From d036fca78b81d78039616c423282547574802fd2 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 1 Nov 2024 13:29:45 +0000
Subject: [PATCH] Fix analyzer and add license header and __all__.

---
 emle/_analyzer.py | 58 +++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 48 insertions(+), 10 deletions(-)

diff --git a/emle/_analyzer.py b/emle/_analyzer.py
index 0c91328..634d9b6 100644
--- a/emle/_analyzer.py
+++ b/emle/_analyzer.py
@@ -1,15 +1,50 @@
-from abc import ABC, abstractmethod
+######################################################################
+# EMLE-Engine: https://github.com/chemle/emle-engine
+#
+# Copyright: 2023-2024
+#
+# Authors: Lester Hedges   <lester.hedges@gmail.com>
+#          Kirill Zinovjev <kzinovjev@gmail.com>
+#
+# EMLE-Engine is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# EMLE-Engine is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EMLE-Engine If not, see <http://www.gnu.org/licenses/>.
+######################################################################
+
+# Note that this file is empty since EMLECalculator and Socket should
+# be directly imported from their respective sub-modules. This is to
+# avoid severe module import overheads when running the client code,
+# which requires no EMLE functionality.
+
+"""
+Analyser for EMLE simulation output.
+"""
+
+__all__ = ["ANI2xBackend", "DeepMDBackend", "EMLEAnalyzer"]
+
+
+from abc import ABC as _ABC
+from abc import abstractmethod as _abstractmethod
 import os as _os
 
 import numpy as _np
 import torch as _torch
 import ase as _ase
 
-from ._utils import pad_to_max
-from .models._emle_pc import EMLEPC
+from ._utils import pad_to_max as _pad_to_max
+from .models._emle_pc import EMLEPC as _EMLEPC
 
 
-class BaseBackend(ABC):
+class BaseBackend(_ABC):
 
     def __init__(self, torch_device=None):
         self._device = torch_device
@@ -42,7 +77,7 @@ def __call__(self, atomic_numbers, xyz, gradient=False):
             return e, f
         return result.detach().cpu().numpy()
 
-    @abstractmethod
+    @_abstractmethod
     def eval(self, atomic_numbers, xyz, gradient=False):
         """
         atomic_numbers: (N_BATCH, N_QM_ATOMS,)
@@ -117,6 +152,9 @@ def __init__(
         dtype = emle_base._dtype
         device = emle_base._device
 
+        # Create the point charge utility class.
+        emle_pc = _EMLEPC()
+
         atomic_numbers, qm_xyz = self._parse_qm_xyz(qm_xyz_filename)
         pc_charges, pc_xyz = self._parse_pc_xyz(pc_xyz_filename)
 
@@ -137,11 +175,11 @@ def __init__(
         )
         self.alpha = self._get_mol_alpha(self.A_thole, self.atomic_numbers)
 
-        mesh_data = EMLEPC._get_mesh_data(self.qm_xyz, self.pc_xyz, self.s)
-        self.e_static = EMLEPC.get_E_static(
+        mesh_data = emle_pc._get_mesh_data(self.qm_xyz, self.pc_xyz, self.s)
+        self.e_static = emle_pc.get_E_static(
             self.q_core, self.q_val, self.pc_charges, mesh_data
         )
-        self.e_induced = EMLEPC.get_E_induced(
+        self.e_induced = emle_pc.get_E_induced(
             self.A_thole, self.pc_charges, self.s, mesh_data
         )
 
@@ -151,7 +189,7 @@ def __init__(
     @staticmethod
     def _parse_qm_xyz(qm_xyz_filename):
         atoms = _ase.io.read(qm_xyz_filename, index=":")
-        atomic_numbers = pad_to_max([_.get_atomic_numbers() for _ in atoms], -1)
+        atomic_numbers = _pad_to_max([_.get_atomic_numbers() for _ in atoms], -1)
         xyz = _np.array([_.get_positions() for _ in atoms])
         return atomic_numbers, xyz
 
@@ -166,7 +204,7 @@ def _parse_pc_xyz(pc_xyz_filename):
                     file.readline()
                 except ValueError:
                     break
-        padded_frames = pad_to_max(frames)
+        padded_frames = _pad_to_max(frames)
         return padded_frames[:, :, 0], padded_frames[:, :, 1:]
 
     @staticmethod