rdkit / conda-rdkit Goto Github PK

View Code? Open in Web Editor NEW

49.0 49.0 30.0 209 KB

Conda build recipe for the rdkit

Shell 5.04% C 82.06% Python 0.84% Batchfile 5.15% Dockerfile 6.91%

conda-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.

conda-rdkit's People

Contributors

Stargazers

Watchers

conda-rdkit's Issues

Cannot import rdEHTTools

According to this blog post, 2019.03 RDKit release conda package has EHT integration. I installed RDKit version 2019.03.4 using conda but cannot import rdEHTTools

2019.03.4
Thu Oct 10 11:08:44 2019
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-2-4d87bc54f7ec> in <module>
     18 
     19 # this is the package including the connection to YAeHMOP
---> 20 from rdkit.Chem import rdEHTTools
     21 from rdkit.Chem import AllChem
     22 

ImportError: cannot import name 'rdEHTTools' from 'rdkit.Chem' (/Users/sternc1/anaconda3/envs/rd-test/lib/python3.7/site-packages/rdkit/Chem/__init__.py)

Do I need to install it separately or enable it in some way?

consider porting to conda-forge?

Have you considered hosting these recipes on conda-forge?
It might be a bit more automated/centralized than the anaconda-cloud option.

is it expected that boost is pulled from conda3 main channel and not rdkit?

$ conda install --channel rdkit rdkit
Solving environment: done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs: 
    - rdkit


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    rdkit-2018.03.4.0          |   py36h71b666b_1        19.5 MB  rdkit
    py-boost-1.65.1            |   py36hf484d3e_4         297 KB
    libboost-1.65.1            |       habcd387_4        19.2 MB
    ------------------------------------------------------------
                                           Total:        39.0 MB

The following NEW packages will be INSTALLED:

    libboost: 1.65.1-habcd387_4               
    py-boost: 1.65.1-py36hf484d3e_4           
    rdkit:    2018.03.4.0-py36h71b666b_1 rdkit

switch to using conda postgresql

Now that conda has postgresql 9.5 builds available for all platforms, I think we should consider switching the rdkit-postgresql recipe over to using those. This would simplify things, lessen the amount of work that we need to do, and possibly make things easier for users (since it's easy to imagine others starting to take advantage of the conda postgresql builds.

When we do that we can remove the postgresql and postgresql95 recipes along with the rdkit-postgresql95 recipe. Unless, of course, you see a reason to maintain support for older postgresql versions in the conda recipes.

rdkit installs libboost 1.67.0 rdkit-postgresql wants 1.65.1

doing the following install as of today on an ubuntu 18.04.2 LTS

bash /tmp/Anaconda3-2019.03-Linux-x86_64.sh
conda create -c rdkit -n my-rdkit rdkit
conda activate my-rdkit
conda install -c rdkit rdkit-postgresql
mkdir postgres
mkdir postgres/data
mkdir postgres/log
anaconda3/envs/my-rdkit/bin/initdb -D /home/username/postgres/data/
anaconda3/envs/my-rdkit/bin/pg_ctl -D /home/username/postgres/data/ -l /home/username/postgres/log/logfile start
createdb my_rdkit_db

you end up with the following happening:
psql my_rdkit_db
psql (11.2)
Type "help" for help.

my_rdkit_db=# create extension rdkit;
ERROR: could not load library "/home/username/anaconda3/envs/my-rdkit/lib/rdkit.so": libboost_system.so.1.65.1: cannot open shared object file: No such file or directory
my_rdkit_db=# \q

if you look in said directory:

anaconda3/envs/my-rdkit/lib/libboost_system.so.1.67.0

if you downgrade with the following:

conda install -y boost-cpp=1.65.1 boost=1.65.1 py-boost=1.65.1

<<< snip >>>

The following NEW packages will be INSTALLED:

boost pkgs/main/linux-64::boost-1.65.1-py36_4
boost-cpp pkgs/main/linux-64::boost-cpp-1.65.1-h14c3975_4

The following packages will be REMOVED:

rdkit-2019.03.3.0-py36hc20afe1_1

The following packages will be DOWNGRADED:

libboost 1.67.0-h46d08c1_4 --> 1.65.1-habcd387_4
py-boost 1.67.0-py36h04863e7_4 --> 1.65.1-py36hf484d3e_4

<<< snip >>>

psql at that point is happy... but... it removed rdkit... so... there is dissonance between what the two packages want.

clean install of conda python 3.7 rdkit rdkit for postgres on ubuntu 18.04 has boost version issues

demonstration of issue

psql --port=15432 my-rdkit-db
psql (11.2)
Type "help" for help.

my-rdkit-db=# create extension rdkit;
ERROR: could not load library "/home/username/anaconda3/envs/my-rdkit/lib/rdkit.so": libboost_regex.so.1.65.1: cannot open shared object file: No such file or directory

versions of relevant things:

conda --version
conda 4.7.10

python --version
Python 3.7.3

uname -a
Linux iapetus 4.15.0-55-generic rdkit/rdkit#60-Ubuntu SMP Tue Jul 2 18:22:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

boost is installed however a more recent version:

cd ~/anaconda3/envs/my-rdkit/lib
ls libboost_regex.so*
libboost_regex.so libboost_regex.so.1.67.0

this workaround worked several weeks ago on another clean install.

try installing a prior version:

conda install -y boost=1.65.1 py-boost=1.65.1

Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

boost=1.65.1 -> python[version='>=2.7,<2.8.0a0,>=3.6,<3.7.0a0']
py-boost=1.65.1 -> python[version='>=2.7,<2.8.0a0,>=3.6,<3.7.0a0']

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Your current python version
is (python=3.7). Note that conda will not change your python version to a different minor version
unless you explicitly specify that.

The following specifications were found to be incompatible with each other:

Package setuptools conflicts for:

snip

a masive list of stuff **

Conda Docker build fails

Hi,

If I checkout and either use master or develop, the Docker build ("docker build .") breaks (Docker runs on Fedora):

[...]
[100%] Built target rdMolDescriptors
[100%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so
[100%] Built target rdChemReactions
[100%] Linking CXX executable testReaction
[100%] Built target testReaction
++ uname

[[ Linux == \L\i\n\u\x ]]
RDBASE=/home/rdkit/bld/rdkit_1494777495800/work
LD_LIBRARY_PATH=/home/rdkit/bld/rdkit_1494777495800/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib:/home/rdkit/bld/rdkit_1494777495800/work/lib
PYTHONPATH=/home/rdkit/bld/rdkit_1494777495800/work
ctest -j4 --output-on-failure
Test project /home/rdkit/bld/rdkit_1494777495800/work
Start 1: testInchi
Start 2: testAvalonLib1
Start 3: pyAvalonTools
Start 4: testDict
1/118 Test #3: pyAvalonTools ...................... Passed 0.19 sec
Start 5: testRDValue
2/118 Test #5: testRDValue ........................ Passed 0.30 sec
Start 6: testDataStructs
3/118 Test #6: testDataStructs .................... Passed 0.20 sec
Start 7: testFPB
4/118 Test #7: testFPB ............................ Passed 0.30 sec
Start 8: testMultiFPB
5/118 Test #8: testMultiFPB ....................... Passed 0.01 sec
Start 9: pyBV
6/118 Test #9: pyBV ............................... Passed 0.42 sec
Start 10: pyDiscreteValueVect
7/118 Test #4: testDict ........................... Passed 2.53 sec
8/118 Test #10: pyDiscreteValueVect ................ Passed 0.30 sec
Start 11: pySparseIntVect
Start 12: pyFPB
9/118 Test #11: pySparseIntVect .................... Passed 0.20 sec
Start 13: testTransforms
10/118 Test #12: pyFPB .............................. Passed 0.30 sec
11/118 Test #13: testTransforms ..................... Passed 0.20 sec
Start 14: testGrid
Start 15: testPyGeometry
12/118 Test #14: testGrid ........................... Passed 0.11 sec
13/118 Test #15: testPyGeometry ..................... Passed 0.12 sec
Start 16: testMatrices
Start 17: testAlignment
14/118 Test #17: testAlignment ...................... Passed 0.10 sec
15/118 Test #16: testMatrices ....................... Passed 0.20 sec
Start 18: pyAlignment
Start 19: testOptimizer
16/118 Test #19: testOptimizer ...................... Passed 0.10 sec
17/118 Test #18: pyAlignment ........................ Passed 0.20 sec
Start 20: testUFFForceField
Start 21: testMMFFForceField
18/118 Test #20: testUFFForceField .................. Passed 0.11 sec
Start 22: pyForceFieldConstraints
19/118 Test #22: pyForceFieldConstraints ............ Passed 0.91 sec
20/118 Test #1: testInchi .......................... Passed 4.99 sec
Start 23: testDistGeom
Start 24: pyDistGeom
21/118 Test #24: pyDistGeom ......................... Passed 0.10 sec
22/118 Test #23: testDistGeom ....................... Passed 0.10 sec
Start 25: graphmolTest1
Start 26: graphmolcpTest
23/118 Test #26: graphmolcpTest ..................... Passed 0.10 sec
24/118 Test #25: graphmolTest1 ...................... Passed 0.10 sec
Start 27: graphmolqueryTest
Start 28: graphmolMolOpsTest
25/118 Test #27: graphmolqueryTest .................. Passed 0.20 sec
Start 29: graphmoltestCanon
26/118 Test #29: graphmoltestCanon .................. Passed 0.20 sec
Start 30: graphmoltestChirality
27/118 Test #30: graphmoltestChirality .............. Passed 0.20 sec
Start 31: graphmoltestPickler
28/118 Test #28: graphmolMolOpsTest ................. Passed 1.05 sec
29/118 Test #31: graphmoltestPickler ................ Passed 0.22 sec
Start 32: graphmoltestPicklerGlobalSetting
Start 33: graphmolIterTest
30/118 Test #32: graphmoltestPicklerGlobalSetting ... Passed 0.10 sec
31/118 Test #33: graphmolIterTest ................... Passed 0.20 sec
Start 34: hanoiTest
Start 35: graphmolMemTest1
32/118 Test #35: graphmolMemTest1 ................... Passed 0.20 sec
Start 36: resMolSupplierTest
33/118 Test #36: resMolSupplierTest ................. Passed 1.11 sec
Start 37: testDepictor
34/118 Test #37: testDepictor ....................... Passed 0.30 sec
Start 38: pyDepictor
35/118 Test #38: pyDepictor ......................... Passed 0.60 sec
Start 39: smiTest1
36/118 Test #39: smiTest1 ........................... Passed 0.30 sec
Start 40: cxsmilesTest
37/118 Test #40: cxsmilesTest ....................... Passed 0.20 sec
Start 41: smaTest1
38/118 Test #41: smaTest1 ........................... Passed 1.11 sec
Start 42: fileParsersTest1
39/118 Test #21: testMMFFForceField ................. Passed 8.44 sec
Start 43: testMolSupplier
40/118 Test #43: testMolSupplier .................... Passed 0.40 sec
Start 44: testMolWriter
41/118 Test #44: testMolWriter ...................... Passed 0.40 sec
Start 45: testTplParser
42/118 Test #45: testTplParser ...................... Passed 0.02 sec
Start 46: testMol2ToMol
43/118 Test #46: testMol2ToMol ...................... Passed 0.04 sec
Start 47: testSequence
44/118 Test #47: testSequence ....................... Passed 0.05 sec
Start 48: testSubstructMatch
45/118 Test #2: testAvalonLib1 ..................... Passed 14.73 sec
Start 49: testReaction
46/118 Test #48: testSubstructMatch ................. Passed 0.71 sec
47/118 Test #49: testReaction ....................... Passed 0.41 sec
Start 50: testReactionFingerprints
Start 51: testEnumeration
48/118 Test #50: testReactionFingerprints ........... Passed 0.03 sec
49/118 Test #51: testEnumeration .................... Passed 0.23 sec
Start 52: pyChemReactions
Start 53: pyChemReactionEnumerations
50/118 Test #52: pyChemReactions .................... Passed 0.30 sec
Start 54: pyChemReactionSanitize
51/118 Test #54: pyChemReactionSanitize ............. Passed 0.16 sec
Start 55: testChemTransforms
52/118 Test #55: testChemTransforms ................. Passed 0.31 sec
Start 56: testSubgraphs1
53/118 Test #53: pyChemReactionEnumerations ......... Passed 1.05 sec
Start 57: testSubgraphs2
54/118 Test #57: testSubgraphs2 ..................... Passed 0.01 sec
55/118 Test #56: testSubgraphs1 ..................... Passed 0.39 sec
Start 58: filterCatalogTest
Start 59: pyFilterCatalog
56/118 Test #58: filterCatalogTest .................. Passed 0.40 sec
Start 60: testFragCatalog
57/118 Test #59: pyFilterCatalog .................... Passed 1.01 sec
Start 61: pyFragCatalog
58/118 Test #60: testFragCatalog .................... Passed 0.50 sec
59/118 Test #61: pyFragCatalog ...................... Passed 0.20 sec
Start 62: testDescriptors
Start 63: testPBF
60/118 Test #63: testPBF ............................ Passed 0.30 sec
Start 64: test3D
61/118 Test #64: test3D ............................. Passed 0.92 sec
Start 65: pyMolDescriptors
62/118 Test #65: pyMolDescriptors ................... Passed 0.52 sec
Start 66: testFingerprints
63/118 Test #62: testDescriptors .................... Passed 3.66 sec
Start 67: testPartialCharges
64/118 Test #67: testPartialCharges ................. Passed 0.04 sec
Start 68: pyPartialCharges
65/118 Test #68: pyPartialCharges ................... Passed 0.32 sec
Start 69: testMolTransforms
66/118 Test #69: testMolTransforms .................. Passed 0.04 sec
Start 70: pyMolTransforms
67/118 Test #42: fileParsersTest1 ................... Passed 12.46 sec
Start 71: testMMFFForceFieldHelpers
68/118 Test #70: pyMolTransforms .................... Passed 0.32 sec
Start 72: testUFFForceFieldHelpers
69/118 Test #66: testFingerprints ................... Passed 8.58 sec
Start 73: testCrystalForceField
70/118 Test #73: testCrystalForceField .............. Passed 0.05 sec
Start 74: pyForceFieldHelpers
71/118 Test #74: pyForceFieldHelpers ................ Passed 0.42 sec
72/118 Test #34: hanoiTest .......................... Passed 23.39 sec
Start 75: testDistGeomHelpers
Start 76: pyDistGeom
73/118 Test #76: pyDistGeom ......................... Passed 5.56 sec
Start 77: testMolAlign
74/118 Test #71: testMMFFForceFieldHelpers .......... Passed 17.79 sec
Start 78: pyMolAlign
75/118 Test #72: testUFFForceFieldHelpers ........... Passed 20.72 sec
Start 79: testFeatures
76/118 Test #79: testFeatures ....................... Passed 0.20 sec
Start 80: pyChemicalFeatures
77/118 Test #80: pyChemicalFeatures ................. Passed 0.25 sec
Start 81: testShapeHelpers
78/118 Test #81: testShapeHelpers ................... Passed 0.22 sec
Start 82: pyShapeHelpers
79/118 Test #82: pyShapeHelpers ..................... Passed 0.29 sec
Start 83: testMolCatalog
80/118 Test #83: testMolCatalog ..................... Passed 0.21 sec
Start 84: pyMolCatalog
81/118 Test #84: pyMolCatalog ....................... Passed 0.29 sec
Start 85: moldraw2DTest1
82/118 Test #85: moldraw2DTest1 ..................... Passed 2.62 sec
Start 86: pyMolDraw2D
83/118 Test #86: pyMolDraw2D ........................ Passed 0.26 sec
Start 87: testFMCS
84/118 Test #87: testFMCS ........................... Passed 1.42 sec
Start 88: pyFMCS
85/118 Test #88: pyFMCS ............................. Passed 1.42 sec
Start 89: FMCStest
86/118 Test #89: FMCStest ........................... Passed 0.21 sec
Start 90: testMolHash
87/118 Test #90: testMolHash ........................ Passed 0.21 sec
Start 91: pyMolHash
88/118 Test #91: pyMolHash .......................... Passed 0.23 sec
Start 92: testMMPA
89/118 Test #92: testMMPA ........................... Passed 0.21 sec
Start 93: pyMMPA
90/118 Test #78: pyMolAlign ......................... Passed 14.35 sec
91/118 Test #93: pyMMPA ............................. Passed 1.74 sec
Start 94: testStructChecker
Start 95: pyStructChecker
92/118 Test #94: testStructChecker .................. Passed 0.10 sec
93/118 Test #95: pyStructChecker .................... Passed 0.15 sec
Start 96: testReducedGraphs
Start 97: pyReducedGraphs
94/118 Test #97: pyReducedGraphs .................... Passed 0.12 sec
95/118 Test #96: testReducedGraphs .................. Passed 0.12 sec
Start 98: trajectoryTest
Start 99: testSLNParse
96/118 Test #98: trajectoryTest ..................... Passed 0.16 sec
97/118 Test #99: testSLNParse ....................... Passed 0.16 sec
Start 100: pySLNParse
Start 101: pyGraphMolWrap
98/118 Test #100: pySLNParse ......................... Passed 0.20 sec
Start 102: pyTestConformerWrap
99/118 Test #102: pyTestConformerWrap ................ Passed 0.20 sec
Start 103: pyTestTrajectory
100/118 Test #103: pyTestTrajectory ................... Passed 0.60 sec
Start 104: pyTestThreads
101/118 Test #104: pyTestThreads ...................... Passed 1.45 sec
Start 105: testQuery
102/118 Test #105: testQuery .......................... Passed 0.30 sec
Start 106: testMatCalc
103/118 Test #106: testMatCalc ........................ Passed 0.21 sec
Start 107: pyMatCalc
104/118 Test #107: pyMatCalc .......................... Passed 0.50 sec
Start 108: pySimDivPickers
105/118 Test #108: pySimDivPickers .................... Passed 3.02 sec
Start 109: pyRanker
106/118 Test #109: pyRanker ........................... Passed 0.14 sec
Start 110: testChemicalFeatures
107/118 Test #110: testChemicalFeatures ............... Passed 0.30 sec
Start 111: pyFeatures
108/118 Test #111: pyFeatures ......................... Passed 0.30 sec
Start 112: pythonTestDbCLI
109/118 Test #101: pyGraphMolWrap ..................... Passed 8.75 sec
Start 113: pythonTestDirML
110/118 Test #113: pythonTestDirML .................... Passed 6.53 sec
Start 114: pythonTestDirDataStructs
111/118 Test #114: pythonTestDirDataStructs ........... Passed 0.91 sec
Start 115: pythonTestDirDbase
112/118 Test #115: pythonTestDirDbase ................. Passed 0.50 sec
Start 116: pythonTestDirSimDivFilters
113/118 Test #116: pythonTestDirSimDivFilters ......... Passed 0.19 sec
Start 117: pythonTestDirVLib
114/118 Test #117: pythonTestDirVLib .................. Passed 0.51 sec
Start 118: pythonTestDirChem
115/118 Test #112: pythonTestDbCLI .................... Passed 12.67 sec
116/118 Test #75: testDistGeomHelpers ................ Passed 52.92 sec
117/118 Test #77: testMolAlign ....................... Passed 78.98 sec
118/118 Test #118: pythonTestDirChem ..................***Failed 40.60 sec
Errors while running CTest
....

Ran 4 tests in 0.031s

OK
......

Ran 6 tests in 0.031s

OK
....[16:07:34]

Pre-condition Violation
valence not defined for atoms not associated with molecules
Violation occurred on line 267 in file /home/rdkit/bld/rdkit_1494777495800/work/Code/GraphMol/Atom.cpp
Failed Expression: dp_mol

.

Ran 5 tests in 0.007s

OK
....

Ran 4 tests in 0.006s

OK
..

Ran 2 tests in 0.007s

OK
......................

Ran 22 tests in 0.025s

OK
.....s.................ss

Ran 25 tests in 0.102s

OK (skipped=3)
..s

Ran 3 tests in 0.125s

OK (skipped=1)
...................................

Ran 35 tests in 1.056s

OK
....

Ran 4 tests in 0.013s

OK
.

Ran 1 test in 0.007s

OK
......

Ran 6 tests in 0.025s

OK
...

Ran 3 tests in 0.045s

OK
.ss.ss.......

Ran 13 tests in 0.786s

OK (skipped=4)
...[16:07:38] WARNING: More than one matching pattern found - picking one
[16:07:38] WARNING: More than one matching pattern found - picking one
.[16:07:38] WARNING: More than one matching pattern found - picking one
..

Ran 6 tests in 0.061s

OK
........

Ran 8 tests in 0.084s

OK
.....

Ran 5 tests in 3.380s

OK
[16:07:42] WARNING: Omitted undefined stereo
[16:07:42] WARNING: Proton(s) added/removed
.....

Ran 5 tests in 8.343s

InChI write Summary: 1164 identical, 0 suffix variance, 17 reasonable

InChI read Summary: 620 identical, 0 variance, 561 reasonable variance
....

Ran 4 tests in 2.088s

OK
......

Ran 6 tests in 0.286s

OK
Traceback (most recent call last):
File "UnitTestPandasTools.py", line 12, in
from rdkit.Chem import PandasTools
File "/home/rdkit/bld/rdkit_1494777495800/work/rdkit/Chem/PandasTools.py", line 154, in
from pandas.core import format as fmt # older versions
ImportError: cannot import name format
..

Ran 2 tests in 0.000s

OK
UnitTestDocTestsChem.py:5: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.
from rdkit.Chem import MCS, FragmentMatcher, MACCSkeys, Descriptors, TemplateAlign
/home/rdkit/bld/rdkit_1494777495800/work/rdkit/Chem/MCS.py:1: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.

This work was funded by Roche and generously donated to the free

OK (skipped=1)
..........

Ran 10 tests in 0.425s

OK
..[16:08:14] reaction has no reactants
[16:08:14] reaction has no products
[16:08:14] initialization failed
[16:08:14] reaction has no reactants
[16:08:14] reaction has no products
.

Ran 3 tests in 0.020s

OK
................[16:08:14] ERROR:
[16:08:14] ERROR:
.

Ran 17 tests in 0.026s

OK
!!! TEST FAILURE: python UnitTestPandasTools.py {}
Exception TypeError: "'NoneType' object is not callable" in <function _removeHandlerRef at 0x7f4b48a6b668> ignored

99% tests passed, 1 tests failed out of 118

Total Test time (real) = 115.91 sec

The following tests FAILED:
118 - pythonTestDirChem (Failed)
BUILD START: rdkit-conda_version-np111py27_1
(actual version deferred until further download or env creation)

The following NEW packages will be INSTALLED:

boost:           1.56.0-py27_3      local
bzip2:           1.0.6-3                 
cairo:           1.14.6-nox_0       local [nox]
cmake:           3.6.3-0                 
curl:            7.52.1-0                
eigen:           3.2.8-2            local
expat:           2.1.0-0                 
fontconfig:      2.11.1-6                
freetype:        2.5.5-2                 
jbig:            2.1-0                   
jpeg:            9b-0                    
libiconv:        1.14-0                  
libpng:          1.6.27-0                
libtiff:         4.0.6-3                 
libxml2:         2.9.4-0                 
mkl:             2017.0.1-0              
ncurses:         5.9-10                  
nox:             1.0-0              local
numpy:           1.11.3-py27_0           
olefile:         0.44-py27_0             
openssl:         1.0.2k-2                
pandas:          0.20.1-np111py27_0      
pillow:          4.1.1-py27_0            
pip:             9.0.1-py27_1            
pixman:          0.32.6-0                
pkg-config:      0.28-1                  
python:          2.7.13-0                
python-dateutil: 2.6.0-py27_0            
pytz:            2017.2-py27_0           
readline:        6.2-2                   
requests:        2.14.2-py27_0           
setuptools:      27.2.0-py27_0           
six:             1.10.0-py27_0           
sqlite:          3.13.0-0                
tk:              8.5.18-0                
wheel:           0.29.0-py27_0           
xz:              5.2.2-1                 
zlib:            1.2.8-3

Applying patch: u'/home/rdkit/conda-rdkit/rdkit/rdpaths.patch'
Patch level ambiguous, selecting least deep
BUILD START (revised): rdkit-conda_version-np111py27_1
Package: rdkit-conda_version-np111py27_1
source tree in: /home/rdkit/bld/rdkit_1494777495800/work
Traceback (most recent call last):
File "/home/rdkit/miniconda/bin/conda-build", line 6, in
sys.exit(conda_build.cli.main_build.main())
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 334, in main
execute(sys.argv[1:])
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 325, in execute
noverify=args.no_verify)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/api.py", line 97, in build
need_source_download=need_source_download, config=config)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/build.py", line 1518, in build_tree
config=config)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/build.py", line 1143, in build
utils.check_call_env(cmd, env=env, cwd=src_dir)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/utils.py", line 628, in check_call_env
return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
File "/home/rdkit/miniconda/lib/python2.7/site-packages/conda_build/utils.py", line 624, in _func_defaulting_env_to_os_environ
return func(_args, **kwargs)
File "/home/rdkit/miniconda/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e', '/home/rdkit/bld/rdkit_1494777495800/work/conda_build.sh']' returned non-zero exit status 8
The command '/bin/sh -c conda build boost --quiet --no-anaconda-upload && conda build nox --quiet --no-anaconda-upload && conda build cairo_nox --quiet --no-anaconda-upload && conda build cairocffi --quiet --no-anaconda-upload && conda build eigen --quiet --no-anaconda-upload && conda build rdkit --quiet --no-anaconda-upload && conda build ncurses --quiet --no-anaconda-upload && conda build postgresql --quiet --no-anaconda-upload && conda build rdkit-postgresql --quiet --no-anaconda-upload && conda build postgresql95 --quiet --no-anaconda-upload && conda build rdkit-postgresql95 --quiet --no-anaconda-upload && CONDA_PY=35 conda build boost --quiet --no-anaconda-upload && CONDA_PY=35 conda build nox --quiet --no-anaconda-upload && CONDA_PY=35 conda build cairo_nox --quiet --no-anaconda-upload && CONDA_PY=35 conda build cairocffi --quiet --no-anaconda-upload && CONDA_PY=35 conda build eigen --quiet --no-anaconda-upload && CONDA_PY=35 conda build rdkit --quiet --no-anaconda-upload && CONDA_PY=35 conda build postgresql --quiet --no-anaconda-upload && CONDA_PY=35 conda build rdkit-postgresql --quiet --no-anaconda-upload && CONDA_PY=35 conda build postgresql95 --quiet --no-anaconda-upload && CONDA_PY=35 conda build rdkit-postgresql95 --quiet --no-anaconda-upload && CONDA_NPY=110 conda build rdkit --quiet --no-anaconda-upload && CONDA_PY=35 CONDA_NPY=110 conda build rdkit --quiet --no-anaconda-upload' returned a non-zero code: 1
[sitzmann@green conda-rdkit]$

Test in `conda build rdkit` fails in Ubuntu 14.04

I followed the instruction in README and encountered the following error when I ran conda build rdkit. Let me know what kind of information is needed for investigation. Thanks in advance.

Environment:

Ubuntu 14.04
Use pyenv to install anaconda3 with conda 4.3.14

The following tests FAILED:
         42 - testMolWriter (SEGFAULT)
        111 - pythonTestDirML (Failed)
Errors while running CTest
Traceback (most recent call last):
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/bin/conda-build", line 6, in <module>
    sys.exit(conda_build.cli.main_build.main())
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 322, in main
    execute(sys.argv[1:])
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 313, in execute
    noverify=args.no_verify)
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/api.py", line 97, in build
    need_source_download=need_source_download, config=config)
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/build.py", line 1493, in build_tree
    config=config)
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/build.py", line 1132, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir)
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/utils.py", line 611, in check_call_env
    return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/conda_build/utils.py", line 607, in _func_defaulting_env_to_os_environ
    return func(_args, **kwargs)
  File "/home/delta/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e', '/home/delta/.pyenv/versions/anaconda3-4.3.0/conda-bld/rdkit_1488846112051/work/conda_build.sh']' returned non-zero exit status 8.

build fails on CentOS 6.4

The following tests FAILED:
6 - testFPB (ILLEGAL)
10 - pyFPB (ILLEGAL)

Digging through the entire build log I see no obvious errors.
Any thoughts on how to proceed?

postgressql95

I think the meta.yaml is incorrect

  fn: https://ftp.postgresql.org/pub/source/v9.5.2/postgresql-9.5.2.tar.bz2
  url: https://ftp.postgresql.org/pub/source/v9.5.2/postgresql-9.5.2.tar.bz2

should probably be

  fn: postgresql-9.5.2.tar.bz2
  url: https://ftp.postgresql.org/pub/source/v9.5.2/postgresql-9.5.2.tar.bz2

That got it to work for me at least.

Failure with conda build rdkit in Linux

I follow the instructions in https://github.com/rdkit/conda-rdkit/
But it constantly pumped out the error with

!!! TEST FAILURE: python PandasTools.py {}
!!! TEST FAILURE: python UnitTestPandasTools.py {}

98% tests passed, 2 tests failed out of 116

Total Test time (real) = 70.02 sec

The following tests FAILED:
111 - pythonTestDirML (Failed)
116 - pythonTestDirChem (Failed)
Errors while running CTest

Can someone help with it?

conda-build v3.0 breaks the rdkit recipes

It seems that the mechanism used to manage the package version in the rdkit and rdkit-postgresql* recipes is no longer supported. Once the build has completed, packaging fails with the error below:

ValueError: support for __conda_version__ has been removed as of Conda-build 3.0.Try Jinja templates instead: http://conda.pydata.org/docs/building/meta-yaml.html#templating-with-jinja

py-boost runtime should be = not >=

conda-rdkit/rdkit/meta.yaml

Line 37 in 92017d1

- py-boost >=1.65.1

This pulls the wrong rdkit version at runtime if a new one exists.

ArgumentError: Python argument types in rdkit.Chem.rdMolDescriptors.CalcCrippenDescriptors(NoneType) did not match C++ signature:

I installed rdkit using conda as mentioned on #84.

conda create -c rdkit -n my-rdkit-env rdkit=2019.09.2

Then, when I try to use MolLogP:

df['mol'] = df.inchi.apply(MolFromInchi)
df['logp'] = df.mol.apply(Descriptors.MolLogP)

rdkit always fail with:

---------------------------------------------------------------------------
ArgumentError                             Traceback (most recent call last)
<ipython-input-7-d1600f543d97> in <module>
----> 1 df['logp'] = df.mol.apply(Descriptors.MolLogP)

~/anaconda3/envs/my-rdkit-env/lib/python3.6/site-packages/pandas/core/series.py in apply(self, func, convert_dtype, args, **kwds)
   4043             else:
   4044                 values = self.astype(object).values
-> 4045                 mapped = lib.map_infer(values, f, convert=convert_dtype)
   4046 
   4047         if len(mapped) and isinstance(mapped[0], Series):

pandas/_libs/lib.pyx in pandas._libs.lib.map_infer()

~/anaconda3/envs/my-rdkit-env/lib/python3.6/site-packages/rdkit/Chem/Crippen.py in <lambda>(*x, **y)
    168 _pyMolMR.version = "1.1.0"
    169 
--> 170 MolLogP = lambda *x, **y: rdMolDescriptors.CalcCrippenDescriptors(*x, **y)[0]
    171 MolLogP.version = rdMolDescriptors._CalcCrippenDescriptors_version
    172 MolLogP.__doc__ = """ Wildman-Crippen LogP value

ArgumentError: Python argument types in
    rdkit.Chem.rdMolDescriptors.CalcCrippenDescriptors(NoneType)
did not match C++ signature:
    CalcCrippenDescriptors(RDKit::ROMol mol, bool includeHs=True, bool force=False)

The C++ version used I suppose is the one shipped by anaconda:

py-boost                  1.67.0           py36h04863e7_4

The complete list:

# packages in environment at /home/muammar/anaconda3/envs/my-rdkit-env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
ase                       3.19.0                   pypi_0    pypi
attrs                     19.3.0                     py_0  
backcall                  0.1.0                    py36_0  
blas                      1.0                         mkl  
bleach                    3.1.0                    py36_0  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2019.11.27                    0  
cairo                     1.14.12              h8948797_3  
certifi                   2019.11.28               py36_0  
cycler                    0.10.0                   pypi_0    pypi
decorator                 4.4.1                      py_0  
defusedxml                0.6.0                      py_0  
entrypoints               0.3                      py36_0  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1                h8a8886c_1  
glib                      2.63.1               h5a9c865_0  
gmp                       6.1.2                h6c8ec71_1  
icu                       58.2                 h9c2bf20_1  
importlib_metadata        1.3.0                    py36_0  
intel-openmp              2019.4                      243  
ipykernel                 5.1.3            py36h39e3cac_0  
ipython                   7.10.2           py36h39e3cac_0  
ipython_genutils          0.2.0                    py36_0  
jedi                      0.15.1                   py36_0  
jinja2                    2.10.3                     py_0  
jpeg                      9b                   h024ee3a_2  
json5                     0.8.5                      py_0  
jsonschema                3.2.0                    py36_0  
jupyter_client            5.3.4                    py36_0  
jupyter_core              4.6.1                    py36_0  
jupyterlab                1.2.4              pyhf63ae98_0  
jupyterlab_server         1.0.6                      py_0  
kiwisolver                1.1.0                    pypi_0    pypi
libboost                  1.67.0               h46d08c1_4  
libedit                   3.1                  heed3624_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
libpng                    1.6.37               hbc83047_0  
libsodium                 1.0.16               h1bed415_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.1.0                h2733197_0  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.9                hea5a465_1  
markupsafe                1.1.1            py36h7b6447c_0  
matplotlib                3.1.2                    pypi_0    pypi
mistune                   0.8.4            py36h7b6447c_0  
mkl                       2019.4                      243  
mkl-service               2.3.0            py36he904b0f_0  
mkl_fft                   1.0.15           py36ha843d7b_0  
mkl_random                1.1.0            py36hd6b4f25_0  
more-itertools            8.0.2                      py_0  
nbconvert                 5.6.1                    py36_0  
nbformat                  4.4.0                    py36_0  
ncurses                   6.0                           0    rdkit
notebook                  6.0.2                    py36_0  
numpy                     1.17.4           py36hc1035e2_0  
numpy-base                1.17.4           py36hde5b4d6_0  
olefile                   0.46                     py36_0  
openssl                   1.0.2u               h7b6447c_0  
pandas                    0.25.3           py36he6710b0_0  
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py36_1  
parso                     0.5.2                      py_0  
pcre                      8.43                 he6710b0_0  
pexpect                   4.7.0                    py36_0  
pickleshare               0.7.5                    py36_0  
pillow                    6.2.1            py36h34e0f95_0  
pip                       19.3.1                   py36_0  
pixman                    0.38.0               h7b6447c_0  
prometheus_client         0.7.1                      py_0  
prompt_toolkit            3.0.2                      py_0  
ptyprocess                0.6.0                    py36_0  
py-boost                  1.67.0           py36h04863e7_4  
pygments                  2.5.2                      py_0  
pyparsing                 2.4.6                    pypi_0    pypi
pyrsistent                0.15.6           py36h7b6447c_0  
python                    3.6.5                hc3d631a_2  
python-dateutil           2.8.1                      py_0  
pytz                      2019.3                     py_0  
pyzmq                     18.1.0           py36he6710b0_0  
rdkit                     2019.09.2.0      py36hc20afe1_1    rdkit
readline                  7.0                  ha6073c6_4  
scipy                     1.4.1                    pypi_0    pypi
send2trash                1.5.0                    py36_0  
setuptools                42.0.2                   py36_0  
six                       1.13.0                   py36_0  
sqlite                    3.23.1               he433501_0  
terminado                 0.8.3                    py36_0  
testpath                  0.4.4                      py_0  
tk                        8.6.8                hbc83047_0  
tornado                   6.0.3            py36h7b6447c_0  
traitlets                 4.3.3                    py36_0  
wcwidth                   0.1.7                    py36_0  
webencodings              0.5.1                    py36_1  
wheel                     0.33.6                   py36_0  
xz                        5.2.4                h14c3975_4  
zeromq                    4.3.1                he6710b0_3  
zipp                      0.6.0                      py_0  
zlib                      1.2.11               h7b6447c_3  
zstd                      1.3.7                h0b5b093_0

What is the right version of C++/Boost to be installed? I would appreaciate any help.

Conda package rdkit-postgresql downgrades my rdkit conda package

I try to install the postgresql cartridge via conda install rdkit-postgresql but this does not work with the latest version of RDKit 2019.03.3

It either installs 2018 version if run with

conda create -c rdkit -n rdkit2 rdkit rdkit-postgresql

Or if I try -- I get a ton of dependency errors

conda install -c rdkit -n rdkit rdkit-postgresql

rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> numpy[version='>=1.12'] -> mkl_fft[version='>=1.0.6,<2.0a0'] -> python[version='>=2.7,<2.8.0a0'] -> readline[version='>=7.0,<8.0a0']
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> numpy[version='>=1.12'] -> mkl_fft[version='>=1.0.6,<2.0a0'] -> python[version='>=2.7,<2.8.0a0'] -> sqlite[version='>=3.27.2,<4.0a0'] -> libedit[version='>=3.1.20181209,<3.2.0a0']
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> numpy[version='>=1.12'] -> mkl_fft[version='>=1.0.6,<2.0a0'] -> python[version='>=2.7,<2.8.0a0'] -> tk[version='>=8.6.8,<8.7.0a0']
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> numpy[version='>=1.12'] -> mkl_random[version='>=1.0.2,<2.0a0']
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> pandas
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> pillow -> jpeg[version='>=9b,<10a']
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> pillow -> libtiff[version='>=4.0.10,<5.0a0'] -> zstd[version='>=1.3.7,<1.3.8.0a0']
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> pillow -> olefile
rdkit/linux-64::rdkit==2019.03.3.0=py37hc20afe1_1 -> py-boost
RDKit Version: 2019.03.3
Platform: Ubuntu 18.04

conda build of Release_2016_09_2 on Kubuntu 16.10 64bit fails

Hi, the RDkit build of Release_2016_09_2 fails on Kubuntu 16.10 64bit with the following (not very informative) error:

[ 61%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so
[ 61%] Built target rdchem
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
Command failed: /bin/bash -x -e /home/pahl/anaconda3/conda-bld/work/conda_build.sh

The build of boost 1.56.0 by the respective recipe wass successful.

Any ideas?

Kind regards,
Axel

Boost in conda anaconda channel not compatible with rdkit.

The boost library available in the anaconda channel (built using this recipe I think) doesn't link to python and so doesn't work for rdkit. This is a problem, as conda install rdkit no longer generates a working install in a fresh environment (at least on linux) as the anaconda boost is installed in preference to that bundled with rdkit (the anaconda boost is selected as the package to satisfy the dependency, as it is version 1.57, not sure if it still would be if the rdkit channel boost was the same version as anacondas).

We can either set a requirement somewhere in meta.yml for using the rdkit bundled boost (such as requiring boost-1.56), or modifying the anaconda boost recipe - I think this may be better in the long run.

Note that conda install rdkit will work if you previously conda install boost==1.56.

Moving builds over to bioconda

Hi,

is there any interest in moving these great recipes over to the bioconda channel? The bioconda community is trying hard to create sustainable packages that runs on most if not all distributions, including HPC. Moreover they have invested a lot of effort to test every PR and package before submitting automatically to anaconda.

https://github.com/bioconda/bioconda-recipes

Let me know what you think or if you have anything against me pushing these recopies also to bioconda.

Thanks,
Bjoern

Issues with pandas on Ubuntu.

I have just installed rdkit through conda in two different machines—one with Windows 10 and another one with Ubuntu 18.04. The environment in Windows runs well just out of the box. But the environment in Ubuntu is producing an 'NoneType' object has no attribute 'core' error (see below).

Conda installed pandas 1.0.1 on my windows machine. I was able to fix the issue on my Ubuntu machine, reverting pandas to version 0.23.4. Is there a better solution?

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-4-b77fb46287cc> in <module>
      3 
      4 # Read SDF
----> 5 moldf = PandasTools.LoadSDF(file);
      6 # Rename ROMol
      7 moldf = moldf.rename(columns={'ROMol': 'Mol'})

~/anaconda3/envs/my-rdkit-env/lib/python3.6/site-packages/rdkit/Chem/PandasTools.py in LoadSDF(filename, idName, molColName, includeFingerprints, isomericSmiles, smilesName, embedProps)
    358   if close is not None:
    359     close()
--> 360   RenderImagesInAllDataFrames(images=True)
    361   return pd.DataFrame(records, index=indices)
    362 

~/anaconda3/envs/my-rdkit-env/lib/python3.6/site-packages/rdkit/Chem/PandasTools.py in RenderImagesInAllDataFrames(images)
    282   '''
    283   if images:
--> 284     pd.core.frame.DataFrame.to_html = patchPandasHTMLrepr
    285   else:
    286     pd.core.frame.DataFrame.to_html = defPandasRendering

AttributeError: 'NoneType' object has no attribute 'core'

Update the boost version to 1.62

Are we constrained to stick with boost 1.56 or could we go ahead and update to the most recent version?

Import error in jupyter and pycharm (Windows10)

Dear representative,

I installed according to the procedure. It works normally on the command line.
However, importing RDkit with jupyter or pycharm will cause DLL import error.
Changing the environment variable or working space does not change this error.

c:\programdata\anaconda3\envs\my-rdkit-env\lib\site-packages\rdkit_init_.py in ()
1 try:
----> 2 from .rdBase import rdkitVersion as version
3 except ImportError:
4 version = 'Unknown'
5 raise
ImportError: DLL load failed:

Sincerely,**

Default rdkit from conda uses outdated version

Hello,

Installing rdkit via conda on Ubuntu 18.04 as follows:

conda create -c rdkit -n my-rdkit-env rdkit

tries to install an older version for me: rdkit-2017.09.1

However, the following works fine for getting the latest:
conda create -c rdkit -n my-rdkit-env rdkit=2019.09.2

Thanks
Vin

rdkit builds fail because of sourceforge.net downloads?

Hi Greg,

I don't know but either something weird is going on or things from sourceforge.net are broken.

The Docker build of rdkit_containers/docker/centos7_base fails with this message:

Step 13/25 : RUN wget --quiet https://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.bz2 && tar xjf boost_1_63_0.tar.bz2 ---> Running in f4896efda246 bzip2: (stdin) is not a bzip2 file. tar: Child returned status 2 tar: Error is not recoverable: exiting now The command '/bin/sh -c wget --quiet https://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.bz2 && tar xjf boost_1_63_0.tar.bz2' returned a non-zero code: 2

The reason why I tried this, is: I wanted to attempt some basic and independent builds after this file https://github.com/spitzenidee/postgresql_rdkit/blob/master/Dockerfile failed with the following message (it worked for me nicely until recently):

== Using strict rotor definition Downloading http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar... CMake Error at Code/cmake/Modules/RDKitUtils.cmake:174 (MESSAGE): The md5 checksum for /opt/rdkit/External/AvalonTools/AvalonToolkit_1.2.0.source.tar is incorrect; expected: 092a94f421873f038aa67d4a6cc8cb54, found: cb530d737c8f2d1023797cf0587b4e05 Call Stack (most recent call first): External/AvalonTools/CMakeLists.txt:29 (downloadAndCheckMD5)

If I skip the AvalonTools, it works again (BTW, for what are the AvalonTools used?)

Thanks,
Markus

switch to using pillow instead of pil for all python versions

Now that pillow is fully supported in anaconda I don't think there's any reason to keep using PIL.

Package not found on macOS: rdkit-postgresql

Trying to conda install -c rdkit rdkit-postgresql fails on macOS:

PackageNotFoundError: Package not found: Conda could not find '

Meanwhile rdkit package can be installed fine.

Appreciative RDKit user here (usually on Linux), just flagging this issue in anticipation of the 2017.03 release. Thanks.

psql error

Description:

When attempting to start psql, including to execute: psql -c 'create extension rdkit' emolecules

I am getting the following error:
psql: error while loading shared libraries: libncursesw.so.6: cannot open shared object file: No such file or directory

I am using:
-UBUNTU 18.04 LTS installed as Windows Subsystem for Linux (WSL)
-rdkit: 2019.03.3
-Python 3.6.5 |Anaconda, Inc.

Thanks for your help.

Valery

Conda build fails on MacOS

The
conda build rdkit
command fails with this error:

Exceeded max retries, giving upLock error:
LOCKERROR: It looks like conda is already doing something.
The lock [u'/Users/admin/anaconda2/pkgs/fontconfig-2.11.1-py27_3.tar.bz2.pid48308.conda_lock'] was found. Wait for it to finish before continuing.
If you are sure that conda is not running, remove it and try again.
You can also use: $ conda clean --lock

Lots of test failed on CentOS7

Lots of tests failed on CentOS7
when conda build rdkit

The following tests FAILED:
          3 - pyAvalonTools (Failed)
          9 - pyBV (Failed)
         10 - pyDiscreteValueVect (Failed)
         18 - pyAlignment (Failed)
         22 - pyForceFieldConstraints (Failed)
         24 - pyDistGeom (Failed)
         37 - pyDepictor (Failed)
         42 - testMolWriter (SEGFAULT)
         50 - pyChemReactions (Failed)
         51 - pyChemReactionEnumerations (Failed)
         52 - pyChemReactionSanitize (Failed)
         57 - pyFilterCatalog (Failed)
         59 - pyFragCatalog (Failed)
         63 - pyMolDescriptors (Failed)
         66 - pyPartialCharges (Failed)
         68 - pyMolTransforms (Failed)
         72 - pyForceFieldHelpers (Failed)
         74 - pyDistGeom (Failed)
         76 - pyMolAlign (Failed)
         78 - pyChemicalFeatures (Failed)
         80 - pyShapeHelpers (Failed)
         82 - pyMolCatalog (Failed)
         84 - pyMolDraw2D (Failed)
         86 - pyFMCS (Failed)
         89 - pyMolHash (Failed)
         91 - pyMMPA (Failed)
         93 - pyStructChecker (Failed)
         95 - pyReducedGraphs (Failed)
         98 - pySLNParse (Failed)
         99 - pyGraphMolWrap (Failed)
        100 - pyTestConformerWrap (Failed)
        101 - pyTestTrajectory (Failed)
        102 - pyTestThreads (Failed)
        105 - pyMatCalc (Failed)
        106 - pySimDivPickers (Failed)
        107 - pyRanker (Failed)
        109 - pyFeatures (Failed)
        110 - pythonTestDbCLI (Failed)
        111 - pythonTestDirML (Failed)
        112 - pythonTestDirDataStructs (Failed)
        114 - pythonTestDirSimDivFilters (Failed)
        115 - pythonTestDirVLib (Failed)
        116 - pythonTestDirChem (Failed)
Errors while running CTest
Command failed: /bin/bash -x -e /home/guest/guest12/anaconda2/conda-bld/rdkit_1481389733299/work/conda_build.sh

rdkit build fail

Trying to build RDKit and have got down to one failed test from six (improvement from adding pandas<0.2 to meta.yaml and using a Python 5.3 environment), but still have one failed test #111 'pythonTestDirML'.

Can anyone tell me how to solve it?

Currently using:
Python 3.5.4 :: Anaconda custom (64-bit)
conda-build 3.2.2
Ubuntu 16.04.3 LTS

Test output (all tests prior, pass):


### ```
108/116 Test #111: pythonTestDirML ..................***Failed   12.64 sec
.......
----------------------------------------------------------------------
Ran 7 tests in 0.681s
OK
............
----------------------------------------------------------------------
Ran 12 tests in 0.308s
OK
F
======================================================================
FAIL: test1_Issue163 (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "UnitTestAnalyzeComposite.py", line 59, in test1_Issue163
    self.assertTrue(res[0][0] == 'BALABANJ')
AssertionError: False is not true
----------------------------------------------------------------------
Ran 1 test in 0.043s
FAILED (failures=1)
...
----------------------------------------------------------------------
Ran 3 tests in 0.001s
OK
.......
----------------------------------------------------------------------
Ran 7 tests in 0.001s
OK
...
----------------------------------------------------------------------
Ran 3 tests in 0.353s
OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.003s
OK
/home/marks/projects/MDC/anaconda3/conda-bld/rdkit_1516631519704/work/rdkit/ML/Data/DataUtils.py:199: FutureWarning: split() requires a non-empty pattern match.
  resArr = expr2.split(inLine)[:-1]
.../home/marks/projects/MDC/anaconda3/conda-bld/rdkit_1516631519704/work/rdkit/ML/Data/DataUtils.py:163: FutureWarning: split() requires a non-empty pattern match.
  resArr = expr2.split(inLine)
...
----------------------------------------------------------------------
Ran 6 tests in 0.004s
OK
............
----------------------------------------------------------------------
Ran 12 tests in 0.002s
OK
.....
----------------------------------------------------------------------
Ran 5 tests in 0.034s
OK
........
----------------------------------------------------------------------
Ran 8 tests in 0.001s
OK
testing AddChild: 
testing GetName: 
testing GetChildren: 
testing PruneChild: 
testing tree equals: 
testing pickled tree equals: 
testing deepcopy on trees: 
testing list membership: ...
----------------------------------------------------------------------
Ran 3 tests in 0.103s
OK
use selection with replacement: 
test the results of CrossValidation: 
test that the CrossValidationDriver runs: ......
----------------------------------------------------------------------
Ran 6 tests in 0.019s
OK
testing basic tree growth: 
testing basic tree classification: 
testing multivalued tree growth: 
testing basic tree growth (python entropy code): 
testing tree classification (python entropy code): 
testing multivalued tree growth (python entropy code): .
----------------------------------------------------------------------
Ran 1 test in 0.007s
OK
.........
----------------------------------------------------------------------
Ran 9 tests in 0.014s
OK
testing tree comparisons: 
testing tree1: 
testing tree2: 
testing classification: 
testing unused variables: 
a more extensive test of the cmp stuff using hand-built trees: 
a more extensive test of the cmp stuff using pickled trees: 
try recycling descriptors: 
try random forests descriptors: ....
----------------------------------------------------------------------
Ran 4 tests in 0.107s
OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.002s
OK
testing calculation of a single descriptor: 
testing calculation of multiple descriptors: ...
----------------------------------------------------------------------
Ran 3 tests in 0.009s
OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.006s
OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.299s
OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.580s
OK
.....
----------------------------------------------------------------------
Ran 5 tests in 0.256s
OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.010s
OK
...
----------------------------------------------------------------------
Ran 3 tests in 0.552s
OK
testing backprop training on and: 
testing backprop training on a linear function: 
testing backprop training on or: ..
----------------------------------------------------------------------
Ran 2 tests in 0.000s
OK

testing Burges empirical risk bound: 
testing Cherkassky empirical risk bound: !!! TEST FAILURE:  python UnitTestAnalyzeComposite.py {}

        Start 112: pythonTestDirDataStructs
109/116 Test  #83: moldraw2DTest1 ...................   Passed   41.63 sec
        Start 113: pythonTestDirDbase
110/116 Test #113: pythonTestDirDbase ...............   Passed    1.21 sec
        Start 114: pythonTestDirSimDivFilters
111/116 Test #112: pythonTestDirDataStructs .........   Passed    2.11 sec
        Start 115: pythonTestDirVLib
112/116 Test #114: pythonTestDirSimDivFilters .......   Passed    0.70 sec
        Start 116: pythonTestDirChem
113/116 Test #115: pythonTestDirVLib ................   Passed    3.21 sec
114/116 Test #110: pythonTestDbCLI ..................   Passed   23.57 sec
115/116 Test  #75: testMolAlign .....................   Passed  116.37 sec
116/116 Test #116: pythonTestDirChem ................   Passed   62.71 sec

99% tests passed, 1 tests failed out of 116

Total Test time (real) = 202.15 sec

The following tests FAILED:
        111 - pythonTestDirML (Failed)
Errors while running CTest

conda build fails with latest anaconda on Windows 10

The conda build using the current version of Anaconda (4.3.1) fails in the conda build boost stage due to a mismatch in the Python version (the build recipe does not recognize Python 3.6).

(K:\Anaconda3-64\conda-bld\boost_1494361869825_b_env) K:\Anaconda3-64\conda-bld\boost_1494361869825\work>if "3.6" == "2.7" (set BOOST_TOOLSET=msvc-9.0 ) else if "3.6" == "3.4" (set BOOST_TOOLSET=msvc-10.0 ) else if "3.6" == "3.5" (set BOOST_TOOLSET=msvc-14.0 ) else (
echo "Unexpected version of python"
exit 1
)
"Unexpected version of python"

Error building conda-rdkit behind a firewall

Hello,

I'm trying to build binary RDKit packages on conda. As I'm behind a firewall I've configured the corresponding proxy server in both the environment (export {https,http,ftp}_proxy=https://user:password@proxy:port/) and the conda configuration file (.condarc).

Everything goes smoothly on running the "conda build rdkit" until the program tries to build the InChI support when, apparently, curl is not able to download the source code from http://www.inchi-trust.org:

-- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR)
Downloading http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (6) Could not resolve host: www.inchi-trust.org
CMake Error at Code/cmake/Modules/RDKitUtils.cmake:194 (MESSAGE):
  The md5 checksum for
  /software/anaconda2/conda-bld/rdkit_1566988838557/work/External/INCHI-API/INCHI-1-SRC.zip
  is incorrect; expected: ccc497c7e6ced1521a6953d859e49af4, found:
  d41d8cd98f00b204e9800998ecf8427e
Call Stack (most recent call first):
  Code/cmake/Modules/FindInchi.cmake:50 (downloadAndCheckMD5)
  CMakeLists.txt:172 (find_package)

-- Configuring incomplete, errors occurred!

However, I've tried curl manually and it works just fine:

curl -O http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   178  100   178    0     0   2373      0 --:--:-- --:--:-- --:--:--  2373

Is there any trick to bypass this situation?

RDKit for python 3.6

Would it be possible to have a version for python 3.6 available? (ideally in https://anaconda.org/rdkit).

Need some way to lock the version of boost to what we build against

Boost version numbers end up in the library names, so using DLLs from newer boost versions does not work.

This is connected to this rdkit issue.
rdkit/rdkit#1957

review the dependency from ICU

if the boost package is linking the ICU libraries, the recipe should pick them from anaconda and specify the build/runtime dependency.

(ref deepchem/deepchem#857 although I'm not fully clear if rdkit was the actual cause in that case)

conda and $RDBASE

When a standard conda RDKit build is done in an environment, it doesn't look like $RDBASE is created. This causes some pieces of the RDKit to fail at runtime:

>>> from rdkit.Chem import SaltRemover
>>> sr = SaltRemover.SaltRemover()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/glandrum/anaconda/envs/rdkit-py3/lib/python3.4/site-packages/rdkit/Chem/SaltRemover.py", line 48, in __init__
    self._initPatterns()
  File "/home/glandrum/anaconda/envs/rdkit-py3/lib/python3.4/site-packages/rdkit/Chem/SaltRemover.py", line 67, in _initPatterns
    inF = open(self.defnFilename,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'Data/Salts.txt'
>>> import os
>>> os.environ['RDBASE']
''

It does look like the build creates the correct directories in $ENV/share/RDKit, but $RDBASE isn't being set.

Note: I experienced this after running a build, I didn't actually do a "conda install rdkit" yet

RuntimeError when using numpy <1.13

Hi,

I have troubles working with the newest version of RDKit together with not-the-newest version of numpy.

It seems like rdkit package requires numpy=1.13, although it is not stated in the dependencies. The simplest example that doesn't work (tested on Ubuntu 16.04):

conda create -c rdkit -n rdkit_test python=3.6 numpy=1.12 rdkit=2017.09.1
source activate rdkit_test

and then in Python I get this error:

>>> import rdkit
>>> from rdkit import Chem
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/martas/miniconda3/envs/rdkit_test/lib/python3.6/site-packages/rdkit/Chem/__init__.py", line 25, in <module>
    from rdkit.Chem.rdmolops import *
SystemError: initialization of rdmolops raised unreported exception

Note that importing rdkit doesn't raise the exception. Also, when I use Python 2.7 I get slightly different error:

>>> from rdkit import Chem
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/martas/miniconda3/envs/rdkit_py27/lib/python2.7/site-packages/rdkit/Chem/__init__.py", line 25, in <module>
    from rdkit.Chem.rdmolops import *
ImportError: numpy.core.multiarray failed to import

When I create the environment with numpy v. 1.13 everything works fine (checked in Py3.6 and Py2.7).

RDkit 2020.09.4 release issues with Conda-forge build and other modules (Python3-saml)

What:
Fresh install on Ubuntu 20.04 with miniconda3, python 3.7 RDKit installs ok but Python3-saml has become incompatible.
First noted with 2020.09.04 but after experiments found first version where break occurred - 2020.03.6

Terse:
Demonstrated with
python3-saml

Some issues with rpy2 but:

$ conda install -c conda-forge rpy2

appears to install and work ok on Ubuntu 20.04 (not Mac OSX)

TERSE:
Up to, and including rdkit==2019.09.3 python3-saml==1.9.0 would install and work together

With a python 3.7 condo env:

$ conda install -c conda-forge rdkit==2020.03.6 -y
$ conda install -c conda-forge python3-saml

Python3-saml failed to install with multiple conflicts
- there are references to Python 3.8 - did we miss something and RDkit is Python3.8 now?

rdkit==2020.09.3 and rdkit==2020.09.4 also are incompatible

Good News - There is compatibility with (this is a section of our build script)

pip install mod_wsgi==4.7.1
pip install -i https://pypi.anaconda.org/OpenEye/simple OpenEye-toolkits
conda install -c conda-forge rpy2 -y
conda install -c conda-forge scikit-learn==0.21.3 -y
conda install -c conda-forge matplotlib==3.3.3 -y

For addition clarity:

pip install python3-saml

does not work - this is PEP517 related but it does reveal that libxml2 and libxmlsec might be the issue
[Spent about a day try to work around this one without success]

These are the results on Ubuntu 20, on Mac OSX Catalina things are worse (that will required another day of experimentation - Rdkit 2018 appears stable here with all other module combinations)

Verbose (-vvv)

These are the experiments I performed focussing on just RDkit and Python3-saml for reproducibility.

Experiment details:

All builds were:
- performed on Amazon Web Services (AWS) Ubuntu 20.04 instances (unless otherwise stated), using t2.large
- MINICONDA="Miniconda3-4.5.12-Linux-x86_64.sh"
- with Python 3.7 environments
- as root user

After each experiment the AWS instance was terminated and a new instance used each time.

Control - 1 - establish older version of RDkit installs with

Ubuntu 20.04

pip install --upgrade pip
conda install -c conda-forge rdkit==2019.03.1.0 -y
conda install -c conda-forge python3-saml

Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.9.2

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /root/miniconda3/envs/test_rdkit

added / updated specs:
- python3-saml

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
defusedxml-0.6.0           |             py_0          22 KB  conda-forge
isodate-0.6.0              |             py_1          25 KB  conda-forge
libgcrypt-1.8.7            |       h36c2ea0_0         610 KB  conda-forge
libgpg-error-1.41          |       h2531618_0         235 KB
libtool-2.4.6              |    h58526e2_1007         497 KB  conda-forge
libxml2-2.9.10             |       hb55368b_3         1.2 MB
libxmlsec1-1.2.29          |       h8fe84ac_0         516 KB
libxslt-1.1.34             |       hc22bd24_0         432 KB
lxml-4.6.2                 |   py37h9120a33_0         1.2 MB
python3-saml-1.9.0         |             py_0         227 KB
xmlsec-1.3.3               |   py37h0e8eec6_0         289 KB
------------------------------------------------------------
                                       Total:         5.2 MB

The following NEW packages will be INSTALLED:

defusedxml conda-forge/noarch::defusedxml-0.6.0-py_0
isodate conda-forge/noarch::isodate-0.6.0-py_1
libgcrypt conda-forge/linux-64::libgcrypt-1.8.7-h36c2ea0_0
libgpg-error pkgs/main/linux-64::libgpg-error-1.41-h2531618_0
libtool conda-forge/linux-64::libtool-2.4.6-h58526e2_1007
libxmlsec1 pkgs/main/linux-64::libxmlsec1-1.2.29-h8fe84ac_0
libxslt pkgs/main/linux-64::libxslt-1.1.34-hc22bd24_0
lxml pkgs/main/linux-64::lxml-4.6.2-py37h9120a33_0
python3-saml pkgs/main/noarch::python3-saml-1.9.0-py_0
xmlsec pkgs/main/linux-64::xmlsec-1.3.3-py37h0e8eec6_0

The following packages will be UPDATED:

libxml2 conda-forge::libxml2-2.9.9-h13577e0_2 --> pkgs/main::libxml2-2.9.10-hb55368b_3

....lots

conda list

...
python-dateutil 2.8.1 py_0 conda-forge
python3-saml 1.9.0 py_0
python_abi 3.7 1_cp37m conda-forge
pytz 2021.1 pyhd8ed1ab_0 conda-forge
rdkit 2019.03.1 py37h9c20d5c_0 conda-forge
readline 8.1 h27cfd23_0
...

SUCCESSFUL build***

Control 2 - newer version of RDkit and Python3-saml

Ubuntu 20.04

pip install --upgrade pip
conda install -c conda-forge rdkit==2019.09.3 -y
conda install -c conda-forge python3-saml

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.9.2

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /root/miniconda3/envs/test_rdkit

added / updated specs:
- python3-saml

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
boost-1.70.0               |   py37h9de70de_1         337 KB  conda-forge
boost-cpp-1.70.0           |       ha2d47e9_1        21.1 MB  conda-forge
cairo-1.16.0               |    h18b612c_1001         1.5 MB  conda-forge
defusedxml-0.6.0           |             py_0          22 KB  conda-forge
fontconfig-2.13.1          |    he4413a7_1000         327 KB  conda-forge
gettext-0.19.8.1           |       h5e8e0c9_1         3.5 MB  conda-forge
icu-58.2                   |    hf484d3e_1000        22.6 MB  conda-forge
isodate-0.6.0              |             py_1          25 KB  conda-forge
libgcrypt-1.8.7            |       h36c2ea0_0         610 KB  conda-forge
libgpg-error-1.39          |       he1b5a44_0         269 KB  conda-forge
libtool-2.4.6              |    h58526e2_1007         497 KB  conda-forge
libxml2-2.9.9              |       h13577e0_2         1.3 MB  conda-forge
libxmlsec1-1.2.29          |       h8fe84ac_0         516 KB
libxslt-1.1.33             |       h7d1a2b0_0         426 KB
lxml-4.4.1                 |   py37h7ec2d77_0         1.5 MB  conda-forge
python3-saml-1.9.0         |             py_0         227 KB
rdkit-2019.09.3            |   py37hb31dc5d_0        23.7 MB  conda-forge
xmlsec-1.3.3               |   py37h0e8eec6_0         289 KB
------------------------------------------------------------
                                       Total:        78.8 MB

The following NEW packages will be INSTALLED:

defusedxml conda-forge/noarch::defusedxml-0.6.0-py_0
gettext conda-forge/linux-64::gettext-0.19.8.1-h5e8e0c9_1
isodate conda-forge/noarch::isodate-0.6.0-py_1
libgcrypt conda-forge/linux-64::libgcrypt-1.8.7-h36c2ea0_0
libgpg-error conda-forge/linux-64::libgpg-error-1.39-he1b5a44_0
libtool conda-forge/linux-64::libtool-2.4.6-h58526e2_1007
libxmlsec1 pkgs/main/linux-64::libxmlsec1-1.2.29-h8fe84ac_0
libxslt pkgs/main/linux-64::libxslt-1.1.33-h7d1a2b0_0
lxml conda-forge/linux-64::lxml-4.4.1-py37h7ec2d77_0
python3-saml pkgs/main/noarch::python3-saml-1.9.0-py_0
xmlsec pkgs/main/linux-64::xmlsec-1.3.3-py37h0e8eec6_0

The following packages will be DOWNGRADED:

boost 1.72.0-py37h48f8a5e_1 --> 1.70.0-py37h9de70de_1
boost-cpp 1.72.0-h9359b55_3 --> 1.70.0-ha2d47e9_1
cairo 1.16.0-h3fc0475_1005 --> 1.16.0-h18b612c_1001
fontconfig 2.13.1-h7e3eb15_1002 --> 2.13.1-he4413a7_1000
icu 67.1-he1b5a44_0 --> 58.2-hf484d3e_1000
libxml2 2.9.10-h68273f3_2 --> 2.9.9-h13577e0_2
rdkit 2019.09.3-py37he9dd633_1 --> 2019.09.3-py37hb31dc5d_0

conda list

...
python-dateutil 2.8.1 py_0 conda-forge
python3-saml 1.9.0 py_0
python_abi 3.7 1_cp37m conda-forge
pytz 2021.1 pyhd8ed1ab_0 conda-forge
rdkit 2019.09.3 py37hb31dc5d_0 conda-forge
readline 8.1 h27cfd23_0
setuptools 52.0.0 py37h06a4308_0
...

SUCCESSFUL build***

Expt 1 - moving newer version of RDkit and Python3-saml

Ubuntu 20.04

export MINICONDA="Miniconda3-py37_4.8.3-Linux-x86_64.sh"
wget https://repo.continuum.io/miniconda/$MINICONDA
bash $MINICONDA -b -p /root/miniconda3
export PATH="/root/miniconda3/bin:$PATH"
conda create -n test_rdkit python=3.7 -y
source activate test_rdkit
pip install --upgrade pip
conda install -c conda-forge rdkit==2020.03.6 -y
conda install -c conda-forge python3-saml

!!!!!!!!UNSUCCESSFUL INSTALL!!!!!!!!

Conda detects conflicts between RDkit install and Python3-SAML

Expt 2 - newer version of RDkit and Python3-saml

Ubuntu 20.04

#Conda init bash
#

source activate test_rdkit

pip install --upgrade pip
conda install -c conda-forge rdkit==2020.09.3 -y
conda install -c conda-forge python3-saml

!!!!!!!!UNSUCCESSFUL INSTALL!!!!!!!!

--> Fails to install python3-saml and reports a huge amount of output - see included file.

Expt 3 - latest version of RDkit and Python3-saml

Ubuntu 20.04

!!!!!!!!UNSUCCESSFUL INSTALL!!!!!!!!

--> Fails to install python3-saml and reports a huge amount of output - see included file.

Expt 4 - Install Python3-saml first then RDkit - check if it works the other way

Ubuntu 20.04

export MINICONDA="Miniconda3-py37_4.8.3-Linux-x86_64.sh"
wget https://repo.continuum.io/miniconda/$MINICONDA
bash $MINICONDA -b -p /root/miniconda3
export PATH="/root/miniconda3/bin:$PATH"
conda create -n test_rdkit python=3.7 -y
source activate test_rdkit
pip install --upgrade pip
conda install -c conda-forge python3-saml -y
conda install -c conda-forge rdkit==2020.09.4 -y

!!!!!!!!UNSUCCESSFUL INSTALL!!!!!!!!

Enable parallel builds

Doing conda build rdkit on windows takes forever since it doesn't use parallel builds. I think nmake isn't really capable of doing this, though there's some information here:
http://stackoverflow.com/questions/601970/how-do-i-utilise-all-the-cores-for-nmake

Sounds like using JOM could work, and I know that creating vcproj files with cmake (using `-G"Visual Studio 1X". where X is whatever you have installed) and then building using MSBuild.exe works, but I'm not going to pretend to be an expert on building on windows, so I don't know what the implications might be.

Any thoughts?

Explicit valence for atom # 1 O, 3, is greater than permitted

Hello everyone, please i need help
I want to generate the xyz coordinates of all possible functionalized naphthalene molecules where the functionalized positions are the (1,4,6,9) positions and the possible functional groups are (COOH, C(CN)2, Br, Me, COCH3 and NO2)" with python. I wrote this code:

from rdkit import Chem
from rdkit.Chem import AllChem
naphtalene = Chem.MolFromSmiles("c1c2ccccc2ccc1")
functional_groups = [Chem.MolFromSmiles("C(=O)O"), Chem.MolFromSmiles("C(CN)C#N"), Chem.MolFromSmiles("Br"), Chem.MolFromSmiles("C"), Chem.MolFromSmiles("C(=O)C"), Chem.MolFromSmiles("N(=O)[O]")]
patterns = []
for i in [0, 3, 5, 8]:
for fg in functional_groups:
patt = Chem.MolFromSmiles("" + Chem.MolToSmiles(fg))
m = AllChem.ReplaceSubstructs(naphtalene, patt, replaceAll = False)[0]
m = AllChem.ReplaceSubstructs(m, Chem.MolFromSmiles(""), Chem.MolFromSmiles("[H]"), replaceAll = False, replacementConnectionPoint = 0, useChirality = false)[0]
AllChem.Compute2DCoords(m)
patterns.append(m)
for p in patterns:
AllChem.EmbedMolecule(p)
print(Chem.MolToMolBlock(p))

But I get error

[00:36:31] Explicit valence for atom # 1 O, 3, is greater than permitted

ArgumentError Traceback (most recent call last)
Cell In [32], line 5
3 for fg in functional_groups:
4 patt = Chem.MolFromSmiles("" + Chem.MolToSmiles(fg))
----> 5 m = AllChem.ReplaceSubstructs(naphtalene, patt, replaceAll = False)[0]
6 m = AllChem.ReplaceSubstructs(m, Chem.MolFromSmiles(""), Chem.MolFromSmiles("[H]"), replaceAll = False, replacementConnectionPoint = 0, useChirality = false)[0]
7 AllChem.Compute2DCoords(m)

ArgumentError: Python argument types in
rdkit.Chem.rdmolops.ReplaceSubstructs(Mol, NoneType)
did not match C++ signature:
ReplaceSubstructs(RDKit::ROMol mol, RDKit::ROMol query, RDKit::ROMol replacement, bool replaceAll=False, unsigned int replacementConnectionPoint=0, bool useChirality=False)

I don't know how to fix the problem

2016.09.2 rdkit build error on fedora 25

On fedora 25, with gcc 6.2.1, the rdkit conda recipe fails with the following error

In file included from /home/ric/miniconda3/conda-bld/rdkit_1480453840975/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config.hpp:61:0, from /home/ric/miniconda3/conda-bld/rdkit_1480453840975/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/cstdint.hpp:36, from /home/ric/miniconda3/conda-bld/rdkit_1480453840975/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/multiprecision/cpp_int.hpp:11, from /home/ric/miniconda3/conda-bld/rdkit_1480453840975/work/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp:36: /home/ric/miniconda3/conda-bld/rdkit_1480453840975/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/multiprecision/cpp_int.hpp:181:4: error: right operand of shift expression ‘(1u << 63u)’ is >= than the precision of the left operand [-fpermissive] BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1)); ^ /home/ric/miniconda3/conda-bld/rdkit_1480453840975/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/multiprecision/cpp_int.hpp:401:4: error: right operand of shift expression ‘(1u << 63u)’ is >= than the precision of the left operand [-fpermissive] BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1)); ^ /home/ric/miniconda3/conda-bld/rdkit_1480453840975/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/multiprecision/cpp_int.hpp:548:4: error: right operand of shift expression ‘(1u << 63u)’ is >= than the precision of the left operand [-fpermissive] BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1)); ^ Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make:350: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o' failed

the version of boost required by the rdkit recipe on unix is boost 1.56.0

rdkit / conda-rdkit Goto Github PK

conda-rdkit's Introduction

RDKit

Community

Code

Web presence

Materials from user group meetings

Documentation

Installation

Binary distributions, anaconda, homebrew

Projects using RDKit

License

conda-rdkit's People

Contributors

Stargazers

Watchers

Forkers

conda-rdkit's Issues

demonstration of issue

versions of relevant things:

boost is installed however a more recent version:

this workaround worked several weeks ago on another clean install.

try installing a prior version:

snip

a masive list of stuff **

OK ......

.

OK ....

OK ..

OK ......................

OK .....s.................ss

OK (skipped=3) ..s

OK (skipped=1) ...................................

OK ....

OK .

OK ......

OK ...

OK .ss.ss.......

OK (skipped=4) ...[16:07:38] WARNING: More than one matching pattern found - picking one [16:07:38] WARNING: More than one matching pattern found - picking one .[16:07:38] WARNING: More than one matching pattern found - picking one ..

OK ........

OK .....

OK [16:07:42] WARNING: Omitted undefined stereo [16:07:42] WARNING: Proton(s) added/removed .....

InChI read Summary: 620 identical, 0 variance, 561 reasonable variance ....

OK ......

This work was funded by Roche and generously donated to the free

.............[16:07:55] WARNING: More than one matching pattern found - picking one [16:07:55] WARNING: More than one matching pattern found - picking one ........

OK ..

OK ..................

OK ...

OK ........

OK ..

OK ..

OK .

OK ........

OK ...

OK ...

OK ....

OK ......

OK ....

OK ....

OK ..........

OK .

OK ..........

OK .....

OK .....................

OK .

.

OK ..

OK ..

OK ...

OK ....

OK ..........

OK ssssss...s.....

OK (skipped=7) s

OK (skipped=1) ..........

OK ..[16:08:14] reaction has no reactants [16:08:14] reaction has no products [16:08:14] initialization failed [16:08:14] reaction has no reactants [16:08:14] reaction has no products .

OK ................[16:08:14] ERROR: [16:08:14] ERROR: .

I installed according to the procedure. It works normally on the command line. However, importing RDkit with jupyter or pycharm will cause DLL import error. Changing the environment variable or working space does not change this error.

c:\programdata\anaconda3\envs\my-rdkit-env\lib\site-packages\rdkit_init_.py in () 1 try: ----> 2 from .rdBase import rdkitVersion as version 3 except ImportError: 4 version = 'Unknown' 5 raise ImportError: DLL load failed:

Package Plan

OK
......

OK
....

OK
..

OK
......................

OK
.....s.................ss

OK (skipped=3)
..s

OK (skipped=1)
...................................

OK
....

OK
.

OK
......

OK
...

OK
.ss.ss.......

OK (skipped=4)
...[16:07:38] WARNING: More than one matching pattern found - picking one
[16:07:38] WARNING: More than one matching pattern found - picking one
.[16:07:38] WARNING: More than one matching pattern found - picking one
..

OK
........

OK
.....

OK
[16:07:42] WARNING: Omitted undefined stereo
[16:07:42] WARNING: Proton(s) added/removed
.....

InChI read Summary: 620 identical, 0 variance, 561 reasonable variance
....

OK
......

.............[16:07:55] WARNING: More than one matching pattern found - picking one
[16:07:55] WARNING: More than one matching pattern found - picking one
........

OK
..

OK
..................

OK
...

OK
........

OK
..

OK
..

OK
.

OK
........

OK
...

OK
...

OK
....

OK
......

OK
....

OK
....

OK
..........

OK
.

OK
..........

OK
.....

OK
.....................

OK
.

OK
..

OK
..

OK
...

OK
....

OK
..........

OK
ssssss...s.....

OK (skipped=7)
s

OK (skipped=1)
..........

OK
..[16:08:14] reaction has no reactants
[16:08:14] reaction has no products
[16:08:14] initialization failed
[16:08:14] reaction has no reactants
[16:08:14] reaction has no products
.

OK
................[16:08:14] ERROR:
[16:08:14] ERROR:
.

I installed according to the procedure. It works normally on the command line.
However, importing RDkit with jupyter or pycharm will cause DLL import error.
Changing the environment variable or working space does not change this error.

c:\programdata\anaconda3\envs\my-rdkit-env\lib\site-packages\rdkit_init_.py in ()
1 try:
----> 2 from .rdBase import rdkitVersion as version
3 except ImportError:
4 version = 'Unknown'
5 raise
ImportError: DLL load failed: