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Home modified by Greg Landrum

Greg Landrum — Fri, 24 Apr 2020 06:23:49 -0000

--- v1
+++ v2
@@ -1,8 +1,13 @@
-Welcome to your wiki!
+A collection of cheminformatics and machine-learning software written in C++ and Python.

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java.

-The wiki uses [Markdown](/p/rdkit/wiki/markdown_syntax/) syntax.
+Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.

+Please note that the development of RDKit has been moved to [github](https://github.com/rdkit/rdkit).
+
+If you have questions please join the [RDKit-discuss](https://sourceforge.net/projects/rdkit/lists/rdkit-discuss) mailing list and ask there or use the [github issue tracker](https://github.com/rdkit/rdkit/issues). Questions left here or sent to the admin's sourceforge address cannot be answered.
+
+[[project_screenshots]]
 [[project_admins]]
 [[download_button]]

Discussion for Home page

Srinivas Hanumsetty — Fri, 24 Apr 2020 06:17:09 -0000

Hello

I installed the new version of rdkit 2020.03.1 using confa forge. When do the import rdkit, I got an error message ModuleNotFoundError: No module named 'rdkit'. I am using python 3.6 and installed it on MACOS catalina. I am going throguht he posts and found that I need to link the python and rdkit using RDBASE. I am not sure how do I do that . Can I get some help.

Discussion for Home page

َAmmar Hasan — Mon, 02 Mar 2020 16:10:28 -0000

Hi every one,
I'm new to Rdkit
I need to generate fingerprint in integrer/count form
I try manys but always I got the messeg:

DataStructs.ConvertToNumpyArray(fps2[i], arr[i])
ArgumentError: Python argument types in
rdkit.DataStructs.cDataStructs.ConvertToNumpyArray(UIntSparseIntVect, numpy.ndarray)
did not match C++ signature:
ConvertToNumpyArray(RDKit::DiscreteValueVect bv, boost::python::api::object destArray)
ConvertToNumpyArray(ExplicitBitVect bv, boost::python::api::object destArray)

My Code as below:
import numpy as np
from rdkit.Chem import AllChem as Chem
from rdkit import DataStructs
from rdkit.Chem.AtomPairs import Pairs

suppl = Chem.SDMolSupplier('5ht3ligs.sdf')

fps1 = [Chem.RDKFingerprint(x, fpSize=1024, minPath=1, maxPath=4) for x in suppl]
fps2 = [Chem.GetHashedMorganFingerprint(x, radius=2, nBits=1024) for x in suppl]
fps3 = [Chem.GetMorganFingerprint(x, radius=2, useCounts= True) for x in suppl]
fps4 = [Pairs.GetAtomPairFingerprintAsIntVect(x) for x in suppl]

arr = np.zeros((4,1024), dtype = np.int8)

for i in range(0,len(suppl)):
DataStructs.ConvertToNumpyArray(fps2[i], arr[i])

print(arr)

I am also wondering if there is a direct way in rdkit to print the fingerprint directly to the text file similar to "Chem.SDwrite" but to save fingerprint. However, If I can convert the count fingerprint to an array then I can use python code to save to text file.
Any help will be highly appreciated.
looking forward to your help.

Thanks
Ammar

Discussion for Home page

OMR ATTR — Sun, 17 Mar 2019 04:48:16 -0000

Hi,
I'm novel user of RDKit. I have a question:
How can I import a set of molecules in an SDF file with their 3D conformations preserved ?

Thank you

Discussion for Home page

Vlad Vassiliev — Wed, 04 Jul 2018 06:54:02 -0000

Hi RDKit Gurus,
While checking the sp3 chiral centers I found out that for a molecule
161
-OEChem-03231300073D

48 49 0 1 0 0 0 0 0999 V2000
1.9053 -2.5277 0.5377 P 0 0 1 0 0 0 0 0 0 0 0 0
3.6553 -0.1610 0.5790 P 0 0 2 0 0 0 0 0 0 0 0 0
2.8753 2.0660 -1.1917 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.1084 -1.2538 -2.9903 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.2015 -3.1270 0.1545 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7029 -2.8790 -0.4812 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.4976 3.0662 -0.6946 O 0 0 0 0 0 0 0 0 0 0 0 0
2.5228 -1.1432 -0.0205 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1619 -2.0776 1.9022 O 0 0 0 0 0 0 0 0 0 0 0 0
2.9151 -3.6241 0.7151 O 0 0 0 0 0 0 0 0 0 0 0 0
3.8594 0.9330 -0.5921 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0083 -1.0430 0.5105 O 0 0 0 0 0 0 0 0 0 0 0 0
3.3493 0.4186 1.9286 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7154 2.6570 -2.4398 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7000 1.2120 -1.8994 O 0 0 0 0 0 0 0 0 0 0 0 0
2.4145 3.0864 -0.1931 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.5515 0.7828 0.4148 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1631 0.5362 -1.0715 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.6788 0.8788 2.0068 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7099 1.9587 1.3157 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7308 0.7069 3.2807 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.3726 1.5204 0.8798 C 0 0 1 0 0 0 0 0 0 0 0 0
-2.4780 1.7558 -0.3278 C 0 0 1 0 0 0 0 0 0 0 0 0
-2.9608 -0.4708 -0.9714 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6297 -1.7159 -1.7557 C 0 0 2 0 0 0 0 0 0 0 0 0
-4.1752 -0.5370 -0.0744 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6284 -2.6255 -1.0551 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.1515 2.3565 0.0668 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3165 -1.9161 -0.7304 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4313 1.1663 2.1968 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7280 2.4914 1.2483 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9632 2.4631 -1.0137 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5561 -2.2655 -1.9574 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.9608 -1.2069 0.7644 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.0130 -0.9687 -0.6314 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.9935 1.3053 -0.3420 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.4095 -3.4895 -1.6944 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4318 -1.2733 0.1479 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0310 -1.3079 -1.5706 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2280 2.2368 1.5897 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.8277 -0.8037 -3.4657 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.0178 -3.5993 -0.0825 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2481 0.9359 3.4140 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1713 0.1185 3.9796 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6991 -1.9374 2.7109 H 0 0 0 0 0 0 0 0 0 0 0 0
5.8303 -0.6831 0.9068 H 0 0 0 0 0 0 0 0 0 0 0 0
3.3643 3.4354 -2.9225 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9251 1.6855 -2.2701 H 0 0 0 0 0 0 0 0 0 0 0 0
1 6 1 0 0 0 0
1 8 1 0 0 0 0
1 9 1 0 0 0 0
1 10 2 0 0 0 0
2 8 1 0 0 0 0
2 11 1 0 0 0 0
2 12 1 0 0 0 0
2 13 2 0 0 0 0
3 11 1 0 0 0 0
3 14 1 0 0 0 0
3 15 1 0 0 0 0
3 16 2 0 0 0 0
4 25 1 0 0 0 0
4 41 1 0 0 0 0
5 27 1 0 0 0 0
5 42 1 0 0 0 0
6 29 1 0 0 0 0
7 28 2 0 0 0 0
9 45 1 0 0 0 0
12 46 1 0 0 0 0
14 47 1 0 0 0 0
15 48 1 0 0 0 0
17 22 1 0 0 0 0
17 26 1 0 0 0 0
17 36 1 0 0 0 0
18 23 1 0 0 0 0
18 24 2 0 0 0 0
19 22 1 0 0 0 0
19 30 2 0 0 0 0
20 28 1 0 0 0 0
20 30 1 0 0 0 0
20 40 1 0 0 0 0
21 30 1 0 0 0 0
21 43 1 0 0 0 0
21 44 1 0 0 0 0
22 23 1 0 0 0 0
22 31 1 0 0 0 0
23 28 1 0 0 0 0
23 32 1 0 0 0 0
24 25 1 0 0 0 0
24 26 1 0 0 0 0
25 27 1 0 0 0 0
25 33 1 0 0 0 0
26 34 1 0 0 0 0
26 35 1 0 0 0 0
27 29 1 0 0 0 0
27 37 1 0 0 0 0
29 38 1 0 0 0 0
29 39 1 0 0 0 0
M END

Atom 2 (phosphorus) has symbol "S". However, according to "RULES FOR THE NOMENCLATURE OF ORGANIC CHEMISTRY. SECTION E: STEREOCHEMISTRY. (RECOMMENDATIONS 1974)" page 28, the double and triple bonds are supposed to be splitted and the phantom atoms should be generated.
In this particular case, the bond P=O should become O-P-O-P. After adding a phantom phosphorus atom to Oxygen the P(2) atom becomes "R".

My question is: what is the proper way to treat such cases?

Thanks,
Vlad

WikiPage Home modified by Greg Landrum

Greg Landrum — Fri, 17 Aug 2012 05:45:08 -0000

Welcome to your wiki! This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/rdkit/wiki/markdown_syntax/) syntax. [[project_admins]] [[download_button]]