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Update README.md
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lucagl authored Mar 6, 2021
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Expand Up @@ -4,7 +4,7 @@ This script was originally conceived to build reliable databases of structures (
However, this tool could be handy in general. Indeed, is not always obvious how to identify the ligand within a pdb and the naming scheme can be cumbersome (combinations of Residue ID, Chain, Residue Name can represent a single ligand or not). I hope this script could help navigate through this.
Ligand names are fetched from the **binding MOAD database**: "http://bindingmoad.org/pdbrecords/index/" . Only valid ligands (according to MOAD's criteria) are considered.
The naming scheme is un-ambiguous and inspired from the binding MOAD database.
**CAREFUL**: if a (ligand) file with the same name exist,
*Note*: if a (ligand) file with the same name exist,
a number will be appended to the created ligand (pdb or xyz) file (see also below).

**NOTE**: The ligands extracted contain only HEAVY atoms (purged of hidrogens). Please, if this behavior is not always desiderable, write me a feedback to make it user-defined.
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