Now the Secondary structure works with the manual and the new shorcuts

Author: Iximiel

src/secondarystructure/AlphaRMSD.cpp

@@ -108,7 +108,7 @@ class AlphaRMSD : public ActionShortcut {
 PLUMED_REGISTER_ACTION(AlphaRMSD,"ALPHARMSD")
 
 void AlphaRMSD::registerKeywords( Keywords& keys ) {
-  SecondaryStructureBase<Vector>::registerKeywords( keys );
+  SecondaryStructureInput::registerKeywords( keys );
   keys.remove("ATOMS");
   keys.remove("SEGMENT");
   keys.remove("STRUCTURE");
@@ -122,11 +122,11 @@ AlphaRMSD::AlphaRMSD(const ActionOptions&ao):
   ActionShortcut(ao) {
   // Read in the input and create a string that describes how to compute the less than
   std::string ltmap;
-  bool uselessthan=SecondaryStructureBase<Vector>::readShortcutWords( ltmap, this );
+  bool uselessthan=SecondaryStructureInput::readShortcutWords( ltmap, this );
   // read in the backbone atoms
   std::vector<unsigned> chains;
   std::vector<std::string> all_atoms;
-  SecondaryStructureBase<Vector>::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
+  SecondaryStructureInput::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
 
   // This constructs all conceivable sections of alpha helix in the backbone of the chains
   unsigned nprevious=0, segno=1;

src/secondarystructure/AntibetaRMSD.cpp

@@ -116,7 +116,7 @@ class AntibetaRMSD : public ActionShortcut {
 PLUMED_REGISTER_ACTION(AntibetaRMSD,"ANTIBETARMSD")
 
 void AntibetaRMSD::registerKeywords( Keywords& keys ) {
-  SecondaryStructureBase<Vector>::registerKeywords( keys );
+  SecondaryStructureInput::registerKeywords( keys );
   keys.remove("ATOMS");
   keys.remove("SEGMENT");
   keys.remove("STRUCTURE");
@@ -140,11 +140,11 @@ AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao):
   ActionShortcut(ao) {
   // Read in the input and create a string that describes how to compute the less than
   std::string ltmap;
-  bool uselessthan=SecondaryStructureBase<Vector>::readShortcutWords( ltmap, this );
+  bool uselessthan=SecondaryStructureInput::readShortcutWords( ltmap, this );
   // read in the backbone atoms
   std::vector<unsigned> chains;
   std::vector<std::string> all_atoms;
-  SecondaryStructureBase<Vector>::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
+  SecondaryStructureInput::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
 
   bool intra_chain(false), inter_chain(false);
   std::string style;

src/secondarystructure/ParabetaRMSD.cpp

@@ -116,7 +116,7 @@ class ParabetaRMSD : public ActionShortcut {
 PLUMED_REGISTER_ACTION(ParabetaRMSD,"PARABETARMSD")
 
 void ParabetaRMSD::registerKeywords( Keywords& keys ) {
-  SecondaryStructureBase<Vector>::registerKeywords( keys );
+  SecondaryStructureInput::registerKeywords( keys );
   keys.remove("ATOMS");
   keys.remove("SEGMENT");
   keys.remove("STRUCTURE");
@@ -141,11 +141,11 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao):
   ActionShortcut(ao) {
   // Read in the input and create a string that describes how to compute the less than
   std::string ltmap;
-  bool uselessthan=SecondaryStructureBase<Vector>::readShortcutWords( ltmap, this );
+  bool uselessthan=SecondaryStructureInput::readShortcutWords( ltmap, this );
   // read in the backbone atoms
   std::vector<unsigned> chains;
   std::vector<std::string> all_atoms;
-  SecondaryStructureBase<Vector>::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
+  SecondaryStructureInput::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
 
   bool intra_chain(false), inter_chain(false);
   std::string style;

src/secondarystructure/SecondaryStructureBase.h

@@ -29,6 +29,7 @@
 #include "core/GenericMolInfo.h"
 #include "core/ParallelTaskManager.h"
 #include "tools/ColvarOutput.h"
+#include "tools/TypeUtils.h"
 #include <vector>
 #include <type_traits>
 
@@ -86,6 +87,9 @@ class SecondaryStructureBase: public ActionWithVector {
   static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, const T& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices );
 };
 
+//this is used to get some of the static non template dependant functionalities for Secondary structure
+using SecondaryStructureInput=SecondaryStructureBase<Empty>;
+
 template <class T,typename myPTM>
 unsigned SecondaryStructureBase<T,myPTM>::getNumberOfDerivatives() {
   return 3*getNumberOfAtoms()+virialSize;
@@ -112,6 +116,7 @@ bool SecondaryStructureBase<T,myPTM>::readShortcutWords( std::string& ltmap, Act
 template <class T,typename myPTM>
 void SecondaryStructureBase<T,myPTM>::registerKeywords( Keywords& keys ) {
   ActionWithVector::registerKeywords( keys );
+  T::registerKeywords( keys );
   PTM::registerKeywords( keys );
   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions");
   keys.addInputKeyword("optional","MASK","vector","a vector which is used to determine which elements of the secondary structure variable should be computed");

src/secondarystructure/SecondaryStructureDRMSD.h

@@ -99,6 +99,9 @@ class SecondaryStructureDRMSDInput {
   flexibleMemory<unsigned> drmsd_atoms{};
 /// The general input for the secondary structure variable
 public:
+  static void registerKeywords( Keywords& keys ) {
+    keys.setDisplayName("SECONDARY_STRUCTURE_DRMSD");
+  }
   static constexpr bool needsBondLength=true;
   typedef T precision;
   size_t natoms{0};

src/secondarystructure/SecondaryStructureRMSD.cpp

@@ -125,6 +125,9 @@ class SecondaryStructureRMSDInput {
 /// The list of reference configurations
   std::vector<RMSD> myrmsd;
 public:
+  static void registerKeywords( Keywords& keys ) {
+    keys.setDisplayName("SECONDARY_STRUCTURE_RMSD");
+  }
   static constexpr bool needsType=true;
 /// The number of atoms
   std::size_t natoms;

src/tools/TypeUtils.cpp

@@ -0,0 +1,22 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2025 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "TypeUtils.h"

src/tools/TypeUtils.h

@@ -0,0 +1,32 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2025 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_tools_TypeUtils_h
+#define __PLUMED_tools_TypeUtils_h
+namespace PLMD {
+class Keywords;
+// An empty type witha a empty registerKeywords
+// This is useful when setting up certains shortcuts (see ANTIBETARMSD for example)
+struct Empty {
+  static void registerKeywords( Keywords& keys ) {}
+};
+} //namespace PLMD
+#endif // __PLUMED_tools_TypeUtils_h