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When I search a Protein in PDB Bank, the result could be viewed by ligand, is there any way to retrieve these ligand SMILES by pypdb? 

In the examples of [exploring label relationships](http://scikit.ml/labelrelations.html#Detecting-communities-in-Label-Relations-Graph), when I use the ordinary random forest model with a simple multitask setting, I can get the accuracy score of 0.30. But the...

checkpointing for model sharding

1

I split my model on two GPUs and use checkpointing to reduce memory usage, but I still got an OOM error when calling `backward()` , it seem like all the...

Recently, I've been reproduce the Freesolv result by YANK, I've encounterd lots of `NAN` in my experiments, here I'd like to conclude some solutions I've founded. 1. For some molecules,...

Two stage RESP fit

3

Hi, As far as I know, the standard resp fit schedule need two steps fit. Here only one step was performed, is that enough?

Add parameters to merge region of interest

11

Hi, this PR adds parameters for the merge function, allowing users select regions of interest to merge, which might be useful for modeling protein mutation and covalent binding. A unit...

Implement of the soft bond potential

2

See https://github.com/michellab/Sire/pull/364 for detail.

Hi guys, I cloned the repo and tried to run the following code provided in the paper, but it complained: ``` File "/root/group_ceph/espaloma/example.py", line 3, in dataset = esp.data.dataset.GraphDataset.load('gen2').view(batch_size=128) File...

stage2_helper failed when molecule contained atom 'Cl' or 'Br'

6

See http://www.psicode.org/psi4manual/master/_modules/psi4/driver/qcdb/parker.html, only ``` 'H': 1, 'C': 4, 'N': 3, 'O': 2, 'F': 1, 'P': 3, 'S': 2, ``` was allowed.

Hi, I'd like to update my plugin when a new object is loaded in PyMOL, a watch process is created for this task: ```python def find_proteins(): """ Find all proteins...