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[WIP] Add support of SDF/MOL2 Files #22

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[WIP] Add support of SDF/MOL2 Files #22

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13 changes: 11 additions & 2 deletions mdonatello/mdonatello.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,8 @@ class MoleculeVisualizer:

def __init__(
self,
ag: mda.core.groups.AtomGroup,
name: str,
ag: str = None,
show_atom_indices: bool = False,
width: int = -1,
height: int = -1,
Expand All @@ -67,7 +68,15 @@ def __init__(
self.height = height
self.show_atom_indices = show_atom_indices

self.mol: Chem.Mol = ag.convert_to("RDKit")
self.name = name
self.ag = ag

if ".sdf" not in self.name and ".mol2" not in self.name:
self.u = mda.Universe(self.name)
if self.ag != None:
self.ag = u.select_atoms(f"resname {self.ag}")
self.mol: Chem.Mol = ag.convert_to("RDKit")

self.mol_noh: Chem.Mol = Chem.RemoveHs(self.mol)
AllChem.Compute2DCoords(self.mol_noh)

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