 2014 15:23
> *To:* rdkit-discuss@lists.sourceforge.net Discuss
> *Subject:* [Rdkit-discuss] SMARTS behaviour
>
>
>
> Hi RDKitters,
>
>
>
> This isn't strictly an RDKit based issue, but I guess someone here will be
> able to help me. I'm trying to identify the index of atoms in a molecule
> which have one or more hydrogen bonded to them but are not bonded to a
> dummy atom ([*]).
>
>
>
> >>> mol = Chem.MolFromSmiles('[*]CCC[*]')
>
> >>> patt = Chem.MolFromSmarts('[*H1,H2,H3,H4]!~[#0]')
>
> >>> print mol.GetSubstructMatches(patt)
>
> ()
>
>
>
> I'd expect this to return (1). But it would appear that I'm in the wrong,
> as Pipeline Pilot give the same result. Is there a SMARTS query that will
> give me the matches that I want or do I have to go back to iterating over
> atoms?
>
>
>
> Many thanks in advance.
>
>
> Best,
>
> Nick
>
>
>
> *Nicholas C. Firth* | PhD Student | Cancer Therapeutics
>
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Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?
you can try use razi:
http://razi.readthedocs.org/en/latest/database_creation_tutorial.html
pozdrawiam
Adrian
2014-02-26 18:34 GMT+01:00 Greg Landrum :
> Hi Hari,
>
> You can use "mol_from_pkl()". Here's a quick demo:
> In [20]: m = Chem.MolFromSmiles('c1cnccc1')
>
> In [21]: pkl = buffer(m.ToBinary())
>
> In [22]: curs.execute('select mol_from_pkl(%s)',(pkl,))
>
> In [23]: curs.fetchone()
> Out[23]: ('c1ccncc1',)
>
> Is that enough to get you started?
> -greg
>
>
>
> On Tue, Feb 25, 2014 at 8:28 PM, hari jayaram wrote:
>
>> Hi ,
>> I am a newbie to postgres and the rdkit postgres database cartridge.
>>
>> I have gotten the cartridge installed and can query sub-structure
>> similarity and do other things as documented in the cartridge documentation
>> page.
>>
>> To create a molecule from the cartridge the documentation
>> recommends something like:
>>
>>
>> >>> curs.execute('select molregno,mol_send(m) from rdk.mols where m@
>> >%s',('c12c1nncc2',))
>> >>> row = curs.fetchone()
>> >>> row
>> (9830, )
>>
>> Then the pickled output of mol_send will be used to create a new molecule
>>
>> >>> from rdkit import Chem
>> >>> m = Chem.Mol(str(row[1]))
>> >>> Chem.MolToSmiles(m,True)
>> 'CC(C)Sc1ccc(CC2CCN(C3CCN(C(=O)c4cnnc5c54)CC3)CC2)cc1'
>>
>>
>> My question is : how about the other way .Is the only way to use the
>> smiles and do an sql insert with the smiles and the mol_from_smiles
>> function as in :
>>
>> insert into compounds (smiles,rdkit_mol,internal,external) VALUES
>> ('C',mol_from_smiles('C);'ID-111','EI-222');
>>
>> Is there a way to insert the python rdkit mol object into the database
>> rdkit "mol" column directly.
>>
>> This is in some ways connected to a question I just asked ( django
>> related) on stack
>> overflow.
>>
>> Thanks a tonne for your help in advance
>> Hari
>>
>>
>>
>>
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Re: [Rdkit-discuss] generate 2D figure
m = Chem.MolFromSmiles('ccc[nH]c', sanitize=False)
I think that in this example there is a problem with your SMILES.
Why you use lower case?
In SMILES format it's a aromatic molecule but you don't have the beginning
and ending of aromatic bond noted by number.
If you have aromatic molecule you should write it like that:
>>>> m = Chem.MolFromSmiles('c1cc[nH]c1')
if it is not aromatic than use upper case:
>>>> m = Chem.MolFromSmiles('CCC[NH]C')
and than try:
>>>> AllChem.Compute2DCoords(m)
for second example:
>>>> m = Chem.MolFromSmiles('C(=O)OCCO')
>>>> AllChem.Compute2DCoords(m)
2014-02-19 21:46 GMT+01:00 Yingfeng Wang :
> Here are more details.
>
> If I use
>
> m = Chem.MolFromSmiles('ccc[nH]c', sanitize=False)
> AllChem.Compute2DCoords(m)
>
> It works.
>
> But I get trouble with
> >>> m = Chem.MolFromSmiles('C(=O)OCCO', sanitize=False)
> >>> AllChem.Compute2DCoords(m)
>
> I got
>
>
> Pre-condition Violation
> getNumImplicitHs() called without preceding call to calcImplicitValence()
> Violation occurred on line 170 in file
> /home/yf1/software/RDKit/install_version/latest/Code/GraphMol/Atom.cpp
> Failed Expression: d_implicitValence>-1
>
>
>
> Traceback (most recent call last):
> File "", line 1, in
> RuntimeError: Pre-condition Violation
>
>
>
> On Wed, Feb 19, 2014 at 3:27 PM, Yingfeng Wang wrote:
>
>> Adrian,
>>
>> I meet a weird case.
>>
>> >>> import matplotlib.offsetbox
>> >>> from rdkit import Chem
>> >>> from rdkit.Chem import AllChem
>> >>> from rdkit.Chem import Draw
>> >>> m = Chem.MolFromSmiles('ccc[nH]c')
>>
>> I got
>> non-ring atom 0 marked aromatic
>> >>> AllChem.Compute2DCoords(m)
>> Traceback (most recent call last):
>> File "", line 1, in
>> Boost.Python.ArgumentError: Python argument types in
>> rdkit.Chem.rdDepictor.Compute2DCoords(NoneType)
>> did not match C++ signature:
>> Compute2DCoords(RDKit::ROMol {lvalue} mol, bool canonOrient=True,
>> bool clearConfs=True, boost::python::dict {lvalue} coordMap={}, unsigned
>> int nFlipsPerSample=0, unsigned int nSample=0, int sampleSeed=0, bool
>> permuteDeg4Nodes=False, double bondLength=-1.0)
>>
>>
>> Actually, "ccc[nH]c" is a fragment. Could you please help me to know
>> whether there is a work around to this case?
>>
>> Thanks.
>>
>> Yingfeng
>>
>>
>>
>>
>> On Mon, Feb 17, 2014 at 2:58 PM, Yingfeng Wang wrote:
>>
>>> Adrian,
>>>
>>> Thanks, it works.
>>>
>>> Yingfeng
>>>
>>>
>>> On Mon, Feb 17, 2014 at 12:50 PM, Adrian Jasiński <
>>> jasinski.adr...@gmail.com> wrote:
>>>
>>>> If you read all from tutorial you will find a example:
>>>>
>>>> >>> suppl = Chem.SDMolSupplier('data/cdk2.sdf')>>> ms = [x for x in suppl
>>>> >>> if x is not None]>>> for m in ms: tmp=AllChem.Compute2DCoords(m)>>>
>>>> >>> from rdkit.Chem import Draw>>>
>>>> >>> Draw.MolToFile(ms[0],'images/cdk2_mol1.png')>>>
>>>> >>> Draw.MolToFile(ms[1],'images/cdk2_mol2.png')
>>>>
>>>>
>>>> for this example with you pasted you can just write mol to file:
>>>>
>>>>
>>>> >>> from rdkit.Chem import AllChem
>>>>
>>>>
>>>>
>>>>
>>>> >>> from rdkit import Chem
>>>> >>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
>>>>
>>>> >>> AllChem.Compute2DCoords(m)
>>>>
>>>> Draw.MolToFile(m,'example.png')
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> pozdrawiam
>>>> Adrian Jasiński
>>>>
>>>>
>>>> 2014-02-17 18:34 GMT+01:00 Yingfeng Wang :
>>>>
>>>>> I want to draw a 2D figure of a compound. And I follow the example
>>>>> given at the following link,
>>>>>
>>>>> http://www.rdkit.org/docs/GettingStartedInPython.html
>>>>>
>>>>> My code is given as follows,
>>>>>
>>>>> >>>
Re: [Rdkit-discuss] generate 2D figure
If you read all from tutorial you will find a example:
>>> suppl = Chem.SDMolSupplier('data/cdk2.sdf')>>> ms = [x for x in suppl if x
>>> is not None]>>> for m in ms: tmp=AllChem.Compute2DCoords(m)>>> from
>>> rdkit.Chem import Draw>>> Draw.MolToFile(ms[0],'images/cdk2_mol1.png')>>>
>>> Draw.MolToFile(ms[1],'images/cdk2_mol2.png')
for this example with you pasted you can just write mol to file:
>>> from rdkit.Chem import AllChem
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
>>> AllChem.Compute2DCoords(m)
Draw.MolToFile(m,'example.png')
pozdrawiam
Adrian Jasiński
2014-02-17 18:34 GMT+01:00 Yingfeng Wang :
> I want to draw a 2D figure of a compound. And I follow the example given
> at the following link,
>
> http://www.rdkit.org/docs/GettingStartedInPython.html
>
> My code is given as follows,
>
> >>> from rdkit.Chem import AllChem
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
> >>> AllChem.Compute2DCoords(m)
> 0
> >>> template = Chem.MolFromSmiles('c1nccc2n1ccc2')
> >>> AllChem.Compute2DCoords(template)
> 0
> >>> AllChem.GenerateDepictionMatching2DStructure(m,template)
> >>>
>
>
> However, I got nothing. I am wondering what the correct way is to generate
> the 2D figure of "c1nccc2n1ccc2". Thanks.
>
> Yingfeng
>
>
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Re: [Rdkit-discuss] SDMolSupplier doesn't support file handlers?
Example from tutorial:
>>> import gzip>>> inf = gzip.open('data/actives_5ht3.sdf.gz')>>> gzsuppl =
>>> Chem.ForwardSDMolSupplier(inf)>>> ms = [x for x in gzsuppl if x is not
>>> None]>>> len(ms)180
pozdrawiam
Adrian Jasiński
2014-01-31 Michał Nowotka :
> Hi,
>
> I need to process large, compressed SDF file. I was planning to use
> SDMolSupplier but there is a problem:
>
> 1. I can't just pass a file name, as this is compressed file and if I
> understand, SDMolSupplier doesn't support compressed files.
> 2. I can't read a file to string and then call setData() method of
> SDMolSupplier, because size of uncompressed string will be larger than
> available memory.
>
> The solution would be to obtain file handler (f = gzip.open(...)) but
> the problem is that there is no way (at least I don't know any) to
> pass it to SDMolSupplier.
>
> Any ideas?
>
> Kind regards,
> Michał Nowotka
>
>
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Re: [Rdkit-discuss] rdkit mol objects from sql
One of the solutions is razi but it's for sqlalchemy
https://razi.readthedocs.org/en/latest/database_creation_tutorial.html
pozdrawiam
Adrian Jasiński
2013/10/23 George Papadatos
> Yes it does; many thanks!
> I've just found the notebook I mentioned:
> http://nbviewer.ipython.org/4316426/
> (Scroll to bottom)
> I prefer Greg's first solution though, as it avoids the conversion from
> smiles completely.
>
> Best,
>
> George
>
> Sent from my gPad
>
> On 23 Oct 2013, at 20:39, JP wrote:
>
> Does the following help you george?
> http://comments.gmane.org/gmane.science.chemistry.rdkit.user/860
>
>
>
> On 23 October 2013 17:11, George Papadatos wrote:
>
>> Hi RDKitters,
>> I must have seen this in an ipython notebook but can't find it right now:
>> If I have a table of rdkit mols generated by the cartridge, is there a
>> way to retrieve them using a psycopg2 connection within python - ideally
>> inside a pandas dataframe?
>>
>> I've got this snippet:
>> import pandas as pd
>> import psycopg2
>> conn = psycopg2.connect("port=5432 user=chembl dbname=chembl_17")
>> data = pd.read_sql(sql, conn)
>>
>> ...but I'm missing the step where I retrieve rdkit mol objects somehow
>> instead of smiles.
>>
>> Many thanks in advance,
>> George
>>
>>
>>
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[Rdkit-discuss] IUPAC nomenclature
Is there a way to converting IUPAC nomenclature into SMILES, InChI, or Molfile formats? I didn't found any clues in RDKit Documentation. it would be nice if you can add such functionality. Fast way for that can be using OPSIN library: https://bitbucket.org/dan2097/opsin/ http://opsin.ch.cam.ac.uk/ I found that something like this is added to Rubidium, some chemical-informatics tool written in Ruby http://depth-first.com/articles/2007/10/19/easily-convert-iupac-nomenclature-to-smiles-inchi-or-molfile-with-rubidium/ regards Adrian Jasinski -- 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] IUPAC nomenclature
Is there a way to converting IUPAC nomenclature into SMILES, InChI, or Molfile formats? I didn't found any clues in RDKit Documentation. it would be nice if you can add such functionality. Fast way for that can be using OPSIN library: https://bitbucket.org/dan2097/opsin/ http://opsin.ch.cam.ac.uk/ I found that something like this is added to Rubidium, some chemical-informatics tool written in Ruby http://depth-first.com/articles/2007/10/19/easily-convert-iupac-nomenclature-to-smiles-inchi-or-molfile-with-rubidium/ regards Adrian Jasiński -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] image font size
Hi all, Greg thanks for new release. By the way I have the question: How can I change font size on image? When I create small images the font is too big and on some big size images it is too small. Regards Adrian -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled
I have the question connected with the topic, Is there any temporary plan of the meeting or topics which will be discussed during this event? If yes where I can find it? If no will it be announced and when? I suggest to publish such a list of topics and to vote for most interesting of them. 2012/7/6 Greg Landrum : > On Fri, Jul 6, 2012 at 11:06 AM, JP wrote: >> I just noticed that this is a "user" meeting and not a "dev" one - so >> perhaps such a topic is out of scope... >> > > eh, that depends. C++ users of the code are also users. I'm more > concerned about having a session that only 2 people are interested in. > To accommodate that we would have to do breakout sessions, and we > hadn't planned to do such a thing. > > I will see if I can come up with a sensible demo that shows how to > create a new python extension module using RDKit functionality. This > should at least make some stuff easier for others in the future. > > -greg > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] problem with overlap in drawing.
Thanks for that, I hope it will help. I will wait for next release and
check other structures drawing.
Unfortunately I can't publish all structures with errors (for security
reasons), but I will try next version and I let you know if I will
find any similar errors.
2012/7/2 Greg Landrum :
> An update on this thread:
>
> On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński
> wrote:
>>
>> There is some example code:
>>
>> from rdkit import Chem
>> from rdkit.Chem import Draw
>> mol = Chem.MolFromSmiles('CC(=O)Nc1c1C(=O)C11C1C1')
>> Draw.MolToFile(mol,'test.png')
>>
>
> I made some change to the depictor this morning that handle this case
> as well as a few other problematic cases. These will be in the next
> release
>
> There are definitely still some problems in the depictor, but it's
> better now than it was. Adrian: thanks for reporting this failure.
>
> -greg
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Re: [Rdkit-discuss] problem with overlap in drawing.
I have many others examples where I have found overlapping. Even rings
overlap in some of them.
It will be nice if it will be fixed for next realize.
Best Regards
Adrian
2012/6/20 Greg Landrum :
> Dear Adrian,
>
> On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński
> wrote:
>>
>> I have some problem with drawing. When I draw molecules using RDkit
>> sometimes I have some structure overlap.
>> But when I draw it using for example marvin it's look fine.
>>
>> There is some example code:
>>
>> from rdkit import Chem
>> from rdkit.Chem import Draw
>> mol = Chem.MolFromSmiles('CC(=O)Nc1c1C(=O)C11C1C1')
>> Draw.MolToFile(mol,'test.png')
>>
>> In attachment I added example image.
>
> Thanks for reporting the problem. That's definitely a bug in the depiction
> code.
>
>>
>> I'm using Ubuntu 12.04 x64.
>>
>> Is there any solution?
>
> There is not at the moment an easy one. I will take a look at your
> specific molecule and see if I can fix the problem for the next
> release.
>
> Best Regards,
> -greg
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[Rdkit-discuss] problem with overlap in drawing.
Hi All
I have some problem with drawing. When I draw molecules using RDkit
sometimes I have some structure overlap.
But when I draw it using for example marvin it's look fine.
There is some example code:
from rdkit import Chem
from rdkit.Chem import Draw
mol = Chem.MolFromSmiles('CC(=O)Nc1c1C(=O)C11C1C1')
Draw.MolToFile(mol,'test.png')
In attachment I added example image.
I'm using Ubuntu 12.04 x64.
Is there any solution?
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