diff --git a/examples/docking/docking.toml b/examples/docking/docking.toml index 554c145b3..2d1b2ddc8 100644 --- a/examples/docking/docking.toml +++ b/examples/docking/docking.toml @@ -3,7 +3,7 @@ [input] # in which order the steps must be executed? -order = ["topology", "rigidbody", "flexref", "waterref"] +order = ["topology", "rigidbody", "flexref", "mdref"] # directory in which the scoring will be done project_dir = "run1" @@ -30,7 +30,7 @@ ambig = 'ambig.tbl' ambig = 'ambig.tbl' cool1_steps = 500 -[stage.waterref] +[stage.mdref] ambig = 'ambig.tbl' cool1_steps = 10 diff --git a/src/haddock/modules/waterref/__init__.py b/src/haddock/modules/mdref/__init__.py similarity index 100% rename from src/haddock/modules/waterref/__init__.py rename to src/haddock/modules/mdref/__init__.py diff --git a/src/haddock/modules/waterref/cns/boxtyp20.pdb b/src/haddock/modules/mdref/cns/boxtyp20.pdb similarity index 100% rename from src/haddock/modules/waterref/cns/boxtyp20.pdb rename to src/haddock/modules/mdref/cns/boxtyp20.pdb diff --git a/src/haddock/modules/waterref/cns/calc_free-ene.cns b/src/haddock/modules/mdref/cns/calc_free-ene.cns similarity index 100% rename from src/haddock/modules/waterref/cns/calc_free-ene.cns rename to src/haddock/modules/mdref/cns/calc_free-ene.cns diff --git a/src/haddock/modules/waterref/cns/centroids_create.cns b/src/haddock/modules/mdref/cns/centroids_create.cns similarity index 100% rename from src/haddock/modules/waterref/cns/centroids_create.cns rename to src/haddock/modules/mdref/cns/centroids_create.cns diff --git a/src/haddock/modules/waterref/cns/centroids_initialize.cns b/src/haddock/modules/mdref/cns/centroids_initialize.cns similarity index 100% rename from src/haddock/modules/waterref/cns/centroids_initialize.cns rename to src/haddock/modules/mdref/cns/centroids_initialize.cns diff --git a/src/haddock/modules/waterref/cns/cg-to-aa.cns b/src/haddock/modules/mdref/cns/cg-to-aa.cns similarity index 100% rename from src/haddock/modules/waterref/cns/cg-to-aa.cns rename to src/haddock/modules/mdref/cns/cg-to-aa.cns diff --git a/src/haddock/modules/waterref/cns/charge-beads-interactions.cns b/src/haddock/modules/mdref/cns/charge-beads-interactions.cns similarity index 100% rename from src/haddock/modules/waterref/cns/charge-beads-interactions.cns rename to src/haddock/modules/mdref/cns/charge-beads-interactions.cns diff --git a/src/haddock/modules/waterref/cns/contactairs.cns b/src/haddock/modules/mdref/cns/contactairs.cns similarity index 100% rename from src/haddock/modules/waterref/cns/contactairs.cns rename to src/haddock/modules/mdref/cns/contactairs.cns diff --git a/src/haddock/modules/waterref/cns/def_solv_param.cns b/src/haddock/modules/mdref/cns/def_solv_param.cns similarity index 100% rename from src/haddock/modules/waterref/cns/def_solv_param.cns rename to src/haddock/modules/mdref/cns/def_solv_param.cns diff --git a/src/haddock/modules/waterref/cns/em_calc_lcc.cns b/src/haddock/modules/mdref/cns/em_calc_lcc.cns similarity index 100% rename from src/haddock/modules/waterref/cns/em_calc_lcc.cns rename to src/haddock/modules/mdref/cns/em_calc_lcc.cns diff --git a/src/haddock/modules/waterref/cns/em_read_data.cns b/src/haddock/modules/mdref/cns/em_read_data.cns similarity index 100% rename from src/haddock/modules/waterref/cns/em_read_data.cns rename to src/haddock/modules/mdref/cns/em_read_data.cns diff --git a/src/haddock/modules/waterref/cns/flex_segment_back.cns b/src/haddock/modules/mdref/cns/flex_segment_back.cns similarity index 100% rename from src/haddock/modules/waterref/cns/flex_segment_back.cns rename to src/haddock/modules/mdref/cns/flex_segment_back.cns diff --git a/src/haddock/modules/waterref/cns/flex_segment_side.cns b/src/haddock/modules/mdref/cns/flex_segment_side.cns similarity index 100% rename from src/haddock/modules/waterref/cns/flex_segment_side.cns rename to src/haddock/modules/mdref/cns/flex_segment_side.cns diff --git a/src/haddock/modules/waterref/cns/flexauto-neighbors.cns b/src/haddock/modules/mdref/cns/flexauto-neighbors.cns similarity index 100% rename from src/haddock/modules/waterref/cns/flexauto-neighbors.cns rename to src/haddock/modules/mdref/cns/flexauto-neighbors.cns diff --git a/src/haddock/modules/waterref/cns/generate_water.cns b/src/haddock/modules/mdref/cns/generate_water.cns similarity index 100% rename from src/haddock/modules/waterref/cns/generate_water.cns rename to src/haddock/modules/mdref/cns/generate_water.cns diff --git a/src/haddock/modules/waterref/cns/initialize.cns b/src/haddock/modules/mdref/cns/initialize.cns similarity index 100% rename from src/haddock/modules/waterref/cns/initialize.cns rename to src/haddock/modules/mdref/cns/initialize.cns diff --git a/src/haddock/modules/waterref/cns/mini_tensor.cns b/src/haddock/modules/mdref/cns/mini_tensor.cns similarity index 100% rename from src/haddock/modules/waterref/cns/mini_tensor.cns rename to src/haddock/modules/mdref/cns/mini_tensor.cns diff --git a/src/haddock/modules/waterref/cns/mini_tensor_dani.cns b/src/haddock/modules/mdref/cns/mini_tensor_dani.cns similarity index 100% rename from src/haddock/modules/waterref/cns/mini_tensor_dani.cns rename to src/haddock/modules/mdref/cns/mini_tensor_dani.cns diff --git a/src/haddock/modules/waterref/cns/mini_tensor_para.cns b/src/haddock/modules/mdref/cns/mini_tensor_para.cns similarity index 100% rename from src/haddock/modules/waterref/cns/mini_tensor_para.cns rename to src/haddock/modules/mdref/cns/mini_tensor_para.cns diff --git a/src/haddock/modules/waterref/cns/print_coorheader.cns b/src/haddock/modules/mdref/cns/print_coorheader.cns similarity index 100% rename from src/haddock/modules/waterref/cns/print_coorheader.cns rename to src/haddock/modules/mdref/cns/print_coorheader.cns diff --git a/src/haddock/modules/waterref/cns/read_data.cns b/src/haddock/modules/mdref/cns/read_data.cns similarity index 100% rename from src/haddock/modules/waterref/cns/read_data.cns rename to src/haddock/modules/mdref/cns/read_data.cns diff --git a/src/haddock/modules/waterref/cns/read_noes.cns b/src/haddock/modules/mdref/cns/read_noes.cns similarity index 100% rename from src/haddock/modules/waterref/cns/read_noes.cns rename to src/haddock/modules/mdref/cns/read_noes.cns diff --git a/src/haddock/modules/waterref/cns/read_struc-cg.cns b/src/haddock/modules/mdref/cns/read_struc-cg.cns similarity index 100% rename from src/haddock/modules/waterref/cns/read_struc-cg.cns rename to src/haddock/modules/mdref/cns/read_struc-cg.cns diff --git a/src/haddock/modules/waterref/cns/read_struc.cns b/src/haddock/modules/mdref/cns/read_struc.cns similarity index 100% rename from src/haddock/modules/waterref/cns/read_struc.cns rename to src/haddock/modules/mdref/cns/read_struc.cns diff --git a/src/haddock/modules/waterref/cns/read_water1.cns b/src/haddock/modules/mdref/cns/read_water1.cns similarity index 100% rename from src/haddock/modules/waterref/cns/read_water1.cns rename to src/haddock/modules/mdref/cns/read_water1.cns diff --git a/src/haddock/modules/waterref/cns/run.cns b/src/haddock/modules/mdref/cns/run.cns similarity index 100% rename from src/haddock/modules/waterref/cns/run.cns rename to src/haddock/modules/mdref/cns/run.cns diff --git a/src/haddock/modules/waterref/cns/scale_cg-to-aa.cns b/src/haddock/modules/mdref/cns/scale_cg-to-aa.cns similarity index 100% rename from src/haddock/modules/waterref/cns/scale_cg-to-aa.cns rename to src/haddock/modules/mdref/cns/scale_cg-to-aa.cns diff --git a/src/haddock/modules/waterref/cns/scale_inter.cns b/src/haddock/modules/mdref/cns/scale_inter.cns similarity index 100% rename from src/haddock/modules/waterref/cns/scale_inter.cns rename to src/haddock/modules/mdref/cns/scale_inter.cns diff --git a/src/haddock/modules/waterref/cns/scale_inter_final.cns b/src/haddock/modules/mdref/cns/scale_inter_final.cns similarity index 100% rename from src/haddock/modules/waterref/cns/scale_inter_final.cns rename to src/haddock/modules/mdref/cns/scale_inter_final.cns diff --git a/src/haddock/modules/waterref/cns/scale_intra_only.cns b/src/haddock/modules/mdref/cns/scale_intra_only.cns similarity index 100% rename from src/haddock/modules/waterref/cns/scale_intra_only.cns rename to src/haddock/modules/mdref/cns/scale_intra_only.cns diff --git a/src/haddock/modules/waterref/cns/set_noe_scale.cns b/src/haddock/modules/mdref/cns/set_noe_scale.cns similarity index 100% rename from src/haddock/modules/waterref/cns/set_noe_scale.cns rename to src/haddock/modules/mdref/cns/set_noe_scale.cns diff --git a/src/haddock/modules/waterref/cns/setflags.cns b/src/haddock/modules/mdref/cns/setflags.cns similarity index 100% rename from src/haddock/modules/waterref/cns/setflags.cns rename to src/haddock/modules/mdref/cns/setflags.cns diff --git a/src/haddock/modules/waterref/cns/symmultimer.cns b/src/haddock/modules/mdref/cns/symmultimer.cns similarity index 100% rename from src/haddock/modules/waterref/cns/symmultimer.cns rename to src/haddock/modules/mdref/cns/symmultimer.cns diff --git a/src/haddock/modules/waterref/cns/water_rest.cns b/src/haddock/modules/mdref/cns/water_rest.cns similarity index 100% rename from src/haddock/modules/waterref/cns/water_rest.cns rename to src/haddock/modules/mdref/cns/water_rest.cns diff --git a/src/haddock/modules/waterref/cns/waterref.cns b/src/haddock/modules/mdref/cns/waterref.cns similarity index 100% rename from src/haddock/modules/waterref/cns/waterref.cns rename to src/haddock/modules/mdref/cns/waterref.cns diff --git a/src/haddock/modules/waterref/cns/waterref.toml b/src/haddock/modules/mdref/cns/waterref.toml similarity index 100% rename from src/haddock/modules/waterref/cns/waterref.toml rename to src/haddock/modules/mdref/cns/waterref.toml diff --git a/src/haddock/modules/waterref/default.py b/src/haddock/modules/mdref/default.py similarity index 96% rename from src/haddock/modules/waterref/default.py rename to src/haddock/modules/mdref/default.py index 970321e5f..31d4bf28b 100644 --- a/src/haddock/modules/waterref/default.py +++ b/src/haddock/modules/mdref/default.py @@ -54,12 +54,12 @@ class HaddockModule(BaseHaddockModule): def __init__(self, stream, order, path): self.stream = stream recipe_path = Path(__file__).resolve().parent.absolute() - cns_script = recipe_path / "cns" / "waterref.cns" - defaults = recipe_path / "cns" / "waterref.toml" + cns_script = recipe_path / "cns" / "mdref.cns" + defaults = recipe_path / "cns" / "mdref.toml" super().__init__(order, path, cns_script, defaults) def run(self, module_information): - logger.info("Running [waterref] module") + logger.info("Running [mdref] module") # Pool of jobs to be executed by the CNS engine jobs = []