From 79728d33c41f0fc6397be24131d8c2475eb97083 Mon Sep 17 00:00:00 2001 From: Lorenzo Rovigatti Date: Mon, 20 Nov 2023 12:48:05 +0100 Subject: [PATCH] Fix some bugs and docs errors due to the DRH -> NA change --- docs/source/configurations.md | 2 +- docs/source/install.md | 2 +- src/Backends/VMMC_CPUBackend.cpp | 2 +- src/Interactions/DNAInteraction.cpp | 2 +- src/Interactions/RNAInteraction.cpp | 2 +- test/TestSuite.py | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source/configurations.md b/docs/source/configurations.md index 98001993a..ec86d1580 100644 --- 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 index 3a4493ae2..ed5be4b42 100644 --- 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 index f4bc58fff..374deeea4 100644 --- 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 index 9bb619d58..c4eecabaa 100644 --- 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 index febc17eca..0e87dfff8 100644 --- 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 index 41bbd5778..1216a4286 100755 --- 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: