Merge pull request #2 from luevano/rewrite

Rewrite

1 files changed, 153 insertions, 0 deletions

diff --git a/ml_exp/compound.py b/ml_exp/compound.py
new file mode 100644
index 000000000..1598fa482
--- /dev/null
+++ b/ml_exp/compound.py
@@ -0,0 +1,153 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+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.
+"""
+import numpy as np
+from ml_exp.data import NUCLEAR_CHARGE
+from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
+    first_neighbor_matrix, adjacency_matrix, bag_of_stuff
+
+
+class Compound:
+    def __init__(self,
+                 xyz=None):
+        """
+        Initialization of the Compound.
+        xyz: (path to) the xyz file.
+        """
+        self.name = None
+
+        self.n = None
+        self.extra = None  # In case a comment is in the compound file.
+        self.atoms = None
+        self.atoms_nc = None
+        self.coordinates = None
+        self.pbe0 = None
+        self.delta = None
+
+        self.cm = None
+        self.ljm = None
+        self.am = None
+        self.bos = None
+
+        if xyz is not None:
+            self.read_xyz(xyz)
+
+    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.
+        bohr_ru: if radius units should be in bohr's radius units.
+        """
+        self.cm = coulomb_matrix(self.coordinates,
+                                 self.atoms_nc,
+                                 size=size,
+                                 as_eig=as_eig,
+                                 bohr_ru=bohr_ru)
+
+    def gen_ljm(self,
+                diag_value=None,
+                sigma=1.0,
+                epsilon=1.0,
+                size=23,
+                as_eig=True,
+                bohr_ru=False):
+        """
+        Generate the Lennard-Jones Matrix for the compund.
+        diag_value: if special diagonal value is to be used.
+        sigma: sigma value.
+        epsilon: epsilon value.
+        size: compound size.
+        as_eig: if the representation should be as the eigenvalues.
+        bohr_ru: if radius units should be in bohr's radius units.
+        """
+        self.ljm = lennard_jones_matrix(self.coordinates,
+                                        self.atoms_nc,
+                                        diag_value=diag_value,
+                                        sigma=sigma,
+                                        epsilon=epsilon,
+                                        size=size,
+                                        as_eig=as_eig,
+                                        bohr_ru=bohr_ru)
+
+    def gen_am(self,
+               use_forces=False,
+               size=23,
+               bohr_ru=False):
+        """
+        Generate the Adjacency Matrix for the compund.
+        use_forces: if the use of forces instead of k_cx should be used.
+        size: compound size.
+        bohr_ru: if radius units should be in bohr's radius units.
+        """
+        # First, generate the first neighor matrix.
+        fnm, bonds, forces = first_neighbor_matrix(self.coordinates,
+                                                   self.atoms_nc,
+                                                   self.atoms,
+                                                   size=size,
+                                                   use_forces=use_forces,
+                                                   bohr_ru=bohr_ru)
+
+        # Now, generate the adjacency matrix.
+        self.am = adjacency_matrix(fnm,
+                                   bonds,
+                                   forces,
+                                   size=size)
+
+    def gen_bos(self,
+                size=23,
+                stuff='bonds'):
+        """
+        Generate the Bag of Stuff for the compound.
+        size: compound size.
+        stuff: elements of the bag, by default the known bag of bonds.
+        """
+        self.bos = bag_of_stuff(self.cm,
+                                self.atoms,
+                                size=size,
+                                stuff=stuff)
+
+    def read_xyz(self,
+                 filename):
+        """
+        Reads an xyz file and adds the corresponding data to the Compound.
+        filename: (path to) the xyz file.
+        """
+        with open(filename, 'r') as f:
+            lines = f.readlines()
+
+        self.name = filename.split('/')[-1]
+        self.n = int(lines[0])
+        self.extra = lines[1]
+        self.atoms = []
+        self.atoms_nc = np.empty(self.n, dtype=int)
+        self.coordinates = np.empty((self.n, 3), dtype=float)
+
+        for i, atom in enumerate(lines[2:self.n + 2]):
+            atom_d = atom.split()
+
+            self.atoms.append(atom_d[0])
+            self.atoms_nc[i] = NUCLEAR_CHARGE[atom_d[0]]
+            self.coordinates[i] = np.asarray(atom_d[1:4], dtype=float)