Aaron Virshup

This is a small view of the much larger issue of calculation caching. This is dependent on good semantic storage of calculation results, plus a way to determine whether two...

Master list of dependencies to update: - AmberTools (16 -> 17) - PySCF (1.1 -> 1.3) - OpenMM (7 -> 7.1) - OpenBabel (???) - Docker (keep up with latest)...

The following test should pass, currently fails: ```python mol = mdt.from_pdb('1YU8') sidechain_atoms = list(mol.residues[5].sidechain) m2 = mol.copy() sa2 = list(m2.residues[5].sidechain) for atom in sa2: assert atom.molecule is m2 ```

Wrong bonding between residues surrounding missing ones

1

This is a residue that appears right before several missing residues: ```python mol = mdt.from_pdb('3p3k') res = mol.residues[46] ``` MDT currently shows a bond between this and the next available...

Most output formats destroy non-standard bond information

1

```python mol = mdt.from_smiles('CCCC') print mol.write('pdb') ``` Gives ``` HETATM 1 C0 UNL 1 0.928 -0.017 -0.007 0.00 0.00 C [...] HETATM 14 H9 UNL 1 0.809 2.183 1.709 0.00...

We're getting clashes and overlaps in the generated 3D structures for big complicated ring systems. To wit: ```python artim = mdt.from_inchi('InChI=1S/C15H22O5/c1-8-4-5-11-9(2)12(16)17-13-15(11)10(8)6-7-14(3,18-13)19-20-15/h8-11,13H,4-7H2,1-3H3/t8-,9-,10+,11+,13-,14-,15-/m1/s1')') artim.draw() ``` gives  Need to detect these as...

git and hg: ignore tags that can't be normalized to version numbers

1

As discussed in #229, when determining the latest tag, it would be ideal to use a general, unambiguous test for whether or not to ignore a given SCM tag. For...

No tests yet, just a build and optional publishing step

Ribbons representation not displaying for DNA

4

To reproduce: ``` mol = mdt.build_dna_helix('ACTGCGTA') viewer = mol.draw(display=True) viewer.ribbon() ``` ## got:  ## Result with moldesign 0.7.2 / nbmolviz 0.6.5: 

Orbitals not showing up

4

This is in the most recent `master` fb2eee08faca347444dc7bbf85de2d8792ccd6f2 and also MDT. You'll also need to check out the `visualization_json` branch of MDT, or this will throw an exception because of...