Aleaverfay/dlin2

tmol/database/default/scoring/ljlk.yaml

@@ -1,7 +1,7 @@
 global_parameters:
   max_dis : 6.0
   spline_start : 4.5 #max_dis - 1.5
-  lj_switch_dis2sigma : 0.6
+  lj_dlin_sigma_factor : 0.6
   lj_hbond_OH_donor_dis : 2.6
   lj_hbond_hdis : 1.75
   lj_hbond_dis : 3.0

tmol/database/scoring/ljlk.py

@@ -15,7 +15,7 @@ class LJLKGlobalParameters:
     lj_hbond_OH_donor_dis: float
     lj_hbond_dis: float
     lj_hbond_hdis: float
-    lj_switch_dis2sigma: float
+    lj_dlin_sigma_factor: float
     lk_min_dis2sigma: float
     lkb_water_dist: float
     lkb_water_angle_sp2: Angle

tmol/score/ljlk/ljlk_energy_term.py

@@ -116,6 +116,7 @@ def _t(ts):
         global_params = torch.stack(
             _t(
                 [
+                    self.global_params.lj_dlin_sigma_factor,
                     self.global_params.lj_hbond_dis,
                     self.global_params.lj_hbond_OH_donor_dis,
                     self.global_params.lj_hbond_hdis,

tmol/score/ljlk/params.py

@@ -21,10 +21,10 @@
 class LJLKGlobalParams(TensorGroup):
     max_dis: Tensor[torch.float32][...]
     spline_start: Tensor[torch.float32][...]
+    lj_dlin_sigma_factor: Tensor[torch.float32][...]
     lj_hbond_OH_donor_dis: Tensor[torch.float32][...]
     lj_hbond_dis: Tensor[torch.float32][...]
     lj_hbond_hdis: Tensor[torch.float32][...]
-    lj_switch_dis2sigma: Tensor[torch.float32][...]
     lk_min_dis2sigma: Tensor[torch.float32][...]
 
     # not clear if this belongs here or in a separate class

tmol/score/ljlk/potentials/lj.hh

@@ -80,7 +80,7 @@ struct lj_score {
     } else {
       Real sigma = lj_sigma<Real>(i, j, global);
       Real epsilon = std::sqrt(i.lj_wdepth * j.lj_wdepth);
-      Real d_lin = sigma * 0.6;
+      Real d_lin = sigma * global.lj_dlin_sigma_factor;
       Real cpoly_dmin =
           sigma > 4.5 ? (sigma > cpoly_dmax - 0.1 ? cpoly_dmax - 0.1 : sigma)
                       : 4.5;
@@ -122,7 +122,9 @@ struct lj_score {
     Real weight = connectivity_weight<Real, Real>(bonded_path_length);
     Real epsilon = std::sqrt(i.lj_wdepth * j.lj_wdepth);
 
-    Real d_lin = sigma * 0.6;
+    // Real d_lin = sigma * 0.6;
+    Real d_lin = sigma * global.lj_dlin_sigma_factor;
+
     Real cpoly_dmin = 4.5;
     if (sigma > cpoly_dmin) cpoly_dmin = sigma;
 

tmol/score/ljlk/potentials/params.hh

@@ -62,6 +62,7 @@ struct LJLKTypeParams {
 
 template <typename Real>
 struct LJGlobalParams {
+  Real lj_dlin_sigma_factor;
   Real lj_hbond_dis;
   Real lj_hbond_OH_donor_dis;
   Real lj_hbond_hdis;
@@ -115,14 +116,18 @@ struct LKTypeParamTensors {
 
 template <typename Real, tmol::Device D>
 struct LJGlobalParamTensors {
+  TView<Real, 1, D> lj_dlin_sigma_factor;
   TView<Real, 1, D> lj_hbond_dis;
   TView<Real, 1, D> lj_hbond_OH_donor_dis;
   TView<Real, 1, D> lj_hbond_hdis;
 
   template <typename Idx>
   auto operator[](Idx i) const {
     return LJGlobalParams<Real>{
-        lj_hbond_dis[i], lj_hbond_OH_donor_dis[i], lj_hbond_hdis[i]};
+        lj_dlin_sigma_factor[i],
+        lj_hbond_dis[i],
+        lj_hbond_OH_donor_dis[i],
+        lj_hbond_hdis[i]};
   }
 };
 

tmol/score/ljlk/potentials/params.pybind.hh

@@ -114,6 +114,7 @@ struct type_caster<tmol::score::ljlk::potentials::LJGlobalParams<Real>> {
   bool load(handle src, bool convert) {
     nvtx_range_function();
 
+    CAST_ATTR(src, value, lj_dlin_sigma_factor);
     CAST_ATTR(src, value, lj_hbond_dis);
     CAST_ATTR(src, value, lj_hbond_OH_donor_dis);
     CAST_ATTR(src, value, lj_hbond_hdis);
@@ -133,6 +134,7 @@ struct type_caster<
   bool load(handle src, bool convert) {
     nvtx_range_function();
 
+    CAST_ATTR(src, value, lj_dlin_sigma_factor);
     CAST_ATTR(src, value, lj_hbond_dis);
     CAST_ATTR(src, value, lj_hbond_OH_donor_dis);
     CAST_ATTR(src, value, lj_hbond_hdis);