Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

2017-02-20 Thread 杨弘宾 

Hi Greg,    I am using 32-bit python27 and anaconda (with 64-bit windows 10). 
So I cannot update to latest version and test  as you proposed several days ago.     
Since it did not trouble me, I plan to upgrade all this environment in the 
future.
BTW, is it necessary to upgrade python into 3.6 in case that RDkit won't 
support python2. I prefer 2.7 at least for now :)


Hongbin Yang 

 From: Greg LandrumDate: 2017-02-20 23:02To: Michal KrompiecCC: 
rdkit-discuss@lists.sourceforge.netSubject: Re: [Rdkit-discuss] problems with 
installation on conda with python 3.5 32-bitHi Michal,
We've only ever done python2.7 builds for win32 and we stopped doing those with 
the 2016.03 release.I will have to check, but I think I probably can start 
doing these again, but I'm reluctant due to the amount of effort required.How 
many users do you need to support who are stuck on 32bit machines?
-greg

On Mon, Feb 20, 2017 at 2:18 PM, Michal Krompiec  
wrote:
Hello,I can't install rdkit on anaconda with 32-bit python3 on Windows 7.
When I try "the usual", conda tries to install python2.7 into the environment:
>conda create -c rdkit -n my-rdkit-env rdkit
Fetching package metadata .
Solving package specifications: .Package plan for installation in environment 
C:\Anaconda3_32\envs\my-rdkit-env:The following NEW packages will be INSTALLED: 
   boost:  1.56.0-py27_3 rdkit
    bzip2:  1.0.6-vc9_3 [vc9]
    mkl:    2017.0.1-0
    numpy:  1.11.3-py27_0
    pip:    9.0.1-py27_1
    python: 2.7.13-0
    rdkit:  2016.03.1-np111py27_1 rdkit
    setuptools: 27.2.0-py27_1
    vs2008_runtime: 9.00.30729.5054-0
    wheel:  0.29.0-py27_0
    zlib:   1.2.8-vc9_3 [vc9]
If I create an empty environment, load python 3.5 into it and try installing 
rdkit, I get an error:
>conda create -n my-rdkit-env python=3.5
Fetching package metadata ...
Solving package specifications: .Package plan for installation in environment 
C:\Anaconda3_32\envs\my-rdkit-env:The following NEW packages will be INSTALLED: 
   pip:    9.0.1-py35_1
    python: 3.5.2-0
    setuptools: 27.2.0-py35_1
    vs2015_runtime: 14.0.25123-0
    wheel:  0.29.0-py35_0Proceed ([y]/n)?#
# To activate this environment, use:
# > activate my-rdkit-env
#
# To deactivate this environment, use:
# > deactivate my-rdkit-env
#
# * for power-users using bash, you must source
#
>conda install --name my-rdkit-env -f --channel 
>https://conda.anaconda.org/rdkit rdkit
Fetching package metadata .
Solving package specifications: .
UnsatisfiableError: The following specifications were found to be in conflict:
  - python 3.5*
  - rdkit -> python 2.7*
Use "conda info " to see the dependencies for each package.

I managed to install rdkit without any problems on the same machine in 64-bit 
anaconda with python3.5, but I need a separate 32-bit build to support users 
with 32-bit machines. Any help will be appreciated.
Thanks and best regards,
Michal


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Re: [Rdkit-discuss] jupyter cracked when drawing with "abnormal" operation of rdMolDraw2D

2017-02-17 Thread 杨弘宾 






Hi, greg,    DrawMolecules did not work in my compute, I guess it is a future 
feature from my version (v2016.3.1), isn't it?     And I tried your second 
suggestion but it still cracked.  Maybe the old version of MolDraw2D is buggy.
    The following are fake compouns for test, and each one is drawable.
# mycompounds.smiSMILESc1cc1[N+]([O-])=O1CCC[N+]([O-])=O
2CC[N+]([O-])=O 3C[N+]([O-])=O  4c1c(CC)1[N+]([O-])=O   5
# codefrom rdkit import Chemfrom rdkit.Chem.Draw import rdMolDraw2Dfrom 
rdkit.Chem import Drawfrom rdkit.Chem import rdDepictorfrom rdkit.Chem import 
rdMolTransformsmols = 
Chem.SmilesMolSupplier('mycompounds.smi',delimiter='\t')len(mols)mols = 
list(mols)def centerMol(mol):    conf = mol.GetConformer()    pt = 
rdMolTransforms.ComputeCentroid(conf)    for i in range(conf.GetNumAtoms()):    
    conf.SetAtomPosition(i,conf.GetAtomPosition(i) - pt)        drawer = 
rdMolDraw2D.MolDraw2DSVG(400,400) smarts = Chem.MolFromSmarts('N(-O)=O')i=0 for 
mol in mols:     if not mol.HasSubstructMatch(smarts):        continue    
rdDepictor.Compute2DCoords(mol)    tm = Chem.Mol(mol)    centerMol(tm)    
Draw.PrepareMolForDrawing(tm)    
#drawer.DrawMolecule(mol,highlightAtoms=mol.GetSubstructMatch(p))     
drawer.DrawMolecule(tm,highlightAtoms=tm.GetSubstructMatch(smarts)) 
drawer.FinishDrawing() svg = drawer.GetDrawingText().replace('svg:','') 



Hongbin Yang 

 From: Greg LandrumDate: 2017-02-18 12:59To: 杨弘宾CC: rdkit-discussSubject: Re: 
[Rdkit-discuss] jupyter cracked when drawing with "abnormal" operation of 
rdMolDraw2DHi,

On Fri, Feb 17, 2017 at 6:31 AM, 杨弘宾 <yanyangh...@163.com> wrote:

Hi, everyone,    I want to draw two molecules in a svg file with rdMolDraw2D. 
When I executed the following code, the jupyter cracked without any error or 
warning.```drawer = rdMolDraw2D.MolDraw2DSVG(400,400)

i=0

for mol in mols:

  if mol.HasSubstructMatch(smarts):

    rdDepictor.Compute2DCoords(mol)     #if i == 1:    #  continue
    drawer.DrawMolecule(mol,highlightAtoms=mol.GetSubstructMatch(smarts))

    i+=1

    if i > 1:

      break

drawer.FinishDrawing()

svg = drawer.GetDrawingText().replace('svg:','')

SVG(svg)```
It seems that we cannot directly draw two molecules with the same drawer? So 
how can I draw as I wanted?
Do you want to draw the molecules on top of each other (somewhat problematic at 
the moment, but doable) or in a grid?If you want to have them in a grid, the 
solution is:
drawer = rdMolDraw2D.MolDraw2DSVG(400,400,200,200) p = 
Chem.MolFromSmarts('c1n1')drawer.DrawMolecules(mols[:4])drawer.FinishDrawing()
 svg = drawer.GetDrawingText().replace('svg:','') 
That's an overall image size of 400x400 with 200x200 panes for the individual 
molecules. At the moment molecular highlighting does not work when you do this 
(there's a github item for that here: 
https://github.com/rdkit/rdkit/issues/1323)
If you want to put them on top of each other, what you show above should kind 
of work. You probably should center each of the molecules first though:
from rdkit.Chem import rdMolTransformsdef centerMol(mol):    conf = 
mol.GetConformer()    pt = rdMolTransforms.ComputeCentroid(conf)    for i in 
range(conf.GetNumAtoms()):        
conf.SetAtomPosition(i,conf.GetAtomPosition(i) - pt)        drawer = 
rdMolDraw2D.MolDraw2DSVG(400,400) p = Chem.MolFromSmarts('c1n1')i=0 for mol 
in mols:     tm = Chem.Mol(mol)    centerMol(tm)    
Draw.PrepareMolForDrawing(tm)    
#drawer.DrawMolecule(mol,highlightAtoms=mol.GetSubstructMatch(p))     
drawer.DrawMolecule(tm,highlightAtoms=tm.GetSubstructMatch(p))     i+=1     if 
i > 1:       break drawer.FinishDrawing() svg = 
drawer.GetDrawingText().replace('svg:','') 
Note that this can end up being somewhat ugly since the drawing code will 
determine the scaling factors to make the molecules fit in the canvas from the 
first molecule.
I think it is fixable by adding some additional logic to DrawMolecules() but 
I'm going to have to look into it. that's this item in github: 
https://github.com/rdkit/rdkit/issues/1325 

By the way, I've no idea why it cracked. From the experiment of the commented 
code, I can conclude it was caused by the drawer. So is it possible to fix the 
bug, adding error or warning instead of "KernelRestarter: restarting kernel" in 
console.
I can't reproduce a crash there. Which version of the RDKit are you using?
-greg


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[Rdkit-discuss] jupyter cracked when drawing with "abnormal" operation of rdMolDraw2D

2017-02-16 Thread 杨弘宾 






Hi, everyone,? ??I want to draw two molecules in a svg file with rdMolDraw2D. 
When I executed the following code, the jupyter cracked without any error or 
warning.```drawer = rdMolDraw2D.MolDraw2DSVG(400,400)

i=0

for mol in mols:

? if mol.HasSubstructMatch(smarts):

? ? rdDepictor.Compute2DCoords(mol)?? ? #if i == 1:? ? # ?continue
? ? drawer.DrawMolecule(mol,highlightAtoms=mol.GetSubstructMatch(smarts))

? ? i+=1

? ? if i > 1:

? ? ? break

drawer.FinishDrawing()

svg = drawer.GetDrawingText().replace('svg:','')

SVG(svg)```
It seems that we cannot directly draw two molecules with the same drawer? So 
how can I draw as I wanted?
By the way, I've no idea why it cracked. From the experiment of the commented 
code, I can conclude it was caused by the drawer. So is it possible to fix the 
bug, adding error or warning instead of "KernelRestarter: restarting kernel" in 
console.


Hongbin Yang?


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Re: [Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread 杨弘宾 






Hi, Menaka,    An easy way I suggest is to install boost via package manager, 
for example:    $ sudo apt-get install libboost-dev libboost-system-dev 
libboost-thread-dev libboost-serialization-dev libboost-python-dev 
libboost-regex-dev     When installing boost from source, remember to add 
python-library    $ ./bootstrap.sh --with-libraries=python,regex; ./b2; ./b2 
install
reference: http://www.rdkit.org/docs/Install.html#ubuntu-12-04-and-later  hope 
it is helpful
PS  Other troubles may cause the error,  for example:Problem:Your system has a 
version of boost installed in /usr/lib, but you would like to force the RDKit 
to use a more recent one.Solution:This can be solved by using cmake version 
2.8.3 (or more recent) and providing the -D Boost_NO_SYSTEM_PATHS=ON 
argument:cmake -D BOOST_ROOT=/usr/local -D Boost_NO_SYSTEM_PATHS=ON ..
reference: 
http://www.rdkit.org/docs/Install.html#frequently-encountered-problems 
Hope it is helpful.

Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology 

 From: Menaka JayawardenaDate: 2016-09-06 00:05To: rdkit-discussSubject: 
[Rdkit-discuss] Error when building RdKit 2013_09_1Hello,
When I try to build the above version of RDKit, I got the following error.
CMake Error at /usr/share/cmake-2.8/Modules/FindBoost.cmake:1131 (message):  
Unable to find the requested Boost libraries.
  Boost version: 1.55.0
  Boost include path: /home/menaka/Downloads/boost_1_55_0/include
  Could not find the following Boost libraries:
          boost_python
  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):  CMakeLists.txt:113 (find_package)
I'd be very grateful if someone could help me in solving this issue. 
Best regardsMenaka
-- 
Menaka Madushanka JayawardenaFaculty of Engineering,University of 
Peradeniyaya.LinkedIn
TP:- 071 885 1183/ 071 350 5470


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[Rdkit-discuss] a SMILES that rdkit cannot read

2016-09-18 Thread 杨弘宾 






hi,? ? When I used rdkit to parse a smi file, I found that there was a SMILES 
that rdkit cannot parse, and no any error or?warning.

version: Release_2016_03_1>>>?mol = 
Chem.MolFromSmiles('N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')>>> print molNone

This compound can be read by OpenBabel. But I have no idea why it didnot work.



Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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Re: [Rdkit-discuss] a SMILES that rdkit cannot read

2016-09-19 Thread 杨弘宾 






Thanks. It's really a obvious error.I ran it in jupyter via browser. Both 
docker/ubuntu and windows were tested and found that jupyter won't give error. 
Ipython or python in terminal(cmd) would show this error.
Why not raise a python error or warning?

Hongbin Yang 

 From: Greg LandrumDate: 2016-09-19 12:08To: 杨弘宾CC: rdkit-discussSubject: Re: 
[Rdkit-discuss] a SMILES that rdkit cannot readHi,

On Mon, Sep 19, 2016 at 5:33 AM, 杨弘宾 <yanyangh...@163.com> wrote:

   When I used rdkit to parse a smi file, I found that there was a SMILES that 
rdkit cannot parse, and no any error or warning.


version: Release_2016_03_1>>> mol = 
Chem.MolFromSmiles('N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')>>> print molNone

This compound can be read by OpenBabel. But I have no idea why it didnot work.
I don't know why OpenBabel accepts it, but there's definitely an error in that 
SMILES. This part: "=N/#N" has a single bond (the "/") directly followed by a 
triple bond (the "#"), and that's not legal SMILES.
I do see an error message when I try the SMILES:In [2]: mol = 
Chem.MolFromSmiles('N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')[06:04:54] SMILES 
Parse Error: syntax error for input: 
'N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O'and find it a bit odd that you don't. 
What operating system are you using and how are you running the code?
Best,-greg


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[Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected

2016-10-27 Thread 杨弘宾 






Hi,? ? I tryied using rdkit to match fragments with compounds only to find that 
rdkit performed not well in SMARTS. The following is the notebook I worked.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole
In?[49]:p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')
In?[50]:mol  = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol
Out[50]:In?[51]:p.HasMatch(mol)
Out[51]:0In?[52]:print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')
None
However, openbabel worked well in matching the substrcutre. Even "or operator" 
was avaiable such as "[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]".?
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')

>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')

>>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')

>>> s.findall(a)

[(6, 7, 8, 9)]
It is a pity that rdkit can calculate the topological distance between two 
atoms while it cannot match the fragments... Is there any better API which I 
didn't find?


Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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Re: [Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected

2016-10-27 Thread 杨弘宾 



  




Thanks, it works!    I appreciate that Rdkit is so strict in representation of 
the the molecules and the substructures. I learned a lot in the mail list.


Hongbin Yang 

 From: Paolo ToscoDate: 2016-10-27 17:19To: 杨弘宾; rdkit-discussSubject: Re: 
[Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as 
expected
  

  
  
Dear Hongbin,
I am afraid The SMARTS you are using is not valid, as no SSSR can
  have less than 3 terms, or it wouldn't be a ring. If you
  change[a!r0] into, for instance, [a!r3], then you'll find the
  match you are looking for.
Cheers,

  p.


On 27/10/2016 09:36, 杨弘宾 wrote:



  
  
  Hi,
      I
  tryied using rdkit to match fragments with compounds only to
  find that rdkit performed not well in SMARTS. The following is
  the notebook I worked.
  

  
  

  

  

  from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole


  

  


  
In [49]:

  

  p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')


  

  


  
In [50]:

  

  mol  = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol


  

  
  

  
Out[50]:

  

  


  
In [51]:

  

  p.HasMatch(mol)


  

  
  

  
Out[51]:

  0

  

  


  
In [52]:

  

  print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')


  

  
  

  

  None

  

  

  
  However, openbabel worked well in matching the substrcutre.
Even "or operator" was avaiable such as 
"[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]". 
  

  
  >>>
  s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
  

  >>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
  

  >>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')
  

  >>> s.findall(a)
  

  [(6, 7, 8, 9)]
  

  
  It is a pity that rdkit can calculate the topological
distance between two atoms while it cannot match the
fragments... Is there any better API which I didn't find?
  

  
  

      
  
  
  Hongbin
  Yang 杨弘宾
  

  Research: Toxicophore and Chemoinformatics

  Pharmaceutical Science, School of Pharmacy
  

  East China University of Science and Technology 



  

  
  

  
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Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-23 Thread 杨弘宾 






Hi，Peter S. Shenkin,    I think this blog may help you draw molecule with 
labels and it told more about drawing with rdMolDraw2D.    
http://rdkit.blogspot.com/2015/02/new-drawing-code.html


Hongbin Yang From: Peter S. ShenkinDate: 2016-10-24 10:18To: Dimitri Maziuk; 
RDKit DiscussSubject: [Rdkit-discuss] 2D drawing with atoms labeled by indexHi,

How do you get RDKit to label the atoms in a 2D drawing with their indices?
There was some discussion of this that included Dimitri Maziuk in September, 
but it wasn't clear to me whether he actually had to modify the underlying 
drawing code to get this behavior.
-P.

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Re: [Rdkit-discuss] Fwd: 2D drawing with atoms labeled by index

2016-10-25 Thread 杨弘宾 






Hi, Peter,    I don't know whether it can help you since I did not repeat your 
code. But it acturally works in my computer:        change the extended name 
from .svg into .html and open it via chrome.    It should be valid with 
svg2.svg (the namespace of svg were removed).

Hongbin Yang 

 From: Peter S. ShenkinDate: 2016-10-25 13:27To: Dmitri MaziukCC: RDKit 
DiscussSubject: Re: [Rdkit-discuss] Fwd:  2D drawing with atoms labeled by 
indexHi,
Dima wrote:Try saving the text (svg/svg2) to a file and opening it in chrome 
(if you can actually open a file in chrome) or some other application.
I actually did that, and in a second email I reported:Chrome thinks svg.svg is 
emptyWhen I load svg2.svg, Chrome complains, "This XML file does not appear to 
have any style information associated with it. The document tree is shown 
below" -P.
On Tue, Oct 25, 2016 at 12:28 AM, Dmitri Maziuk  wrote:
OK, my turn: that went out too soon.



It seems to me that jypiter, ipython, or whatever, has no idea how render MIME 
type image/svg+xml. It can display an "SVG" object, but the bit that turned 
image/svg+xml into "SVG" does not understand XML namespaces (that's been around 
since at least 2009).



Try saving the text (svg/svg2) to a file and opening it in chrome (if you can 
actually open a file in chrome) or some other application.



Dima






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[Rdkit-discuss] Is there a way to init the conformations of smiles supplier to improve the performance for substructure matching.

2016-11-01 Thread 杨弘宾 






Hi,? ??Supposing I'd like to matching 100 substructures with 1000 compounds 
represented as smiles.What I did is:
suppl = AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')l = 
len(suppl)for j in range(ll): ?# I have to make substructures in the first 
loop.? ??for i in range(l):

? ??? ??suppl[i].GetSubstructMatches(s[j])?and found the performance is not 
good.
Then I did a comparison and found that it was because the conformation of the 
compounds where not initiated.If I use MolFromSmiles，the performance will 
improve a lot.start = time.clock()suppl = 
AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')

l=len(suppl)?print time.clock()-start ? # >>>?0.0373735355168 ?indicating that 
the molecules were not initiated.
for i in range(l):

? ??suppl[i].GetSubstructMatches(sa)

? ??suppl[i].GetSubstructMatches(sa2)

print time.clock()-start ? # >>>?11.1884715172
start = time.clock()

f = open('allmoleculenew.smi')

for i in range(l):

? ??mol = Chem.MolFromSmiles(f.next().split('\t')[0])

? ??mol.GetSubstructMatches(sa)

? ??mol.GetSubstructMatches(sa2)print time.clock()-start # >>>?5.44030582111
The second method was double faster than the first, indicating that the "init" 
is more time consuming compared to matching.I think?SmilesMolSupplier is a good 
API to load multiple compounds but it didnot parse the smiles immediately, 
which adds the?time complexity to the further application. So is it possible to 
manually initiate the compounds?


Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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Re: [Rdkit-discuss] Is there a way to init the conformations of smiles supplier to improve the performance for substructure matching.

2016-11-01 Thread 杨弘宾 






Hi, Brian,    The first point you mentioned was acturally what I guessed and it 
is deprecated in my context, I think.    Thanks for the second suggestion, I 
tried this and the performance improved:
suppl = AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')l = 
len(suppl)  # This line is crucialsuppl = list(suppl)
And the types of suppl are repectively: , ,
So, though the second suppl (after len(suppl) ) is selectable, it was not a 
list indeed. It is amazing that the all molecules were instantiated after the 
`list` operator.
: )

Hongbin Yang

 From: Brian KelleyDate: 2016-11-01 19:56To: 杨弘宾CC: rdkit-discussSubject: Re: 
[Rdkit-discuss] Is there a way to init the conformations of smiles supplier to 
improve the performance for substructure matching.I'll make two more points ( 
thanks to Greg Landrum for pointing this out )
1). In your code each call to suppl[i] makes a new molecule, calling it twice 
in a row is twice as slow.  This explains your last result.
2) in my example, I was assuming that the queries were already in a python list 
and not from a supplier.  If they are being read from a supplier, you can 
easily keep them all in memory with:
queries = list(query_supplier)

Note that for large files, this can take up a lot of memory.
Thanks for the clarification Greg.
Brian Kelley
On Nov 1, 2016, at 4:22 AM, 杨弘宾 <yanyangh...@163.com> wrote:


Hi,    Supposing I'd like to matching 100 substructures with 1000 compounds 
represented as smiles.What I did is:
suppl = AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')l = 
len(suppl)for j in range(ll):  # I have to make substructures in the first 
loop.    for i in range(l):

        suppl[i].GetSubstructMatches(s[j]) and found the performance is not 
good.
Then I did a comparison and found that it was because the conformation of the 
compounds where not initiated.If I use MolFromSmiles，the performance will 
improve a lot.start = time.clock()suppl = 
AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')

l=len(suppl) print time.clock()-start   # >>> 0.0373735355168  indicating that 
the molecules were not initiated.
for i in range(l):

    suppl[i].GetSubstructMatches(sa)

    suppl[i].GetSubstructMatches(sa2)

print time.clock()-start   # >>> 11.1884715172
start = time.clock()

f = open('allmoleculenew.smi')

for i in range(l):

    mol = Chem.MolFromSmiles(f.next().split('\t')[0])

    mol.GetSubstructMatches(sa)

    mol.GetSubstructMatches(sa2)print time.clock()-start # >>> 5.44030582111
The second method was double faster than the first, indicating that the "init" 
is more time consuming compared to matching.I think SmilesMolSupplier is a good 
API to load multiple compounds but it didnot parse the smiles immediately, 
which adds the time complexity to the further application. So is it possible to 
manually initiate the compounds?


Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology 

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[Rdkit-discuss] property of name in smilesMolSupplier

2016-10-13 Thread 杨弘宾 






Hi，? ? I spent a lot of time to explorer "How to get the property of name when 
using SmilesMolSupplier"
I had a smiles file like this:===c1c1\t1\n...===where 1 means that it is 
positve
So I wanted to read this smiles file via SMilesMolSupplier and I knew that the 
second column is the default name column.suppl = 
Chem.SmilesMolSupplier('compounds.smi',delimiter='\t',titleLine=False)
However, I could not get the property of 1 because I had no idea what the 
property_name was.In the document, it shows that :If the input file has a title 
line and more than two columns (smiles and id), the
additional columns will be used to set properties on each molecule.  The 
properties
are accessible using the mol.GetProp(propName) method.But It was a "no title 
table", So I thought its property_name of "their names" should be "Name" or 
"name" as default. And I failed...After read the source code, I found that it 
should be 
_Namehttps://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp#L194?I
 think the document should be improved so that others may know how to get the 
name of each compoundBTW, I tried to use suppl[0].GetPropNames() but only to 
get ",class std::allocator > at 0x7402e90>" that seemed 
tell nothing. I wondered that is there any way to make it readable in python?



Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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Re: [Rdkit-discuss] property of name in smilesMolSupplier

2016-10-13 Thread 杨弘宾 



  




Hi Paolo,?? ? Thank you for your answer. I tried and found an interesting issue:
>>> mol = suppl[1]

>>> print mol.GetProp('_Name')

>>> print list(mol.GetPropNames())---output---1[]
I guess that the _Name property is a hidden variable. ?Maybe the user cannot 
find this property_name untill he read the source code, or define the 
property_name through adding headers.



Hongbin Yang 杨弘宾


?From:?Paolo ToscoDate:?2016-10-13?18:56To:?杨弘宾; rdkit-discussSubject:?Re: 
[Rdkit-discuss] property of name in smilesMolSupplier
  

  
  
Hi Hongbin,



  suppl[0].GetPropNames() is an
  interable object, so you can use it in for loops such as:

  

  for i in suppl[0].GetPropNames():

  ? print (i)

  

  or you may convert it to a list:

  

  l = list(suppl[0].GetPropNames())

  print (l)

  

  Cheers,

  p.

    

On 10/13/16 11:31, 杨弘宾 wrote:



  
  
  Hi，
  ? ? I spent
  a lot of time to explorer "How to get the property of name
  when using SmilesMolSupplier"
  


  I had a
  smiles file like this:
  ===
  c1c1\t1\n
  ...
  ===
  where 1 means that it is positve
  

  
  So I wanted to read this smiles file via SMilesMolSupplier
and I knew that the second column is the default name column.
  suppl =
  Chem.SmilesMolSupplier('compounds.smi',delimiter='\t',titleLine=False)
  


  However, I could not get the property of 1 because I had no
idea what the property_name was.
  In the document, it shows that :
  
If the input file has a title line and more than two columns (smiles 
and id), the
additional columns will be used to set properties on each molecule.  The 
properties
are accessible using the mol.GetProp(propName) method.
But It was a "no title table", So I thought its property_name of "their 
names" should be "Name" or "name" as default. And I failed...
After read the source code, I found that it should be _Name

https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp#L194?
I think the document should be improved so that others may know how to 
get the name of each compound
BTW, I tried to use suppl[0].GetPropNames() but only to get 
",class std::allocator > at 0x7402e90>" that seemed 
tell nothing. I wondered that is there any way to make it readable in python?
    

  
  

  
  
  
  Hongbin
  Yang 杨弘宾
  

  Research: Toxicophore and Chemoinformatics

  Pharmaceutical Science, School of Pharmacy
  

  East China University of Science and Technology?



  

  
  

  
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[Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

2017-03-28 Thread 杨弘宾 






Hi, rdkiters,
? ? Have you tried install rdkit from source? It's ok when I installed rdkit by 
conda in my PC. But when I tried installing it in a server in which I am only a 
user who cannot use "sudo" and the "python" is in a read-only directory.
Here is my cmake command:`~applic/cmake/bin/cmake -D 
PYTHON_LIBRARY=/home/yccai/Programs/Anaconda/lib/python2.7/config/libpython2.7.a
 -D PYTHON_INCLUDE_DIR=/home/yccai/Programs/Anaconda/include/python2.7 -D 
PYTHON_EXECUTABLE=/home/yccai/Programs/Anaconda/bin/python -D 
BOOST_ROOT=/home/yccai/Programs/Anaconda -D Boost_NO_SYSTEM_PATHS=ON ..`
And output:
-- The C compiler identification is GNU 4.1.2

-- The CXX compiler identification is GNU 4.1.2

-- Check for working C compiler: /usr/bin/cc

-- Check for working C compiler: /usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working CXX compiler: /usr/bin/c++

-- Check for working CXX compiler: /usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check if the system is big endian

-- Searching 16 bit integer

-- Looking for sys/types.h

-- Looking for sys/types.h - found

-- Looking for stdint.h

-- Looking for stdint.h - found

-- Looking for stddef.h

-- Looking for stddef.h - found

-- Check size of unsigned short

-- Check size of unsigned short - done

-- Using unsigned short

-- Check if the system is big endian - little endian

-- Found PythonInterp: /home/yccai/Programs/Anaconda/bin/python (found version 
"2.7.12") 

-- Found PythonLibs: 
/home/yccai/Programs/Anaconda/lib/python2.7/config/libpython2.7.a (found 
version "2.7.12") 

-- Boost version: 1.56.0

-- Found the following Boost libraries:

--   python

-- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) 
(Required is at least version "2.91.0")

Eigen3 not found, disabling the Descriptors3D build.

-- Looking for include file pthread.h

-- Looking for include file pthread.h - found

-- Looking for pthread_create

-- Looking for pthread_create - not found

-- Looking for pthread_create in pthreads

-- Looking for pthread_create in pthreads - not found

-- Looking for pthread_create in pthread

-- Looking for pthread_create in pthread - found

-- Found Threads: TRUE  

-- Boost version: 1.56.0

-- Found the following Boost libraries:

--   thread

--   system

-- Boost version: 1.56.0

-- Found the following Boost libraries:

--   serialization

== Using strict rotor definition

== Updating Filters.cpp from pains file

== Done updating pains files

-- Boost version: 1.56.0

-- Found the following Boost libraries:

--   regex

-- Configuring done

-- Generating done

-- Build files have been written to: 
/home/hbyang/applic/rdkit-Release_2016_09_4/build?

There was no error in `make` and `make install`.
But when I used:`from rdkit import rdBase`error happened:ImportError: 
/home/yccai/Programs/Anaconda/bin/../lib/libboost_serialization.so.1.56.0: 
undefined 
symbol:?_ZN5boost13serialization6detail17singleton_wrapperINS_7archive6detail12extra_detail3mapINS3_15binary_oarchive14m_is_destroyedE
I tried the older version of rdkit and got similar error 
(libboost_python.so.1.56.0).
I don't think the problem is in the boost in conda but.. ? So what can I do to 
install it (or find where is the problem)?
I want to use rdkit to draw molecules in my tool. Is there any alternative way 
to do so?


Hongbin Yang?


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Re: [Rdkit-discuss] delete a substructure

2017-03-08 Thread 杨弘宾 



网易邮箱






Hi Chemyang,
    Your issue was caused by the definition of "-OH(phenol)", I think.  If you 
define this pattern as "cO", the atom 3 will be matched since it is the 
aromatic carbon bond to an oxygen.  I guess you just wanted to match exactly 
the oxygen and restrict it with "bonding with an aromatic carbon". So the 
SMARTS should ber "[$(Oc)]", which indicates an oxygen with the environment of 
"bonding with an aromatic carbon".
    m = Chem.MolFromSmiles('CC1=CC(=C(C=C1)C(=O)O)O')    
m.GetSubstructMatches(Chem.MolFromSmiles('[$(Oc)]'))    >>> ((10,),)
Then only atom 10 will be matched and it won't interfere with other counts.
Reference: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html  4.4


Hongbin Yang 

 From: Chenyang ShiDate: 2017-03-09 01:32To: Greg LandrumCC: rdkit-discuss; 
杨弘宾Subject: Re: [Rdkit-discuss] delete a substructure



网易邮箱



Dear Hongbin,
I tried your method on a molecule, 4-Methylsalicylic acid 
(CC1=CC(=C(C=C1)C(=O)O)O). I looped through all groups defined in Joback method 
(using SMARTS), and used m.GetSubstructMatches to print out all atom positions. 
The result is summarized in the table. 
We can see there are duplicated counts--coming from COOH group. As suggested by 
Hongbin, we can remove duplicated atoms by looking at their positions--in this 
case, ((9),), ((7,8,),), ((7,),), and ((8,),) are subsets of ((7,8,9)) from 
-COOH. Indeed we can get rid of these duplicates. However, I also noticed that 
Atom (3,) from =C< (ring) group is also a part of -OH (phenol) ((10,3),). If we 
apply the same algorithm to remove duplicates, the =C<(ring) group will be only 
counted twice instead of three times.  
Greg, you mentioned as an alternative I can delete substructure using chemical 
reaction method. It would be greatly appreciated if you could show me (point me 
to) a simple example code, perhaps on a simple molecule? I find myself at a 
loss when browsing the manual. I would like to try also in that direction.
Thanks,Chenyang





On Mon, Mar 6, 2017 at 1:52 AM, Greg Landrum <greg.land...@gmail.com> wrote:
The solution that Hongbin proposes to the double-counting problem is a good 
one. Just be sure to sort your substructure queries in the right order so that 
the more complex ones come first.
Another thing you might think about is making your queries more specific. For 
example, as you pointed out "[OH]" is very general and matches parts of 
carboxylic acids and a number of other functional groups. The RDKit has a set 
of fairly well tested (though certainly not perfect) functional group 
definitions in $RDBASE/Data/Functional_Group_Hierarchy.txt. The alcohol 
definition from there looks like this:[O;H1;$(O-!@[#6;!$(C=!@[O,N,S])])]


-greg

On Mon, Mar 6, 2017 at 7:20 AM, 杨弘宾 <yanyangh...@163.com> wrote:

Hi, Chenyang,    You don't need to delete the substructure from the molecule. 
Just check whehter the mapped atoms have been matched. For example:
m = Chem.MolFromSmiles('CC(=O)O')OH = Chem.MolFromSmarts('[OH]')COOH = 
Chem.MolFromSmarts('C(O)=O')
m.GetSubstructMatches(OH)>> ((3,),)m.GetSubstructMatchs(COOH)>> ((1, 3, 2),)
Since atom "3" has been already matched, it should be ignored. So you can 
create a "set" to record the matched atoms to avoid repetitive count.


Hongbin Yang 杨弘宾


 From: Chenyang ShiDate: 2017-03-06 14:04To: Greg LandrumCC: RDKit 
DiscussSubject: Re: [Rdkit-discuss] delete a substructureHi Greg,
Thanks for a prompt reply. I did try "GetSubstructMatches()" and it returns 
correct numbers of substructures for CH3COOH. The potential problem with this 
approach is that if the molecule is getting complicated, it will possibly 
generate duplicate numbers for certain functional groups. For example, --OH 
(alcohol) group will be likely also counted in --COOH. A safer way, in my mind, 
is to remove the substructure that has been counted. 
Greg, you mentioned "chemical reaction functionality", can you show me a demo 
script with that using CH3COOH as an example. I will definitely delve into the 
manual to learn more. But reading your code will be a good start. 
Thanks,Chenyang
 
On Sun, Mar 5, 2017 at 10:15 PM, Greg Landrum <greg.land...@gmail.com> wrote:
Hi Chenyang,
If you're really interested in counting the number of times the substructure 
appears, you can do that much quicker with `GetSubstructMatches()`:
In [2]: m = Chem.MolFromSmiles('CC(C)CCO')In [3]: 
len(m.GetSubstructMatches(Chem.MolFromSmarts('[CH3;X4]')))
Out[3]: 2
Is that sufficient, or do you actually want to sequentially remove all of the 
groups in your list?
If you actually want to remove them, you are probably better off using the 
chemical reaction functionality instead of DeleteSubstructs(), which 
recalculates the number of implicit Hs on atoms after each call.
-greg

On Mon, Mar 6, 2017 at 4:21 AM, Chenyang Shi <c

Re: [Rdkit-discuss] delete a substructure

2017-03-05 Thread 杨弘宾 






Hi, Chenyang,    You don't need to delete the substructure from the molecule. 
Just check whehter the mapped atoms have been matched. For example:
m = Chem.MolFromSmiles('CC(=O)O')OH = Chem.MolFromSmarts('[OH]')COOH = 
Chem.MolFromSmarts('C(O)=O')
m.GetSubstructMatches(OH)>> ((3,),)m.GetSubstructMatchs(COOH)>> ((1, 3, 2),)
Since atom "3" has been already matched, it should be ignored. So you can 
create a "set" to record the matched atoms to avoid repetitive count.


Hongbin Yang 杨弘宾


 From: Chenyang ShiDate: 2017-03-06 14:04To: Greg LandrumCC: RDKit 
DiscussSubject: Re: [Rdkit-discuss] delete a substructureHi Greg,
Thanks for a prompt reply. I did try "GetSubstructMatches()" and it returns 
correct numbers of substructures for CH3COOH. The potential problem with this 
approach is that if the molecule is getting complicated, it will possibly 
generate duplicate numbers for certain functional groups. For example, --OH 
(alcohol) group will be likely also counted in --COOH. A safer way, in my mind, 
is to remove the substructure that has been counted. 
Greg, you mentioned "chemical reaction functionality", can you show me a demo 
script with that using CH3COOH as an example. I will definitely delve into the 
manual to learn more. But reading your code will be a good start. 
Thanks,Chenyang
 
On Sun, Mar 5, 2017 at 10:15 PM, Greg Landrum <greg.land...@gmail.com> wrote:
Hi Chenyang,
If you're really interested in counting the number of times the substructure 
appears, you can do that much quicker with `GetSubstructMatches()`:
In [2]: m = Chem.MolFromSmiles('CC(C)CCO')In [3]: 
len(m.GetSubstructMatches(Chem.MolFromSmarts('[CH3;X4]')))
Out[3]: 2
Is that sufficient, or do you actually want to sequentially remove all of the 
groups in your list?
If you actually want to remove them, you are probably better off using the 
chemical reaction functionality instead of DeleteSubstructs(), which 
recalculates the number of implicit Hs on atoms after each call.
-greg

On Mon, Mar 6, 2017 at 4:21 AM, Chenyang Shi <cs3...@columbia.edu> wrote:
I am new to rdkit but I am already impressed by its vibrant community. I have a 
question regarding deleting substructure. In the RDKIT documentation, this is a 
snippet of code describing how to delete substructure:
>>>m = Chem.MolFromSmiles("CC(=O)O")>>>patt = 
>>>Chem.MolFromSmarts("C(=O)[OH]")>>>rm = AllChem.DeleteSubstructs(m, 
>>>patt)>>>Chem.MolToSmiles(rm)'C'
This block of code first loads a molecule CH3COOH using SMILES code, then 
defines a substructure COOH using SMARTS code which is to be deleted. After 
final line of code, the program outputs 'C', in SMILES form. 
I had wanted to develop a method for detecting number of groups in a molecule. 
In CH3COOH case, I can search number of --CH3 and --COOH group by using their 
respective SMARTS code with no problem. However, when molecule becomes more 
complicated, it is preferred to delete the substructure that has been searched 
before moving to next search using SMARTS code. Well, in current case, after 
searching -COOH group and deleting it, the leftover is 'C' which is essentially 
CH4 instead of --CH3. I cannot proceed with searching with SMARTS code for 
--CH3 ([CH3;A;X4!R]). 
Is there any way to work around this?Thanks,Chenyang 
 

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Re: [Rdkit-discuss] Chem.MolToSmarts(mol) out put

2017-07-14 Thread 杨弘宾 
Hi, Alexis,

Why don’t you output the molecule as “Smiles” format since the “Smarts” you 
wanted to output was really a molecule.

And it is possible to remove the dummy atom via mol object. For example:

In [26]: x = Chem.MolFromSmiles('CC*')

In [27]: x.GetSubstructMatch(Chem.MolFromSmiles('*'))
Out[27]: (2,)

In [28]: mw = Chem.RWMol(x)

In [29]: mw.RemoveAtom(2)

In [30]: Chem.MolToSmiles(mw)
Out[30]: 'CC'

But I don’t know whether it can handle SMARTS. Hope that it is helpful for you.

Hongbin Yang 

> On 14 Jul 2017, at 4:59 PM, Alexis Parenty  
> wrote:
> 
>  <>Dear Rdkiters,
> 
> 
> 
> I sometimes get smarts from mol in atomic number notation such as:
> 
> [#6]-[#7+]1=[#6]2-[#6]3:[#7]:[#6]:[#6]:[#6]:[#6]:3-[#6]3:[#6]:[#6]:[#6]:[#6]:[#6]:3-[#7]-2-[#6]-[#6]-1
> 
> 
> 
> Is there a way to force the method Chem.MolToSmarts(mol) to output a smarts 
> using alphabetic letters instead of atomic numbers?
> 
> The reason I am asking is because I need to remove dummy atoms [*] from 
> smarts using string manipulation and I would rather use only one method. 
> Unless I can do that from the mol object?
> 
> 
> 
> Many thanks,
> 
> 
> 
> Alexis
> 
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