biosimspace

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Support for openff-bespokefit

9

It would be desirable to make it easier for users to combine molecules parameterised with openff-bespokefit with other system components. This would lower barriers for benchmarking studies with forcefield parameters...

jmichel80

alchemlyb dependency pulling in invalid Jaxlib version on Python 3.9 and 3.10

1

Despite our package building against the correct version of `jaxlib`, i.e.: ``` jax: 0.4.19-pyhd8ed1ab_0 conda-forge jaxlib: 0.4.19-cpu_py39h45b9b01_0 conda-forge ``` when installing the Python 3.9 development version of BioSimSpace you end...

lohedges

[BUG] Protein parametrization fails if detects a disulfide bridge between reduced cysteine residues (CYS and not CYX)

2

**Describe the bug** When using BSS.Parameters.parametrise() on a protein system, If BioSimSpace detects a disulfide bridge between cystein residues, it will add a "bond" command to the leap script: ...

cespos

Matching atoms and merging ring systems (fused rings, different hybridisation states) - issues

8

Hello! I'm currently matching and merging molecules for MCL1 ligands. The basic code used to replicate these is: ```python # ligands lig0 = "lig_27" lig1 = "lig_42" # options prematch...

annamherz

Faster MCS Calculation

7

The current matchAtoms() uses the entire molecule to get MCS, a simple idea to accelerate it is to get MCS for heavy atoms and then match up hydrogens hanging off...

kexul

This PR introduces protein FEP functionality to BioSimSpace and allows for creating of hybrid protein/peptide systems with single or multiple simultaneous modifications, which can include point mutations to canonical or...

akalpokas

[BUG] BSS.Convert.toRDKit() appears to lose stereochemical information

9

Hey again, I think I've encountered a bug with the Convert module (or I might be overlooking a crucial bit of code). Converting from a BioSimSpace / Sire mol to...

noahharrison64

Fix issue #330

4

This PR closes #330 by preserving SMILES based molecule properties when parameterising. Previously, `BioSimSpace.Convert.smiles` was only used to create an intermediate molecule during parameterisation, so any properties that were generated...

lohedges

Alchemical Transfer Method

1

This PR adds functionality for creating, running and analysing RBFE calculations using the Alchemical Transfer Method (AToM). Functionality is contained in a pair of key locations and is as follows:...

mb2055

Prepare systems with multiple ligands

9

**Is your feature request related to a problem? Please describe.** I was trying to prepare a system with a protein and 2 ligands (given as SDF files). However, both ligands...

cespos