diff options
| -rw-r--r-- | ml_exp/compound.py | 13 | ||||
| -rw-r--r-- | ml_exp/representations.py | 18 |
2 files changed, 29 insertions, 2 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 03cfb8519..a85daefa4 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -78,12 +78,14 @@ class Compound: def gen_cm(self, size=23, + sort=False, flatten=True, as_eig=True, bohr_ru=False): """ Generate the Coulomb Matrix for the compund. size: compound size. + sort: if the representation should be sorted row-norm-wise. flatten: if the representation should be 1D. as_eig: if the representation should be as the eigenvalues. bohr_ru: if radius units should be in bohr's radius units. @@ -91,15 +93,17 @@ class Compound: self.cm = coulomb_matrix(self.coordinates, self.nc, size=size, + sort=sort, + flatten=flatten, as_eig=as_eig, - bohr_ru=bohr_ru, - flatten=flatten) + bohr_ru=bohr_ru) def gen_ljm(self, diag_value=None, sigma=1.0, epsilon=1.0, size=23, + sort=False, flatten=True, as_eig=True, bohr_ru=False): @@ -109,6 +113,7 @@ class Compound: sigma: sigma value. epsilon: epsilon value. size: compound size. + sort: if the representation should be sorted row-norm-wise. flatten: if the representation should be 1D. as_eig: if the representation should be as the eigenvalues. bohr_ru: if radius units should be in bohr's radius units. @@ -119,6 +124,7 @@ class Compound: sigma=sigma, epsilon=epsilon, size=size, + sort=sort, flatten=flatten, as_eig=as_eig, bohr_ru=bohr_ru) @@ -142,11 +148,13 @@ class Compound: def gen_am(self, use_forces=False, size=23, + sort=False, flatten=True): """ Generate the Adjacency Matrix for the compund. use_forces: if the use of forces instead of k_cx should be used. size: compound size. + sort: if the representation should be sorted row-norm-wise. flatten: if the representation should be 1D. """ self.am = adjacency_matrix(self.bonds_i, @@ -154,6 +162,7 @@ class Compound: self.bonds_f, use_forces=use_forces, size=size, + sort=sort, flatten=flatten) def gen_ei(self, diff --git a/ml_exp/representations.py b/ml_exp/representations.py index fcaa0f33a..47164ca7c 100644 --- a/ml_exp/representations.py +++ b/ml_exp/representations.py @@ -28,6 +28,7 @@ from ml_exp.data import POSSIBLE_BONDS def coulomb_matrix(coords, nc, size=23, + sort=False, flatten=True, as_eig=True, bohr_ru=False): @@ -36,6 +37,7 @@ def coulomb_matrix(coords, coords: compound coordinates. nc: nuclear charge data. size: compound size. + sort: if the representation should be sorted row-norm-wise. flatten: if the representation should be 1D. as_eig: if the representation should be as the eigenvalues. bohr_ru: if radius units should be in bohr's radius units. @@ -77,6 +79,10 @@ size. Arrays are not of the right shape.') return np.pad(cm_eigs, (0, size - n), 'constant') else: + if sort: + si = np.argsort(np.linalg.norm(cm, axis=-1))[::-1] + cm = cm[si] + if flatten: return np.pad(cm, ((0, size - n), (0, size - n)), 'constant').flatten() @@ -90,6 +96,7 @@ def lennard_jones_matrix(coords, sigma=1.0, epsilon=1.0, size=23, + sort=False, flatten=True, as_eig=True, bohr_ru=False): @@ -101,6 +108,7 @@ def lennard_jones_matrix(coords, sigma: sigma value. epsilon: epsilon value. size: compound size. + sort: if the representation should be sorted row-norm-wise. flatten: if the representation should be 1D. as_eig: if the representation should be as the eigenvalues. bohr_ru: if radius units should be in bohr's radius units. @@ -149,6 +157,10 @@ size. Arrays are not of the right shape.') return np.pad(lj_eigs, (0, size - n), 'constant') else: + if sort: + si = np.argsort(np.linalg.norm(lj, axis=-1))[::-1] + lj = lj[si] + if flatten: return np.pad(lj, ((0, size - n), (0, size - n)), 'constant').flatten() @@ -216,6 +228,7 @@ def adjacency_matrix(bonds_i, bonds_f, use_forces=False, size=23, + sort=False, flatten=True): """ Calculates the adjacency matrix given the bond list. @@ -225,6 +238,7 @@ def adjacency_matrix(bonds_i, bonds_f: list of force values. use_forces: if the use of forces instead of k_cx should be used. size: compund size. + sort: if the representation should be sorted row-norm-wise. flatten: if the representation should be 1D. """ if bonds_i is None: @@ -249,6 +263,10 @@ the current compound.') am[i, j] = bonds_k[i] am[j, i] = am[i, j] + if sort: + si = np.argsort(np.linalg.norm(am, axis=-1)) + am = am[si] + if flatten: return np.pad(am, ((0, size - n), (0, size - n)), 'constant').flatten() else: |