Fix some bugs and docs errors due to the DRH -> NA change

lorenzo-rovigatti · Nov 20, 2023 · 79728d3 · 79728d3
1 parent aaebaeb
commit 79728d3
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/docs/source/configurations.md b/docs/source/configurations.md
@@ -117,7 +117,7 @@ CGCAAC type=DNA
 ```
 
 ```{note}
-Setting `type` only affects the force field when using the DNA/RNA hybrid model (`interaction_type=DRH`). For normal DNA or RNA, the interactions will be determined by the `interaction_type=DNA|DNA2|RNA|RNA2|DRH|LJ...` parameter in the [input file](input.md)
+Setting `type` only affects the force field when using the DNA/RNA hybrid model (`interaction_type=NA`). For normal DNA or RNA, the interactions will be determined by the `interaction_type=DNA|DNA2|RNA|RNA2|NA|LJ...` parameter in the [input file](input.md)
 ```
 
 ```{note}

diff --git a/docs/source/install.md b/docs/source/install.md
@@ -118,7 +118,7 @@ cmake -DPython=1 -DPYTHON_EXECUTABLE=$HOME/miniconda3/bin/python -DPYTHON_INCLUD
 
 ## Testing
 
-* `make test_run` runs quick tests to check that oxDNA has been correctly compiled, and that the core interactions (`DNA2`, `RNA2` and `DRH`) compute the energy contributions in a nicked double strand correctly.
+* `make test_run` runs quick tests to check that oxDNA has been correctly compiled, and that the core interactions (`DNA2`, `RNA2` and `NA`) compute the energy contributions in a nicked double strand correctly.
 * `make test_quick` runs longer tests to check that oxDNA works.
 * `make test_oxpy` checks that the Python bindings work.
 * `make test` runs all sets of tests above.

diff --git a/src/Backends/VMMC_CPUBackend.cpp b/src/Backends/VMMC_CPUBackend.cpp
@@ -193,7 +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");
+	ok_interactions.push_back("NA");
 	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()) {

diff --git a/src/Interactions/DNAInteraction.cpp b/src/Interactions/DNAInteraction.cpp
@@ -236,7 +236,7 @@ void DNAInteraction::get_settings(input_file &inp) {
 			std::string inter_type;
 			getInputString(&inp, "interaction_type", inter_type, 0);
 
-			if(inter_type.compare("DRH") || inter_type.compare("DRH_relax")) {
+			if(inter_type.compare("NA") || inter_type.compare("NA_relax")) {
 				getInputString(&inp, "seq_dep_file_DNA", _seq_filename, 1);
 			} else {
 				getInputString(&inp, "seq_dep_file", _seq_filename, 1);

diff --git a/src/Interactions/RNAInteraction.cpp b/src/Interactions/RNAInteraction.cpp
@@ -54,7 +54,7 @@ void RNAInteraction::get_settings(input_file &inp) {
 		if(!_average) {
 			std::string inter_type;
 			getInputString(&inp, "interaction_type", inter_type, 0);
-			if(inter_type.compare("DRH") || inter_type.compare("DRH_relax")) {
+			if(inter_type.compare("NA") || inter_type.compare("NA_relax")) {
 				getInputString(&inp, "seq_dep_file_RNA", _seq_filename, 1);
 			} else {
 				getInputString(&inp, "seq_dep_file", _seq_filename, 1);

diff --git a/test/TestSuite.py b/test/TestSuite.py
@@ -346,7 +346,7 @@ def __init__(self, list_file, executable, level, threads=1):
     def launch(self):
         for i in range(self.threads):
             runner = Runner(i)
-            runner.setDaemon(True)
+            runner.daemon = True
             runner.start()
 
         for system in self.systems: