CHANGELOG.md
CITING.md
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DEVELOPMENT.md
DISCLAIMER.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
docs/CNS.md
docs/INSTALL.md
docs/USAGE.md
docs/citing.rst
docs/conf.py
docs/contributing.rst
docs/examples.md
docs/index.rst
docs/intro.md
docs/figs/HADDOCK2-stages.png
docs/figs/HADDOCK3-logo.png
docs/figs/HADDOCK3-workflow-scheme.png
docs/modules/index.rst
docs/reference/index.rst
docs/testing/index.rst
docs/testing/integration_tests.md
docs/tutorials/benchmark.md
docs/tutorials/continuing_runs.md
docs/tutorials/index.rst
docs/tutorials/mpi.md
docs/tutorials/user_config.rst
src/haddock/__init__.py
src/haddock/clis/__init__.py
src/haddock/clis/cli.py
src/haddock/clis/cli_analyse.py
src/haddock/clis/cli_bm.py
src/haddock/clis/cli_cfg.py
src/haddock/clis/cli_clean.py
src/haddock/clis/cli_cp.py
src/haddock/clis/cli_dmn.py
src/haddock/clis/cli_mpi.py
src/haddock/clis/cli_pp.py
src/haddock/clis/cli_re.py
src/haddock/clis/cli_restraints.py
src/haddock/clis/cli_score.py
src/haddock/clis/cli_traceback.py
src/haddock/clis/cli_unpack.py
src/haddock/clis/re/__init__.py
src/haddock/clis/re/clustfcc.py
src/haddock/clis/re/clustrmsd.py
src/haddock/clis/re/score.py
src/haddock/clis/restraints/__init__.py
src/haddock/clis/restraints/active_passive_to_ambig.py
src/haddock/clis/restraints/calc_accessibility.py
src/haddock/clis/restraints/naccess.config
src/haddock/clis/restraints/passive_from_active.py
src/haddock/clis/restraints/restrain_bodies.py
src/haddock/clis/restraints/validate_tbl.py
src/haddock/clis/restraints/webservice.py
src/haddock/clis/restraints/z_surface_restraints.py
src/haddock/cns/toppar/boxtyp20.pdb
src/haddock/cns/toppar/carbohydrate.param
src/haddock/cns/toppar/carbohydrate.top
src/haddock/cns/toppar/dmso.pdb
src/haddock/cns/toppar/dna-rna-1.3.link
src/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p-break.top
src/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.link
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src/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.param
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src/haddock/cns/toppar/dna-rna-pho-1.3.link
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src/haddock/cns/toppar/fragment_probes.param
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src/haddock/cns/toppar/heme.pdb
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src/haddock/cns/toppar/hemeB.pdb
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src/haddock/cns/toppar/hemes-allhdg.param
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src/haddock/cns/toppar/hemes.pep
src/haddock/cns/toppar/ion.param
src/haddock/cns/toppar/ion.top
src/haddock/cns/toppar/ligand.param
src/haddock/cns/toppar/ligand.pep
src/haddock/cns/toppar/ligand.top
src/haddock/cns/toppar/metalcenter.tbl
src/haddock/cns/toppar/par_axis.pro
src/haddock/cns/toppar/par_axis_dani.pro
src/haddock/cns/toppar/protein-CG-Martini-2-2.link
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src/haddock/cns/toppar/protein-CG-Martini-2-2.top
src/haddock/cns/toppar/protein-CG-Martini.link
src/haddock/cns/toppar/protein-CG-Martini.param
src/haddock/cns/toppar/protein-CG-Martini.top
src/haddock/cns/toppar/protein-allhdg5-4-noCter.link
src/haddock/cns/toppar/protein-allhdg5-4-noNter.link
src/haddock/cns/toppar/protein-allhdg5-4-noter.link
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src/haddock/cns/toppar/solvent-allhdg5-4.param
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src/haddock/cns/toppar/tensor.pdb
src/haddock/cns/toppar/tensor.psf
src/haddock/cns/toppar/tensor_dani.pdb
src/haddock/cns/toppar/tensor_dani.psf
src/haddock/cns/toppar/tensor_para.pdb
src/haddock/cns/toppar/tensor_para.psf
src/haddock/cns/toppar/top_axis.pro
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src/haddock/cns/toppar/initial_positions/trans_vector_0
src/haddock/cns/toppar/initial_positions/trans_vector_1
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src/haddock/cns/toppar/initial_positions/trans_vector_3
src/haddock/cns/toppar/initial_positions/trans_vector_30
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src/haddock/cns/toppar/initial_positions/trans_vector_32
src/haddock/cns/toppar/initial_positions/trans_vector_33
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src/haddock/cns/toppar/initial_positions/trans_vector_35
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src/haddock/cns/toppar/initial_positions/trans_vector_37
src/haddock/cns/toppar/initial_positions/trans_vector_38
src/haddock/cns/toppar/initial_positions/trans_vector_39
src/haddock/cns/toppar/initial_positions/trans_vector_4
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src/haddock/cns/toppar/initial_positions/trans_vector_41
src/haddock/cns/toppar/initial_positions/trans_vector_42
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src/haddock/cns/toppar/initial_positions/trans_vector_46
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src/haddock/cns/toppar/initial_positions/trans_vector_48
src/haddock/cns/toppar/initial_positions/trans_vector_49
src/haddock/cns/toppar/initial_positions/trans_vector_5
src/haddock/cns/toppar/initial_positions/trans_vector_50
src/haddock/cns/toppar/initial_positions/trans_vector_6
src/haddock/cns/toppar/initial_positions/trans_vector_7
src/haddock/cns/toppar/initial_positions/trans_vector_8
src/haddock/cns/toppar/initial_positions/trans_vector_9
src/haddock/core/__init__.py
src/haddock/core/cns_paths.py
src/haddock/core/defaults.py
src/haddock/core/exceptions.py
src/haddock/core/mandatory.yaml
src/haddock/core/optional.yaml
src/haddock/core/supported_molecules.py
src/haddock/core/typing.py
src/haddock/deps/contact_fcc.cpp
src/haddock/deps/fast-rmsdmatrix.c
src/haddock/fcc/__init__.py
src/haddock/fcc/calc_fcc_matrix.py
src/haddock/fcc/cluster_fcc.py
src/haddock/gear/__init__.py
src/haddock/gear/clean_steps.py
src/haddock/gear/config.py
src/haddock/gear/expandable_parameters.py
src/haddock/gear/extend_run.py
src/haddock/gear/greetings.py
src/haddock/gear/haddockmodel.py
src/haddock/gear/known_cns_errors.py
src/haddock/gear/parameters.py
src/haddock/gear/prepare_run.py
src/haddock/gear/preprocessing.py
src/haddock/gear/restart_run.py
src/haddock/gear/validations.py
src/haddock/gear/yaml2cfg.py
src/haddock/gear/zerofill.py
src/haddock/libs/__init__.py
src/haddock/libs/libalign.py
src/haddock/libs/libcli.py
src/haddock/libs/libclust.py
src/haddock/libs/libcns.py
src/haddock/libs/libfcc.py
src/haddock/libs/libfunc.py
src/haddock/libs/libhpc.py
src/haddock/libs/libinteractive.py
src/haddock/libs/libio.py
src/haddock/libs/liblog.py
src/haddock/libs/libmath.py
src/haddock/libs/libmpi.py
src/haddock/libs/libontology.py
src/haddock/libs/libparallel.py
src/haddock/libs/libpdb.py
src/haddock/libs/libplots.py
src/haddock/libs/librestraints.py
src/haddock/libs/libstructure.py
src/haddock/libs/libsubprocess.py
src/haddock/libs/libtimer.py
src/haddock/libs/libutil.py
src/haddock/libs/libworkflow.py
src/haddock/libs/assets/__init__.py
src/haddock/libs/assets/index.css
src/haddock/libs/assets/report.bundle.js
src/haddock/modules/__init__.py
src/haddock/modules/base_cns_module.py
src/haddock/modules/defaults.yaml
src/haddock/modules/_template_cat/README.md
src/haddock/modules/_template_cat/_template_mod/__init__.py
src/haddock/modules/_template_cat/_template_mod/defaults.yaml
src/haddock/modules/analysis/__init__.py
src/haddock/modules/analysis/alascan/__init__.py
src/haddock/modules/analysis/alascan/defaults.yaml
src/haddock/modules/analysis/alascan/scan.py
src/haddock/modules/analysis/caprieval/__init__.py
src/haddock/modules/analysis/caprieval/capri.py
src/haddock/modules/analysis/caprieval/defaults.yaml
src/haddock/modules/analysis/clustfcc/__init__.py
src/haddock/modules/analysis/clustfcc/clustfcc.py
src/haddock/modules/analysis/clustfcc/defaults.yaml
src/haddock/modules/analysis/clustrmsd/__init__.py
src/haddock/modules/analysis/clustrmsd/clustrmsd.py
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src/haddock/modules/analysis/contactmap/__init__.py
src/haddock/modules/analysis/contactmap/contmap.py
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src/haddock/modules/analysis/ilrmsdmatrix/__init__.py
src/haddock/modules/analysis/ilrmsdmatrix/defaults.yaml
src/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.py
src/haddock/modules/analysis/rmsdmatrix/__init__.py
src/haddock/modules/analysis/rmsdmatrix/defaults.yaml
src/haddock/modules/analysis/rmsdmatrix/rmsd.py
src/haddock/modules/analysis/seletop/__init__.py
src/haddock/modules/analysis/seletop/defaults.yaml
src/haddock/modules/analysis/seletopclusts/__init__.py
src/haddock/modules/analysis/seletopclusts/defaults.yaml
src/haddock/modules/analysis/seletopclusts/seletopclusts.py
src/haddock/modules/extras/__init__.py
src/haddock/modules/extras/exit/__init__.py
src/haddock/modules/extras/exit/defaults.yaml
src/haddock/modules/refinement/__init__.py
src/haddock/modules/refinement/emref/__init__.py
src/haddock/modules/refinement/emref/defaults.yaml
src/haddock/modules/refinement/emref/cns/calc_free-ene.cns
src/haddock/modules/refinement/emref/cns/contactairs.cns
src/haddock/modules/refinement/emref/cns/def_solv_param.cns
src/haddock/modules/refinement/emref/cns/dna-rna_restraints.cns
src/haddock/modules/refinement/emref/cns/emref.cns
src/haddock/modules/refinement/emref/cns/flex_segment_back.cns
src/haddock/modules/refinement/emref/cns/flexauto-neighbors.cns
src/haddock/modules/refinement/emref/cns/print_coorheader.cns
src/haddock/modules/refinement/emref/cns/protein-ss-restraints-all.cns
src/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha-beta.cns
src/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha.cns
src/haddock/modules/refinement/emref/cns/read_data.cns
src/haddock/modules/refinement/emref/cns/read_noes.cns
src/haddock/modules/refinement/emref/cns/read_param.cns
src/haddock/modules/refinement/emref/cns/restrain-ions.cns
src/haddock/modules/refinement/emref/cns/scale_inter.cns
src/haddock/modules/refinement/emref/cns/scale_inter_final.cns
src/haddock/modules/refinement/emref/cns/scale_intra_only.cns
src/haddock/modules/refinement/emref/cns/setflags.cns
src/haddock/modules/refinement/emref/cns/symmultimer.cns
src/haddock/modules/refinement/flexref/__init__.py
src/haddock/modules/refinement/flexref/defaults.yaml
src/haddock/modules/refinement/flexref/cns/calc_free-ene.cns
src/haddock/modules/refinement/flexref/cns/check-homomers.cns
src/haddock/modules/refinement/flexref/cns/cm-restraints.cns
src/haddock/modules/refinement/flexref/cns/contactairs.cns
src/haddock/modules/refinement/flexref/cns/covalions.cns
src/haddock/modules/refinement/flexref/cns/def_solv_param.cns
src/haddock/modules/refinement/flexref/cns/dna-rna_restraints.cns
src/haddock/modules/refinement/flexref/cns/flex_segment.cns
src/haddock/modules/refinement/flexref/cns/flex_segment_back.cns
src/haddock/modules/refinement/flexref/cns/flex_segment_side.cns
src/haddock/modules/refinement/flexref/cns/flexauto-neighbors.cns
src/haddock/modules/refinement/flexref/cns/flexref.cns
src/haddock/modules/refinement/flexref/cns/numtrees.cns
src/haddock/modules/refinement/flexref/cns/print_coorheader.cns
src/haddock/modules/refinement/flexref/cns/protein-ss-restraints-all.cns
src/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha-beta.cns
src/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha.cns
src/haddock/modules/refinement/flexref/cns/random_rotations.cns
src/haddock/modules/refinement/flexref/cns/read_data.cns
src/haddock/modules/refinement/flexref/cns/read_noes.cns
src/haddock/modules/refinement/flexref/cns/read_param.cns
src/haddock/modules/refinement/flexref/cns/restrain-ions.cns
src/haddock/modules/refinement/flexref/cns/sa_ltad_cool1.cns
src/haddock/modules/refinement/flexref/cns/sa_ltad_cool2.cns
src/haddock/modules/refinement/flexref/cns/sa_ltad_cool3.cns
src/haddock/modules/refinement/flexref/cns/sa_ltad_hightemp.cns
src/haddock/modules/refinement/flexref/cns/scale_inter.cns
src/haddock/modules/refinement/flexref/cns/scale_inter_final.cns
src/haddock/modules/refinement/flexref/cns/scale_inter_only.cns
src/haddock/modules/refinement/flexref/cns/scale_intra_only.cns
src/haddock/modules/refinement/flexref/cns/separate.cns
src/haddock/modules/refinement/flexref/cns/setflags.cns
src/haddock/modules/refinement/flexref/cns/symmultimer.cns
src/haddock/modules/refinement/flexref/cns/torsiontop.cns
src/haddock/modules/refinement/mdref/__init__.py
src/haddock/modules/refinement/mdref/defaults.yaml
src/haddock/modules/refinement/mdref/cns/calc_free-ene.cns
src/haddock/modules/refinement/mdref/cns/cm-restraints.cns
src/haddock/modules/refinement/mdref/cns/contactairs.cns
src/haddock/modules/refinement/mdref/cns/def_solv_param.cns
src/haddock/modules/refinement/mdref/cns/dna-rna_restraints.cns
src/haddock/modules/refinement/mdref/cns/flex_segment_back.cns
src/haddock/modules/refinement/mdref/cns/flex_segment_side.cns
src/haddock/modules/refinement/mdref/cns/flexauto-neighbors.cns
src/haddock/modules/refinement/mdref/cns/generate_dmso.cns
src/haddock/modules/refinement/mdref/cns/generate_water.cns
src/haddock/modules/refinement/mdref/cns/mdref.cns
src/haddock/modules/refinement/mdref/cns/print_coorheader.cns
src/haddock/modules/refinement/mdref/cns/protein-ss-restraints-all.cns
src/haddock/modules/refinement/mdref/cns/protein-ss-restraints-alpha-beta.cns
src/haddock/modules/refinement/mdref/cns/protein-ss-restraints-alpha.cns
src/haddock/modules/refinement/mdref/cns/read_data.cns
src/haddock/modules/refinement/mdref/cns/read_noes.cns
src/haddock/modules/refinement/mdref/cns/read_param.cns
src/haddock/modules/refinement/mdref/cns/restrain-ions.cns
src/haddock/modules/refinement/mdref/cns/scale_inter.cns
src/haddock/modules/refinement/mdref/cns/scale_inter_final.cns
src/haddock/modules/refinement/mdref/cns/scale_intra_only.cns
src/haddock/modules/refinement/mdref/cns/setflags.cns
src/haddock/modules/refinement/mdref/cns/symmultimer.cns
src/haddock/modules/refinement/openmm/__init__.py
src/haddock/modules/refinement/openmm/defaults.yaml
src/haddock/modules/refinement/openmm/openmm.py
src/haddock/modules/sampling/__init__.py
src/haddock/modules/sampling/gdock/__init__.py
src/haddock/modules/sampling/gdock/defaults.yaml
src/haddock/modules/sampling/lightdock/__init__.py
src/haddock/modules/sampling/lightdock/defaults.yaml
src/haddock/modules/sampling/rigidbody/__init__.py
src/haddock/modules/sampling/rigidbody/defaults.yaml
src/haddock/modules/sampling/rigidbody/cns/bestener.cns
src/haddock/modules/sampling/rigidbody/cns/bsa.cns
src/haddock/modules/sampling/rigidbody/cns/charge-beads-interactions.cns
src/haddock/modules/sampling/rigidbody/cns/check-homomers.cns
src/haddock/modules/sampling/rigidbody/cns/cm-restraints.cns
src/haddock/modules/sampling/rigidbody/cns/def_solv_param.cns
src/haddock/modules/sampling/rigidbody/cns/get_random_rotation.cns
src/haddock/modules/sampling/rigidbody/cns/print_coorheader.cns
src/haddock/modules/sampling/rigidbody/cns/random_rotations.cns
src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
src/haddock/modules/sampling/rigidbody/cns/read_noes.cns
src/haddock/modules/sampling/rigidbody/cns/read_param.cns
src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
src/haddock/modules/sampling/rigidbody/cns/rotation180.cns
src/haddock/modules/sampling/rigidbody/cns/scale_inter_final.cns
src/haddock/modules/sampling/rigidbody/cns/scale_inter_mini.cns
src/haddock/modules/sampling/rigidbody/cns/scale_inter_only.cns
src/haddock/modules/sampling/rigidbody/cns/scale_intra_only.cns
src/haddock/modules/sampling/rigidbody/cns/separate.cns
src/haddock/modules/sampling/rigidbody/cns/surf-restraints.cns
src/haddock/modules/sampling/rigidbody/cns/symmultimer.cns
src/haddock/modules/scoring/__init__.py
src/haddock/modules/scoring/emscoring/__init__.py
src/haddock/modules/scoring/emscoring/defaults.yaml
src/haddock/modules/scoring/emscoring/cns/calc_free-ene.cns
src/haddock/modules/scoring/emscoring/cns/def_solv_param.cns
src/haddock/modules/scoring/emscoring/cns/emscoring.cns
src/haddock/modules/scoring/emscoring/cns/print_coorheader.cns
src/haddock/modules/scoring/emscoring/cns/read_param.cns
src/haddock/modules/scoring/emscoring/cns/restrain-ions.cns
src/haddock/modules/scoring/emscoring/cns/scale_inter_final.cns
src/haddock/modules/scoring/emscoring/cns/scale_intra_only.cns
src/haddock/modules/scoring/mdscoring/__init__.py
src/haddock/modules/scoring/mdscoring/defaults.yaml
src/haddock/modules/scoring/mdscoring/cns/calc_free-ene.cns
src/haddock/modules/scoring/mdscoring/cns/contactairs.cns
src/haddock/modules/scoring/mdscoring/cns/def_solv_param.cns
src/haddock/modules/scoring/mdscoring/cns/dna-rna_restraints.cns
src/haddock/modules/scoring/mdscoring/cns/flex_segment_back.cns
src/haddock/modules/scoring/mdscoring/cns/flex_segment_side.cns
src/haddock/modules/scoring/mdscoring/cns/flexauto-neighbors.cns
src/haddock/modules/scoring/mdscoring/cns/generate_dmso.cns
src/haddock/modules/scoring/mdscoring/cns/generate_water.cns
src/haddock/modules/scoring/mdscoring/cns/mdscoring.cns
src/haddock/modules/scoring/mdscoring/cns/print_coorheader.cns
src/haddock/modules/scoring/mdscoring/cns/protein-ss-restraints-all.cns
src/haddock/modules/scoring/mdscoring/cns/protein-ss-restraints-alpha-beta.cns
src/haddock/modules/scoring/mdscoring/cns/protein-ss-restraints-alpha.cns
src/haddock/modules/scoring/mdscoring/cns/read_param.cns
src/haddock/modules/scoring/mdscoring/cns/restrain-ions.cns
src/haddock/modules/scoring/mdscoring/cns/scale_inter_final.cns
src/haddock/modules/scoring/mdscoring/cns/scale_intra_only.cns
src/haddock/modules/scoring/mdscoring/cns/setflags.cns
src/haddock/modules/topology/__init__.py
src/haddock/modules/topology/topoaa/__init__.py
src/haddock/modules/topology/topoaa/defaults.yaml
src/haddock/modules/topology/topoaa/cns/auto-his.cns
src/haddock/modules/topology/topoaa/cns/bondglycans.cns
src/haddock/modules/topology/topoaa/cns/build-missing.cns
src/haddock/modules/topology/topoaa/cns/coval-ace-cys.cns
src/haddock/modules/topology/topoaa/cns/covalheme.cns
src/haddock/modules/topology/topoaa/cns/dna_break.cns
src/haddock/modules/topology/topoaa/cns/generate-topology.cns
src/haddock/modules/topology/topoaa/cns/patch-bb-cg.cns
src/haddock/modules/topology/topoaa/cns/patch-types-cg.cns
src/haddock/modules/topology/topoaa/cns/prot_break.cns
src/haddock/modules/topology/topocg/__init__.py
src/haddock/modules/topology/topocg/defaults.yaml
src/haddock3.egg-info/PKG-INFO
src/haddock3.egg-info/SOURCES.txt
src/haddock3.egg-info/dependency_links.txt
src/haddock3.egg-info/entry_points.txt
src/haddock3.egg-info/requires.txt
src/haddock3.egg-info/top_level.txt
varia/cns1.3/README.md
varia/cns1.3/instlib/machine/supported/arm-aarch64-linux/machine_f.f
varia/cns1.3/instlib/machine/supported/intel-x86_64bit-linux/machine_f.f
varia/cns1.3/instlib/machine/supported/linux/machine_f.f
varia/cns1.3/instlib/machine/supported/mac-arm-darwin/machine_f.f
varia/cns1.3/instlib/machine/supported/mac-intel-darwin/machine_f.f
varia/cns1.3/source/cns.f
varia/cns1.3/source/cns.inc
varia/cns1.3/source/cnst.inc
varia/cns1.3/source/collapse.inc
varia/cns1.3/source/collapse_rgyr.f
varia/cns1.3/source/connect.f
varia/cns1.3/source/cstran.f
varia/cns1.3/source/ener.inc
varia/cns1.3/source/energy.f
varia/cns1.3/source/fantacross.f
varia/cns1.3/source/fantalin.f
varia/cns1.3/source/fantaxplor.inc
varia/cns1.3/source/genic.f
varia/cns1.3/source/initia.f
varia/cns1.3/source/machvar.f
varia/cns1.3/source/param.inc
varia/cns1.3/source/rtf.inc
varia/cns1.3/source/segmnt.f
varia/cns1.3/source/selrpn.f
varia/cns1.3/source/sup2.inc
varia/cns1.3/source/supccr.inc
varia/cns1.3/source/vector.f
varia/cns1.3/source/version.inc
varia/cns1.3/source/xangle.f
varia/cns1.3/source/xangle.inc
varia/cns1.3/source/xccr.f
varia/cns1.3/source/xccr.inc
varia/cns1.3/source/xdipo_pcs.f
varia/cns1.3/source/xdipo_pcs.inc
varia/cns1.3/source/xdipo_rdc.f
varia/cns1.3/source/xdipo_rdc.inc
varia/cns1.3/source/xfantaccr.f
varia/cns1.3/source/xfantadipo.f
varia/cns1.3/source/xt1dist.f
varia/lmod/README.md
varia/lmod/haddock3/3.0.0.lua