geom: use hydrogen torsion angles

keitaroyam · Dec 1, 2023 · 4d8006e · 4d8006e
1 parent 29376cb
commit 4d8006e
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/servalcat/__init__.py b/servalcat/__init__.py
@@ -6,5 +6,5 @@
 Mozilla Public License, version 2.0; see LICENSE.
 """
 
-__version__ = '0.4.41'
-__date__ = '2023-11-30'
+__version__ = '0.4.42'
+__date__ = '2023-12-01'
diff --git a/src/refine.cpp b/src/refine.cpp
@@ -622,6 +622,8 @@ void add_refine(py::module& m) {
     .def_readwrite("dinc_dummy", &Geometry::dinc_dummy)
     .def_readwrite("vdw_sdi_dummy", &Geometry::vdw_sdi_dummy)
     .def_readwrite("max_vdw_radius", &Geometry::max_vdw_radius)
+    // torsion parameters
+    .def_readwrite("use_hydr_tors", &Geometry::use_hydr_tors)
     // ADP restraint parameters
     .def_readwrite("adpr_max_dist", &Geometry::adpr_max_dist)
     .def_readwrite("adpr_d_power", &Geometry::adpr_d_power)

diff --git a/src/refine/geom.hpp b/src/refine/geom.hpp
@@ -604,6 +604,9 @@ struct Geometry {
   //double dvdw_cut_min_x  = 1.75; // used as twice in fast_hessian_tabulation.f // VDWR VDWC val
   double max_vdw_radius = 2.0;
 
+  // torsion
+  bool use_hydr_tors = true;
+
   // ADP restraints
   float adpr_max_dist = 4.;
   double adpr_d_power = 4;
@@ -665,12 +668,17 @@ inline void Geometry::load_topo(const gemmi::Topo& topo) {
                }
              };
 
-  auto test_link_r = [&topo](const gemmi::Topo::Rule& rule, const std::string& link_id) {
+  auto test_hydr_tors = [&](const gemmi::Topo::Torsion &t) {
+    return use_hydr_tors && (t.atoms[0]->is_hydrogen() || t.atoms[3]->is_hydrogen());
+  };
+  auto test_link_r = [&topo,&test_hydr_tors](const gemmi::Topo::Rule& rule, const std::string& link_id) {
                        if (rule.rkind != gemmi::Topo::RKind::Torsion)
                          return true;
                        const gemmi::Topo::Torsion& t = topo.torsions[rule.index];
                        if (t.restr->label.find("sp2_sp2") == 0)
                          return true;
+                       if (test_hydr_tors(t))
+                           return true;
                        return ((link_id == "TRANS"   || link_id != "CIS"  ||
                                 link_id == "PTRANS"  || link_id != "PCIS" ||
                                 link_id == "NMTRANS" || link_id != "NMCIS") &&
@@ -691,6 +699,7 @@ inline void Geometry::load_topo(const gemmi::Topo& topo) {
         for (const gemmi::Topo::Rule& rule : ri.monomer_rules) {
           if (rule.rkind != gemmi::Topo::RKind::Torsion ||
               topo.torsions[rule.index].restr->label.find("sp2_sp2") == 0 ||
+              test_hydr_tors(topo.torsions[rule.index]) ||
               (ri.orig_chemcomp && ri.orig_chemcomp->group == gemmi::ChemComp::Group::Peptide &&
                topo.torsions[rule.index].restr->label.find("chi") == 0))
             add(rule, true);