Add support for small (ABn-type) molecules for sGNN

Author: KuangYu

dmff/sgnn/gnn.py

@@ -8,7 +8,8 @@
 import jax.nn.initializers
 import jax.numpy as jnp
 import numpy as np
-from .graph import MAX_VALENCE, TopGraph, from_pdb
+from .graph import TopGraph, from_pdb
+from .graph import MAX_VALENCE, ATYPE_INDEX, FSCALE_BOND, FSCALE_ANGLE
 from ..utils import jit_condition
 from jax import value_and_grad, vmap
 
@@ -55,7 +56,12 @@ def __init__(self,
                  nn=1,
                  sigma=162.13039087945623,
                  mu=117.41975505778706,
-                 seed=12345):
+                 seed=12345,
+                 max_valence=MAX_VALENCE,
+                 atype_index=ATYPE_INDEX,
+                 fscale_bond=FSCALE_BOND,
+                 fscale_angle=FSCALE_ANGLE
+                 ):
         """ Constructor for MolGNNForce
 
         Parameters
@@ -77,15 +83,25 @@ def __init__(self,
         mu: float, optional
             a constant shift
             the final total energy would be ${(E_{NN} + \mu) * \sigma}
-        seed: int: optional
+        seed: int, optional
             random seed used in network initialization
             default = 12345
-        
+        max_valence: int, optional
+            Maximal valence number for all atoms inside the graph, use the value in graph.py by default
+        atype_index: dict, optional
+            A dictionary that assign index to each relevant element: e.g., {'H': 0, 'C': 1, 'O': 2}, use the ATYPE_INDEX in graph.py by default
+        fscale_bond: float, optional
+            The scaling factor for bond features, use value in graph.py by default
+        fscale_angle: float, optional
+            The scaling factor for angle features, use value in graph.py by default
         """
         self.nn = nn
         self.G = G
         self.G.get_all_subgraphs(nn, typify=True)
-        self.G.prepare_subgraph_feature_calc()
+        self.G.prepare_subgraph_feature_calc(max_valence=max_valence,
+                atype_index=atype_index,
+                fscale_bond=fscale_bond,
+                fscale_angle=fscale_angle)
         params = OrderedDict()
         key = jax.random.PRNGKey(seed)
         params['w'] = jax.random.uniform(key)
@@ -151,14 +167,14 @@ def message_pass(f_in, nb_connect, w, nn):
                 if nn == 0:
                     return f_in[0]
                 elif nn == 1:
-                    nb_connect0 = nb_connect[0:MAX_VALENCE - 1]
-                    nb_connect1 = nb_connect[MAX_VALENCE - 1:2 *
-                                             (MAX_VALENCE - 1)]
+                    nb_connect0 = nb_connect[0:max_valence - 1]
+                    nb_connect1 = nb_connect[max_valence - 1:2 *
+                                             (max_valence - 1)]
                     nb0 = jnp.sum(nb_connect0)
                     nb1 = jnp.sum(nb_connect1)
                     f = f_in[0] * (1 - jnp.heaviside(nb0, 0)*w - jnp.heaviside(nb1, 0)*w) + \
-                        w * nb_connect0.dot(f_in[1:MAX_VALENCE, :]) / jnp.piecewise(nb0, [nb0<1e-5, nb0>=1e-5], [lambda x: jnp.array(1e-5), lambda x: x]) + \
-                        w * nb_connect1.dot(f_in[MAX_VALENCE:2*MAX_VALENCE-1, :])/ jnp.piecewise(nb1, [nb1<1e-5, nb1>=1e-5], [lambda x: jnp.array(1e-5), lambda x: x])
+                        w * nb_connect0.dot(f_in[1:max_valence, :]) / jnp.piecewise(nb0, [nb0<1e-5, nb0>=1e-5], [lambda x: jnp.array(1e-5), lambda x: x]) + \
+                        w * nb_connect1.dot(f_in[max_valence:2*max_valence-1, :])/ jnp.piecewise(nb1, [nb1<1e-5, nb1>=1e-5], [lambda x: jnp.array(1e-5), lambda x: x])
                     return f
 
             features = fc0(features, params)