Bart Bruininks

Volume from SDF

3

Hello developers, I would like to calculate the total volume of an arbitrary sphere based SDF object. For now I am casting the SDF to a mesh and then use...

Point cloud to SDF?

5

Dear developer, I am trying to convert a point cloud to an SDF object. I have an array of XYZs. I have been trying the following: ``` from sdf import...

adds vsites as bonds between base particles and vsite

4

Partially addresses #1954 Changes made in this Pull Request: - ITP reads vsites PR Checklist ------------ - [ ] Tests? - [ ] Docs? - [ ] CHANGELOG updated? -...

Raise better error in top-parser

3

**Describe the bug** Turorial brush lipids does not finish. Polyply 1.5.0. ``` polyply gen_coords -p system.top -o struct.gro -res PEO OHter -c bilayer_brush.gro -name test -box 8.0 8.0 33.0 -split...

parse_pragma cannot handle #include in .itps files which are in #include in the top

3

Hoi, It seems like the ITP reader cannot handle nested includes in the included itps in the top file. This is used (a lot) in Go models and in any...

Segmentation containment hierarchy

2

### Description When working with point clouds or voxel densities, it is often useful to ask for the content of a component. However, the definition of inside is not trivial...

Heya, Would it be an option to use a seed for the fudge factor and for all other random parts of insane? It would be really nice if it would...