rdkit / rdkit Goto Github PK

The official sources for the RDKit library

License: BSD 3-Clause "New" or "Revised" License

CMake 1.14% C++ 23.93% Python 5.69% C 2.46% JavaScript 0.20% HTML 64.41% Makefile 0.01% QMake 0.01% Smarty 0.01% LLVM 0.06% Shell 0.01% Java 0.58% C# 0.07% Fortran 0.01% Yacc 0.09% Lex 0.01% SMT 0.01% Jupyter Notebook 0.75% Dockerfile 0.01% SWIG 0.56%

cheminformatics c-plus-plus python rdkit

rdkit's Introduction

RDKit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

BSD license - a business friendly license for open source
Core data structures and algorithms in C++
Python 3.x wrapper generated using Boost.Python
Java and C# wrappers generated with SWIG
2D and 3D molecular operations
Descriptor and Fingerprint generation for machine learning
Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
Cheminformatics nodes for KNIME
Contrib folder with useful community-contributed software harnessing the power of the RDKit

Community

Code

GitHub code and bug tracker

Web presence

Materials from user group meetings

Documentation

Available on the RDKit page and in the Docs folder on GitHub

Installation

Installation instructions are available in Docs/Book/Install.md.

Binary distributions, anaconda, homebrew

binaries for conda python or, if you are using the conda-forge stack, the RDKit is also available from conda-forge.
RPMs for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
debs for Ubuntu and other Debian-derived Linux distros. Contributed by the Debichem team.
homebrew formula for building on the Mac. Contributed by Eddie Cao.
recipes for building using the excellent conda package manager. Contributed by Riccardo Vianello.
APKs for Alpine Linux. Contributed by da Verona
Wheels at PyPi for all major platforms and python versions. Contributed by Christopher Kuenneth

Projects using RDKit

ROBERT - Automated Machine Learning Protocols
AQME - Automated Quantum Mechanical Environment
chemprop - message passing neural networks for molecular property prediction
RMG - Reaction Mechanism Generator
RDMC - Reaction Data and Molecular Conformers - package for dealing with reactions, molecules, conformers, mainly in 3D
pychemprojections - python library for visualizing various 2D projections of molecules.
pychemovality - python library for estimating the ovality of molecules.
ChEMBL Structure Pipeline - ChEMBL protocols used to standardise and salt strip molecules.
FPSim2 - Simple package for fast molecular similarity searches.
Datamol (docs, repo) - A Python library to intuitively manipulate molecules.
Scopy (docs, paper) - an integrated negative design Python library for desirable HTS/VS database design
stk (docs, paper) - a Python library for building, manipulating, analyzing and automatic design of molecules.
gpusimilarity - A Cuda/Thrust implementation of fingerprint similarity searching
Samson Connect - Software for adaptive modeling and simulation of nanosystems
mol_frame - Chemical Structure Handling for Dask and Pandas DataFrames
RDKit.js - The official JavaScript release of RDKit
DeepChem - python library for deep learning for chemistry
mmpdb - Matched molecular pair database generation and analysis
CheTo (paper)- Chemical topic modeling
OCEAN (paper)- Optimized cross reactivity estimation
ChEMBL Beaker - standalone web server wrapper for RDKit and OSRA
ZINC - Free database of commercially-available compounds for virtual screening
sdf_viewer.py - an interactive SDF viewer
sdf2ppt - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation.
MolGears - A cheminformatics tool for bioactive molecules
PYPL - Simple cartridge that lets you call Python scripts from Oracle PL/SQL.
shape-it-rdkit - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend
WONKA - Tool for analysis and interrogation of protein-ligand crystal structures
OOMMPPAA - Tool for directed synthesis and data analysis based on protein-ligand crystal structures
OCEAN - web-tool for target-prediction of chemical structures which uses ChEMBL as datasource
chemfp - very fast fingerprint searching
rdkit_ipynb_tools - RDKit Tools for the IPython Notebook
Vernalis KNIME nodes
Erlwood KNIME nodes
AZOrange

License

Code released under the BSD license.

rdkit's People

Contributors

Stargazers

Watchers

Forkers

bgruening ckannas nhfechner rochoa85 teaguesterling ericsmoll giallu sriniker zachcp nfirth dawnmy gerebtzoff teng-lin bovee tobywright pzc mwojcikowski janholstjensen johnmay jandom alexandersavelyev skearnes patrickfuller abhik1368 acanada chdon dkoes mcs07 baoilleach dfhahn john-reynolds nadineschneider rwest mark-davies jir322 mnowotka jeprescottroy sixpi acpharis nizamibilal1064 heron1 bp-kelley bach-hardie wshirley jmhernandezlobato jwildenhain proteneer ditti2 bielitzlabs stevenkirkland fchevillard steve-federowicz nextmovesoftware beangoben greglandrum paulbarrett79 adalke strets123 munbo flovering greatlse samoturk lewisacidic doliathgavid mpkotter mcmont ebjerrum nbateshaus hainm kozo2 mojtabah askcos recisic ptosco leelasd odewahn lmmentel connorcoley virajshah thegodone markdoerr ivanov-inin richard-hall coleb flachsenberg anarayanan86 ffsouza githubsniper gedeck mitchondra davidacosgrove d-b-w darkreactions fatmas1982 eberardo jepdavidson dcyou abradle jb-delafosse xaccc

rdkit's Issues

Cannot generate coordinates for output from DeleteSubstructs

As the example shows, this came from problems with salt stripping and is not helped by sanitization.

In [15]: m = Chem.MolFromSmiles('[I-].C[n+]1c(\\C=C\\2/C=CC=CN2CC=C)sc3ccccc13') 

In [16]: sr = SaltRemover.SaltRemover()

In [17]: nm =sr(m)

In [18]: AllChem.Compute2DCoords(nm)
[05:47:08] 

****
Pre-condition Violation

Violation occurred on line 656 in file /scratch/RDKit_trunk/Code/GraphMol/Depictor/EmbeddedFrag.cpp
Failed Expression: d_eatoms.find(aid) == d_eatoms.end()
****

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-18-fbe6edb91321> in <module>()
----> 1 AllChem.Compute2DCoords(nm)

RuntimeError: Pre-condition Violation

In [19]: Chem.SanitizeMol(nm)
Out[19]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE

In [20]: AllChem.Compute2DCoords(nm)
[05:47:18] 

****
Pre-condition Violation

Violation occurred on line 656 in file /scratch/RDKit_trunk/Code/GraphMol/Depictor/EmbeddedFrag.cpp
Failed Expression: d_eatoms.find(aid) == d_eatoms.end()
****

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-20-fbe6edb91321> in <module>()
----> 1 AllChem.Compute2DCoords(nm)

RuntimeError: Pre-condition Violation

In [21]: p = Chem.MolFromSmiles('[I-]')

In [22]: Chem.DeleteSubstructs(m,p)
Out[22]: <rdkit.Chem.rdchem.Mol at 0x3630980>

In [23]: nm2=Chem.DeleteSubstructs(m,p)

In [24]: AllChem.Compute2DCoords(nm2)
[05:47:57] 

****
Pre-condition Violation

Violation occurred on line 656 in file /scratch/RDKit_trunk/Code/GraphMol/Depictor/EmbeddedFrag.cpp
Failed Expression: d_eatoms.find(aid) == d_eatoms.end()
****

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-24-c2a107eeb439> in <module>()
----> 1 AllChem.Compute2DCoords(nm2)

RuntimeError: Pre-condition Violation

In [25]: Chem.MolToSmiles(nm2,True)
Out[25]: 'C=CCN1C=CC=C/C1=C\\c1sc2ccccc2[n+]1C'

fix repeated calls to find_package(Boost) in build system

This commit for 2.8.11:
http://cmake.org/gitweb?p=cmake.git;a=commit;h=0100f88e298c6766d60108537010ede0f83da1dd
breaks things.

MolPickler::molFromPickle() leaks core when query bonds are present

Double bond stereochemistry not preserved in reactions.

Reported by Sabrina Syeda.
Thread here: http://www.mail-archive.com/[email protected]/msg03080.html

>>rxn = AllChem.ReactionFromSmarts('[CX4:4][CH1:3]=[CH1:2][CX4:5].[Br:1]>>[C:5][C:2]=[C:3][C:4][Br:1]')
>>rxn.Initialize()
>>r = [Chem.MolFromSmiles('CCC\C=C\C(C)C'), Chem.MolFromSmiles('Br')]
>>ps = rxn.RunReactants(tuple(r))
>> for p in ps:
    ...:     for m in p:
    ...:         print Chem.MolToSmiles(m, isomericSmiles= True)
    ...:         
[out] CCC(Br)C=CC(C)C
[out] CCCC=CC(C)(C)Br

Docs for Descriptors.MolWt are wrong

In [21]: Descriptors.MolWt?
Type:       function
String Form:<function <lambda> at 0x2f70320>
File:       /scratch/RDKit_trunk/rdkit/Chem/Descriptors.py
Definition: Descriptors.MolWt(*x, **y)
Docstring:
The average molecular weight of the molecule ignoring hydrogens

>>> MolWt(Chem.MolFromSmiles('CC'))
30.07...
>>> MolWt(Chem.MolFromSmiles('[NH4+].[Cl-]'))
53.49...

Install notes

Hi Greg,

Here are the (new) Ubuntu 12.04 installation notes, both for the repository version of RDKit and for building from source.

I've also moved the contents of the http://code.google.com/p/rdkit/wiki/BuildingWithCmake into this doc file.

MCS code does not support stereochemistry

Thread here: http://www.mail-archive.com/[email protected]/msg02934.html

In [2]: mol1 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@@]3(OCc2cc(C#N)ccc23)CCCN(C)C") 
In [3]: mol2 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@]3(OCc2cc(C#N)ccc23)CCCN(C)C")

In [4]: from rdkit.Chem import MCS

In [6]: MCS.FindMCS((mol1,mol2))
Out[6]: MCSResult(numAtoms=24, numBonds=26, smarts='[F]-[#6]:1:[#6]:[#6]:[#6](-[#6]-2(-[#6]-[#6]-[#6]-[#7](-[#6])-[#6])-[#8]-[#6]-[#6]:3:[#6]:[#6](:[#6]:[#6]:[#6]:3-2)-[#6]#[#7]):[#6]:[#6]:1', completed=1)

SDWriter initialized on a file object can produce an unhandled C++ exception

Not calling the flush method of an SDWriter initialized on a file object may produce an unhandled exception and terminate the interpreter:

 In [7]: with open('xyz.sdf', 'w') as xyz:
    ...:     w = Chem.SDWriter(xyz)
    ...:     w.write(Chem.MolFromSmiles('c1ccccc1'))
    ...:     w.write(Chem.MolFromSmiles('c1ccccc1'))
    ...:     w.write(Chem.MolFromSmiles('c1ccccc1'))
    ...:     w.write(Chem.MolFromSmiles('c1ccccc1'))
    ...:     w.write(Chem.MolFromSmiles('c1ccccc1'))
    ...:     
 terminate called after throwing an instance of 'boost::python::error_already_set' 
 Aborted

Molecules from InChI have incorrect molecular weight.

In [24]: m =Chem.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')

In [25]: em = Chem.EditableMol(m)

In [26]: em.RemoveBond(8,7)

In [27]: nm = em.GetMol()

In [29]: frags = Chem.GetMolFrags(nm,asMols=True)

In [30]: [Descriptors.MolWt(x) for x in frags]
Out[30]: [5.04, 6.048]

It doesn't always happen though:

In [31]: m = Chem.MolFromSmiles('CO')
In [32]: em = Chem.EditableMol(m)

In [33]: em.RemoveBond(0,1)

In [34]: nm = em.GetMol()

In [35]: frags = Chem.GetMolFrags(nm,asMols=True)

In [36]: [Descriptors.MolWt(x) for x in frags]
Out[36]: [16.043, 18.015]

Corrected number of iterations in UFFOptimizeMolecule documentation

Says 100, it should be 200.

Seg fault when ChemicalReaction.runReactants is called with a None molecule

In [7]: ps = rxn2.RunReactants((Chem.MolFromSmiles('F[C@H](Cl)(Br)I'),))
[05:01:37] Explicit valence for atom # 1 C, 5, is greater than permitted
Segmentation fault (core dumped)

Compatibility with sdf files served by the PDB

SDFs provided by the PDB (Protein Data Bank) have a slightly different format than what RDKit is expecting.

Example file that would fail with the old code
http://www.rcsb.org/pdb/download/downloadLigandFiles.do?ligandIdList=XK2&structIdList=1HVR&instanceType=all&excludeUnobserved=false&includeHydrogens=false

The old error was:

Post-condition Violation
Element '' not found
Violation occurred on line 91 in file /home/jandom/workspace/rdkit/Code/GraphMol/PeriodicTable.h
Failed Expression: anum>-1

Hashed topological torsion fingerprints not compatible with old version.

2012_12_1:

In [9]: AllChem.GetHashedTopologicalTorsionFingerprint(Chem.MolFromSmiles('CCCCO'),nBits=4192).GetNonzeroElements()
Out[9]: {544: 1, 1760: 1}

2013_03_1:

In [3]: AllChem.GetHashedTopologicalTorsionFingerprint(Chem.MolFromSmiles('CCCCO'),nBits=4192).GetNonzeroElements()
Out[3]: {1974: 1, 3516: 1}

There's no good reason for this to be the case.

Gasteiger charge calculation generating NaNs for boron

In [3]: m = Chem.MolFromSmiles('CB(O)O')

In [4]: from rdkit.Chem import AllChem
Al
In [5]: AllChem.ComputeGasteigerCharges(m)

In [6]: for a in m.GetAtoms(): print a.GetProp('_GasteigerCharge')
-nan
-nan
-nan
-nan

Incorrect atom labels from BRICS

In [4]: m = Chem.MolFromSmiles('CCOC1(C)CCCCC1')

In [5]: Chem.MolToSmiles(BRICS.BreakBRICSBonds(m),True)
Out[5]: '[3*]O[3*].[4*]CC.[4*]C1(C)CCCCC1'

(dupe of sf.net issue 287 to experiment with github issue tracking)

Fix handling of flex/bison dependencies in CMake files

The way things are currently broken with "make clean" should be fixed.

Compatibility with sdf files served by the PDB

SDFs provided by the PDB (Protein Data Bank) have a slightly different format than what RDKit is expecting.

http://www.rcsb.org/pdb/download/downloadLigandFiles.do?ligandIdList=XK2&structIdList=1HVR&instanceType=all&excludeUnobserved=false&includeHydrogens=false

Incorrect InChIs after clearing computed properties

(reported by Francis Atkinson)

from __future__ import print_function

from rdkit import Chem

old_mol=Chem.MolFromMolBlock("""
  Marvin  02211109112D

 13 12  0  0  0  0            999 V2000
   -0.7607  -10.6459    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0457  -10.2343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6692  -10.6459    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3843  -10.2343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0993  -10.6459    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8142  -10.2343    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4740  -10.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6692  -11.4731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3843   -9.4072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0993  -11.4731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5317  -10.6451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2440  -10.2326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8132   -9.4072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  4  9  1  1  0  0  0
  1  2  1  0  0  0  0
  5 10  1  1  0  0  0
  4  5  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
  5  6  1  0  0  0  0
  6 13  1  6  0  0  0
  2  3  1  0  0  0  0
  1  7  1  0  0  0  0
  3  8  1  1  0  0  0
M  END
""")



main_mol = Chem.DeleteSubstructs(old_mol,Chem.MolFromSmiles('O=[Sb](=O)O'))
main_mol.ClearComputedProps()
Chem.SanitizeMol(main_mol)
print(Chem.MolToSmiles(old_mol,True))
print(Chem.MolToSmiles(main_mol,True))

old_mol.Debug()
main_mol.Debug()

print(Chem.MolToInchi(old_mol))
print(Chem.MolToInchi(new_mol))

SWIG wrappers do not expose Atom.SetProp, Bond.SetProp, or Bond.GetProp

Easy enough to copy in from ROMol.i

logLevel bug in MolFromInchi

There is a typo in inchi.py . "logLogLevel" is used where it should be "logLevel". Here is a reproducible:

>>> Chem.MolFromInchi("InChI=1S/CH2/h1H2", logLevel=100)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "..../site-packages/rdkit/Chem/inchi.py", line 76, in MolFromInchi
    if logLogLevel not in logLevelToLogFunctionLookup:
NameError: global name 'logLogLevel' is not defined

Reported by Andrew Dalke

mol fails to transfer to inchi format

from rdkit import Chem
from rdkit.Chem import BRICS
m1 = Chem.inchi.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')
m2 = BRICS.BreakBRICSBonds(m1)
Chem.MolToSmiles(m2,True)

I got

'[14_]c1nnc(C)nc1O.[16_]c1ccccc1'.

But when I try to get inchi format

Chem.inchi.MolToInchi(m2)

I got

[23:56:23] ERROR: Unknown element(s): *
''

By the way,
res = list(BRICS.FindBRICSBonds(m1))
res

I got
[((8, 7), ('14', '16'))]

What are '14' and '16'?

Thanks.

Missing headers upon doing "make install"

(reported by Riccardo Vianello)

There are a set of header files that "make install" does not copy into the install directory when not doing an in-tree install.

Add Bond.GetBondTypeAsDouble() to Python wrapper.

Atom labels at the edge of drawings generated for small molecules are cutoff

It's an old story, but it's an irritating one.

Bad ring query matches for molecules from MolFromSmarts

In [5]: Chem.MolFromSmiles('c:1:c:c:c:c:c1').HasSubstructMatch(Chem.MolFromSmarts('[R2]~[R1]~[R2]'))
Out[5]: False

In [6]: Chem.MolFromSmarts('c:1:c:c:c:c:c1').HasSubstructMatch(Chem.MolFromSmarts('[R2]~[R1]~[R2]'))
Out[6]: True

In [7]: Chem.MolFromSmarts('ccc').HasSubstructMatch(Chem.MolFromSmarts('[R2]~[R1]~[R2]'))
Out[7]: True

Support for Pillow/PIL fork

Pillow is a "friendly" fork of PIL. Effectively it replaces PIL.

It's nearly completely backwards compatible, except that it places things under the "PIL" module. Things like "import Image" need to be "from PIL import Image".

Support for it is a couple of lines to rdkit/sping/PIL/pidPIL.py. Change:

import Image, ImageFont, ImageDraw

to -

try:
from PIL import Image, ImageFont, ImageDraw
except ImportError:
import Image, ImageFont, ImageDraw

BaseFeatures_DIP2_NoMicroSpecies.fdef not parseable

In [7]: ffact = ChemicalFeatures.BuildFeatureFactory('./BaseFeatures_DIP2_NoMicrospecies.fdef')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-7-be7869918589> in <module>()
----> 1 ffact = ChemicalFeatures.BuildFeatureFactory('./BaseFeatures_DIP2_NoMicrospecies.fdef')

ValueError:  pattern->getNumAtoms() != len(feature weight vector)

RDLogger.CRITICAL same as RDLogger.ERROR

reported by Andrew Dalke

Inital take on the USR Descriptor (no tests)

Hi Greg,

Here is my take an the USR Descriptor - it's 2x faster than Adrian's implementation but it's a lot less clearer. It probably can be improved quickly. Numerics agree with Adrian but I should probably add a test case.

Jan

aromatic Si written in SMILES, but cannot be read

In [2]: Chem.MolFromSmiles('Cc1cc[si](-c2cccc3ccc4cc5ccccc5cc4c32)[si](C)n1')
[04:48:35] SMILES Parse Error: syntax error for input: Cc1cc[si](-c2cccc3ccc4cc5ccccc5cc4c32)[si](C)n1

In [3]: Chem.MolFromSmiles('Cc1cc[Si](-c2cccc3ccc4cc5ccccc5cc4c32)[Si](C)n1')
Out[3]: <rdkit.Chem.rdchem.Mol at 0x242d440>

In [5]: Chem.CanonSmiles('C1=CC=CC=[Si]1')
Out[5]: 'c1cc[si]cc1'

cartridge: pg_dump shouldn't use SMILES

Reported by Stephan Reiling: http://www.mail-archive.com/[email protected]/msg02948.html

SDWriter failing with bad boost::any_cast on windows

[reported by Paul C]

In [10]: from rdkit import Chem

In [11]: from rdkit.Chem import Descriptors

In [12]: from rdkit.ML.Descriptors import MoleculeDescriptors

In [13]: m = Chem.MolFromSmiles('CC')

In [15]: nms=[x[0] for x in Descriptors._descList]

In [16]: calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)

In [17]: ds= calc.CalcDescriptors(m)

In [18]: w=Chem.SDWriter('blah.sdf')

In [19]: w.write(m)
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-19-4b04ce05d7ef> in <module>()
----> 1 w.write(m)

RuntimeError: boost::bad_any_cast: failed conversion using boost::any_cast

Add convenience API function for template-based enumeration

The hard bits are already there in $RDBASE/rdkit/Chem/ChemUtils/TemplateExpand.py, it just needs a more user-friendly API and an example or two.
This would be a good one from the cookbook based on the contents of this thread:
http://www.mail-archive.com/[email protected]/msg02931.html

Include a particular version of the avalon toolkit in the RDKit distribution

Error providing atom invariants to AtomPairs and TopologicalTorsion fps from Python

Stereochemistry information influences canonical SMILES even when non-stereo smiles is being generated

In [30]: smi='CC1CCC[C@@]2(C)C1CC[C@@H]2C(C)=O'

In [31]: print Chem.MolToSmiles(Chem.MolFromSmiles(smi.replace('@','')));print Chem.MolToSmiles(Chem.MolFromSmiles(smi))
CC(=O)C1CCC2C(C)CCCC12C
CC(=O)C1CCC2C(C)CCCC21C

Those should definitely be the same.

Reported by Riccardo Vianello

Stereochemistry lost for reacting atoms that don't change connectivity

Reported by Robert Feinstein in this thread: http://www.mail-archive.com/[email protected]/msg02908.html

# Demo of RDKit reaction transform nuking stereocenters
from rdkit import Chem
from rdkit.Chem import AllChem

# Define simple transform that includes possible stereocenter ([C:2])
rxn = AllChem.ReactionFromSmarts('[C:2][C:1]=O>>[C:2][C:1]=S')

# React achiral mol as test
ps = rxn.RunReactants((Chem.MolFromSmiles('CC=O'),))
Chem.MolToSmiles( ps[0][0], isomericSmiles=True )
# Output is 'CC=S'

# React mol with chiral center far removed
ps = rxn.RunReactants((Chem.MolFromSmiles('[Cl][C@H]([Br])CCCC=O'),))
Chem.MolToSmiles( ps[0][0], isomericSmiles=True )
# Output is 'S=CCCC[C@H](Cl)Br'

# React mol with chiral center included in transform component
ps = rxn.RunReactants((Chem.MolFromSmiles('[Cl][C@H](C=O)'),))
Chem.MolToSmiles( ps[0][0], isomericSmiles=True )
# Output is 'S=CCCl' - chriality has been lost.

improper behavior for empty SDMolSuppliers

This is reasonable:

[14]>>> s = Chem.SDMolSupplier()

[15]>>> s.SetData("")

[16]>>> s.next()
---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
/scratch/RDKit_sf/<ipython-input-16-5e5e6532ea26> in <module>()
----> 1 s.next()

StopIteration: End of supplier hit

But this is bad:

[11]>>> s = Chem.SDMolSupplier()

[12]>>> s.SetData("")

[13]>>> len(s)
  [13]: 1

as is this:

[17]>>> s = Chem.SDMolSupplier()

[18]>>> s.SetData("")

[19]>>> s[0]

[20]>>>

and this is incomprehensible:

[17]>>> s = Chem.SDMolSupplier()

[18]>>> s.SetData("")

[19]>>> s[0]

[20]>>> s[1]
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
/scratch/RDKit_sf/<ipython-input-20-88de191fe097> in <module>()
----> 1 s[1]

IndexError: invalid index

[21]>>> s.SetData("")

[22]>>> s[0]

[23]>>> s.next()
---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
/scratch/RDKit_sf/<ipython-input-23-5e5e6532ea26> in <module>()
----> 1 s.next()

StopIteration: End of supplier hit

[24]>>> len(s)
  [24]: 2

MolFromInchi doesn't work

I am using python Python 2.7.3
from rdkit import Chem
m2 = Chem.inchi.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')
I got
Traceback (most recent call last):
File "", line 1, in
AttributeError: 'module' object has no attribute 'MolFromInchi'
But if I use MolFromSmiles
from rdkit import Chem
m2 = Chem.MolFromSmiles('C1CCC1')
It works.

Sanitize fails with very simple smiles: non-ring atom 2 marked aromatic

If we run the following program:

from rdkit import Chem
Chem.MolFromSmiles('O(C)c')

we get an error:
non-ring atom 2 marked aromatic

Everything goes well if we disable sanitization:

Chem.MolFromSmiles('O(C)c', sanitize=False)

Added USR descriptor

Ultrafast Shape Descriptor,
access via rdkit.Chem.Descriptors.USR,
added unit tests (sanity and numeric),
also some docs.

In [2]: smiles = "CCN1CCN(c2cc3[nH]c(C(=O)[C@@]4(CC)CC[C@](C)(O)CC4)nc3cc2Cl)CC1"

In [3]: mol = Chem.MolFromSmiles(smiles)

In [4]: tmp = Chem.EditableMol(mol)

In [5]: for atom in [29, 28, 27, 26, 25, 24, 8, 7, 6, 5, 4, 3, 2, 1, 0]: tmp.RemoveAtom(atom)

In [6]: mol = tmp.GetMol()

In [8]: Chem.MolToSmiles(mol)
[05:00:49] 

****
Range Error
idx
Violation occurred on line 153 in file /scratch/RDKit_git/Code/GraphMol/ROMol.cpp
Failed Expression: 0 <= 18 <= 14
****

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-8-2ae14fafa41a> in <module>()
----> 1 Chem.MolToSmiles(mol)

RuntimeError: Range Error

Remove the chiral spec and things work fine:

In [13]: smiles2 = "CCN1CCN(c2cc3[nH]c(C(=O)[C]4(CC)CC[C](C)(O)CC4)nc3cc2Cl)CC1"

In [14]: mol = Chem.MolFromSmiles(smiles2)

In [15]: tmp = Chem.EditableMol(mol)

In [16]: for atom in [29, 28, 27, 26, 25, 24, 8, 7, 6, 5, 4, 3, 2, 1, 0]: tmp.RemoveAtom(atom)

In [17]: mol = tmp.GetMol()

In [18]: Chem.MolToSmiles(mol)
Out[18]: 'CCC1(C(=O)c(n)[nH])CCC(C)(O)CC1'

reported by Dan Warner

InChI generation code not recognizing stereo

reported by Jan Holst Jensen

> For example: InChI strings generated for spiro.mol (spiro.mol - attached):
>
> IUPAC:
> InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3/t2*7-,8-,9-/m10/s1
> RDKit: InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3

This one still doesn't recognize the stereo. I'll file a bug for it:
In [2]: Chem.MolToInchi(Chem.MolFromMolFile('spiro.mol'))
[09:53:16] WARNING: Omitted undefined stereo
Out[2]: 'InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3'

Here's the file:

spiro.mol
  ACD/Labs0709041010  

 22 24  0  0  0  0  0  0  0  0  1 V2000
    9.2912   -9.4308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8009   -6.9967    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    7.7063   -7.9840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8986   -9.1405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1531   -6.3991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5689   -7.8459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7408   -6.2812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8789   -9.3129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3257   -7.7280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1335   -6.5716    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   15.2311   -8.7153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6519  -14.7621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1616  -12.3280    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    8.0670  -13.3153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2593  -14.4717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5138  -11.7304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9296  -13.1772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1015  -11.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2396  -14.6442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6864  -13.0593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4941  -11.9029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5918  -14.0466    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  1  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  0  0  0  0
  6  8  1  1  0  0  0
  9  7  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
  9 11  1  1  0  0  0
 14 13  1  0  0  0  0
 14 15  1  1  0  0  0
 12 14  1  0  0  0  0
 16 14  1  0  0  0  0
 17 12  1  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  0  0  0  0
 17 19  1  1  0  0  0
 20 18  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 20 22  1  1  0  0  0
M  END
>  <NAME>
spiro 

$$$$

seg fault in Quantize.FindVarMultQuantBounds when passed sequences instead of floats

In [1]: from rdkit.ML.Data import Quantize

In [2]: d = [0,1,2,3,4]

In [3]: a = [0,0,1,1,1]

In [4]: Quantize.FindVarMultQuantBounds(d,1,a,2)
Out[4]: ([1.5], 0.9709505944546688)

In [5]: d2 = [(x,) for x in d]

In [6]: Quantize.FindVarMultQuantBounds(d2,1,a,2)
Segmentation fault

MolFragmentToSmiles generating non-canonical results

In [3]: Chem.MolFragmentToSmiles(Chem.MolFromSmiles('c1c(C)cccc1'),(0,1,2))
Out[3]: 'Ccc'

In [4]: Chem.MolFragmentToSmiles(Chem.MolFromSmiles('c1c(C)cccc1'),(1,2,3))
Out[4]: 'ccC'

In [5]: Chem.MolFragmentToSmiles(Chem.MolFromSmiles('c1c(C)cccc1'),(1,3,2))
Out[5]: 'ccC'