LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
bin/ant_thony.py
bin/lgd_add_chain.py
bin/lgd_calculate_diameter.py
bin/lgd_calculate_reference_points.py
bin/lgd_calculate_scoring.py
bin/lgd_calculate_surface_density.py
bin/lgd_cluster_bsas.py
bin/lgd_copy_structures.py
bin/lgd_create_membrane.py
bin/lgd_filter_membrane.py
bin/lgd_filter_restraints.py
bin/lgd_flatten.py
bin/lgd_generate_conformations.py
bin/lgd_generate_glowworm_positions.py
bin/lgd_generate_trajectory.py
bin/lgd_gso_to_csv.py
bin/lgd_move_anm.py
bin/lgd_prepare_new_simulation.py
bin/lgd_quaternion_to_euler.py
bin/lgd_rank.py
bin/lgd_rank_swarm.py
bin/lgd_stats.py
bin/lgd_success_rate.py
bin/lgd_top.py
bin/lightdock3.py
bin/lightdock3_setup.py
lightdock/__init__.py
lightdock/constants.py
lightdock/version.py
lightdock.egg-info/PKG-INFO
lightdock.egg-info/SOURCES.txt
lightdock.egg-info/dependency_links.txt
lightdock.egg-info/not-zip-safe
lightdock.egg-info/requires.txt
lightdock.egg-info/top_level.txt
lightdock/error/__init__.py
lightdock/error/lightdock_errors.py
lightdock/etc/glowworm.conf
lightdock/gso/__init__.py
lightdock/gso/algorithm.py
lightdock/gso/boundaries.py
lightdock/gso/coordinates.py
lightdock/gso/glowworm.py
lightdock/gso/initializer.py
lightdock/gso/parameters.py
lightdock/gso/swarm.py
lightdock/gso/searchspace/__init__.py
lightdock/gso/searchspace/benchmark_ofunctions.py
lightdock/gso/searchspace/landscape.py
lightdock/gso/searchspace/ofunction.py
lightdock/gso/searchspace/cython/__init__.py
lightdock/gso/searchspace/cython/j1.c
lightdock/gso/searchspace/cython/j2.c
lightdock/gso/searchspace/cython/j3.c
lightdock/gso/searchspace/cython/j4.c
lightdock/gso/searchspace/cython/j5.c
lightdock/gso/searchspace/cython/setup.py
lightdock/mathutil/__init__.py
lightdock/mathutil/constants.py
lightdock/mathutil/ellipsoid.py
lightdock/mathutil/lrandom.py
lightdock/mathutil/cython/__init__.py
lightdock/mathutil/cython/cutil.c
lightdock/mathutil/cython/quaternion.c
lightdock/mathutil/cython/setup.py
lightdock/parallel/__init__.py
lightdock/parallel/kraken.py
lightdock/parallel/util.py
lightdock/pdbutil/PDBIO.py
lightdock/pdbutil/__init__.py
lightdock/prep/__init__.py
lightdock/prep/ftdock.py
lightdock/prep/geometry.py
lightdock/prep/poses.py
lightdock/prep/simulation.py
lightdock/prep/starting_points.py
lightdock/scoring/__init__.py
lightdock/scoring/functions.py
lightdock/scoring/multiple.py
lightdock/scoring/cpydock/__init__.py
lightdock/scoring/cpydock/driver.py
lightdock/scoring/cpydock/data/__init__.py
lightdock/scoring/cpydock/data/amber.py
lightdock/scoring/cpydock/data/solvation.py
lightdock/scoring/cpydock/data/vdw.py
lightdock/scoring/cpydock/energy/__init__.py
lightdock/scoring/cpydock/energy/parameters.py
lightdock/scoring/cpydock/energy/c/__init__.py
lightdock/scoring/cpydock/energy/c/cpydock.c
lightdock/scoring/cpydock/energy/c/setup.py
lightdock/scoring/ddna/__init__.py
lightdock/scoring/ddna/driver.py
lightdock/scoring/ddna/cython/__init__.py
lightdock/scoring/ddna/cython/cddna.c
lightdock/scoring/ddna/cython/setup.py
lightdock/scoring/dfire/__init__.py
lightdock/scoring/dfire/driver.py
lightdock/scoring/dfire/cython/__init__.py
lightdock/scoring/dfire/cython/cdfire.c
lightdock/scoring/dfire/cython/setup.py
lightdock/scoring/dfire/data/DCparams
lightdock/scoring/dfire2/__init__.py
lightdock/scoring/dfire2/driver.py
lightdock/scoring/dfire2/c/__init__.py
lightdock/scoring/dfire2/c/cdfire2.c
lightdock/scoring/dfire2/c/setup.py
lightdock/scoring/dfire2/cython/__init__.py
lightdock/scoring/dfire2/cython/setup.py
lightdock/scoring/dfire2/data/dfire2_energies.npy
lightdock/scoring/dfire2/data/dfire_pair.lib
lightdock/scoring/dna/__init__.py
lightdock/scoring/dna/driver.py
lightdock/scoring/dna/data/__init__.py
lightdock/scoring/dna/data/amber.py
lightdock/scoring/dna/data/vdw.py
lightdock/scoring/dna/energy/__init__.py
lightdock/scoring/dna/energy/parameters.py
lightdock/scoring/dna/energy/c/__init__.py
lightdock/scoring/dna/energy/c/cdna.c
lightdock/scoring/dna/energy/c/setup.py
lightdock/scoring/fastdfire/__init__.py
lightdock/scoring/fastdfire/driver.py
lightdock/scoring/fastdfire/c/__init__.py
lightdock/scoring/fastdfire/c/cdfire.c
lightdock/scoring/fastdfire/c/setup.py
lightdock/scoring/fastdfire/data/DCparams
lightdock/scoring/mj3h/__init__.py
lightdock/scoring/mj3h/driver.py
lightdock/scoring/mj3h/data/MJ_potentials.dat
lightdock/scoring/pisa/__init__.py
lightdock/scoring/pisa/driver.py
lightdock/scoring/pisa/cython/__init__.py
lightdock/scoring/pisa/cython/cpisa.c
lightdock/scoring/pisa/cython/setup.py
lightdock/scoring/pisa/data/pisa.params
lightdock/scoring/sd/__init__.py
lightdock/scoring/sd/driver.py
lightdock/scoring/sd/data/__init__.py
lightdock/scoring/sd/data/amber.py
lightdock/scoring/sd/data/vdw.py
lightdock/scoring/sd/energy/__init__.py
lightdock/scoring/sd/energy/c/__init__.py
lightdock/scoring/sd/energy/c/sd.c
lightdock/scoring/sd/energy/c/setup.py
lightdock/scoring/sipper/__init__.py
lightdock/scoring/sipper/driver.py
lightdock/scoring/sipper/c/__init__.py
lightdock/scoring/sipper/c/setup.py
lightdock/scoring/sipper/c/sipper.c
lightdock/scoring/sipper/data/__init__.py
lightdock/scoring/sipper/data/energy.py
lightdock/scoring/template/__init__.py
lightdock/scoring/template/driver.py
lightdock/scoring/tobi/__init__.py
lightdock/scoring/tobi/driver.py
lightdock/scoring/tobi/data/TOBI_SC_step1.dat
lightdock/scoring/tobi/data/TOBI_SC_step2.dat
lightdock/scoring/vdw/__init__.py
lightdock/scoring/vdw/driver.py
lightdock/scoring/vdw/data/__init__.py
lightdock/scoring/vdw/data/amber.py
lightdock/scoring/vdw/data/vdw.py
lightdock/scoring/vdw/energy/__init__.py
lightdock/scoring/vdw/energy/c/__init__.py
lightdock/scoring/vdw/energy/c/cvdw.c
lightdock/scoring/vdw/energy/c/setup.py
lightdock/simulation/__init__.py
lightdock/simulation/docking_mpi.py
lightdock/simulation/docking_multiprocessing.py
lightdock/structure/__init__.py
lightdock/structure/atom.py
lightdock/structure/chain.py
lightdock/structure/complex.py
lightdock/structure/model.py
lightdock/structure/nm.py
lightdock/structure/residue.py
lightdock/structure/space.py
lightdock/test/__init__.py
lightdock/test/bin/__init__.py
lightdock/test/bin/regression.py
lightdock/test/bin/test_dfire.py
lightdock/test/bin/test_dfire2.py
lightdock/test/bin/test_dna.py
lightdock/test/bin/test_fastdfire.py
lightdock/test/bin/test_mj3h.py
lightdock/test/bin/test_pisa.py
lightdock/test/bin/test_pydock.py
lightdock/test/bin/test_setup.py
lightdock/test/bin/test_setup_membrane.py
lightdock/test/bin/test_setup_restraints.py
lightdock/test/bin/test_tobi.py
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lightdock/test/prep/golden_data/starting_points.pdb
lightdock/test/prep/golden_data/test.bild
lightdock/test/prep/golden_data/3p0g/ligand.pdb
lightdock/test/prep/golden_data/3p0g/lightdock_ligand.pdb
lightdock/test/prep/golden_data/3p0g/lightdock_ligand.pdb.xyz.npy
lightdock/test/prep/golden_data/3p0g/lightdock_receptor_membrane.pdb
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lightdock/test/prep/golden_data/3p0g/receptor_membrane.pdb
lightdock/test/prep/golden_data/3p0g/restraints.list
lightdock/test/prep/golden_data/3p0g/setup.json
lightdock/test/prep/golden_data/3p0g/init/cluster_centers.pdb
lightdock/test/prep/golden_data/3p0g/init/initial_positions_0.dat
lightdock/test/prep/golden_data/3p0g/init/initial_positions_1.dat
lightdock/test/prep/golden_data/3p0g/init/starting_poses_0.bild
lightdock/test/prep/golden_data/3p0g/init/starting_poses_1.bild
lightdock/test/prep/golden_data/3p0g/init/starting_positions_0.pdb
lightdock/test/prep/golden_data/3p0g/init/starting_positions_1.pdb
lightdock/test/prep/golden_data/create_simulation_info_file/setup.json
lightdock/test/prep/golden_data/load_starting_positions/ok/init/cluster_centers.pdb
lightdock/test/prep/golden_data/load_starting_positions/ok/init/initial_positions_0.dat
lightdock/test/prep/golden_data/load_starting_positions/ok/init/initial_positions_1.dat
lightdock/test/prep/golden_data/load_starting_positions/ok/init/starting_poses_0.bild
lightdock/test/prep/golden_data/load_starting_positions/ok/init/starting_poses_1.bild
lightdock/test/prep/golden_data/load_starting_positions/ok/init/starting_positions_0.pdb
lightdock/test/prep/golden_data/load_starting_positions/ok/init/starting_positions_1.pdb
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/cluster_centers.pdb
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/initial_positions_0.dat
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/initial_positions_1.dat
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/starting_poses_0.bild
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/starting_poses_1.bild
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/starting_positions_0.pdb
lightdock/test/prep/golden_data/load_starting_positions/wrong_dat/init/starting_positions_1.pdb
lightdock/test/scoring/__init__.py
lightdock/test/scoring/test_ddna_function.py
lightdock/test/scoring/test_dfire2_function.py
lightdock/test/scoring/test_dfire_function.py
lightdock/test/scoring/test_dna_function.py
lightdock/test/scoring/test_fastdfire_function.py
lightdock/test/scoring/test_function_interface.py
lightdock/test/scoring/test_mj_function.py
lightdock/test/scoring/test_pisa_function.py
lightdock/test/scoring/test_pydock_function.py
lightdock/test/scoring/test_tobi_function.py
lightdock/test/scoring/golden_data/1AY7_lig.pdb.H
lightdock/test/scoring/golden_data/1AY7_lig.pdb.amber
lightdock/test/scoring/golden_data/1AY7_rec.pdb.H
lightdock/test/scoring/golden_data/1AY7_rec.pdb.amber
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lightdock/test/scoring/golden_data/1AY7rec.pdb
lightdock/test/scoring/golden_data/1EAWlig.pdb
lightdock/test/scoring/golden_data/1EAWrec.pdb
lightdock/test/scoring/golden_data/1PPElig.pdb
lightdock/test/scoring/golden_data/1PPErec.pdb
lightdock/test/scoring/golden_data/1azp_dna.pdb
lightdock/test/scoring/golden_data/1azp_prot.pdb
lightdock/test/scoring/golden_data/3mfk_dna.pdb
lightdock/test/scoring/golden_data/3mfk_homodimer.pdb
lightdock/test/scoring/golden_data/3mfk_homodimer.pdb.H
lightdock/test/structure/__init__.py
lightdock/test/structure/test_atom.py
lightdock/test/structure/test_chain.py
lightdock/test/structure/test_complex.py
lightdock/test/structure/test_model.py
lightdock/test/structure/test_nm.py
lightdock/test/structure/test_residue.py
lightdock/test/structure/golden_data/two_residues.pdb
lightdock/test/structure/golden_data/two_residues_y_180.pdb
lightdock/test/structure/golden_data/two_residues_y_90_x_90.pdb
lightdock/test/structure/golden_data/nm_dna/1DIZ_lig.pdb.H
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lightdock/test/structure/golden_data/nm_prot/2UUY_rec.pdb
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lightdock/test/structure/golden_data/nm_prot/lightdock_rec.nm.npy
lightdock/test/util/__init__.py
lightdock/test/util/test_logger.py
lightdock/test/util/test_parser.py
lightdock/test/util/golden_data/lightdock_1czy_peptide.pdb
lightdock/test/util/golden_data/lightdock_1czy_protein.pdb
lightdock/test/util/golden_data/output_debug.log
lightdock/test/util/golden_data/output_error.log
lightdock/test/util/golden_data/output_warning.log
lightdock/test/util/golden_data/pdbs.list
lightdock/util/__init__.py
lightdock/util/analysis.py
lightdock/util/logger.py
lightdock/util/multiprocessing_pdb.py
lightdock/util/parser.py
lightdock/util/table.py