Merge pull request #125 from martimunicoy/bug_index

Fix bug PDB index
martimunicoy · Jan 22, 2021 · 0dcfff5 · 0dcfff5
2 parents 45bdcda + c99d82f
commit 0dcfff5
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diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -17,6 +17,9 @@ New features
 - `PR #119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Adds explanatory error message when using an invalid Impact Template in the from_impact_template method.
 - `PR #119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Supports Openforcefield-0.8.3 .
 
+Bugfixes
+""""""""
+- `PR #125 <https://github.com/martimunicoy/peleffy/pull/125>`_: A bad index slicing in the molecule.Molecule._pdb_checkup() is now fixed. 
 
 Tests added
 """""""""""

diff --git a/peleffy/topology/molecule.py b/peleffy/topology/molecule.py
@@ -176,9 +176,9 @@ def _pdb_checkup(self, path):
         with open(path) as pdb_file:
             for line in pdb_file:
                 if line.startswith('ATOM') or line.startswith('HETATM'):
-                    atom_id.append(line[13:16])
-                    res_name.append(line[18:20])
-                    res_id.append(line[23:26])
+                    atom_id.append(line[12:16])
+                    res_name.append(line[17:20])
+                    res_id.append(line[22:26])
                 if line.startswith('CONECT'):
                     connectivity = True