From c31ff95907bd03dc858ebc72c68e804685a56f9b Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Fri, 16 Jul 2021 20:29:51 +0200 Subject: [PATCH 1/4] initial restructure into package --- README.md | 6 +- haddock/__init__.py => README.rst | 0 requirements.txt | 1 + requirements.yml | 1 + setup.py | 89 +++++++++++++++++++ {haddock/cns => src/haddock}/__init__.py | 0 {haddock => src/haddock}/cli.py | 0 bin/haddock3.py => src/haddock/clis/cli.py | 0 {haddock/data => src/haddock/cns}/__init__.py | 0 {haddock => src/haddock}/cns/engine.py | 0 {haddock => src/haddock}/cns/topology.py | 0 {haddock => src/haddock}/cns/util.py | 0 {haddock => src/haddock}/cooking.py | 0 .../analysis => src/haddock/data}/__init__.py | 0 {haddock => src/haddock}/data/topology.py | 0 .../haddock}/data/toppar/boxtyp20.pdb | 0 .../haddock}/data/toppar/haddock.param | 0 .../haddock}/data/toppar/haddock.top | 0 .../toppar/initial_positions/trans_vector_0 | 0 .../toppar/initial_positions/trans_vector_1 | 0 .../toppar/initial_positions/trans_vector_10 | 0 .../toppar/initial_positions/trans_vector_11 | 0 .../toppar/initial_positions/trans_vector_12 | 0 .../toppar/initial_positions/trans_vector_13 | 0 .../toppar/initial_positions/trans_vector_14 | 0 .../toppar/initial_positions/trans_vector_15 | 0 .../toppar/initial_positions/trans_vector_16 | 0 .../toppar/initial_positions/trans_vector_17 | 0 .../toppar/initial_positions/trans_vector_18 | 0 .../toppar/initial_positions/trans_vector_19 | 0 .../toppar/initial_positions/trans_vector_2 | 0 .../toppar/initial_positions/trans_vector_20 | 0 .../toppar/initial_positions/trans_vector_21 | 0 .../toppar/initial_positions/trans_vector_22 | 0 .../toppar/initial_positions/trans_vector_23 | 0 .../toppar/initial_positions/trans_vector_24 | 0 .../toppar/initial_positions/trans_vector_25 | 0 .../toppar/initial_positions/trans_vector_26 | 0 .../toppar/initial_positions/trans_vector_27 | 0 .../toppar/initial_positions/trans_vector_28 | 0 .../toppar/initial_positions/trans_vector_29 | 0 .../toppar/initial_positions/trans_vector_3 | 0 .../toppar/initial_positions/trans_vector_30 | 0 .../toppar/initial_positions/trans_vector_31 | 0 .../toppar/initial_positions/trans_vector_32 | 0 .../toppar/initial_positions/trans_vector_33 | 0 .../toppar/initial_positions/trans_vector_34 | 0 .../toppar/initial_positions/trans_vector_35 | 0 .../toppar/initial_positions/trans_vector_36 | 0 .../toppar/initial_positions/trans_vector_37 | 0 .../toppar/initial_positions/trans_vector_38 | 0 .../toppar/initial_positions/trans_vector_39 | 0 .../toppar/initial_positions/trans_vector_4 | 0 .../toppar/initial_positions/trans_vector_40 | 0 .../toppar/initial_positions/trans_vector_41 | 0 .../toppar/initial_positions/trans_vector_42 | 0 .../toppar/initial_positions/trans_vector_43 | 0 .../toppar/initial_positions/trans_vector_44 | 0 .../toppar/initial_positions/trans_vector_45 | 0 .../toppar/initial_positions/trans_vector_46 | 0 .../toppar/initial_positions/trans_vector_47 | 0 .../toppar/initial_positions/trans_vector_48 | 0 .../toppar/initial_positions/trans_vector_49 | 0 .../toppar/initial_positions/trans_vector_5 | 0 .../toppar/initial_positions/trans_vector_50 | 0 .../toppar/initial_positions/trans_vector_6 | 0 .../toppar/initial_positions/trans_vector_7 | 0 .../toppar/initial_positions/trans_vector_8 | 0 .../toppar/initial_positions/trans_vector_9 | 0 .../haddock}/data/toppar/ion.param | 0 {haddock => src/haddock}/data/toppar/ion.top | 0 .../haddock}/data/toppar/ligand.param | 0 .../haddock}/data/toppar/ligand.top | 0 .../haddock}/data/toppar/par_axis.pro | 0 .../haddock}/data/toppar/par_axis_dani.pro | 0 .../data/toppar/protein-allhdg5-4-noter.link | 0 .../data/toppar/protein-allhdg5-4.param | 0 .../data/toppar/protein-allhdg5-4.top | 0 .../haddock}/data/toppar/protein_break.top | 0 .../haddock}/data/toppar/scatter.lib | 0 .../haddock}/data/toppar/tensor.pdb | 0 .../haddock}/data/toppar/tensor.psf | 0 .../haddock}/data/toppar/tensor_dani.pdb | 0 .../haddock}/data/toppar/tensor_dani.psf | 0 .../haddock}/data/toppar/tensor_para.pdb | 0 .../haddock}/data/toppar/tensor_para.psf | 0 .../haddock}/data/toppar/top_axis.pro | 0 .../haddock}/data/toppar/top_axis_dani.pro | 0 .../data/toppar/water-allhdg5-4.param | 0 .../haddock}/data/toppar/water-allhdg5-4.top | 0 {haddock => src/haddock}/defaults.py | 12 ++- {haddock => src/haddock}/error.py | 0 {haddock => src/haddock}/mathutil.py | 0 {haddock => src/haddock}/modules/__init__.py | 0 .../haddock/modules/analysis}/__init__.py | 0 .../haddock/modules/clustering}/__init__.py | 0 .../haddock/modules/sampling}/__init__.py | 0 .../haddock}/modules/sampling/lightdock.py | 0 .../haddock}/modules/sampling/sampling.toml | 0 .../haddock/modules/scoring}/__init__.py | 0 .../modules/scoring/cns/calc_free-ene.cns | 0 .../modules/scoring/cns/def_solv_param.cns | 0 .../modules/scoring/cns/flex_segment_back.cns | 0 .../scoring/cns/flexauto-neighbors.cns | 0 .../modules/scoring/cns/print_coorheader.cns | 0 .../modules/scoring/cns/scale_inter_final.cns | 0 .../modules/scoring/cns/scale_intra_only.cns | 0 .../haddock}/modules/scoring/cns/scoring.cns | 0 .../haddock}/modules/scoring/cns/scoring.toml | 0 .../haddock}/modules/scoring/default.py | 0 src/haddock/modules/topology/__init__.py | 0 .../modules/topology/cns/auto-his.cns | 0 .../modules/topology/cns/build-missing.cns | 0 .../modules/topology/cns/coval-ace-cys.cns | 0 .../modules/topology/cns/covalheme.cns | 0 .../modules/topology/cns/dna_break.cns | 0 .../topology/cns/generate-topology.cns | 0 .../topology/cns/generate-topology.toml | 0 .../modules/topology/cns/patch-bb-cg.cns | 0 .../modules/topology/cns/patch-types-cg.cns | 0 .../modules/topology/cns/prot_break.cns | 0 .../haddock}/modules/topology/default.py | 0 {haddock => src/haddock}/ontology.py | 0 {haddock => src/haddock}/parallel.py | 0 {haddock => src/haddock}/pdbutil.py | 0 {haddock => src/haddock}/structure.py | 0 {haddock => src/haddock}/version.py | 0 {haddock => src/haddock}/workflow.py | 0 128 files changed, 100 insertions(+), 9 deletions(-) rename haddock/__init__.py => README.rst (100%) create mode 100644 setup.py rename {haddock/cns => src/haddock}/__init__.py (100%) rename {haddock => src/haddock}/cli.py (100%) rename bin/haddock3.py => src/haddock/clis/cli.py (100%) rename {haddock/data => src/haddock/cns}/__init__.py (100%) rename {haddock => src/haddock}/cns/engine.py (100%) rename {haddock => src/haddock}/cns/topology.py (100%) rename {haddock => src/haddock}/cns/util.py (100%) rename {haddock => src/haddock}/cooking.py (100%) rename {haddock/modules/analysis => src/haddock/data}/__init__.py (100%) rename {haddock => src/haddock}/data/topology.py (100%) rename {haddock => src/haddock}/data/toppar/boxtyp20.pdb (100%) rename {haddock => src/haddock}/data/toppar/haddock.param (100%) rename {haddock => src/haddock}/data/toppar/haddock.top (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_0 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_1 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_10 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_11 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_12 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_13 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_14 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_15 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_16 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_17 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_18 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_19 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_2 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_20 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_21 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_22 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_23 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_24 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_25 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_26 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_27 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_28 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_29 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_3 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_30 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_31 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_32 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_33 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_34 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_35 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_36 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_37 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_38 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_39 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_4 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_40 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_41 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_42 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_43 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_44 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_45 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_46 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_47 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_48 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_49 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_5 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_50 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_6 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_7 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_8 (100%) rename {haddock => src/haddock}/data/toppar/initial_positions/trans_vector_9 (100%) rename {haddock => src/haddock}/data/toppar/ion.param (100%) rename {haddock => src/haddock}/data/toppar/ion.top (100%) rename {haddock => src/haddock}/data/toppar/ligand.param (100%) rename {haddock => src/haddock}/data/toppar/ligand.top (100%) rename {haddock => src/haddock}/data/toppar/par_axis.pro (100%) rename {haddock => src/haddock}/data/toppar/par_axis_dani.pro (100%) rename {haddock => src/haddock}/data/toppar/protein-allhdg5-4-noter.link (100%) rename {haddock => src/haddock}/data/toppar/protein-allhdg5-4.param (100%) rename {haddock => src/haddock}/data/toppar/protein-allhdg5-4.top (100%) rename {haddock => src/haddock}/data/toppar/protein_break.top (100%) rename {haddock => src/haddock}/data/toppar/scatter.lib (100%) rename {haddock => src/haddock}/data/toppar/tensor.pdb (100%) rename {haddock => src/haddock}/data/toppar/tensor.psf (100%) rename {haddock => src/haddock}/data/toppar/tensor_dani.pdb (100%) rename {haddock => src/haddock}/data/toppar/tensor_dani.psf (100%) rename {haddock => src/haddock}/data/toppar/tensor_para.pdb (100%) rename {haddock => src/haddock}/data/toppar/tensor_para.psf (100%) rename {haddock => src/haddock}/data/toppar/top_axis.pro (100%) rename {haddock => src/haddock}/data/toppar/top_axis_dani.pro (100%) rename {haddock => src/haddock}/data/toppar/water-allhdg5-4.param (100%) rename {haddock => src/haddock}/data/toppar/water-allhdg5-4.top (100%) rename {haddock => src/haddock}/defaults.py (87%) rename {haddock => src/haddock}/error.py (100%) rename {haddock => src/haddock}/mathutil.py (100%) rename {haddock => src/haddock}/modules/__init__.py (100%) rename {haddock/modules/clustering => src/haddock/modules/analysis}/__init__.py (100%) rename {haddock/modules/sampling => src/haddock/modules/clustering}/__init__.py (100%) rename {haddock/modules/scoring => src/haddock/modules/sampling}/__init__.py (100%) rename {haddock => src/haddock}/modules/sampling/lightdock.py (100%) rename {haddock => src/haddock}/modules/sampling/sampling.toml (100%) rename {haddock/modules/topology => src/haddock/modules/scoring}/__init__.py (100%) rename {haddock => src/haddock}/modules/scoring/cns/calc_free-ene.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/def_solv_param.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/flex_segment_back.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/flexauto-neighbors.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/print_coorheader.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/scale_inter_final.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/scale_intra_only.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/scoring.cns (100%) rename {haddock => src/haddock}/modules/scoring/cns/scoring.toml (100%) rename {haddock => src/haddock}/modules/scoring/default.py (100%) create mode 100644 src/haddock/modules/topology/__init__.py rename {haddock => src/haddock}/modules/topology/cns/auto-his.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/build-missing.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/coval-ace-cys.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/covalheme.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/dna_break.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/generate-topology.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/generate-topology.toml (100%) rename {haddock => src/haddock}/modules/topology/cns/patch-bb-cg.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/patch-types-cg.cns (100%) rename {haddock => src/haddock}/modules/topology/cns/prot_break.cns (100%) rename {haddock => src/haddock}/modules/topology/default.py (100%) rename {haddock => src/haddock}/ontology.py (100%) rename {haddock => src/haddock}/parallel.py (100%) rename {haddock => src/haddock}/pdbutil.py (100%) rename {haddock => src/haddock}/structure.py (100%) rename {haddock => src/haddock}/version.py (100%) rename {haddock => src/haddock}/workflow.py (100%) diff --git a/README.md b/README.md index f3891201b..3a0d35dfe 100644 --- a/README.md +++ b/README.md @@ -27,12 +27,14 @@ cd haddock3 virtualenv-3.8 venv source venv/bin/activate pip install -r requirements.txt +python setup.py develop --no-deps ``` #### with `conda` ```bash conda env create -f requirements.yml conda activate haddock3 +python setup.py develop --no-deps ``` ### 1.3 Copy CNS binary to the expected path: @@ -43,7 +45,7 @@ mkdir -p bin/cns # on mac ls -s bin/cns/cns /PATH/TO/cns_solve-1.31-UU-MacIntel.exe -# on linux +# on linux, adapt the file name if needed ls -s bin/cns/cns /PATH/TO/CNS_FOLDER/intel-x86_64bit-linux/source/cns_solve-2002171359.exe ``` @@ -69,5 +71,5 @@ source bin/activate_haddock ```bash cd examples/recipes/scoring/ -haddock3.py scoring.toml +haddock3 scoring.toml ``` diff --git a/haddock/__init__.py b/README.rst similarity index 100% rename from haddock/__init__.py rename to README.rst diff --git a/requirements.txt b/requirements.txt index 26c4e1736..504a0d0bd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,3 +3,4 @@ pdb-tools==2.1.0 jsonpickle==2.0.0 numpy==1.20.2 lightdock==0.9.0a2 +libfuncpy>=0.0.3 diff --git a/requirements.yml b/requirements.yml index 5899b19ef..8e20b96b7 100644 --- a/requirements.yml +++ b/requirements.yml @@ -11,3 +11,4 @@ dependencies: - pip: - pdb-tools - lightdock + - libfuncpy diff --git a/setup.py b/setup.py new file mode 100644 index 000000000..af9588ff8 --- /dev/null +++ b/setup.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python +# -*- encoding: utf-8 -*- +"""Setup dot py.""" +from glob import glob +from os.path import basename, dirname, join, splitext + +from setuptools import find_packages, setup + + +def read(*names, **kwargs): + """Read description files.""" + path = join(dirname(__file__), *names) + with open(path, encoding=kwargs.get('encoding', 'utf8')) as fh: + return fh.read() + + +# activate once added, do not remove +#long_description = '{}\n{}'.format( +# read('README.rst'), +# read(join('docs', 'CHANGELOG.rst')), +# ) + + +setup( + name='haddock3', + version='0.0.3-alpha', + description='Haddock 3.', + long_description='',#long_description, + long_description_content_type='text/x-rst', + license='Apache License 2.0', + author='HADDOCK', + author_email='A.M.J.J.Bonvin@uu.nl', + url='https://github.com/haddocking/haddock3', + packages=find_packages('src'), + package_dir={'': 'src'}, + #py_modules=[splitext(basename(i))[0] for i in glob("src/*.py")], + include_package_data=True, + zip_safe=False, + classifiers=[ + # complete classifier list: + # http://pypi.python.org/pypi?%3Aaction=list_classifiers + 'Development Status :: 3 - Alpha', + #'Development Status :: 4 - Beta', + 'License :: OSI Approved :: Apache Software License', + 'Natural Language :: English', + 'Operating System :: POSIX', + 'Operating System :: MacOS', + 'Operating System :: Microsoft', + 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', + ], + project_urls={ + 'webpage': 'https://github.com/haddocking/haddock3', + 'Documentation': 'https://github.com/haddocking/haddock3#readme', + 'Changelog': '', + 'Issue Tracker': 'https://github.com/haddocking/haddock3/issues', + 'Discussion Forum': 'https://github.com/haddocking/haddock3/issues', + }, + keywords=[ + 'Structural Biology', + 'Biochemistry', + 'Docking', + 'Protein docking', + 'Proteins', + ], + python_requires='>=3.8, <3.10', + install_requires=[ + # not added on purpose + ], + extras_require={ + }, + setup_requires=[ + ], + entry_points={ + 'console_scripts': [ + 'haddock3 = haddock.clis.cli:main', + ] + }, + # cmdclass={'build_ext': optional_build_ext}, + # ext_modules=[ + # Extension( + # splitext(relpath(path, 'src').replace(os.sep, '.'))[0], + # sources=[path], + # include_dirs=[dirname(path)] + # ) + # for root, _, _ in os.walk('src') + # for path in glob(join(root, '*.c')) + # ], + ) diff --git a/haddock/cns/__init__.py b/src/haddock/__init__.py similarity index 100% rename from haddock/cns/__init__.py rename to src/haddock/__init__.py diff --git a/haddock/cli.py b/src/haddock/cli.py similarity index 100% rename from haddock/cli.py rename to src/haddock/cli.py diff --git a/bin/haddock3.py b/src/haddock/clis/cli.py similarity index 100% rename from bin/haddock3.py rename to src/haddock/clis/cli.py diff --git a/haddock/data/__init__.py b/src/haddock/cns/__init__.py similarity index 100% rename from haddock/data/__init__.py rename to src/haddock/cns/__init__.py diff --git a/haddock/cns/engine.py b/src/haddock/cns/engine.py similarity index 100% rename from haddock/cns/engine.py rename to src/haddock/cns/engine.py diff --git a/haddock/cns/topology.py b/src/haddock/cns/topology.py similarity index 100% rename from haddock/cns/topology.py rename to src/haddock/cns/topology.py diff --git a/haddock/cns/util.py b/src/haddock/cns/util.py similarity index 100% rename from haddock/cns/util.py rename to src/haddock/cns/util.py diff --git a/haddock/cooking.py b/src/haddock/cooking.py similarity index 100% rename from haddock/cooking.py rename to src/haddock/cooking.py diff --git a/haddock/modules/analysis/__init__.py b/src/haddock/data/__init__.py similarity index 100% rename from haddock/modules/analysis/__init__.py rename to src/haddock/data/__init__.py diff --git a/haddock/data/topology.py b/src/haddock/data/topology.py similarity index 100% rename from haddock/data/topology.py rename to src/haddock/data/topology.py diff --git a/haddock/data/toppar/boxtyp20.pdb b/src/haddock/data/toppar/boxtyp20.pdb similarity index 100% rename from haddock/data/toppar/boxtyp20.pdb rename to src/haddock/data/toppar/boxtyp20.pdb diff --git a/haddock/data/toppar/haddock.param b/src/haddock/data/toppar/haddock.param similarity index 100% rename from haddock/data/toppar/haddock.param rename to src/haddock/data/toppar/haddock.param diff --git a/haddock/data/toppar/haddock.top b/src/haddock/data/toppar/haddock.top similarity index 100% rename from haddock/data/toppar/haddock.top rename to src/haddock/data/toppar/haddock.top diff --git a/haddock/data/toppar/initial_positions/trans_vector_0 b/src/haddock/data/toppar/initial_positions/trans_vector_0 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_0 rename to src/haddock/data/toppar/initial_positions/trans_vector_0 diff --git 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haddock/data/toppar/initial_positions/trans_vector_12 rename to src/haddock/data/toppar/initial_positions/trans_vector_12 diff --git a/haddock/data/toppar/initial_positions/trans_vector_13 b/src/haddock/data/toppar/initial_positions/trans_vector_13 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_13 rename to src/haddock/data/toppar/initial_positions/trans_vector_13 diff --git a/haddock/data/toppar/initial_positions/trans_vector_14 b/src/haddock/data/toppar/initial_positions/trans_vector_14 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_14 rename to src/haddock/data/toppar/initial_positions/trans_vector_14 diff --git a/haddock/data/toppar/initial_positions/trans_vector_15 b/src/haddock/data/toppar/initial_positions/trans_vector_15 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_15 rename to src/haddock/data/toppar/initial_positions/trans_vector_15 diff --git a/haddock/data/toppar/initial_positions/trans_vector_16 b/src/haddock/data/toppar/initial_positions/trans_vector_16 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_16 rename to src/haddock/data/toppar/initial_positions/trans_vector_16 diff --git a/haddock/data/toppar/initial_positions/trans_vector_17 b/src/haddock/data/toppar/initial_positions/trans_vector_17 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_17 rename to src/haddock/data/toppar/initial_positions/trans_vector_17 diff --git a/haddock/data/toppar/initial_positions/trans_vector_18 b/src/haddock/data/toppar/initial_positions/trans_vector_18 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_18 rename to src/haddock/data/toppar/initial_positions/trans_vector_18 diff --git a/haddock/data/toppar/initial_positions/trans_vector_19 b/src/haddock/data/toppar/initial_positions/trans_vector_19 similarity index 100% rename from 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a/haddock/data/toppar/initial_positions/trans_vector_22 b/src/haddock/data/toppar/initial_positions/trans_vector_22 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_22 rename to src/haddock/data/toppar/initial_positions/trans_vector_22 diff --git a/haddock/data/toppar/initial_positions/trans_vector_23 b/src/haddock/data/toppar/initial_positions/trans_vector_23 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_23 rename to src/haddock/data/toppar/initial_positions/trans_vector_23 diff --git a/haddock/data/toppar/initial_positions/trans_vector_24 b/src/haddock/data/toppar/initial_positions/trans_vector_24 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_24 rename to src/haddock/data/toppar/initial_positions/trans_vector_24 diff --git a/haddock/data/toppar/initial_positions/trans_vector_25 b/src/haddock/data/toppar/initial_positions/trans_vector_25 similarity index 100% rename from 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a/haddock/data/toppar/initial_positions/trans_vector_35 b/src/haddock/data/toppar/initial_positions/trans_vector_35 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_35 rename to src/haddock/data/toppar/initial_positions/trans_vector_35 diff --git a/haddock/data/toppar/initial_positions/trans_vector_36 b/src/haddock/data/toppar/initial_positions/trans_vector_36 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_36 rename to src/haddock/data/toppar/initial_positions/trans_vector_36 diff --git a/haddock/data/toppar/initial_positions/trans_vector_37 b/src/haddock/data/toppar/initial_positions/trans_vector_37 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_37 rename to src/haddock/data/toppar/initial_positions/trans_vector_37 diff --git a/haddock/data/toppar/initial_positions/trans_vector_38 b/src/haddock/data/toppar/initial_positions/trans_vector_38 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_38 rename to src/haddock/data/toppar/initial_positions/trans_vector_38 diff --git a/haddock/data/toppar/initial_positions/trans_vector_39 b/src/haddock/data/toppar/initial_positions/trans_vector_39 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_39 rename to src/haddock/data/toppar/initial_positions/trans_vector_39 diff --git a/haddock/data/toppar/initial_positions/trans_vector_4 b/src/haddock/data/toppar/initial_positions/trans_vector_4 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_4 rename to src/haddock/data/toppar/initial_positions/trans_vector_4 diff --git a/haddock/data/toppar/initial_positions/trans_vector_40 b/src/haddock/data/toppar/initial_positions/trans_vector_40 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_40 rename to src/haddock/data/toppar/initial_positions/trans_vector_40 diff --git 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a/haddock/data/toppar/initial_positions/trans_vector_48 b/src/haddock/data/toppar/initial_positions/trans_vector_48 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_48 rename to src/haddock/data/toppar/initial_positions/trans_vector_48 diff --git a/haddock/data/toppar/initial_positions/trans_vector_49 b/src/haddock/data/toppar/initial_positions/trans_vector_49 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_49 rename to src/haddock/data/toppar/initial_positions/trans_vector_49 diff --git a/haddock/data/toppar/initial_positions/trans_vector_5 b/src/haddock/data/toppar/initial_positions/trans_vector_5 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_5 rename to src/haddock/data/toppar/initial_positions/trans_vector_5 diff --git a/haddock/data/toppar/initial_positions/trans_vector_50 b/src/haddock/data/toppar/initial_positions/trans_vector_50 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_50 rename to src/haddock/data/toppar/initial_positions/trans_vector_50 diff --git a/haddock/data/toppar/initial_positions/trans_vector_6 b/src/haddock/data/toppar/initial_positions/trans_vector_6 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_6 rename to src/haddock/data/toppar/initial_positions/trans_vector_6 diff --git a/haddock/data/toppar/initial_positions/trans_vector_7 b/src/haddock/data/toppar/initial_positions/trans_vector_7 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_7 rename to src/haddock/data/toppar/initial_positions/trans_vector_7 diff --git a/haddock/data/toppar/initial_positions/trans_vector_8 b/src/haddock/data/toppar/initial_positions/trans_vector_8 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_8 rename to src/haddock/data/toppar/initial_positions/trans_vector_8 diff --git a/haddock/data/toppar/initial_positions/trans_vector_9 b/src/haddock/data/toppar/initial_positions/trans_vector_9 similarity index 100% rename from haddock/data/toppar/initial_positions/trans_vector_9 rename to src/haddock/data/toppar/initial_positions/trans_vector_9 diff --git a/haddock/data/toppar/ion.param b/src/haddock/data/toppar/ion.param similarity index 100% rename from haddock/data/toppar/ion.param rename to src/haddock/data/toppar/ion.param diff --git a/haddock/data/toppar/ion.top b/src/haddock/data/toppar/ion.top similarity index 100% rename from haddock/data/toppar/ion.top rename to src/haddock/data/toppar/ion.top diff --git a/haddock/data/toppar/ligand.param b/src/haddock/data/toppar/ligand.param similarity index 100% rename from haddock/data/toppar/ligand.param rename to src/haddock/data/toppar/ligand.param diff --git a/haddock/data/toppar/ligand.top b/src/haddock/data/toppar/ligand.top similarity index 100% rename from haddock/data/toppar/ligand.top rename to src/haddock/data/toppar/ligand.top diff --git a/haddock/data/toppar/par_axis.pro b/src/haddock/data/toppar/par_axis.pro similarity index 100% rename from haddock/data/toppar/par_axis.pro rename to src/haddock/data/toppar/par_axis.pro diff --git a/haddock/data/toppar/par_axis_dani.pro b/src/haddock/data/toppar/par_axis_dani.pro similarity index 100% rename from haddock/data/toppar/par_axis_dani.pro rename to src/haddock/data/toppar/par_axis_dani.pro diff --git a/haddock/data/toppar/protein-allhdg5-4-noter.link b/src/haddock/data/toppar/protein-allhdg5-4-noter.link similarity index 100% rename from haddock/data/toppar/protein-allhdg5-4-noter.link rename to src/haddock/data/toppar/protein-allhdg5-4-noter.link diff --git a/haddock/data/toppar/protein-allhdg5-4.param b/src/haddock/data/toppar/protein-allhdg5-4.param similarity index 100% rename from haddock/data/toppar/protein-allhdg5-4.param rename to src/haddock/data/toppar/protein-allhdg5-4.param diff --git a/haddock/data/toppar/protein-allhdg5-4.top b/src/haddock/data/toppar/protein-allhdg5-4.top similarity index 100% rename from haddock/data/toppar/protein-allhdg5-4.top rename to src/haddock/data/toppar/protein-allhdg5-4.top diff --git a/haddock/data/toppar/protein_break.top b/src/haddock/data/toppar/protein_break.top similarity index 100% rename from haddock/data/toppar/protein_break.top rename to src/haddock/data/toppar/protein_break.top diff --git a/haddock/data/toppar/scatter.lib b/src/haddock/data/toppar/scatter.lib similarity index 100% rename from haddock/data/toppar/scatter.lib rename to src/haddock/data/toppar/scatter.lib diff --git a/haddock/data/toppar/tensor.pdb b/src/haddock/data/toppar/tensor.pdb similarity index 100% rename from haddock/data/toppar/tensor.pdb rename to src/haddock/data/toppar/tensor.pdb diff --git a/haddock/data/toppar/tensor.psf b/src/haddock/data/toppar/tensor.psf similarity index 100% rename from haddock/data/toppar/tensor.psf rename to src/haddock/data/toppar/tensor.psf diff --git a/haddock/data/toppar/tensor_dani.pdb b/src/haddock/data/toppar/tensor_dani.pdb similarity index 100% rename from haddock/data/toppar/tensor_dani.pdb rename to src/haddock/data/toppar/tensor_dani.pdb diff --git a/haddock/data/toppar/tensor_dani.psf b/src/haddock/data/toppar/tensor_dani.psf similarity index 100% rename from haddock/data/toppar/tensor_dani.psf rename to src/haddock/data/toppar/tensor_dani.psf diff --git a/haddock/data/toppar/tensor_para.pdb b/src/haddock/data/toppar/tensor_para.pdb similarity index 100% rename from haddock/data/toppar/tensor_para.pdb rename to src/haddock/data/toppar/tensor_para.pdb diff --git a/haddock/data/toppar/tensor_para.psf b/src/haddock/data/toppar/tensor_para.psf similarity index 100% rename from haddock/data/toppar/tensor_para.psf rename to src/haddock/data/toppar/tensor_para.psf diff --git a/haddock/data/toppar/top_axis.pro b/src/haddock/data/toppar/top_axis.pro similarity index 100% rename from haddock/data/toppar/top_axis.pro rename to src/haddock/data/toppar/top_axis.pro diff --git a/haddock/data/toppar/top_axis_dani.pro b/src/haddock/data/toppar/top_axis_dani.pro similarity index 100% rename from haddock/data/toppar/top_axis_dani.pro rename to src/haddock/data/toppar/top_axis_dani.pro diff --git a/haddock/data/toppar/water-allhdg5-4.param b/src/haddock/data/toppar/water-allhdg5-4.param similarity index 100% rename from haddock/data/toppar/water-allhdg5-4.param rename to src/haddock/data/toppar/water-allhdg5-4.param diff --git a/haddock/data/toppar/water-allhdg5-4.top b/src/haddock/data/toppar/water-allhdg5-4.top similarity index 100% rename from haddock/data/toppar/water-allhdg5-4.top rename to src/haddock/data/toppar/water-allhdg5-4.top diff --git a/haddock/defaults.py b/src/haddock/defaults.py similarity index 87% rename from haddock/defaults.py rename to src/haddock/defaults.py index b17cbe535..587a403ee 100644 --- a/haddock/defaults.py +++ b/src/haddock/defaults.py @@ -37,13 +37,11 @@ class Default: LINK_FILE = data_path / "toppar/protein-allhdg5-4-noter.link" - TRANSLATION_VECTORS = { - f"trans_vector_{i}": Path(data_path, - 'toppar', - 'initial_positions', - f'trans_vector_{i}') - for i in range(51) - } + TRANSLATION_VECTORS = {} + for i in range(51): + _s = f"trans_vector_{i}" + _p = Path(data_path, 'toppar', 'initial_positions', _s) + TRANSLATION_VECTORS[_s] = _p TENSORS = { "tensor_psf": data_path / "toppar/tensor.psf", diff --git a/haddock/error.py b/src/haddock/error.py similarity index 100% rename from haddock/error.py rename to src/haddock/error.py diff --git a/haddock/mathutil.py b/src/haddock/mathutil.py similarity index 100% rename from haddock/mathutil.py rename to src/haddock/mathutil.py diff --git a/haddock/modules/__init__.py b/src/haddock/modules/__init__.py similarity index 100% rename from haddock/modules/__init__.py rename to src/haddock/modules/__init__.py diff --git a/haddock/modules/clustering/__init__.py b/src/haddock/modules/analysis/__init__.py similarity index 100% rename from haddock/modules/clustering/__init__.py rename to src/haddock/modules/analysis/__init__.py diff --git a/haddock/modules/sampling/__init__.py b/src/haddock/modules/clustering/__init__.py similarity index 100% rename from haddock/modules/sampling/__init__.py rename to src/haddock/modules/clustering/__init__.py diff --git a/haddock/modules/scoring/__init__.py b/src/haddock/modules/sampling/__init__.py similarity index 100% rename from haddock/modules/scoring/__init__.py rename to src/haddock/modules/sampling/__init__.py diff --git a/haddock/modules/sampling/lightdock.py b/src/haddock/modules/sampling/lightdock.py similarity index 100% rename from haddock/modules/sampling/lightdock.py rename to src/haddock/modules/sampling/lightdock.py diff --git a/haddock/modules/sampling/sampling.toml b/src/haddock/modules/sampling/sampling.toml similarity index 100% rename from haddock/modules/sampling/sampling.toml rename to src/haddock/modules/sampling/sampling.toml diff --git a/haddock/modules/topology/__init__.py b/src/haddock/modules/scoring/__init__.py similarity index 100% rename from haddock/modules/topology/__init__.py rename to src/haddock/modules/scoring/__init__.py diff --git a/haddock/modules/scoring/cns/calc_free-ene.cns b/src/haddock/modules/scoring/cns/calc_free-ene.cns similarity index 100% rename from haddock/modules/scoring/cns/calc_free-ene.cns rename to src/haddock/modules/scoring/cns/calc_free-ene.cns diff --git a/haddock/modules/scoring/cns/def_solv_param.cns b/src/haddock/modules/scoring/cns/def_solv_param.cns similarity index 100% rename from haddock/modules/scoring/cns/def_solv_param.cns rename to src/haddock/modules/scoring/cns/def_solv_param.cns diff --git a/haddock/modules/scoring/cns/flex_segment_back.cns b/src/haddock/modules/scoring/cns/flex_segment_back.cns similarity index 100% rename from haddock/modules/scoring/cns/flex_segment_back.cns rename to src/haddock/modules/scoring/cns/flex_segment_back.cns diff --git a/haddock/modules/scoring/cns/flexauto-neighbors.cns b/src/haddock/modules/scoring/cns/flexauto-neighbors.cns similarity index 100% rename from haddock/modules/scoring/cns/flexauto-neighbors.cns rename to src/haddock/modules/scoring/cns/flexauto-neighbors.cns diff --git a/haddock/modules/scoring/cns/print_coorheader.cns b/src/haddock/modules/scoring/cns/print_coorheader.cns similarity index 100% rename from haddock/modules/scoring/cns/print_coorheader.cns rename to src/haddock/modules/scoring/cns/print_coorheader.cns diff --git a/haddock/modules/scoring/cns/scale_inter_final.cns b/src/haddock/modules/scoring/cns/scale_inter_final.cns similarity index 100% rename from haddock/modules/scoring/cns/scale_inter_final.cns rename to src/haddock/modules/scoring/cns/scale_inter_final.cns diff --git a/haddock/modules/scoring/cns/scale_intra_only.cns b/src/haddock/modules/scoring/cns/scale_intra_only.cns similarity index 100% rename from haddock/modules/scoring/cns/scale_intra_only.cns rename to src/haddock/modules/scoring/cns/scale_intra_only.cns diff --git a/haddock/modules/scoring/cns/scoring.cns b/src/haddock/modules/scoring/cns/scoring.cns similarity index 100% rename from haddock/modules/scoring/cns/scoring.cns rename to src/haddock/modules/scoring/cns/scoring.cns diff --git a/haddock/modules/scoring/cns/scoring.toml b/src/haddock/modules/scoring/cns/scoring.toml similarity index 100% rename from haddock/modules/scoring/cns/scoring.toml rename to src/haddock/modules/scoring/cns/scoring.toml diff --git a/haddock/modules/scoring/default.py b/src/haddock/modules/scoring/default.py similarity index 100% rename from haddock/modules/scoring/default.py rename to src/haddock/modules/scoring/default.py diff --git a/src/haddock/modules/topology/__init__.py b/src/haddock/modules/topology/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/haddock/modules/topology/cns/auto-his.cns b/src/haddock/modules/topology/cns/auto-his.cns similarity index 100% rename from haddock/modules/topology/cns/auto-his.cns rename to src/haddock/modules/topology/cns/auto-his.cns diff --git a/haddock/modules/topology/cns/build-missing.cns b/src/haddock/modules/topology/cns/build-missing.cns similarity index 100% rename from haddock/modules/topology/cns/build-missing.cns rename to src/haddock/modules/topology/cns/build-missing.cns diff --git a/haddock/modules/topology/cns/coval-ace-cys.cns b/src/haddock/modules/topology/cns/coval-ace-cys.cns similarity index 100% rename from haddock/modules/topology/cns/coval-ace-cys.cns rename to src/haddock/modules/topology/cns/coval-ace-cys.cns diff --git a/haddock/modules/topology/cns/covalheme.cns b/src/haddock/modules/topology/cns/covalheme.cns similarity index 100% rename from haddock/modules/topology/cns/covalheme.cns rename to src/haddock/modules/topology/cns/covalheme.cns diff --git a/haddock/modules/topology/cns/dna_break.cns b/src/haddock/modules/topology/cns/dna_break.cns similarity index 100% rename from haddock/modules/topology/cns/dna_break.cns rename to src/haddock/modules/topology/cns/dna_break.cns diff --git a/haddock/modules/topology/cns/generate-topology.cns b/src/haddock/modules/topology/cns/generate-topology.cns similarity index 100% rename from haddock/modules/topology/cns/generate-topology.cns rename to src/haddock/modules/topology/cns/generate-topology.cns diff --git a/haddock/modules/topology/cns/generate-topology.toml b/src/haddock/modules/topology/cns/generate-topology.toml similarity index 100% rename from haddock/modules/topology/cns/generate-topology.toml rename to src/haddock/modules/topology/cns/generate-topology.toml diff --git a/haddock/modules/topology/cns/patch-bb-cg.cns b/src/haddock/modules/topology/cns/patch-bb-cg.cns similarity index 100% rename from haddock/modules/topology/cns/patch-bb-cg.cns rename to src/haddock/modules/topology/cns/patch-bb-cg.cns diff --git a/haddock/modules/topology/cns/patch-types-cg.cns b/src/haddock/modules/topology/cns/patch-types-cg.cns similarity index 100% rename from haddock/modules/topology/cns/patch-types-cg.cns rename to src/haddock/modules/topology/cns/patch-types-cg.cns diff --git a/haddock/modules/topology/cns/prot_break.cns b/src/haddock/modules/topology/cns/prot_break.cns similarity index 100% rename from haddock/modules/topology/cns/prot_break.cns rename to src/haddock/modules/topology/cns/prot_break.cns diff --git a/haddock/modules/topology/default.py b/src/haddock/modules/topology/default.py similarity index 100% rename from haddock/modules/topology/default.py rename to src/haddock/modules/topology/default.py diff --git a/haddock/ontology.py b/src/haddock/ontology.py similarity index 100% rename from haddock/ontology.py rename to src/haddock/ontology.py diff --git a/haddock/parallel.py b/src/haddock/parallel.py similarity index 100% rename from haddock/parallel.py rename to src/haddock/parallel.py diff --git a/haddock/pdbutil.py b/src/haddock/pdbutil.py similarity index 100% rename from haddock/pdbutil.py rename to src/haddock/pdbutil.py diff --git a/haddock/structure.py b/src/haddock/structure.py similarity index 100% rename from haddock/structure.py rename to src/haddock/structure.py diff --git a/haddock/version.py b/src/haddock/version.py similarity index 100% rename from haddock/version.py rename to src/haddock/version.py diff --git a/haddock/workflow.py b/src/haddock/workflow.py similarity index 100% rename from haddock/workflow.py rename to src/haddock/workflow.py From d6e55cad82b1db0d3e3640c16e3e517c7801e1ce Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Fri, 16 Jul 2021 21:24:07 +0200 Subject: [PATCH 2/4] pyversion above 3.8 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index af9588ff8..b6ed2d8f8 100644 --- a/setup.py +++ b/setup.py @@ -63,7 +63,7 @@ def read(*names, **kwargs): 'Protein docking', 'Proteins', ], - python_requires='>=3.8, <3.10', + python_requires='>=3.8, <4', install_requires=[ # not added on purpose ], From 29df072b99b52adc957af1faded613e934e7d881 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Fri, 16 Jul 2021 21:51:01 +0200 Subject: [PATCH 3/4] removes libfuncpy for now --- requirements.txt | 1 - requirements.yml | 1 - 2 files changed, 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 504a0d0bd..26c4e1736 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,4 +3,3 @@ pdb-tools==2.1.0 jsonpickle==2.0.0 numpy==1.20.2 lightdock==0.9.0a2 -libfuncpy>=0.0.3 diff --git a/requirements.yml b/requirements.yml index 8e20b96b7..5899b19ef 100644 --- a/requirements.yml +++ b/requirements.yml @@ -11,4 +11,3 @@ dependencies: - pip: - pdb-tools - lightdock - - libfuncpy From ec71edb5f3e77f618b511eff39bfd3d4153e3110 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Mon, 19 Jul 2021 20:42:28 +0200 Subject: [PATCH 4/4] add update instructions --- README.md | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 81f9d1355..ccb358dca 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ - # WARNING: The `main` branch is not production-ready The `main` branch is a prototype of newly refined architecture and it @@ -65,6 +64,21 @@ Save and exit. Source the file: source bin/activate_haddock ``` +You need to `source bin/activate_haddock` at each new terminal window +you wish to use `haddock3`. + +### 1.5 Keep up to date + +In the `github` folder of `haddock3` run: + +```bash +git pull +``` + +This will pull the latest changes to your local folder and because you +installed `haddock3` with the option `develop` those changes become +available immediately. + ## 2. Examples ### 2.1. Basic scoring of an ensemble of 5 structures: