DNA-RNA hybrids

.github/workflows/test-linux.yml

@@ -22,4 +22,5 @@ jobs:
     - name: Run Simple Test Script
       run: |
         pushd build
+        make test_run
         make test_quick

DRH_sequence_dependent_parameters.txt

@@ -0,0 +1,4 @@
+HYDR_A_U = 1.21
+HYDR_A_T = 1.37
+HYDR_rC_dG = 1.61
+HYDR_rG_dC = 1.77

src/Backends/FFS_MD_CPUBackend.cpp

@@ -218,6 +218,7 @@ number FFS_MD_CPUBackend::pair_interaction_nonbonded_DNA_with_op(BaseParticle *p
 
 	_interaction->set_computed_r(computed_r);
 	number energy = _interaction->pair_interaction_term(DNAInteraction::HYDROGEN_BONDING, p, q, false, update_forces);
+
 	if(energy <= MAX_BOND_CUTOFF) {
 		_op.add_hb(q->index, p->index, energy);
 	}
@@ -235,6 +236,8 @@ number FFS_MD_CPUBackend::pair_interaction_nonbonded_DNA_with_op(BaseParticle *p
 		energy += _interaction->pair_interaction_term(RNA2Interaction::DEBYE_HUCKEL, p, q, false, update_forces);
 	}
 
+
+
 	return energy;
 }
 

src/Backends/VMMC_CPUBackend.cpp

@@ -7,6 +7,7 @@
 #include "../Utilities/Utils.h"
 #include "../Interactions/RNAInteraction2.h"
 #include "../Interactions/DNA2Interaction.h"
+#include "../Interactions/DRHInteraction.h"
 
 #include <set>
 #include <sstream>
@@ -192,6 +193,7 @@ void VMMC_CPUBackend::get_settings(input_file & inp) {
 	ok_interactions.push_back("DNA2_nomesh");
 	ok_interactions.push_back("RNA");
 	ok_interactions.push_back("RNA2");
+	ok_interactions.push_back("DRH");
 	if(getInputString(&inp, "interaction_type", inter, 0) == KEY_FOUND) {
 		// std::find points is equal to ok_interactions.end() if it can't find inter in ok_interactions.
 		if(std::find(ok_interactions.begin(), ok_interactions.end(), inter) == ok_interactions.end()) {
@@ -424,17 +426,26 @@ inline number VMMC_CPUBackend::_particle_particle_nonbonded_interaction_VMMC(Bas
 	energy += _interaction->pair_interaction_term(DNAInteraction::NONBONDED_EXCLUDED_VOLUME, p, q, false, false);
 	energy += _interaction->pair_interaction_term(DNAInteraction::CROSS_STACKING, p, q, false, false);
 
-	// all interactions except DNA2Interaction use the DNAInteraction coaxial stacking
-	if(dynamic_cast<DNA2Interaction *>(_interaction.get()) == NULL)
-	energy += _interaction->pair_interaction_term(DNAInteraction::COAXIAL_STACKING, p, q, false, false);
+	// all interactions except DNA2Interaction use the DNAInteraction coaxial stacking*
+	// *the hybrid interaction is a second exception
+	if( (dynamic_cast<DNA2Interaction *>(_interaction.get()) == NULL) || (dynamic_cast<DRHInteraction *>(_interaction.get()) == NULL) ) {
+		energy += _interaction->pair_interaction_term(DNAInteraction::COAXIAL_STACKING, p, q, false, false);
+	}
 
-	if(dynamic_cast<DNA2Interaction *>(_interaction.get()) != NULL) {
+	if(dynamic_cast<DRHInteraction *>(_interaction.get()) != NULL) {
+		energy += _interaction->pair_interaction_term(DRHInteraction::COAXIAL_STACKING, p, q, false, false);
+		energy += _interaction->pair_interaction_term(DRHInteraction::DEBYE_HUCKEL, p, q, false, false);
+	}
+
+	else if(dynamic_cast<DNA2Interaction *>(_interaction.get()) != NULL) {
 		energy += _interaction->pair_interaction_term(DNA2Interaction::COAXIAL_STACKING, p, q, false, false);
 		energy += _interaction->pair_interaction_term(DNA2Interaction::DEBYE_HUCKEL, p, q, false, false);
 	}
 	else if(dynamic_cast<RNA2Interaction *>(_interaction.get()) != NULL) {
 		energy += _interaction->pair_interaction_term(RNA2Interaction::DEBYE_HUCKEL, p, q, false, false);
 	}
+
+
 
 	return energy;
 }

src/CMakeLists.txt

@@ -122,6 +122,8 @@ SET(interactions_SOURCES
 	Interactions/PatchyInteractionDan.cpp
 	Interactions/KFInteraction.cpp
 	Interactions/CustomInteraction.cpp
+	Interactions/DRHInteraction.cpp
+	Interactions/DRHInteraction_relax.cpp
 )
 
 SET(move_SOURCES

src/Interactions/DNA2Interaction.h

@@ -25,7 +25,7 @@
 
 #include "DNAInteraction.h"
 
-class DNA2Interaction: public DNAInteraction {
+class DNA2Interaction: virtual public DNAInteraction {
 
 protected:
 	float _salt_concentration;

src/Interactions/DNAInteraction.cpp

@@ -233,7 +233,15 @@ void DNAInteraction::get_settings(input_file &inp) {
 
 	if(getInputBool(&inp, "use_average_seq", &_average, 0) == KEY_FOUND) {
 		if(!_average) {
-			getInputString(&inp, "seq_dep_file", _seq_filename, 1);
+			std::string inter_type;
+			getInputString(&inp, "interaction_type", inter_type, 0);
+
+			if(inter_type.compare("DRH") || inter_type.compare("DRH_relax")) {
+				getInputString(&inp, "seq_dep_file_DNA", _seq_filename, 1);
+			} else {
+				getInputString(&inp, "seq_dep_file", _seq_filename, 1);
+			}
+
 			OX_LOG(Logger::LOG_INFO, "Using '%s' as the input for sequence-dependent values", _seq_filename.c_str());
 		}
 	}

src/Interactions/DNAInteraction.h

@@ -12,7 +12,7 @@
  * This is the default interaction.
  */
 
-class DNAInteraction : public BaseInteraction {
+class DNAInteraction : virtual public BaseInteraction {
 protected:
 	bool _average;
 	std::string _seq_filename;