rdCoordGen.AddCoords returning empty conformer for large system

[jasondbiggs]

I have coordgen set as the default layout function for systems with many rings, and this large molecule triggers that, but the conformer returned is empty in this case.

mol = MolFromSmiles('OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc23)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc23)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc23)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc23)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1OP(=S)(O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc23)C[C@@H]1O')
rdCoordGen.AddCoords(mol)

for x in range(5):
    pos = mol.GetConformer().GetAtomPosition(x)
    print(pos.x, pos.y, pos.z)

0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0

Obviously this molecule is large and difficult to lay out in 2D, but I would have expected AddCoords to return -1 to indicate failure.

For what it's worth, I am finding the avalon tools to be the best layout for these larger biomolecules.

>>>from rdkit import rdBase
>>>rdBase.rdkitVersion

 "2021.03.1"

[greglandrum]

This seems likely to be a coordgen bug, can you please create an issue for it here? https://github.com/schrodinger/coordgenlibs/issues

[jasondbiggs]

@greglandrum reported. The only reason I reported here originally is I don't have a standalone example calling coordgen directly.

[greglandrum]

@greglandrum reported. The only reason I reported here originally is I don't have a standalone example calling coordgen directly.

oh, no worries, I wasn't complaining about you opening it here. I just wanted to be sure it was on the coordgen team's radar.

Thanks for creating that other issue.