From efaa8eeb58d8e19d32f94ec4e91ec794574dfd32 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 18:13:33 -0700
Subject: Coulomb matrix done, fix init

---
 ml_exp/__init__.py        | 27 ++++-----------------------
 ml_exp/compound.py        | 28 ++++++++++++++++++++++++----
 ml_exp/representations.py | 10 +++++-----
 3 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index 06425f6a2..8e803b37e 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -20,29 +20,10 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
-from ml_exp.read_qm7_data import read_nc_data, read_db_data, read_qm7_data
-from ml_exp.c_matrix import c_matrix, c_matrix_multiple
-from ml_exp.lj_matrix import lj_matrix, lj_matrix_multiple
-from ml_exp.frob_norm import frob_norm
-from ml_exp.gauss_kernel import gauss_kernel
-from ml_exp.cholesky_solve import cholesky_solve
-from ml_exp.do_ml import do_ml
-from ml_exp.parallel_create_matrices import parallel_create_matrices
-from ml_exp.misc import plot_benchmarks
-
+from ml_exp.compound import Compound
+from ml_exp.representations import coulomb_matrix
 
 # If somebody does "from package import *", this is what they will
 # be able to access:
-__all__ = ['read_nc_data',
-           'read_db_data',
-           'read_qm7_data',
-           'c_matrix',
-           'c_matrix_multiple',
-           'lj_matrix',
-           'lj_matrix_multiple',
-           'frob_norm',
-           'gauss_kernel',
-           'cholesky_solve',
-           'do_ml',
-           'parallel_create_matrices',
-           'plot_benchmarks']
+__all__ = ['Compound',
+           'coulomb_matrix']
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 9536767a7..3ea377826 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -22,10 +22,16 @@ SOFTWARE.
 """
 import numpy as np
 from ml_exp.data import NUCLEAR_CHARGE
+from ml_exp.representations import coulomb_matrix
 
 
 class Compound:
-    def __init__(self, xyz=None):
+    def __init__(self,
+                 xyz=None):
+        """
+        Initialization of the Compound.
+        xyz: (path to) the xyz file.
+        """
         # empty_array = np.asarray([], dtype=float)
 
         self.n = None
@@ -41,10 +47,24 @@ class Compound:
         if xyz is not None:
             self.read_xyz(xyz)
 
-    def gen_cm(self):
-        pass
+    def gen_cm(self,
+               size=23,
+               as_eig=True,
+               bohr_ru=False):
+        """
+        Generate the Coulomb Matrix for the compund.
+        size: compound size.
+        as_eig: if the representation should be as the eigenvalues.
+        bhor_ru: if radius units should be in bohr's radius units.
+        """
+        self.coulomb_matrix = coulomb_matrix(self.coordinates,
+                                             self.atoms_nc,
+                                             size=size,
+                                             as_eig=as_eig,
+                                             bhor_ru=bohr_ru)
 
-    def read_xyz(self, filename):
+    def read_xyz(self,
+                 filename):
         """
         Reads an xyz file and adds the corresponding data to the Compound.
         filename: (path to) the xyz file.
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index bbc538ae6..c503c310d 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -28,16 +28,16 @@ def coulomb_matrix(coords,
                    nc,
                    size=23,
                    as_eig=True,
-                   bohr_radius_units=False):
+                   bhor_ru=False):
     """
     Creates the Coulomb Matrix from the molecule data given.
     coords: compound coordinates.
     nc: nuclear charge data.
     size: compound size.
-    as_eig: if data should be returned as matrix or array of eigenvalues.
-    bohr_radius_units: if units should be in bohr's radius units.
+    as_eig: if the representation should be as the eigenvalues.
+    bhor_ru: if radius units should be in bohr's radius units.
     """
-    if bohr_radius_units:
+    if bhor_ru:
         cr = 0.52917721067
     else:
         cr = 1
@@ -54,7 +54,7 @@ def coulomb_matrix(coords,
         size = n
 
     nr = range(size)
-    cm = np.empty((size, size), dtype=float)
+    cm = np.zeros((size, size), dtype=float)
 
     # Actual calculation of the coulomb matrix.
     for i in nr:
-- 
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