mdinterface 1.5.2__tar.gz → 1.5.3__tar.gz

{mdinterface-1.5.2/mdinterface.egg-info → mdinterface-1.5.3}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: mdinterface
-Version: 1.5.2
+Version: 1.5.3
 Summary: Build Interface Systems for Molecular Dynamics Simulations
 Author-email: Fabrice Roncoroni <fabrice.roncoroni@gmail.com>
 License-Expression: Apache-2.0
-Project-URL: Homepage, https://gitlab.com/roncofaber/mdinterface
-Project-URL: Repository, https://gitlab.com/roncofaber/mdinterface.git
-Project-URL: Documentation, https://gitlab.com/roncofaber/mdinterface
-Project-URL: Bug Tracker, https://gitlab.com/roncofaber/mdinterface/-/issues
+Project-URL: Homepage, https://github.com/roncofaber/mdinterface
+Project-URL: Repository, https://github.com/roncofaber/mdinterface.git
+Project-URL: Documentation, https://roncofaber.github.io/mdinterface
+Project-URL: Bug Tracker, https://github.com/roncofaber/mdinterface/issues
 Keywords: molecular dynamics,simulation,interface,chemistry,materials science
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
@@ -41,12 +41,10 @@ Requires-Dist: pymbxas; extra == "all"
 Requires-Dist: fairchem-core; extra == "all"
 Dynamic: license-file
 
-<div style="display: flex; align-items: center;">
-  <img src="./assets/mdinterface.png" alt="Logo" width="80"  style="margin-right: 10px;">
-  <div style="display: flex; flex-direction: column;">
-    <h1 style="margin: 0;">mdinterface: Build Interface Systems for Molecular Dynamics Simulations</h1>
-  </div>
-</div>
+<h1>
+  <img src="./assets/mdinterface.png" alt="Logo" width="60" style="vertical-align: middle; margin-right: 10px;">
+  mdinterface: Build Interface Systems for Molecular Dynamics Simulations
+</h1>
 
 [![PyPI version](https://badge.fury.io/py/mdinterface.svg?icon=si%3Apython)](https://pypi.org/project/mdinterface/) [![GitHub version](https://badge.fury.io/gh/roncofaber%2Fmdinterface.svg?icon=si%3Agithub)](https://github.com/roncofaber/mdinterface) [![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://roncofaber.github.io/mdinterface)
 

{mdinterface-1.5.2 → mdinterface-1.5.3}/README.md

@@ -1,9 +1,7 @@
-<div style="display: flex; align-items: center;">
-  <img src="./assets/mdinterface.png" alt="Logo" width="80"  style="margin-right: 10px;">
-  <div style="display: flex; flex-direction: column;">
-    <h1 style="margin: 0;">mdinterface: Build Interface Systems for Molecular Dynamics Simulations</h1>
-  </div>
-</div>
+<h1>
+  <img src="./assets/mdinterface.png" alt="Logo" width="60" style="vertical-align: middle; margin-right: 10px;">
+  mdinterface: Build Interface Systems for Molecular Dynamics Simulations
+</h1>
 
 [![PyPI version](https://badge.fury.io/py/mdinterface.svg?icon=si%3Apython)](https://pypi.org/project/mdinterface/) [![GitHub version](https://badge.fury.io/gh/roncofaber%2Fmdinterface.svg?icon=si%3Agithub)](https://github.com/roncofaber/mdinterface) [![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://roncofaber.github.io/mdinterface)
 

{mdinterface-1.5.2 → mdinterface-1.5.3}/mdinterface/__init__.py

@@ -6,8 +6,8 @@ Initially developed to construct electrolyte/electrode interfaces, it is also we
 
 """
 
-__version__ = '1.5.2'
-__date__ = '28 Apr. 2026'
+__version__ = '1.5.3'
+__date__ = '09 Jul. 2026'
 __author__ = 'Fabrice Roncoroni'
 __all__ = ['SimulationBox', 'SimCell', 'BoxBuilder', "Specie", "Polymer"]
 

{mdinterface-1.5.2 → mdinterface-1.5.3}/mdinterface/build/builder.py

@@ -669,7 +669,7 @@ class SimCell:
         padding: float,
         layered: bool,
         do_match: bool,
-    ) -> Tuple[mda.Universe, float]:
+    ) -> Tuple[mda.Universe, float, float]:
         """
         Second pass: assemble all layers into a single Universe.
 

{mdinterface-1.5.2 → mdinterface-1.5.3}/mdinterface/core/specie.py

@@ -857,9 +857,10 @@ class Specie(object):
             charges, atoms = calculate_RESP_charges(self, **respargs)
             
         if assign:
-            self.atoms.set_positions(atoms.get_positions())
             self.atoms.set_initial_charges(charges)
-        
+            if method == "resp":
+                self.atoms.set_positions(atoms.get_positions())
+
         return charges
 
     def estimate_OPLSAA_parameters(self, charge=None):

{mdinterface-1.5.2 → mdinterface-1.5.3}/mdinterface/io/lammpswriter.py

@@ -96,9 +96,10 @@ class DATAWriter(base.WriterBase):
         moltags = atoms.resindices
         m_l = len(str(moltags.max()))+1
     
+        coordinates = atoms.positions.copy()
         if self.convert_units:
-            coordinates = self.convert_pos_to_native(atoms.positions, inplace=False)
-            
+            coordinates = self.convert_pos_to_native(coordinates, inplace=False)
+
         b_l = len(str(int(coordinates.max()))) + 1
         b_t = b_l + 6
 
@@ -173,9 +174,9 @@ class DATAWriter(base.WriterBase):
         """Convert dimensions to triclinic vectors, convert lengths to native
         units and then write the dimensions section
         """
+        triv = mdamath.triclinic_vectors(dimensions)
         if self.convert_units:
-            triv = self.convert_pos_to_native(mdamath.triclinic_vectors(
-                                              dimensions),inplace=False)
+            triv = self.convert_pos_to_native(triv, inplace=False)
         self.f.write('\n')
         self.f.write('{:f} {:f} xlo xhi\n'.format(0., triv[0][0]))
         self.f.write('{:f} {:f} ylo yhi\n'.format(0., triv[1][1]))
@@ -407,7 +408,7 @@ def write_lammps_coefficients(
         if improper.id not in np.array(system.impropers.types(), dtype=int):
             continue
 
-        atype = "{}".format(*improper.symbols)
+        atype = "{}-{}-{}-{}".format(*improper.symbols)
         value = "{:>7.4f}    {:>2d}    {:>2d}".format(*improper.values)
 
         fout.write("{:>5}    {}  #  {:<2} | {}\n".format(improper.id, value, atype, improper.resname))

{mdinterface-1.5.2 → mdinterface-1.5.3}/mdinterface/utils/map.py

@@ -140,7 +140,7 @@ def map_dihedrals(dihedrals):
 def map_impropers(impropers):
     
     if impropers is None:
-        return None, None
+        return [], {}, np.array([])
     
     improper_type_ids = []
     type_id = 0
@@ -267,49 +267,39 @@ def generate_missing_interactions(nas, interaction_type):
             continue
 
     for mss_interaction in mss_interactions:
-        found_interaction = False
         stypes = tuple(nas._smap[ii] for ii in mss_interaction)
         stypes_rev = stypes[::-1]
-        
+
         # topology attribute already existing in map
         if stypes in interaction_type_map or stypes_rev in interaction_type_map:
-            if found_interaction:
-                raise ValueError(f"More than one possible {interaction_type[:-1]} found, abort!")
-                
             if stypes in interaction_type_map:
                 ninteraction = interaction_type_map[stypes].copy()
-                
             else:
                 ninteraction = interaction_type_map[stypes_rev].copy()
                 mss_interaction = mss_interaction[::-1]
-            
+
             a1, a2, *rest = mss_interaction
-            
+
             ninteraction._a1 = a1
             ninteraction._a2 = a2
-            
+
             if num_atoms > 2:
                 ninteraction._a3 = rest[0]
             if num_atoms > 3:
                 ninteraction._a4 = rest[1]
             new_interactions.append(ninteraction)
-            found_interaction = True
-        
-        # new topology attribute
+
+        # new topology attribute — type not yet defined, create bare object
         else:
-            if found_interaction:
-                raise ValueError(f"More than one possible {interaction_type[:-1]} found, abort!")
-            
             a1, a2, *rest = mss_interaction
-            
+
             if num_atoms == 2:
                 ninteraction = Bond(a1, a2)
             elif num_atoms == 3:
                 ninteraction = Angle(a1, a2, rest[0])
             elif num_atoms == 4:
                 ninteraction = Dihedral(a1, a2, rest[0], rest[1])
-                
+
             new_interactions.append(ninteraction)
-            found_interaction = True
             
     return new_interactions

{mdinterface-1.5.2 → mdinterface-1.5.3/mdinterface.egg-info}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: mdinterface
-Version: 1.5.2
+Version: 1.5.3
 Summary: Build Interface Systems for Molecular Dynamics Simulations
 Author-email: Fabrice Roncoroni <fabrice.roncoroni@gmail.com>
 License-Expression: Apache-2.0
-Project-URL: Homepage, https://gitlab.com/roncofaber/mdinterface
-Project-URL: Repository, https://gitlab.com/roncofaber/mdinterface.git
-Project-URL: Documentation, https://gitlab.com/roncofaber/mdinterface
-Project-URL: Bug Tracker, https://gitlab.com/roncofaber/mdinterface/-/issues
+Project-URL: Homepage, https://github.com/roncofaber/mdinterface
+Project-URL: Repository, https://github.com/roncofaber/mdinterface.git
+Project-URL: Documentation, https://roncofaber.github.io/mdinterface
+Project-URL: Bug Tracker, https://github.com/roncofaber/mdinterface/issues
 Keywords: molecular dynamics,simulation,interface,chemistry,materials science
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
@@ -41,12 +41,10 @@ Requires-Dist: pymbxas; extra == "all"
 Requires-Dist: fairchem-core; extra == "all"
 Dynamic: license-file
 
-<div style="display: flex; align-items: center;">
-  <img src="./assets/mdinterface.png" alt="Logo" width="80"  style="margin-right: 10px;">
-  <div style="display: flex; flex-direction: column;">
-    <h1 style="margin: 0;">mdinterface: Build Interface Systems for Molecular Dynamics Simulations</h1>
-  </div>
-</div>
+<h1>
+  <img src="./assets/mdinterface.png" alt="Logo" width="60" style="vertical-align: middle; margin-right: 10px;">
+  mdinterface: Build Interface Systems for Molecular Dynamics Simulations
+</h1>
 
 [![PyPI version](https://badge.fury.io/py/mdinterface.svg?icon=si%3Apython)](https://pypi.org/project/mdinterface/) [![GitHub version](https://badge.fury.io/gh/roncofaber%2Fmdinterface.svg?icon=si%3Agithub)](https://github.com/roncofaber/mdinterface) [![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://roncofaber.github.io/mdinterface)
 

{mdinterface-1.5.2 → mdinterface-1.5.3}/pyproject.toml

@@ -38,10 +38,10 @@ dependencies = [
 ]
 
 [project.urls]
-Homepage = "https://gitlab.com/roncofaber/mdinterface"
-Repository = "https://gitlab.com/roncofaber/mdinterface.git"
-Documentation = "https://gitlab.com/roncofaber/mdinterface"
-"Bug Tracker" = "https://gitlab.com/roncofaber/mdinterface/-/issues"
+Homepage = "https://github.com/roncofaber/mdinterface"
+Repository = "https://github.com/roncofaber/mdinterface.git"
+Documentation = "https://roncofaber.github.io/mdinterface"
+"Bug Tracker" = "https://github.com/roncofaber/mdinterface/issues"
 
 [project.optional-dependencies]
 resp = [