mdinterface 1.2.0__tar.gz → 1.3.0__tar.gz

{mdinterface-1.2.0 → mdinterface-1.3.0}/PKG-INFO

@@ -1,24 +1,34 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: mdinterface
-Version: 1.2.0
-Summary: mdinterface: A package for building interface systems in Molecular Dynamics simulations.
+Version: 1.3.0
+Summary: Build Interface Systems for Molecular Dynamics Simulations
 Home-page: https://gitlab.com/roncofaber/mdinterface
+Author: Fabrice Roncoroni
+Author-email: fabrice.roncoroni@gmail.com
 License: Apache-2.0
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: mdanalysis
 Requires-Dist: ase
 Requires-Dist: numpy
 Requires-Dist: networkx
-Requires-Dist: libarvo
 Requires-Dist: platformdirs
 Requires-Dist: configparser
+Provides-Extra: volume
+Requires-Dist: libarvo; extra == "volume"
+Provides-Extra: resp
+Requires-Dist: pyscf; extra == "resp"
+Requires-Dist: pymbxas; extra == "resp"
+Provides-Extra: all
+Requires-Dist: libarvo; extra == "all"
+Requires-Dist: pyscf; 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;">
@@ -37,16 +47,17 @@ Using `mdinterface` you can:
 
 - Create layered simulation boxes with solvents, solutes, and interface slabs.
 - Populate your system with ions and solvents using PACKMOL, and provide the starting concentration profile of the species to get the MD where you want it to be, but faster.
-- Import common molecules/metals/polymers with pre-defined classical force fields parameters from the database, or automatically generate new OPLS-AA force field parameters using [https://github.com/Isra3l/ligpargen](LigParGen).
+- Import common molecules/metals/polymers with pre-defined classical force fields parameters from the database, or automatically generate new OPLS-AA force field parameters using [LigParGen](https://github.com/Isra3l/ligpargen).
 - Generate polymer chains of any length from a starting monomer.
 - Estimate the RESP charges of molecules using the [PySCF  electronic structure code](https://github.com/pyscf/pyscf).
-- Automatically write LAMMPS data files and coefficients, so you can start making them atoms dance!
+- Automatically write LAMMPS data files and coefficients, so you can start making them atoms dance as soon as possible!
+- Integrate your workflow with [MDAnalysis](https://github.com/MDAnalysis/mdanalysis): create your molecules with `mdinterface` and convert them to `mda.Universe` objects with a simple interface.
 
 ## Requirements
 
 Check the file [requirements.txt](requirements.txt) to see which packages are needed. Installing the package using `pip` should already take care of all mandatory dependencies.
 
-Additionaly, you need the `packmol` utility installed to generate MD boxes. You can follow the instructions at [https://m3g.github.io/packmol/](https://m3g.github.io/packmol/) to install it. Alternatively, you can install it using `conda`:
+Additionally, you need the `packmol` utility installed to generate MD boxes. You can follow the instructions at [https://m3g.github.io/packmol/](https://m3g.github.io/packmol/) to install it. Alternatively, you can install it using `conda`:
 
 ```bash
 conda install -c conda-forge packmol
@@ -56,7 +67,7 @@ conda install -c conda-forge packmol
 
 #### Automatic OPLS-AA force field generator with LigParGen
 
-If you want to use LigParGen, please follow the instructions on their [GitHub](https://github.com/Isra3l/ligpargen). To make sure that BOSS is recognized by the package, specify the environment variable `BOSSdir`.
+If you want to use LigParGen, please follow the instructions on their [GitHub](https://github.com/Isra3l/ligpargen). If you are having trouble installing, you can try my own [fork](https://github.com/roncofaber/ligpargen) of the original repo. To make sure that BOSS is recognized by the package, specify the environment variable `BOSSdir`.
 
 You can do this manually every time, or just add the path to the `config.ini` file to your config directory:
 
@@ -70,7 +81,7 @@ The config directory is found using [`platformdirs`](https://pypi.org/project/pl
 
 ### RESP charge analysis with PySCF
 
-To use the RESP charge analysis feature, you need to install [PySCF](https://github.com/pyscf/pyscf) and [PyMBXAS](https://gitlab.com/roncofaber/pymbxas).
+To use the RESP charge analysis feature, you need to install [PySCF](https://github.com/pyscf/pyscf) and [PyMBXAS](https://gitlab.com/roncofaber/pymbxas). To my knowledge, the RESP feature is only implemented in [gpu4pyscf](https://github.com/pyscf/gpu4pyscf) at the moment, so follow the repo instructions on how to install it.
 
 ## Installation
 
@@ -92,25 +103,32 @@ Clone the repository in the desired location:
 git clone git@gitlab.com:roncofaber/mdinterface.git
 ```
 
-Install the required packages:
+Install the package:
 
 ```bash
 cd mdinterface
-conda install -c conda-forge --file requirements.txt
+pip install .
 ```
 
-Install the package with pip:
+### Install a development environment
+
+If you plan of making changes, clone the package and add it to your development environment with:
 
 ```bash
-pip install .
+pip install --no-build-isolation -e .
 ```
 
-### Install a development environment
+### Install optional packages
 
-If you plan of making changes, clone the package and install the requirements but then add it to your development environment with:
+You can install optional dependencies with the following commands:
 
 ```bash
-pip install --no-build-isolation --no-deps -e .
+# install libarvo to estimate species:
+pip install mdinterface[volume] volumes
+# install pyscf and pymbxas (you still need gpu4pyscf):
+pip install mdinterface[resp]
+# install all of the above options:
+pip install mdinterface[all]
 ```
 
 ## Usage
@@ -120,9 +138,16 @@ Creating a new Specie (with its topology attributes) is as simple as doing:
 ```python
 #%% Make a specie, and use LigParGen to estimate FF parameters
 my_specie = Specie("CH3ONO", ligpargen=True) # molecule is in ASE database
+
+# make a specie from any ASE readable file
+my_specie = Specie("methylnitrite.xyz", ligpargen=True)
+
+# convert specie to mdanalysis universe (and all the attributes!)
+my_specie.to_universe()
+
 ```
 
-Please, check the files in [examples](mdinterface/examples/) to learn how to use the package. Including setting up simulation boxes, creating polymers and much more.
+Please, check the files in [examples](mdinterface/examples/) to learn how to use the package. Including setting up simulation boxes, creating polymers, perform RESP analysis and much more!
 
 ## Roadmap
 

mdinterface-1.2.0/mdinterface.egg-info/PKG-INFO → mdinterface-1.3.0/README.md

@@ -1,25 +1,3 @@
-Metadata-Version: 2.2
-Name: mdinterface
-Version: 1.2.0
-Summary: mdinterface: A package for building interface systems in Molecular Dynamics simulations.
-Home-page: https://gitlab.com/roncofaber/mdinterface
-License: Apache-2.0
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Operating System :: OS Independent
-Classifier: Topic :: Software Development
-Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: mdanalysis
-Requires-Dist: ase
-Requires-Dist: numpy
-Requires-Dist: networkx
-Requires-Dist: libarvo
-Requires-Dist: platformdirs
-Requires-Dist: configparser
-
 <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;">
@@ -37,16 +15,17 @@ Using `mdinterface` you can:
 
 - Create layered simulation boxes with solvents, solutes, and interface slabs.
 - Populate your system with ions and solvents using PACKMOL, and provide the starting concentration profile of the species to get the MD where you want it to be, but faster.
-- Import common molecules/metals/polymers with pre-defined classical force fields parameters from the database, or automatically generate new OPLS-AA force field parameters using [https://github.com/Isra3l/ligpargen](LigParGen).
+- Import common molecules/metals/polymers with pre-defined classical force fields parameters from the database, or automatically generate new OPLS-AA force field parameters using [LigParGen](https://github.com/Isra3l/ligpargen).
 - Generate polymer chains of any length from a starting monomer.
 - Estimate the RESP charges of molecules using the [PySCF  electronic structure code](https://github.com/pyscf/pyscf).
-- Automatically write LAMMPS data files and coefficients, so you can start making them atoms dance!
+- Automatically write LAMMPS data files and coefficients, so you can start making them atoms dance as soon as possible!
+- Integrate your workflow with [MDAnalysis](https://github.com/MDAnalysis/mdanalysis): create your molecules with `mdinterface` and convert them to `mda.Universe` objects with a simple interface.
 
 ## Requirements
 
 Check the file [requirements.txt](requirements.txt) to see which packages are needed. Installing the package using `pip` should already take care of all mandatory dependencies.
 
-Additionaly, you need the `packmol` utility installed to generate MD boxes. You can follow the instructions at [https://m3g.github.io/packmol/](https://m3g.github.io/packmol/) to install it. Alternatively, you can install it using `conda`:
+Additionally, you need the `packmol` utility installed to generate MD boxes. You can follow the instructions at [https://m3g.github.io/packmol/](https://m3g.github.io/packmol/) to install it. Alternatively, you can install it using `conda`:
 
 ```bash
 conda install -c conda-forge packmol
@@ -56,7 +35,7 @@ conda install -c conda-forge packmol
 
 #### Automatic OPLS-AA force field generator with LigParGen
 
-If you want to use LigParGen, please follow the instructions on their [GitHub](https://github.com/Isra3l/ligpargen). To make sure that BOSS is recognized by the package, specify the environment variable `BOSSdir`.
+If you want to use LigParGen, please follow the instructions on their [GitHub](https://github.com/Isra3l/ligpargen). If you are having trouble installing, you can try my own [fork](https://github.com/roncofaber/ligpargen) of the original repo. To make sure that BOSS is recognized by the package, specify the environment variable `BOSSdir`.
 
 You can do this manually every time, or just add the path to the `config.ini` file to your config directory:
 
@@ -70,7 +49,7 @@ The config directory is found using [`platformdirs`](https://pypi.org/project/pl
 
 ### RESP charge analysis with PySCF
 
-To use the RESP charge analysis feature, you need to install [PySCF](https://github.com/pyscf/pyscf) and [PyMBXAS](https://gitlab.com/roncofaber/pymbxas).
+To use the RESP charge analysis feature, you need to install [PySCF](https://github.com/pyscf/pyscf) and [PyMBXAS](https://gitlab.com/roncofaber/pymbxas). To my knowledge, the RESP feature is only implemented in [gpu4pyscf](https://github.com/pyscf/gpu4pyscf) at the moment, so follow the repo instructions on how to install it.
 
 ## Installation
 
@@ -92,25 +71,32 @@ Clone the repository in the desired location:
 git clone git@gitlab.com:roncofaber/mdinterface.git
 ```
 
-Install the required packages:
+Install the package:
 
 ```bash
 cd mdinterface
-conda install -c conda-forge --file requirements.txt
+pip install .
 ```
 
-Install the package with pip:
+### Install a development environment
+
+If you plan of making changes, clone the package and add it to your development environment with:
 
 ```bash
-pip install .
+pip install --no-build-isolation -e .
 ```
 
-### Install a development environment
+### Install optional packages
 
-If you plan of making changes, clone the package and install the requirements but then add it to your development environment with:
+You can install optional dependencies with the following commands:
 
 ```bash
-pip install --no-build-isolation --no-deps -e .
+# install libarvo to estimate species:
+pip install mdinterface[volume] volumes
+# install pyscf and pymbxas (you still need gpu4pyscf):
+pip install mdinterface[resp]
+# install all of the above options:
+pip install mdinterface[all]
 ```
 
 ## Usage
@@ -120,9 +106,16 @@ Creating a new Specie (with its topology attributes) is as simple as doing:
 ```python
 #%% Make a specie, and use LigParGen to estimate FF parameters
 my_specie = Specie("CH3ONO", ligpargen=True) # molecule is in ASE database
+
+# make a specie from any ASE readable file
+my_specie = Specie("methylnitrite.xyz", ligpargen=True)
+
+# convert specie to mdanalysis universe (and all the attributes!)
+my_specie.to_universe()
+
 ```
 
-Please, check the files in [examples](mdinterface/examples/) to learn how to use the package. Including setting up simulation boxes, creating polymers and much more.
+Please, check the files in [examples](mdinterface/examples/) to learn how to use the package. Including setting up simulation boxes, creating polymers, perform RESP analysis and much more!
 
 ## Roadmap
 

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/__init__.py

@@ -6,8 +6,8 @@ Initially developed to construct electrolyte/electrode interfaces, it is also we
 
 """
 
-__version__ = '1.2.0'
-__date__ = '28 Mar. 2025'
+__version__ = '1.3.0'
+__date__ = '17 Jul. 2025'
 __author__ = 'Fabrice Roncoroni'
 __all__ = ['SimulationBox', "Specie", "Polymer"]
 

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/core/specie.py

@@ -20,6 +20,7 @@ from mdinterface.utils.auxiliary import as_list, find_smallest_missing, round_li
 from mdinterface.externals import run_ligpargen, run_OBChargeModel, calculate_RESP_charges
 from mdinterface.utils.graphs import molecule_to_graph, find_unique_paths_of_length,\
     find_improper_idxs,find_relevant_distances, find_atom_types
+from mdinterface.utils.draw import draw_bond_markers
 
 import copy
 import numpy as np
@@ -176,7 +177,7 @@ class Specie(object):
     def _atom_types_from_lj(self, lj):
         
         # use function to retrieve IDs
-        atom_type_ids, types_map = find_atom_types(self.atoms, max_depth=1)
+        atom_type_ids, types_map = find_atom_types(self.graph, max_depth=1)
         
         atom_types = []
         for atom_id in atom_type_ids:
@@ -220,7 +221,7 @@ class Specie(object):
         
         self._atoms = atoms
         self._graph = molecule_to_graph(atoms, cutoff_scale=cutoff)
-        
+
         return
     
     def _update_topology(self):
@@ -507,15 +508,21 @@ class Specie(object):
                                                     centers=centers, Ninv=Ninv)
         return unique_pairs_list
 
-    def plot_graph(self, **kwargs):
+    def plot_graph(self, show_bonds=False):
         
         colors = [jmol_colors[a.number] for a in self.atoms]
         
+        # node_pos = nx.spring_layout(self.graph, k=1.5/np.sqrt(self.graph.order()))
+        node_pos = nx.kamada_kawai_layout(self.graph)
+        
         fig, ax = plt.subplots()
-        nx.draw(self.graph, with_labels=True, node_color=colors,
+        nx.draw(self.graph, pos=node_pos, with_labels=True, node_color=colors,
                 node_size=1000, edge_color='black', linewidths=2, font_size=15,
                 edgecolors="black", ax=ax, width=2)
         
+        if show_bonds:
+            draw_bond_markers(ax, self, node_pos, jmol_colors)
+    
         plt.show()
         
         return

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/database/ions.py

@@ -20,7 +20,8 @@ import ase
 # Jorgensen: https://pubs.acs.org/doi/10.1021/ct600252r
 # Cheatham : https://pubs.acs.org/doi/10.1021/jp8001614
 # Sengupta : https://pubs.acs.org/doi/10.1021/acs.jcim.0c01390 (12-6 HFE param)
-# Dang     : 
+# Dang     : https://doi.org/10.1063/1.462555, https://doi.org/10.1063/1.466363
+
 ions_parameters = {
     "F": {
         "charge": -1.0,
@@ -28,7 +29,7 @@ ions_parameters = {
             "jorgensen": [0.71000, 3.0500],
             "cheatham" : [0.00336, 4.1035],
             "sengupta" : [0.24140, 3.2678],
-            "dang"     : [0.18000, 3.1180]
+            "dang"     : [0.20000, 3.1680] # was [0.18000, 3.1180]
         }
     },
     "Cl": {
@@ -107,6 +108,8 @@ ions_parameters = {
 
 def lookup_parameters(element, ffield):
     try:
+        if ffield.lower() == "merz":
+            ffield = "sengupta"
         charge = ions_parameters[element]["charge"]
         lj = ions_parameters[element]["ffield"][ffield.lower()]
         return charge, lj
@@ -125,7 +128,7 @@ class Ion(Specie):
         **kwargs: Additional keyword arguments to pass to the Specie superclass.
     """
     
-    def __init__(self, element, ffield="Jorgensen", chg_scaling=0.8, **kwargs):
+    def __init__(self, element, ffield="Jorgensen", chg_scaling=1.0, **kwargs):
         
         charge, lj = lookup_parameters(element, ffield)
         lj = {element: lj}
@@ -166,7 +169,9 @@ class Perchlorate(Specie):
         return
 
 
-# hydronium https://pubs.acs.org/doi/pdf/10.1021/jp036842c
+# hydronium parameters:
+    # std:  https://pubs.acs.org/doi/pdf/10.1021/jp036842c
+    # netz: https://refubium.fu-berlin.de/bitstream/handle/fub188/15473/1.4942771.pdf
 class Hydronium(Specie):
     def __init__(self, **kwargs):
         
@@ -186,3 +191,22 @@ class Hydronium(Specie):
 
         super().__init__(hyd, charges=charges, bonds=b1, angles=a1, lj=lj, **kwargs)
         return
+
+# hydroxide parameters:
+    # netz: https://refubium.fu-berlin.de/bitstream/handle/fub188/15473/1.4942771.pdf
+class Hydroxide(Specie):
+    def __init__(self, **kwargs):
+        
+        # make ion by cheating and making NH3 first
+        hoh = ase.build.molecule("OH")
+
+        # bond is fixed in paper #FIXME used hydronium bond with r0=1
+        b1 = Bond("O", "H", kr=1085.9565/2, r0=1.000)
+        
+        charges = [-1.000, 0.000]
+        
+        # converted J to cal
+        lj = {"O": [0.01195, 3.8100], "H": [0.000, 0.000]}
+
+        super().__init__(hoh, charges=charges, bonds=b1, lj=lj, **kwargs)
+        return

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/database/molecules.py

@@ -19,15 +19,22 @@ class Water(Specie):
             a1 = Angle("H", "O", "H", kr=55, theta0=104.52)
             charges = [-0.83, 0.415, 0.415]
             lj = {"O": [0.102, 3.188], "H": [0.0, 1.0]}
+        
+        if model.lower() == "charmm":
+            b1 = Bond("O", "H", kr=450, r0=0.9572)
+            a1 = Angle("H", "O", "H", kr=55, theta0=104.52)
+            charges = [-0.834, 0.417, 0.417]
+            lj = {"O": [0.1521, 3.1507], "H": [0.0460, 0.4]}
 
         super().__init__("H2O", charges=charges, bonds=b1, angles=a1, lj=lj, **kwargs)
         return
 
+# 22 Apr. 2025 correction: all bond terms have been divider by 2:
 #oxygen https://pubs.acs.org/doi/10.1021/acs.jctc.0c01132 /!\: divide sig by 2**(1/6)
 class Oxygen(Specie):
     def __init__(self, **kwargs):
         
-        b1 = Bond("O", "O", kr=1640.4, r0=1.2074)
+        b1 = Bond("O", "O", kr=1640.4/2, r0=1.2074)
         lj = {"O" : [0.1047, 2.9373]}
 
         super().__init__("O2", charges = 0.0, lj=lj, bonds=b1, **kwargs)
@@ -37,7 +44,7 @@ class Oxygen(Specie):
 class Hydrogen(Specie):
     def __init__(self, Hset="std", **kwargs):
         
-        b1 = Bond("H", "H", kr=700, r0=0.7414)
+        b1 = Bond("H", "H", kr=700/2, r0=0.7414)
         
         if Hset.lower() == "std":   # standard 12-6 set
             lj = {"H" : [0.0153, 2.5996]}
@@ -51,7 +58,7 @@ class Hydrogen(Specie):
 class Nitrogen(Specie):
     def __init__(self, **kwargs):
         
-        b1 = Bond("N", "N", kr=3190, r0=1.0977)
+        b1 = Bond("N", "N", kr=3190/2, r0=1.0977)
         lj = {"N" : [0.0797, 3.2197]}
 
         super().__init__("N2", charges = 0.0, lj=lj, bonds=b1, **kwargs)

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/externals/pyscf.py

@@ -40,15 +40,18 @@ def calculate_RESP_charges(specie, basis='def2-svpd', xc="b3lyp", calc_type="RKS
         
         atoms = mole_to_ase(mol)
     
+    mol.cart = True    # PySCF uses spherical basis by default
+    
     # run calculation and calculate density matrix
     mf = make_pyscf_calculator(mol, xc=xc, calc_type=calc_type, gpu=gpu)
+    
     mf.kernel()
     dm = mf.make_rdm1()
     
     # now, start RESP with ESP first!
 
     # ESP charge (do I need this?)
-    q0 = esp.esp_solve(mol, dm)
+    # q0 = esp.esp_solve(mol, dm)
 
     # RESP charge // first stage fitting
     q1 = esp.resp_solve(mol, dm, maxit=maxit)
@@ -67,7 +70,7 @@ def calculate_RESP_charges(specie, basis='def2-svpd', xc="b3lyp", calc_type="RKS
             equal_constraints.append(tmp_idx.tolist())
             
     # RESP charge // second stage fitting
-    q2 = esp.resp_solve(mol, dm, resp_a=1e-4,
+    q2 = esp.resp_solve(mol, dm, resp_a=5e-4, resp_b=0.1, tol=1e-7,
                         sum_constraints=sum_constraints,
                         equal_constraints=equal_constraints, maxit=maxit)
 

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/io/lammpswriter.py

@@ -68,17 +68,16 @@ class DATAWriter(base.WriterBase):
         self.units['velocity'] = kwargs.pop('velocityunit',
                                  self.units['length']+'/'+self.units['time'])
 
-    def _write_atoms(self, atoms, data):
+    def _write_atoms(self, atoms, data, atom_style):
         self.f.write('\n')
         self.f.write('Atoms\n')
         self.f.write('\n')
 
         try:
             charges = atoms.charges
+            has_charges = True
         except (NoDataError, AttributeError):
             has_charges = False
-        else:
-            has_charges = True
 
         indices = atoms.indices + 1
         i_l = len(str(indices.max()))
@@ -96,18 +95,26 @@ class DATAWriter(base.WriterBase):
         b_l = len(str(int(coordinates.max()))) + 1
         b_t = b_l + 6
 
-        if has_charges:
-            for index, moltag, atype, charge, coords in zip(indices, moltags,
-                    types, charges, coordinates):
+        if atom_style == "atomic":
+            for index, atype, coords in zip(indices, types, coordinates):
                 x, y, z = coords
-                self.f.write(f"{index:{i_l}d} {moltag:{m_l}d}  {atype:{t_l}d}  {charge: .7f}"
+                self.f.write(f"{index:{i_l}d}  {atype:{t_l}d}"
                              f"  {x:> {b_t}.5f} {y:> {b_t}.5f} {z:> {b_t}.5f}\n")
-        else:
-            for index, moltag, atype, coords in zip(indices, moltags, types,
-                    coordinates):
-                x, y, z = coords
-                self.f.write(f"{index:{i_l}d} {moltag:{m_l}d} {atype:{t_l}d}"
-                             f" {x:> {b_t}.5f} {y:> {b_t}.5f} {z:> {b_t}.5f}\n")
+        elif atom_style == "full":
+            
+            if not has_charges:
+                for index, moltag, atype, coords in zip(indices, moltags, types,
+                        coordinates):
+                    x, y, z = coords
+                    self.f.write(f"{index:{i_l}d} {moltag:{m_l}d} {atype:{t_l}d}"
+                                 f" {x:> {b_t}.5f} {y:> {b_t}.5f} {z:> {b_t}.5f}\n")
+            elif has_charges:
+                for index, moltag, atype, charge, coords in zip(indices, moltags,
+                                                                types, charges, coordinates):
+                    x, y, z = coords
+                    self.f.write(f"{index:{i_l}d} {moltag:{m_l}d} {atype:{t_l}d}"
+                                 f"  {charge: .7f}"
+                                 f" {x:> {b_t}.5f} {y:> {b_t}.5f} {z:> {b_t}.5f}\n")
 
     def _write_velocities(self, atoms):
         self.f.write('\n')
@@ -172,7 +179,7 @@ class DATAWriter(base.WriterBase):
         self.f.write('\n')
 
     @requires('types', 'masses')
-    def write(self, selection, frame=None):
+    def write(self, selection, frame=None, atom_style='full'):
         """Write selection at current trajectory frame to file.
 
         The sections for Atoms, Masses, Velocities, Bonds, Angles,
@@ -233,11 +240,14 @@ class DATAWriter(base.WriterBase):
                 ('dihedral', 'dihedrals'), ('improper', 'impropers')]
 
             for btype, attr_name in attrs:
-                features[btype] = atoms.__getattribute__(attr_name)
-                self.f.write('{:>12d}  {}\n'.format(len(features[btype]),
-                                                    attr_name))
-                features[btype] = features[btype].atomgroup_intersection(
-                                    atoms, strict=True)
+                try:
+                    features[btype] = atoms.__getattribute__(attr_name)
+                    self.f.write('{:>12d}  {}\n'.format(len(features[btype]),
+                                                        attr_name))
+                    features[btype] = features[btype].atomgroup_intersection(
+                                        atoms, strict=True)
+                except:
+                    pass
 
             self.f.write('\n')
             
@@ -251,7 +261,7 @@ class DATAWriter(base.WriterBase):
             self._write_dimensions(atoms.dimensions)
 
             self._write_masses(atoms)
-            self._write_atoms(atoms, u.trajectory.ts.data)
+            self._write_atoms(atoms, u.trajectory.ts.data, atom_style)
             for attr in features.values():
                 if attr is None or len(attr) == 0:
                     continue

{mdinterface-1.2.0 → mdinterface-1.3.0}/mdinterface/simulationbox.py

@@ -142,7 +142,7 @@ class SimulationBox():
     def make_simulation_box(self, xysize, layering, padding=1.5, to_ase=False,
                             write_data=False, filename="data.lammps",
                             center_electrode=False, layered=False, hijack=None,
-                            match_cell=False, remove_charges=False):
+                            match_cell=False, atom_style="full", write_coeff=True):
         
         # define approximate cross_section
         assert len(xysize) == 2, "'xysize' should have length of 2 [xsize, ysize]"
@@ -210,7 +210,8 @@ class SimulationBox():
         
         # write data file
         if write_data:
-            self.write_lammps_file(system, filename=filename, remove_charges=remove_charges)
+            self.write_lammps_file(system, filename=filename,
+                                   atom_style=atom_style, write_coeff=write_coeff)
         
         # convert to ase, or not
         if to_ase:
@@ -218,14 +219,22 @@ class SimulationBox():
         return system
     
     def write_lammps_file(self, system,  write_coeff=True, filename="data.lammps",
-                          remove_charges=False):
+                          atom_style="full"):
         
-        if remove_charges:
-            system.del_TopologyAttr("charges")
+        # just make sure we are not messing things up
+        system = system.copy()
+        
+        # remove coefficients
+        if not write_coeff:
+            for attribute in ["bonds", "angles", "dihedrals", "impropers"]:
+                try:
+                    system.del_TopologyAttr(attribute)
+                except:
+                    pass
         
         # first write data file
         with DATAWriter(filename) as dt:
-            dt.write(system.atoms)
+            dt.write(system.atoms, atom_style=atom_style)
             
         # now write coeff where they belong
         if write_coeff:
@@ -428,7 +437,7 @@ class SimulationBox():
         if not slabs:
             return xsize, ysize
         
-        xsize_t, ysize_t = np.NaN, np.NaN
+        xsize_t, ysize_t = np.nan, np.nan
         
         for tslab in slabs:
             xi, yi, _ = self._get_size_from_slab(tslab)

mdinterface-1.3.0/mdinterface/utils/draw.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jul 14 18:55:16 2025
+
+@author: roncofaber
+"""
+
+import matplotlib.pyplot as plt
+
+def draw_bond_markers(ax, mol, node_pos, jmol_colors):
+    # Assign marker and color for each bond type
+    bond_markers = ['o', 's', 'D', '^', 'v', '*', 'P', 'X']
+    bond_colors = ['red', 'blue', 'green', 'orange', 'purple', 'brown', 'cyan', 'magenta']
+    bondtype_to_marker = {}
+    bondtype_to_color = {}
+    for idx, bond in enumerate(mol._btype):
+        bondtype_to_marker[idx] = bond_markers[idx % len(bond_markers)]
+        bondtype_to_color[idx] = bond_colors[idx % len(bond_colors)]
+    
+    # Draw markers at bond midpoints
+    for (a, b), btype_idx in zip(mol.bonds[0], mol.bonds[1]):
+        marker = bondtype_to_marker[btype_idx]
+        color = bondtype_to_color[btype_idx]
+        x0, y0 = node_pos[a]
+        x1, y1 = node_pos[b]
+        xm, ym = (x0 + x1) / 2, (y0 + y1) / 2
+        ax.scatter(xm, ym, marker=marker, color=color, s=100, zorder=5)
+    
+    # Legend
+    legend_handles = []
+    for idx, bond in enumerate(mol._btype):
+        marker = bondtype_to_marker[idx]
+        color = bondtype_to_color[idx]
+        label = f"$k_r={bond.kr}$, $r_0={bond.r0}$"
+        h = plt.Line2D([0], [0], marker=marker, color='w', markerfacecolor=color, markersize=10, label=label, linestyle='None')
+        legend_handles.append(h)
+    ax.legend(handles=legend_handles, loc='best', fontsize=10, framealpha=1.0, edgecolor='k')
+    
+    return