Re: [Rdkit-discuss] Rdkit atom indexing vs indexing in written pdb file

2017-02-01 Thread Susan Leung
Thank you very much Andrew! Indeed, I did not spot the pattern - how silly of me! From: Andrew Dalke [da...@dalkescientific.com] Sent: 01 February 2017 16:49 To: Susan Leung Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Rdkit atom

Re: [Rdkit-discuss] substructure of a fingerprint position

2017-02-01 Thread George Papadatos
https://iwatobipen.wordpress.com/2017/01/08/get-bit-information-with-rdkit/ George. Sent from my giPhone > On 26 Jan 2017, at 11:02, Gonzalo Colmenarejo > wrote: > > Hi, > > is there a way in RDKit to retrieve the substructure(s) corresponding to a > (hashed

[Rdkit-discuss] ctest fails

2017-02-01 Thread 鈴木 倫太郎
Dear All, I have been used RDKit 2015_03_1 with self-build version of python 2.7 and boost 1.62 on CentOS 5.11. Now I tried to built and install 2016_09_3 in the same environment and I got 13 errors after ctest. 88% tests passed, 13 tests failed out of 112 The following tests FAILED:

Re: [Rdkit-discuss] ctest fails

2017-02-01 Thread 鈴木 倫太郎
Dear Paolo, Thank you for your response. I built boost with the following commands. $ ./bootstrap.sh --prefix=/usr/local/boost_1_62_0 --with-python=/usr/local/bin/python --with-python-root=/usr/local $ ./b2 threading=multi /usr/local/bin/python is my self-built version of Python 2.7. The

[Rdkit-discuss] C++ MolPickler

2017-02-01 Thread David Cosgrove
Hi All, I've got as far as 'Preserving Molecules' in the 'Getting Started with C++' document I'm writing, and it appears that the MolPickler doesn't write properties into the pickle. Is that right? If so, it means the molecule name goes missing, which is an issue when putting multiple molecules

Re: [Rdkit-discuss] Rdkit atom indexing vs indexing in written pdb file

2017-02-01 Thread Andrew Dalke
Dear Susan, If I understand what's going on correctly, you have run across the difference between 0-based and 1-based indexing. See https://en.wikipedia.org/wiki/Zero-based_numbering . RDKit, like most programming libraries and languages, index based on an offset from the beginning, so 0

[Rdkit-discuss] Rdkit atom indexing vs indexing in written pdb file

2017-02-01 Thread Susan Leung
Dear all, I am producing rdkit conformers and writing them to pdb files but am finding the atom indexing in rdkit is different from the written pdb. I would like this because I want to do a substructure search (using rdkit) to give me a handle on these atoms in the pdbfile. Apologies if this