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Rename waterref to mdref #58

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merged 2 commits into from
Aug 2, 2021
Merged

Rename waterref to mdref #58

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b61ce32
rename `waterref` to `mdref`
rvhonorato Aug 2, 2021
5a25b85
Merge remote-tracking branch 'upstream/main' into rename-waterref
rvhonorato Aug 2, 2021
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4 changes: 2 additions & 2 deletions examples/docking/docking.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -30,7 +30,7 @@ ambig = 'ambig.tbl'
ambig = 'ambig.tbl'
cool1_steps = 500

[stage.waterref]
[stage.mdref]
ambig = 'ambig.tbl'
cool1_steps = 10

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0 src/haddock/modules/waterref/__init__.py → src/haddock/modules/mdref/__init__.py
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0 ...haddock/modules/waterref/cns/boxtyp20.pdb → src/haddock/modules/mdref/cns/boxtyp20.pdb
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0 ...ck/modules/waterref/cns/calc_free-ene.cns → ...ddock/modules/mdref/cns/calc_free-ene.cns
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0 ...modules/waterref/cns/centroids_create.cns → ...ck/modules/mdref/cns/centroids_create.cns
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0 ...les/waterref/cns/centroids_initialize.cns → ...odules/mdref/cns/centroids_initialize.cns
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0 ...haddock/modules/waterref/cns/cg-to-aa.cns → src/haddock/modules/mdref/cns/cg-to-aa.cns
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0 ...aterref/cns/charge-beads-interactions.cns → ...s/mdref/cns/charge-beads-interactions.cns
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0 ...dock/modules/waterref/cns/contactairs.cns → ...haddock/modules/mdref/cns/contactairs.cns
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0 ...k/modules/waterref/cns/def_solv_param.cns → ...dock/modules/mdref/cns/def_solv_param.cns
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0 ...dock/modules/waterref/cns/em_calc_lcc.cns → ...haddock/modules/mdref/cns/em_calc_lcc.cns
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0 ...ock/modules/waterref/cns/em_read_data.cns → ...addock/modules/mdref/cns/em_read_data.cns
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0 ...odules/waterref/cns/flex_segment_back.cns → ...k/modules/mdref/cns/flex_segment_back.cns
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0 ...odules/waterref/cns/flex_segment_side.cns → ...k/modules/mdref/cns/flex_segment_side.cns
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0 ...dules/waterref/cns/flexauto-neighbors.cns → .../modules/mdref/cns/flexauto-neighbors.cns
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0 ...k/modules/waterref/cns/generate_water.cns → ...dock/modules/mdref/cns/generate_water.cns
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0 ...ddock/modules/waterref/cns/initialize.cns → src/haddock/modules/mdref/cns/initialize.cns
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0 ...dock/modules/waterref/cns/mini_tensor.cns → ...haddock/modules/mdref/cns/mini_tensor.cns
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0 ...modules/waterref/cns/mini_tensor_dani.cns → ...ck/modules/mdref/cns/mini_tensor_dani.cns
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0 ...modules/waterref/cns/mini_tensor_para.cns → ...ck/modules/mdref/cns/mini_tensor_para.cns
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0 ...modules/waterref/cns/print_coorheader.cns → ...ck/modules/mdref/cns/print_coorheader.cns
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0 ...addock/modules/waterref/cns/read_data.cns → src/haddock/modules/mdref/cns/read_data.cns
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0 ...addock/modules/waterref/cns/read_noes.cns → src/haddock/modules/mdref/cns/read_noes.cns
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0 ...ck/modules/waterref/cns/read_struc-cg.cns → ...ddock/modules/mdref/cns/read_struc-cg.cns
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0 ...ddock/modules/waterref/cns/read_struc.cns → src/haddock/modules/mdref/cns/read_struc.cns
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0 ...dock/modules/waterref/cns/read_water1.cns → ...haddock/modules/mdref/cns/read_water1.cns
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0 src/haddock/modules/waterref/cns/run.cns → src/haddock/modules/mdref/cns/run.cns
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0 ...k/modules/waterref/cns/scale_cg-to-aa.cns → ...dock/modules/mdref/cns/scale_cg-to-aa.cns
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0 ...dock/modules/waterref/cns/scale_inter.cns → ...haddock/modules/mdref/cns/scale_inter.cns
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0 ...odules/waterref/cns/scale_inter_final.cns → ...k/modules/mdref/cns/scale_inter_final.cns
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0 ...modules/waterref/cns/scale_intra_only.cns → ...ck/modules/mdref/cns/scale_intra_only.cns
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0 ...ck/modules/waterref/cns/set_noe_scale.cns → ...ddock/modules/mdref/cns/set_noe_scale.cns
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0 ...haddock/modules/waterref/cns/setflags.cns → src/haddock/modules/mdref/cns/setflags.cns
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0 ...dock/modules/waterref/cns/symmultimer.cns → ...haddock/modules/mdref/cns/symmultimer.cns
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0 ...ddock/modules/waterref/cns/water_rest.cns → src/haddock/modules/mdref/cns/water_rest.cns
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0 ...haddock/modules/waterref/cns/waterref.cns → src/haddock/modules/mdref/cns/waterref.cns
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0 ...addock/modules/waterref/cns/waterref.toml → src/haddock/modules/mdref/cns/waterref.toml
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6 changes: 3 additions & 3 deletions src/haddock/modules/waterref/default.py → src/haddock/modules/mdref/default.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = []
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