coordgenlibs

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Really slow performance with some macrocycles

8

We found an issue when using coordgen with rdkit. When activating coordgen, it is extremely slow to work with such chiral macrocycles. Removing the chirality from the atoms makes it...

bjonnh-work

Add missing dependencies for test_coordgen

1

It will fix #116

jyhpsycho

Failed to build test_coordgen on static mode

1

How to reproduce: 1) Build static maeparser, and install on ../libmaeparser-1.2.4-220427 2) Clone current repository. 3) Create some build directory and chdir into it. 4) Run following command to configure...

jyhpsycho

Hi, my system is CentOS7. when I install the coordgen, there is an error as follows: ``` make -j install [ 85%] Building CXX object example_dir/CMakeFiles/example.dir/example.cpp.o [ 90%] Linking CXX...

lh12565

Poor result for constrained coord generation in rapamycin derivative.

1

Hi, I am calling CoordGen via RDKit, and have had a problem with constrained generation of coords for a rapamycin analogue using rapamycin as the template. The discussion is here:...

DavidACosgrove

The coordinates generated for this molecule are all NaN: `C1C=CC=C2C1=CSC=C3C(=O)OOOC(=O)C(=CC(=O)N3)OC2=O` This was the molecule which caused the crash in #106

greglandrum

This one was reported by @lucasmorin222 in the RDKit tracker (https://github.com/rdkit/rdkit/issues/4845), but I've confirmed that it's a coordgen problem. I don't have a straight reproducible for coordgen, but this bit...

greglandrum

rdCoordGen.AddCoords returning empty conformer for large system

2

Originally reported [here](https://github.com/rdkit/rdkit/issues/4325) I do not have a standalone example for this failure, but the coordgen call made by RDKit in this case is returning an empty conformer. ``` mol...

jasondbiggs

add template for norbornane

2

added template, also modified the ring detection algorithm so that norbornane triggers the template search

ZontaNicola

Distorted depiction

9

I found a combination of ring systems that yields a distorted depiction: ``` from rdkit import Chem from rdkit.Chem import rdDepictor rdDepictor.SetPreferCoordGen(True) Chem.MolFromSmiles("CC1C2CCC1CC(c1cccc3cc(-c4ccc5cccc(S)c5c4)sc13)C2") ```  Interestingly, removing either the methyl...

ptosco