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- IHMCIF
- https://github.com/ihmwg/IHMCIF
- Data dictionary
- Not included in PDB-Dev deployment directly
- python-ihm
- https://github.com/ihmwg/python-ihm/
- Used for reading and …
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Every action in Puppets should cause at most 2 DOM operations: one for removing what used to be there, and another for adding the new content.
I can test this with [MutationObserver](https://develope…
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On testing 4.2 beta User Matt Helgeson expressed dismay that the functional forms for orientational distributions were still the same as those for polydispersity. The issue being that the current dist…
smk78 updated
2 years ago
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I need to rapidly minimize conformations of organic molecules that are anywhere from 250-500 atoms in size (lignin polymers). I was using MMFF in RDKit before, but I would like to access the GPU accel…
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Code:
```
import jax
import jax.numpy as jnp
import numpy as np
import sys
import hoomd
import hoomd.md
from ecv.models import AutoEncoder
from ecv.models.encoders import MLP, EGNN
fr…
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We should add a contribution guideline including our programming style, for instance member functions start with lower case letter followed by camel case style for long function names. Suggestions of …
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Hi,
I installed all the dependencies via conda in an environment called jtvae. Then, after cloning the repository, I ran:
```
(jtvae) hgraph2graph$ pip install .
```
But I got the following…
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@afalty and I just spoke about their hyperspectral image analysis routine and database. They have plans to make the database and analysis routine open source and want to see it applied in Open Specy. …
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According to Polychrom documentation, the timestep of simulation is always fs scale (`integrator="langevin"`). But I need simulation in ms scale to fit experiment data, just setting timestep=1e12 fs w…
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**Expectation**
The atom indices of an OpenMM Topology match those of its associated System, this includes virtual sites.
**Current status**
Creating an OpenMM Topology with virtual sites put…