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martimunicoy / peleffy

The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.

Home Page:https://martimunicoy.github.io/peleffy

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Molecule from SMILES is unnamed

martimunicoy opened this issue · comments

commented

Description

When an offpele Molecule is initialized from a SMILES tag, no name is set to it. This behavior can cause some problems later when generating the template files.

Solution

We should assign a default name in Molecule objects.

commented

Solution 2

A new parameter for Molecule called name could help. In this way, the user could always choose a custom name for the molecule. When this parameter is not given, then, the name could be retrieved from the PDB file (like we are currently doing). Otherwise, a default name like UNL should be set.