restraintmaker.tools_Rdkit package
Submodules
restraintmaker.tools_Rdkit.Rdkit_Functions module
- This module is linking the restraintmaker functionality to rdkit
MCS search
molecule ring filter
etc.
- restraintmaker.tools_Rdkit.Rdkit_Functions._calc_pca_without_scaling(coords, dims, verbose: bool = True)[source]
Analogous to _calc_pca, but it does not do any coordinate transfromations. (Rescaling etc. This should be done before calling this function. This will help save time, if the function is called many times
- restraintmaker.tools_Rdkit.Rdkit_Functions.mcs_selection(mols: List[rdkit.Chem.rdchem.Mol], min_MCS_size: int = 6) List[source]
The selection is getting only the MCS of pairwise molecules
- Warnings: results do not seem reasonable YET.
TODO: Check what exactly is not going as expected
- Parameters
mols (t.List[Chem.Mol]) – molecules
min_MCS_size – what is the minimal MCS size
verbose (bool) – loud and noisy
- Return type
List
- restraintmaker.tools_Rdkit.Rdkit_Functions.parse_pdb_blocks_to_rdkit(pdb_mols: str) List[rdkit.Chem.rdchem.Mol][source]
Convert a pdblock to and rdkit-Mol
- Parameters
pdb_mols (str)
- Returns
an rdkit mol obj
- Return type
rdkit.Mol
- restraintmaker.tools_Rdkit.Rdkit_Functions.ring_atom_filter(selected: list, mols: List[rdkit.Chem.rdchem.Mol], selected_mols: dict) List[int][source]
Filter molecules for rings and remove non-ring atoms from the selection
- Parameters
mols (t.List[Chem.Mol]) – molecules to select from
- Returns
list of stil selected atom indices, inside a ring
- Return type
t.List[int]