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}; 931C004812135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931C004912135A5E009192AB /* attribute_statistics.cpp */, 931C004A12135A5E009192AB /* CommonEndpointPairFilter.cpp */, 931C004B12135A5E009192AB /* interaction_graph.cpp */, 931C004C12135A5E009192AB /* internal */, 931C004E12135A5E009192AB /* LowestRefinedPairScore.cpp */, 931C004F12135A5E009192AB /* SConscript */, 931C005012135A5E009192AB /* StateAdaptor.cpp */, ); name = src; path = ../modules/misc/src; sourceTree = SOURCE_ROOT; }; 931C004C12135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( 931C004D12135A5E009192AB /* SConscript */, ); name = internal; path = ../modules/misc/src/internal; sourceTree = SOURCE_ROOT; }; 931C005112135A5E009192AB /* test */ = { isa = PBXGroup; children = ( 931C005212135A5E009192AB /* input */, 931C005412135A5E009192AB /* SConscript */, 931C005512135A5E009192AB /* test_common_endpoint.py */, 931C005612135A5E009192AB /* test_lrps.py */, 931C005712135A5E009192AB /* test_statistics.py */, 931C005812135A5E009192AB /* test_wlc.py */, ); name = test; path = ../modules/misc/test; sourceTree = SOURCE_ROOT; }; 931C005212135A5E009192AB /* input */ = { isa = PBXGroup; children = ( 931C005312135A5E009192AB /* single_protein.pdb */, ); name = input; path = ../modules/misc/test/input; sourceTree = SOURCE_ROOT; }; 931C005912135A5E009192AB /* modeller */ = { isa = PBXGroup; children = ( 931C005A12135A5E009192AB /* bin */, 931C005C12135A5E009192AB /* data */, 931C005E12135A5E009192AB /* doc */, 931C006012135A5E009192AB /* examples */, 931C006812135A5E009192AB /* include */, 931C006B12135A5E009192AB /* pyext */, 931C006F12135A5E009192AB /* SConscript */, 931C007012135A5E009192AB /* src */, 931C007412135A5E009192AB /* test */, ); name = modeller; path = ../modules/modeller; sourceTree = SOURCE_ROOT; }; 931C005A12135A5E009192AB /* bin */ = { isa = PBXGroup; children = ( 931C005B12135A5E009192AB /* SConscript */, ); name = bin; path = ../modules/modeller/bin; sourceTree = SOURCE_ROOT; }; 931C005C12135A5E009192AB /* data */ = { isa = PBXGroup; children = ( 931C005D12135A5E009192AB /* SConscript */, ); name = data; path = ../modules/modeller/data; sourceTree = SOURCE_ROOT; }; 931C005E12135A5E009192AB /* doc */ = { isa = PBXGroup; children = ( 931C005F12135A5E009192AB /* SConscript */, ); name = doc; path = ../modules/modeller/doc; sourceTree = SOURCE_ROOT; }; 931C006012135A5E009192AB /* examples */ = { isa = PBXGroup; children = ( 931C006112135A5E009192AB /* imp_restraints_in_modeller.py */, 931C006212135A5E009192AB /* imp_restraints_in_modeller.readme */, 931C006312135A5E009192AB /* load_modeller_model.py */, 931C006412135A5E009192AB /* load_modeller_model.readme */, 931C006512135A5E009192AB /* modeller_restraints_in_imp.py */, 931C006612135A5E009192AB /* modeller_restraints_in_imp.readme */, 931C006712135A5E009192AB /* SConscript */, ); name = examples; path = ../modules/modeller/examples; sourceTree = SOURCE_ROOT; }; 931C006812135A5E009192AB /* include */ = { isa = PBXGroup; children = ( 931C006912135A5E009192AB /* MultipleBinormalRestraint.h */, 931C006A12135A5E009192AB /* SConscript */, ); name = include; path = ../modules/modeller/include; sourceTree = SOURCE_ROOT; }; 931C006B12135A5E009192AB /* pyext */ = { isa = PBXGroup; children = ( 931C006C12135A5E009192AB /* IMP_modeller_init.i */, 931C006D12135A5E009192AB /* SConscript */, 931C006E12135A5E009192AB /* swig.i-in */, ); name = pyext; path = ../modules/modeller/pyext; sourceTree = SOURCE_ROOT; }; 931C007012135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931C007112135A5E009192AB /* internal */, 931C007212135A5E009192AB /* MultipleBinormalRestraint.cpp */, 931C007312135A5E009192AB /* SConscript */, ); name = src; path = ../modules/modeller/src; sourceTree = SOURCE_ROOT; }; 931C007112135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/modeller/src/internal; sourceTree = SOURCE_ROOT; }; 931C007412135A5E009192AB /* test */ = { isa = PBXGroup; children = ( 931C007512135A5E009192AB /* input */, 931C007812135A5E009192AB /* SConscript */, 931C007912135A5E009192AB /* test_dynamic_restraints.py */, 931C007A12135A5E009192AB /* test_imp_restraints.py */, 931C007B12135A5E009192AB /* test_load_model_atoms.py */, 931C007C12135A5E009192AB /* test_modeller_restraints.py */, 931C007D12135A5E009192AB /* test_rsr_file_read.py */, ); name = test; path = ../modules/modeller/test; sourceTree = SOURCE_ROOT; }; 931C007512135A5E009192AB /* input */ = { isa = PBXGroup; children = ( 931C007612135A5E009192AB /* single_dna.pdb */, 931C007712135A5E009192AB /* single_protein.pdb */, ); name = input; path = ../modules/modeller/test/input; sourceTree = SOURCE_ROOT; }; 931C007E12135A5E009192AB /* multifit */ = { isa = PBXGroup; children = ( 931C007F12135A5E009192AB /* bin */, 931C008112135A5E009192AB /* data */, 931C008312135A5E009192AB /* doc */, 931C008712135A5E009192AB /* examples */, 931C008B12135A5E009192AB /* include */, 931C009912135A5E009192AB /* pyext */, 931C009D12135A5E009192AB /* README */, 931C009E12135A5E009192AB /* SConscript */, 931C009F12135A5E009192AB /* src */, 931C00AD12135A5E009192AB /* test */, ); name = multifit; path = ../modules/multifit; sourceTree = SOURCE_ROOT; }; 931C007F12135A5E009192AB /* bin */ = { isa = PBXGroup; children = ( 931C008012135A5E009192AB /* SConscript */, ); name = bin; path = ../modules/multifit/bin; sourceTree = SOURCE_ROOT; }; 931C008112135A5E009192AB /* data */ = { isa = PBXGroup; children = ( 931C008212135A5E009192AB /* SConscript */, ); name = data; path = ../modules/multifit/data; sourceTree = SOURCE_ROOT; }; 931C008312135A5E009192AB /* doc */ = { isa = PBXGroup; children = ( 931C008412135A5E009192AB /* generated */, 931C008612135A5E009192AB /* SConscript */, ); name = doc; path = ../modules/multifit/doc; sourceTree = SOURCE_ROOT; }; 931C008412135A5E009192AB /* generated */ = { isa = PBXGroup; children = ( 931C008512135A5E009192AB /* overview.dox */, ); name = generated; path = ../modules/multifit/doc/generated; sourceTree = SOURCE_ROOT; }; 931C008712135A5E009192AB /* examples */ = { isa = PBXGroup; children = ( 9349D76D12164ACD00235135 /* optimize_speicific_mapping.py */, 931C008812135A5E009192AB /* generated */, 931C008A12135A5E009192AB /* SConscript */, ); name = examples; path = ../modules/multifit/examples; sourceTree = SOURCE_ROOT; }; 931C008812135A5E009192AB /* generated */ = { isa = PBXGroup; children = ( 931C008912135A5E009192AB /* examples.dox */, ); name = generated; path = ../modules/multifit/examples/generated; sourceTree = SOURCE_ROOT; }; 931C008B12135A5E009192AB /* include */ = { isa = PBXGroup; children = ( 931C008C12135A5E009192AB /* DataContainer.h */, 931C008D12135A5E009192AB /* fitting_solutions_reader_writer.h */, 931C008E12135A5E009192AB /* fitting_tools.h */, 931C008F12135A5E009192AB /* FittingSolutionRecord.h */, 931C009012135A5E009192AB /* internal */, 931C009112135A5E009192AB /* m_rigid_fitting.h */, 931C009212135A5E009192AB /* restraints_utils.h */, 931C009312135A5E009192AB /* sampling_space.h */, 931C009412135A5E009192AB /* sampling_space_utils.h */, 931C009512135A5E009192AB /* SConscript */, 931C009612135A5E009192AB /* SettingsData.h */, 931C009712135A5E009192AB /* SingleDominoRun.h */, 931C009812135A5E009192AB /* weighted_excluded_volume.h */, ); name = include; path = ../modules/multifit/include; sourceTree = SOURCE_ROOT; }; 931C009012135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/multifit/include/internal; sourceTree = SOURCE_ROOT; }; 931C009912135A5E009192AB /* pyext */ = { isa = PBXGroup; children = ( 931C009A12135A5E009192AB /* multifit.i */, 931C009B12135A5E009192AB /* SConscript */, 931C009C12135A5E009192AB /* swig.i-in */, ); name = pyext; path = ../modules/multifit/pyext; sourceTree = SOURCE_ROOT; }; 931C009F12135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931C00A012135A5E009192AB /* DataContainer.cpp */, 931C00A112135A5E009192AB /* fitting_solutions_reader_writer.cpp */, 931C00A212135A5E009192AB /* fitting_tools.cpp */, 931C00A312135A5E009192AB /* FittingSolutionRecord.cpp */, 931C00A412135A5E009192AB /* internal */, 931C00A512135A5E009192AB /* m_rigid_fitting.cpp */, 931C00A612135A5E009192AB /* restraints_utils.cpp */, 931C00A712135A5E009192AB /* sampling_space.cpp */, 931C00A812135A5E009192AB /* sampling_space_utils.cpp */, 931C00A912135A5E009192AB /* SConscript */, 931C00AA12135A5E009192AB /* SettingsData.cpp */, 931C00AB12135A5E009192AB /* SingleDominoRun.cpp */, 931C00AC12135A5E009192AB /* weighted_excluded_volume.cpp */, ); name = src; path = ../modules/multifit/src; sourceTree = SOURCE_ROOT; }; 931C00A412135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/multifit/src/internal; sourceTree = SOURCE_ROOT; }; 931C00AD12135A5E009192AB /* test */ = { isa = PBXGroup; children = ( 931C00AE12135A5E009192AB /* input */, 931C00E312135A5F009192AB /* restraints */, 931C00E412135A5F009192AB /* SConscript */, 931C00E512135A5F009192AB /* test_add_surface_index.py */, 931C00E612135A5F009192AB /* test_data_container.py */, 931C00E712135A5F009192AB /* test_read_fitting_solutions.py */, 931C00E812135A5F009192AB /* test_rigid_fitting_pca.py */, 931C00E912135A5F009192AB /* test_settings_data.py */, 931C00EA12135A5F009192AB /* test_single_domino_run.py */, 931C00EB12135A5F009192AB /* test_surface_sample_protein.py */, 931C00EC12135A5F009192AB /* test_weighted_excluded_volume_restraint.py */, ); name = test; path = ../modules/multifit/test; sourceTree = SOURCE_ROOT; }; 931C00AE12135A5E009192AB /* input */ = { isa = PBXGroup; children = ( 931C00AF12135A5E009192AB /* 1f7dA00.pdb */, 931C00B012135A5E009192AB /* 1f7dA00_8.mrc */, 931C00B112135A5E009192AB /* 1z5s.jt */, 931C00B212135A5E009192AB /* 1z5s_20.mrc */, 931C00B312135A5E009192AB /* 1z5s_A.pdb */, 931C00B412135A5E009192AB /* 1z5s_A_anchor_points.pdb */, 931C00B512135A5E009192AB /* 1z5s_A_fitted.pdb */, 931C00B612135A5E009192AB /* 1z5s_A_fitting.output */, 931C00B712135A5E009192AB /* 1z5s_A_fitting_solutions.txt */, 931C00B812135A5E009192AB /* 1z5s_anchor_points.pdb */, 931C00B912135A5E009192AB /* 1z5s_B.pdb */, 931C00BA12135A5E009192AB /* 1z5s_B_anchor_points.pdb */, 931C00BB12135A5E009192AB /* 1z5s_B_fitted.pdb */, 931C00BC12135A5E009192AB /* 1z5s_B_fitting.output */, 931C00BD12135A5E009192AB /* 1z5s_C.pdb */, 931C00BE12135A5E009192AB /* 1z5s_C1.pdb */, 931C00BF12135A5E009192AB /* 1z5s_C_anchor_points.pdb */, 931C00C012135A5E009192AB /* 1z5s_C_fitted.pdb */, 931C00C112135A5E009192AB /* 1z5s_C_fitting.output */, 931C00C212135A5E009192AB /* 1z5s_D.pdb */, 931C00C312135A5E009192AB /* 1z5s_D_anchor_points.pdb */, 931C00C412135A5E009192AB /* 1z5s_D_fitted.pdb */, 931C00C512135A5E009192AB /* 1z5s_D_fitting.output */, 931C00C612135A5E009192AB /* assembly.input */, 931C00C712135A5E009192AB /* scoring */, 931C00D612135A5F009192AB /* scoring_complete */, ); name = input; path = ../modules/multifit/test/input; sourceTree = SOURCE_ROOT; }; 931C00C712135A5E009192AB /* scoring */ = { isa = PBXGroup; children = ( 931C00C812135A5E009192AB /* pairwise_terms_A_B.dat */, 931C00C912135A5E009192AB /* pairwise_terms_P1_P4227.dat */, 931C00CA12135A5E009192AB /* pairwise_terms_P1_P6927.dat */, 931C00CB12135A5E009192AB /* pairwise_terms_P2803_P4227.dat */, 931C00CC12135A5E009192AB /* pairwise_terms_P2803_P6927.dat */, 931C00CD12135A5E009192AB /* pairwise_terms_P4227_P6927.dat */, 931C00CE12135A5E009192AB /* rmsd_A.dat */, 931C00CF12135A5E009192AB /* rmsd_B.dat */, 931C00D012135A5E009192AB /* rmsd_C.dat */, 931C00D112135A5E009192AB /* rmsd_D.dat */, 931C00D212135A5F009192AB /* singleton_terms_A.dat */, 931C00D312135A5F009192AB /* singleton_terms_P2803.dat */, 931C00D412135A5F009192AB /* singleton_terms_P4227.dat */, 931C00D512135A5F009192AB /* singleton_terms_P6927.dat */, ); name = scoring; path = ../modules/multifit/test/input/scoring; sourceTree = SOURCE_ROOT; }; 931C00D612135A5F009192AB /* scoring_complete */ = { isa = PBXGroup; children = ( 931C00D712135A5F009192AB /* pairwise_terms_A_B.dat */, 931C00D812135A5F009192AB /* pairwise_terms_A_C.dat */, 931C00D912135A5F009192AB /* pairwise_terms_A_D.dat */, 931C00DA12135A5F009192AB /* pairwise_terms_B_C.dat */, 931C00DB12135A5F009192AB /* pairwise_terms_B_D.dat */, 931C00DC12135A5F009192AB /* pairwise_terms_C_D.dat */, 931C00DD12135A5F009192AB /* pairwise_terms_P10867_P8065.dat */, 931C00DE12135A5F009192AB /* pairwise_terms_P14991_P8065.dat */, 931C00DF12135A5F009192AB /* singleton_terms_A.dat */, 931C00E012135A5F009192AB /* singleton_terms_B.dat */, 931C00E112135A5F009192AB /* singleton_terms_C.dat */, 931C00E212135A5F009192AB /* singleton_terms_D.dat */, ); name = scoring_complete; path = ../modules/multifit/test/input/scoring_complete; sourceTree = SOURCE_ROOT; }; 931C00E312135A5F009192AB /* restraints */ = { isa = PBXGroup; children = ( ); name = restraints; path = ../modules/multifit/test/restraints; sourceTree = SOURCE_ROOT; }; 931C00ED12135A5F009192AB /* npc */ = { isa = PBXGroup; children = ( 931C00EE12135A5F009192AB /* bin */, 931C00F412135A5F009192AB /* data */, 931C00F812135A5F009192AB /* doc */, 931C00FA12135A5F009192AB /* examples */, 931C00FC12135A5F009192AB /* include */, 931C010A12135A5F009192AB /* pyext */, 931C010F12135A5F009192AB /* README */, 931C011012135A5F009192AB /* SConscript */, 931C011112135A5F009192AB /* src */, 931C011E12135A5F009192AB /* test */, ); name = npc; path = ../modules/npc; sourceTree = SOURCE_ROOT; }; 931C00EE12135A5F009192AB /* bin */ = { isa = PBXGroup; children = ( 931C00EF12135A5F009192AB /* create_npc.cpp */, 931C00F012135A5F009192AB /* display_npc.cpp */, 931C00F112135A5F009192AB /* SConscript */, 931C00F212135A5F009192AB /* simulate_npc.cpp */, 931C00F312135A5F009192AB /* simulate_slab.cpp */, ); name = bin; path = ../modules/npc/bin; sourceTree = SOURCE_ROOT; }; 931C00F412135A5F009192AB /* data */ = { isa = PBXGroup; children = ( 931C00F512135A5F009192AB /* google_demo_data */, 931C00F612135A5F009192AB /* SConscript */, 931C00F712135A5F009192AB /* small_data */, ); name = data; path = ../modules/npc/data; sourceTree = SOURCE_ROOT; }; 931C00F812135A5F009192AB /* doc */ = { isa = PBXGroup; children = ( 931C00F912135A5F009192AB /* SConscript */, ); name = doc; path = ../modules/npc/doc; sourceTree = SOURCE_ROOT; }; 931C00FA12135A5F009192AB /* examples */ = { isa = PBXGroup; children = ( 931C00FB12135A5F009192AB /* SConscript */, ); name = examples; path = ../modules/npc/examples; sourceTree = SOURCE_ROOT; }; 931C00FC12135A5F009192AB /* include */ = { isa = PBXGroup; children = ( 931C00FD12135A5F009192AB /* base_types.h */, 931C00FE12135A5F009192AB /* BondBondPairScore.h */, 931C00FF12135A5F009192AB /* ConsecutivePairContainer.h */, 931C010012135A5F009192AB /* DistributePairsScoreState.h */, 931C010112135A5F009192AB /* FGChainFilter.h */, 931C010212135A5F009192AB /* HarmonicDistancePairScore.h */, 931C010312135A5F009192AB /* InteractionPairScore.h */, 931C010412135A5F009192AB /* internal */, 931C010612135A5F009192AB /* npc_simulation.h */, 931C010712135A5F009192AB /* SConscript */, 931C010812135A5F009192AB /* SlabGeometry.h */, 931C010912135A5F009192AB /* SlabSingletonScore.h */, ); name = include; path = ../modules/npc/include; sourceTree = SOURCE_ROOT; }; 931C010412135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( 931C010512135A5F009192AB /* SConscript */, ); name = internal; path = ../modules/npc/include/internal; sourceTree = SOURCE_ROOT; }; 931C010A12135A5F009192AB /* pyext */ = { isa = PBXGroup; children = ( 931C010B12135A5F009192AB /* SConscript */, 931C010C12135A5F009192AB /* src */, 931C010E12135A5F009192AB /* swig.i-in */, ); name = pyext; path = ../modules/npc/pyext; sourceTree = SOURCE_ROOT; }; 931C010C12135A5F009192AB /* src */ = { isa = PBXGroup; children = ( 931C010D12135A5F009192AB /* randomize.py */, ); name = src; path = ../modules/npc/pyext/src; sourceTree = SOURCE_ROOT; }; 931C011112135A5F009192AB /* src */ = { isa = PBXGroup; children = ( 931C011212135A5F009192AB /* BondBondPairScore.cpp */, 931C011312135A5F009192AB /* ConsecutivePairContainer.cpp */, 931C011412135A5F009192AB /* DistributePairsScoreState.cpp */, 931C011512135A5F009192AB /* FGChainFilter.cpp */, 931C011612135A5F009192AB /* HarmonicDistancePairScore.cpp */, 931C011712135A5F009192AB /* InteractionPairScore.cpp */, 931C011812135A5F009192AB /* internal */, 931C011A12135A5F009192AB /* npc_simulation.cpp */, 931C011B12135A5F009192AB /* SConscript */, 931C011C12135A5F009192AB /* SlabGeometry.cpp */, 931C011D12135A5F009192AB /* SlabSingletonScore.cpp */, ); name = src; path = ../modules/npc/src; sourceTree = SOURCE_ROOT; }; 931C011812135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( 931C011912135A5F009192AB /* SConscript */, ); name = internal; path = ../modules/npc/src/internal; sourceTree = SOURCE_ROOT; }; 931C011E12135A5F009192AB /* test */ = { isa = PBXGroup; children = ( 931C011F12135A5F009192AB /* SConscript */, 931C012012135A5F009192AB /* test_bond_bond.py */, 931C012112135A5F009192AB /* test_consecutive_pair_container.py */, 931C012212135A5F009192AB /* test_interaction.py */, 931C012312135A5F009192AB /* test_slab_score.py */, ); name = test; path = ../modules/npc/test; sourceTree = SOURCE_ROOT; }; 931C012412135A5F009192AB /* restrainer */ = { isa = PBXGroup; children = ( 931C012512135A5F009192AB /* bin */, 931C012712135A5F009192AB /* data */, 931C012B12135A5F009192AB /* doc */, 931C012F12135A5F009192AB /* examples */, 931C015612135A5F009192AB /* include */, 931C015812135A5F009192AB /* pyext */, 931C016012135A5F009192AB /* SConscript */, 931C016112135A5F009192AB /* src */, 931C016412135A5F009192AB /* test */, ); name = restrainer; path = ../modules/restrainer; sourceTree = SOURCE_ROOT; }; 931C012512135A5F009192AB /* bin */ = { isa = PBXGroup; children = ( 931C012612135A5F009192AB /* SConscript */, ); name = bin; path = ../modules/restrainer/bin; sourceTree = SOURCE_ROOT; }; 931C012712135A5F009192AB /* data */ = { isa = PBXGroup; children = ( 931C012812135A5F009192AB /* schema.png */, 931C012912135A5F009192AB /* schema.xsd */, 931C012A12135A5F009192AB /* SConscript */, ); name = data; path = ../modules/restrainer/data; sourceTree = SOURCE_ROOT; }; 931C012B12135A5F009192AB /* doc */ = { isa = PBXGroup; children = ( 931C012C12135A5F009192AB /* generated */, 931C012E12135A5F009192AB /* SConscript */, ); name = doc; path = ../modules/restrainer/doc; sourceTree = SOURCE_ROOT; }; 931C012C12135A5F009192AB /* generated */ = { isa = PBXGroup; children = ( 931C012D12135A5F009192AB /* overview.dox */, ); name = generated; path = ../modules/restrainer/doc/generated; sourceTree = SOURCE_ROOT; }; 931C012F12135A5F009192AB /* examples */ = { isa = PBXGroup; children = ( 931C013012135A5F009192AB /* basic_display.py */, 931C013112135A5F009192AB /* basic_display.readme */, 931C013212135A5F009192AB /* basic_setup.py */, 931C013312135A5F009192AB /* basic_setup.readme */, 931C013412135A5F009192AB /* em_restraint.py */, 931C013512135A5F009192AB /* em_restraint.readme */, 931C013612135A5F009192AB /* generated */, 931C013D12135A5F009192AB /* input */, 931C015112135A5F009192AB /* rigid_body_and_excluded_volume_restraint.py */, 931C015212135A5F009192AB /* rigid_body_and_excluded_volume_restraint.readme */, 931C015312135A5F009192AB /* saxs_restraint.py */, 931C015412135A5F009192AB /* saxs_restraint.readme */, 931C015512135A5F009192AB /* SConscript */, ); name = examples; path = ../modules/restrainer/examples; sourceTree = SOURCE_ROOT; }; 931C013612135A5F009192AB /* generated */ = { isa = PBXGroup; children = ( 931C013712135A5F009192AB /* basic_display.py.html */, 931C013812135A5F009192AB /* basic_setup.py.html */, 931C013912135A5F009192AB /* em_restraint.py.html */, 931C013A12135A5F009192AB /* examples.dox */, 931C013B12135A5F009192AB /* rigid_body_and_excluded_volume_restraint.py.html */, 931C013C12135A5F009192AB /* saxs_restraint.py.html */, ); name = generated; path = ../modules/restrainer/examples/generated; sourceTree = SOURCE_ROOT; }; 931C013D12135A5F009192AB /* input */ = { isa = PBXGroup; children = ( 931C013E12135A5F009192AB /* data */, 931C014712135A5F009192AB /* display_representation.xml */, 931C014812135A5F009192AB /* eg1_representation.xml */, 931C014912135A5F009192AB /* eg1_restraint.xml */, 931C014A12135A5F009192AB /* eg2_representation.xml */, 931C014B12135A5F009192AB /* eg2_restraint.xml */, 931C014C12135A5F009192AB /* em_representation.xml */, 931C014D12135A5F009192AB /* em_restraint.xml */, 931C014E12135A5F009192AB /* pdb_display.xml */, 931C014F12135A5F009192AB /* saxs_representation.xml */, 931C015012135A5F009192AB /* saxs_restraint.xml */, ); name = input; path = ../modules/restrainer/examples/input; sourceTree = SOURCE_ROOT; }; 931C013E12135A5F009192AB /* data */ = { isa = PBXGroup; children = ( 931C013F12135A5F009192AB /* 6lyz.pdb */, 931C014012135A5F009192AB /* in.mrc */, 931C014112135A5F009192AB /* lyzexp.dat */, 931C014212135A5F009192AB /* protein1.pdb */, 931C014312135A5F009192AB /* protein2.pdb */, 931C014412135A5F009192AB /* protein3.pdb */, 931C014512135A5F009192AB /* protein4.pdb */, 931C014612135A5F009192AB /* protein5.pdb */, ); name = data; path = ../modules/restrainer/examples/input/data; sourceTree = SOURCE_ROOT; }; 931C015612135A5F009192AB /* include */ = { isa = PBXGroup; children = ( 931C015712135A5F009192AB /* SConscript */, ); name = include; path = ../modules/restrainer/include; sourceTree = SOURCE_ROOT; }; 931C015812135A5F009192AB /* pyext */ = { isa = PBXGroup; children = ( 931C015912135A5F009192AB /* SConscript */, 931C015A12135A5F009192AB /* src */, 931C015F12135A5F009192AB /* swig.i-in */, ); name = pyext; path = ../modules/restrainer/pyext; sourceTree = SOURCE_ROOT; }; 931C015A12135A5F009192AB /* src */ = { isa = PBXGroup; children = ( 931C015B12135A5F009192AB /* _display.py */, 931C015C12135A5F009192AB /* _representation.py */, 931C015D12135A5F009192AB /* _restraint.py */, 931C015E12135A5F009192AB /* _xml_parser.py */, ); name = src; path = ../modules/restrainer/pyext/src; sourceTree = SOURCE_ROOT; }; 931C016112135A5F009192AB /* src */ = { isa = PBXGroup; children = ( 931C016212135A5F009192AB /* internal */, 931C016312135A5F009192AB /* SConscript */, ); name = src; path = ../modules/restrainer/src; sourceTree = SOURCE_ROOT; }; 931C016212135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/restrainer/src/internal; sourceTree = SOURCE_ROOT; }; 931C016412135A5F009192AB /* test */ = { isa = PBXGroup; children = ( 931C016512135A5F009192AB /* input */, 931C017E12135A5F009192AB /* SConscript */, 931C017F12135A5F009192AB /* test_connectivity_for_pdb.py */, 931C018012135A5F009192AB /* test_connectivity_for_sphere.py */, 931C018112135A5F009192AB /* test_diameter_for_pdb.py */, 931C018212135A5F009192AB /* test_diameter_for_sphere.py */, 931C018312135A5F009192AB /* test_display.py */, 931C018412135A5F009192AB /* test_distance_for_pdb.py */, 931C018512135A5F009192AB /* test_distance_for_sphere.py */, 931C018612135A5F009192AB /* test_em.py */, 931C018712135A5F009192AB /* test_get_rigid_body.py */, 931C018812135A5F009192AB /* test_methods_for_pdb.py */, 931C018912135A5F009192AB /* test_methods_for_sphere.py */, 931C018A12135A5F009192AB /* test_representation_mix.py */, 931C018B12135A5F009192AB /* test_representation_pdb.py */, 931C018C12135A5F009192AB /* test_representation_sphere.py */, 931C018D12135A5F009192AB /* test_saxs.py */, ); name = test; path = ../modules/restrainer/test; sourceTree = SOURCE_ROOT; }; 931C016512135A5F009192AB /* input */ = { isa = PBXGroup; children = ( 931C016612135A5F009192AB /* data */, 931C016B12135A5F009192AB /* display_representation.xml */, 931C016C12135A5F009192AB /* em_representation.xml */, 931C016D12135A5F009192AB /* em_restraint.xml */, 931C016E12135A5F009192AB /* mix_representation.xml */, 931C016F12135A5F009192AB /* pdb_connectivity_restraint.xml */, 931C017012135A5F009192AB /* pdb_diameter_restraint.xml */, 931C017112135A5F009192AB /* pdb_display.xml */, 931C017212135A5F009192AB /* pdb_distance_restraint.xml */, 931C017312135A5F009192AB /* pdb_methods_restraint.xml */, 931C017412135A5F009192AB /* pdb_representation.xml */, 931C017512135A5F009192AB /* README */, 931C017612135A5F009192AB /* saxs_representation.xml */, 931C017712135A5F009192AB /* saxs_restraint.xml */, 931C017812135A5F009192AB /* sphere_connectivity_restraint.xml */, 931C017912135A5F009192AB /* sphere_diameter_restraint.xml */, 931C017A12135A5F009192AB /* sphere_display.xml */, 931C017B12135A5F009192AB /* sphere_distance_restraint.xml */, 931C017C12135A5F009192AB /* sphere_methods_restraint.xml */, 931C017D12135A5F009192AB /* sphere_representation.xml */, ); name = input; path = ../modules/restrainer/test/input; sourceTree = SOURCE_ROOT; }; 931C016612135A5F009192AB /* data */ = { isa = PBXGroup; children = ( 931C016712135A5F009192AB /* 6lyz.pdb */, 931C016812135A5F009192AB /* in.mrc */, 931C016912135A5F009192AB /* lyzexp.dat */, 931C016A12135A5F009192AB /* simple_input.pdb */, ); name = data; path = ../modules/restrainer/test/input/data; sourceTree = SOURCE_ROOT; }; 931C018E12135A5F009192AB /* saxs */ = { isa = PBXGroup; children = ( 931C018F12135A5F009192AB /* bin */, 931C019112135A5F009192AB /* data */, 931C019412135A5F009192AB /* doc */, 931C019812135A5F009192AB /* examples */, 931C01A112135A5F009192AB /* include */, 931C01AB12135A5F009192AB /* pyext */, 931C01AE12135A5F009192AB /* SConscript */, 931C01AF12135A5F009192AB /* src */, 931C01B812135A5F009192AB /* test */, ); name = saxs; path = ../modules/saxs; sourceTree = SOURCE_ROOT; }; 931C018F12135A5F009192AB /* bin */ = { isa = PBXGroup; children = ( 931C019012135A5F009192AB /* SConscript */, ); name = bin; path = ../modules/saxs/bin; sourceTree = SOURCE_ROOT; }; 931C019112135A5F009192AB /* data */ = { isa = PBXGroup; children = ( 931C019212135A5F009192AB /* formfactors-int_tab_solvation.lib */, 931C019312135A5F009192AB /* SConscript */, ); name = data; path = ../modules/saxs/data; sourceTree = SOURCE_ROOT; }; 931C019412135A5F009192AB /* doc */ = { isa = PBXGroup; children = ( 931C019512135A5F009192AB /* generated */, 931C019712135A5F009192AB /* SConscript */, ); name = doc; path = ../modules/saxs/doc; sourceTree = SOURCE_ROOT; }; 931C019512135A5F009192AB /* generated */ = { isa = PBXGroup; children = ( 931C019612135A5F009192AB /* overview.dox */, ); name = generated; path = ../modules/saxs/doc/generated; sourceTree = SOURCE_ROOT; }; 931C019812135A5F009192AB /* examples */ = { isa = PBXGroup; children = ( 931C019912135A5F009192AB /* 6lyz.pdb */, 931C019A12135A5F009192AB /* generated */, 931C019D12135A5F009192AB /* lyzexp.dat */, 931C019E12135A5F009192AB /* profile.py */, 931C019F12135A5F009192AB /* profile.readme */, 931C01A012135A5F009192AB /* SConscript */, ); name = examples; path = ../modules/saxs/examples; sourceTree = SOURCE_ROOT; }; 931C019A12135A5F009192AB /* generated */ = { isa = PBXGroup; children = ( 931C019B12135A5F009192AB /* examples.dox */, 931C019C12135A5F009192AB /* profile.py.html */, ); name = generated; path = ../modules/saxs/examples/generated; sourceTree = SOURCE_ROOT; }; 931C01A112135A5F009192AB /* include */ = { isa = PBXGroup; children = ( 931C01A212135A5F009192AB /* Distribution.h */, 931C01A312135A5F009192AB /* FormFactorTable.h */, 931C01A412135A5F009192AB /* internal */, 931C01A512135A5F009192AB /* Profile.h */, 931C01A612135A5F009192AB /* Restraint.h */, 931C01A712135A5F009192AB /* SConscript */, 931C01A812135A5F009192AB /* Score.h */, 931C01A912135A5F009192AB /* SolventAccessibleSurface.h */, 931C01AA12135A5F009192AB /* utility.h */, ); name = include; path = ../modules/saxs/include; sourceTree = SOURCE_ROOT; }; 931C01A412135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/saxs/include/internal; sourceTree = SOURCE_ROOT; }; 931C01AB12135A5F009192AB /* pyext */ = { isa = PBXGroup; children = ( 931C01AC12135A5F009192AB /* SConscript */, 931C01AD12135A5F009192AB /* swig.i-in */, ); name = pyext; path = ../modules/saxs/pyext; sourceTree = SOURCE_ROOT; }; 931C01AF12135A5F009192AB /* src */ = { isa = PBXGroup; children = ( 931C01B012135A5F009192AB /* Distribution.cpp */, 931C01B112135A5F009192AB /* FormFactorTable.cpp */, 931C01B212135A5F009192AB /* internal */, 931C01B312135A5F009192AB /* Profile.cpp */, 931C01B412135A5F009192AB /* Restraint.cpp */, 931C01B512135A5F009192AB /* SConscript */, 931C01B612135A5F009192AB /* Score.cpp */, 931C01B712135A5F009192AB /* SolventAccessibleSurface.cpp */, ); name = src; path = ../modules/saxs/src; sourceTree = SOURCE_ROOT; }; 931C01B212135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/saxs/src/internal; sourceTree = SOURCE_ROOT; }; 931C01B812135A5F009192AB /* test */ = { isa = PBXGroup; children = ( 931C01B912135A5F009192AB /* input */, 931C01BF12135A5F009192AB /* SConscript */, 931C01C012135A5F009192AB /* test_saxs.py */, 931C01C112135A5F009192AB /* test_surface.py */, ); name = test; path = ../modules/saxs/test; sourceTree = SOURCE_ROOT; }; 931C01B912135A5F009192AB /* input */ = { isa = PBXGroup; children = ( 931C01BA12135A5F009192AB /* 6lyz.pdb */, 931C01BB12135A5F009192AB /* formfactors-int_tab_solvation.lib */, 931C01BC12135A5F009192AB /* lyzexp.dat */, 931C01BD12135A5F009192AB /* single_dna.pdb */, 931C01BE12135A5F009192AB /* single_protein.pdb */, ); name = input; path = ../modules/saxs/test/input; sourceTree = SOURCE_ROOT; }; 931C01C312135A5F009192AB /* statistics */ = { isa = PBXGroup; children = ( 931C01C412135A5F009192AB /* bin */, 931C01C612135A5F009192AB /* data */, 931C01C812135A5F009192AB /* doc */, 931C01CC12135A5F009192AB /* examples */, 931C01D312135A5F009192AB /* include */, 931C01E812135A5F009192AB /* pyext */, 931C01EB12135A5F009192AB /* SConscript */, 931C01EC12135A5F009192AB /* src */, 931C01FE12135A5F009192AB /* test */, ); name = statistics; path = ../modules/statistics; sourceTree = SOURCE_ROOT; }; 931C01C412135A5F009192AB /* bin */ = { isa = PBXGroup; children = ( 931C01C512135A5F009192AB /* SConscript */, ); name = bin; path = ../modules/statistics/bin; sourceTree = SOURCE_ROOT; }; 931C01C612135A5F009192AB /* data */ = { isa = PBXGroup; children = ( 931C01C712135A5F009192AB /* SConscript */, ); name = data; path = ../modules/statistics/data; sourceTree = SOURCE_ROOT; }; 931C01C812135A5F009192AB /* doc */ = { isa = PBXGroup; children = ( 931C01C912135A5F009192AB /* generated */, 931C01CB12135A5F009192AB /* SConscript */, ); name = doc; path = ../modules/statistics/doc; sourceTree = SOURCE_ROOT; }; 931C01C912135A5F009192AB /* generated */ = { isa = PBXGroup; children = ( 931C01CA12135A5F009192AB /* overview.dox */, ); name = generated; path = ../modules/statistics/doc/generated; sourceTree = SOURCE_ROOT; }; 931C01CC12135A5F009192AB /* examples */ = { isa = PBXGroup; children = ( 931C01CD12135A5F009192AB /* generated */, 931C01D012135A5F009192AB /* kmeans.py */, 931C01D112135A5F009192AB /* kmeans.readme */, 931C01D212135A5F009192AB /* SConscript */, ); name = examples; path = ../modules/statistics/examples; sourceTree = SOURCE_ROOT; }; 931C01CD12135A5F009192AB /* generated */ = { isa = PBXGroup; children = ( 931C01CE12135A5F009192AB /* examples.dox */, 931C01CF12135A5F009192AB /* kmeans.py.html */, ); name = generated; path = ../modules/statistics/examples/generated; sourceTree = SOURCE_ROOT; }; 931C01D312135A5F009192AB /* include */ = { isa = PBXGroup; children = ( 931C01D412135A5F009192AB /* Histogram.h */, 931C01D512135A5F009192AB /* internal */, 931C01D812135A5F009192AB /* KMCenters.h */, 931C01D912135A5F009192AB /* KMCentersNode.h */, 931C01DA12135A5F009192AB /* KMCentersNodeLeaf.h */, 931C01DB12135A5F009192AB /* KMCentersNodeSplit.h */, 931C01DC12135A5F009192AB /* KMCentersTree.h */, 931C01DD12135A5F009192AB /* KMData.h */, 931C01DE12135A5F009192AB /* KMFilterCenters.h */, 931C01DF12135A5F009192AB /* KMLocalSearch.h */, 931C01E012135A5F009192AB /* KMLocalSearchLloyd.h */, 931C01E112135A5F009192AB /* KMLProxy.h */, 931C01E212135A5F009192AB /* KMRectangle.h */, 931C01E312135A5F009192AB /* KMTerminationCondition.h */, 931C01E412135A5F009192AB /* PartitionalClustering.h */, 931C01E512135A5F009192AB /* point_clustering.h */, 931C01E612135A5F009192AB /* SConscript */, 931C01E712135A5F009192AB /* statistics_macros.h */, ); name = include; path = ../modules/statistics/include; sourceTree = SOURCE_ROOT; }; 931C01D512135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( 931C01D612135A5F009192AB /* random_generator.h */, 931C01D712135A5F009192AB /* SConscript */, ); name = internal; path = ../modules/statistics/include/internal; sourceTree = SOURCE_ROOT; }; 931C01E812135A5F009192AB /* pyext */ = { isa = PBXGroup; children = ( 931C01E912135A5F009192AB /* SConscript */, 931C01EA12135A5F009192AB /* swig.i-in */, ); name = pyext; path = ../modules/statistics/pyext; sourceTree = SOURCE_ROOT; }; 931C01EC12135A5F009192AB /* src */ = { isa = PBXGroup; children = ( 931C01ED12135A5F009192AB /* Histogram.cpp */, 931C01EE12135A5F009192AB /* internal */, 931C01F012135A5F009192AB /* KMCenters.cpp */, 931C01F112135A5F009192AB /* KMCentersNode.cpp */, 931C01F212135A5F009192AB /* KMCentersNodeLeaf.cpp */, 931C01F312135A5F009192AB /* KMCentersNodeSplit.cpp */, 931C01F412135A5F009192AB /* KMCentersTree.cpp */, 931C01F512135A5F009192AB /* KMData.cpp */, 931C01F612135A5F009192AB /* KMFilterCenters.cpp */, 931C01F712135A5F009192AB /* KMLocalSearch.cpp */, 931C01F812135A5F009192AB /* KMLocalSearchLloyd.cpp */, 931C01F912135A5F009192AB /* KMLProxy.cpp */, 931C01FA12135A5F009192AB /* KMRectangle.cpp */, 931C01FB12135A5F009192AB /* PartitionalClustering.cpp */, 931C01FC12135A5F009192AB /* point_clustering.cpp */, 931C01FD12135A5F009192AB /* SConscript */, ); name = src; path = ../modules/statistics/src; sourceTree = SOURCE_ROOT; }; 931C01EE12135A5F009192AB /* internal */ = { isa = PBXGroup; children = ( 931C01EF12135A5F009192AB /* SConscript */, ); name = internal; path = ../modules/statistics/src/internal; sourceTree = SOURCE_ROOT; }; 931C01FE12135A5F009192AB /* test */ = { isa = PBXGroup; children = ( 931C01FF12135A5F009192AB /* SConscript */, 931C020012135A5F009192AB /* test_connectivity_clustering.py */, 931C020112135A5F009192AB /* test_histogram.py */, 931C020212135A5F009192AB /* test_kmeans.py */, 931C020312135A5F009192AB /* test_simple_kmeans.py */, ); name = test; path = ../modules/statistics/test; sourceTree = SOURCE_ROOT; }; 931C020412135A5F009192AB /* scons_tools */ = { isa = PBXGroup; children = ( 931C020512135A5F009192AB /* __init__.py */, 931C020612135A5F009192AB /* application.py */, 931C020712135A5F009192AB /* boost.py */, 931C020812135A5F009192AB /* bug_fixes.py */, 931C020912135A5F009192AB /* build_summary.py */, 931C020A12135A5F009192AB /* cgal.py */, 931C020B12135A5F009192AB /* checks.py */, 931C020C12135A5F009192AB /* colorize_python.py */, 931C020D12135A5F009192AB /* compilation.py */, 931C020E12135A5F009192AB /* config_h.py */, 931C020F12135A5F009192AB /* config_py.py */, 931C021012135A5F009192AB /* doxygen.py */, 931C021112135A5F009192AB /* endian.py */, 931C021212135A5F009192AB /* example-config.py */, 931C021312135A5F009192AB /* examples.py */, 931C021412135A5F009192AB /* gcc.py */, 931C021512135A5F009192AB /* hierarchy.py */, 931C021612135A5F009192AB /* imp_module.py */, 931C021712135A5F009192AB /* link_test.py */, 931C021812135A5F009192AB /* modeller_test.py */, 931C021912135A5F009192AB /* modpage.py */, 931C021A12135A5F009192AB /* pch.py */, 931C021B12135A5F009192AB /* pyscanner.py */, 931C021C12135A5F009192AB /* run-all-tests.py */, 931C021D12135A5F009192AB /* run.py */, 931C021E12135A5F009192AB /* standards.py */, 931C021F12135A5F009192AB /* swig.py */, 931C022012135A5F009192AB /* symlinks.py */, 931C022112135A5F009192AB /* test.py */, 931C022212135A5F009192AB /* version_info.py */, ); name = scons_tools; path = ../scons_tools; sourceTree = SOURCE_ROOT; }; 931C022412135A5F009192AB /* tools */ = { isa = PBXGroup; children = ( 931C022512135A5F009192AB /* apply-standards.pl */, 931C022612135A5F009192AB /* auto-build.sh */, 931C022712135A5F009192AB /* build */, 931C023712135A5F009192AB /* build-release */, 931C023812135A5F009192AB /* check-standards.py */, 931C023912135A5F009192AB /* container_templates */, 931C026112135A5F009192AB /* cpp_format.py */, 931C026212135A5F009192AB /* gdbinit */, 931C026312135A5F009192AB /* imp.xcodeproj */, 931C026612135A5F009192AB /* imppy.sh */, 931C026712135A5F009192AB /* imppy.sh-in */, 931C026812135A5F009192AB /* mac */, 931C026C12135A5F009192AB /* make-class */, 931C026D12135A5F009192AB /* make-container */, 931C026E12135A5F009192AB /* make-module */, 931C026F12135A5F009192AB /* make-sconscripts */, 931C027012135A5F009192AB /* reindent.py */, 931C027112135A5F009192AB /* rpm */, 931C027312135A5F009192AB /* sample_config.py */, 931C027412135A5F009192AB /* SConscript */, 931C027512135A5F009192AB /* setup-out-of-source */, 931C027612135A5F009192AB /* subversion */, 931C027A12135A5F009192AB /* valgrind-python.supp */, 931C027B12135A5F009192AB /* w32 */, ); name = tools; sourceTree = SOURCE_ROOT; }; 931C022712135A5F009192AB /* build */ = { isa = PBXGroup; children = ( 931C022812135A5F009192AB /* imp.build */, ); path = build; sourceTree = SOURCE_ROOT; }; 931C022812135A5F009192AB /* imp.build */ = { isa = PBXGroup; children = ( 931C022912135A5F009192AB /* imp.pbxindex */, ); name = imp.build; path = build/imp.build; sourceTree = SOURCE_ROOT; }; 931C022912135A5F009192AB /* imp.pbxindex */ = { isa = PBXGroup; children = ( 931C022A12135A5F009192AB /* categories.pbxbtree */, 931C022B12135A5F009192AB /* cdecls.pbxbtree */, 931C022C12135A5F009192AB /* decls.pbxbtree */, 931C022D12135A5F009192AB /* files.pbxbtree */, 931C022E12135A5F009192AB /* imports.pbxbtree */, 931C022F12135A5F009192AB /* pbxindex.header */, 931C023012135A5F009192AB /* protocols.pbxbtree */, 931C023112135A5F009192AB /* refs.pbxbtree */, 931C023212135A5F009192AB /* strings.pbxstrings */, 931C023512135A5F009192AB /* subclasses.pbxbtree */, 931C023612135A5F009192AB /* symbols0.pbxsymbols */, ); name = imp.pbxindex; path = build/imp.build/imp.pbxindex; sourceTree = SOURCE_ROOT; }; 931C023212135A5F009192AB /* strings.pbxstrings */ = { isa = PBXGroup; children = ( 931C023312135A5F009192AB /* control */, 931C023412135A5F009192AB /* strings */, ); name = strings.pbxstrings; path = build/imp.build/imp.pbxindex/strings.pbxstrings; sourceTree = SOURCE_ROOT; }; 931C023912135A5F009192AB /* container_templates */ = { isa = PBXGroup; children = ( 931C023A12135A5F009192AB /* container.cc */, 931C023B12135A5F009192AB /* container.hpp */, 931C023C12135A5F009192AB /* corelist.cc */, 931C023D12135A5F009192AB /* corelist.hpp */, 931C023E12135A5F009192AB /* corerestraint.cc */, 931C023F12135A5F009192AB /* corerestraint.hpp */, 931C024012135A5F009192AB /* filter.cc */, 931C024112135A5F009192AB /* filter.hpp */, 931C024212135A5F009192AB /* function.cc */, 931C024312135A5F009192AB /* function.hpp */, 931C024412135A5F009192AB /* helper.cc */, 931C024512135A5F009192AB /* helper.hpp */, 931C024612135A5F009192AB /* in_container.cc */, 931C024712135A5F009192AB /* in_container.hpp */, 931C024812135A5F009192AB /* inactive.cc */, 931C024912135A5F009192AB /* inactive.hpp */, 931C024A12135A5F009192AB /* list.cc */, 931C024B12135A5F009192AB /* list.hpp */, 931C024C12135A5F009192AB /* min.cc */, 931C024D12135A5F009192AB /* min.hpp */, 931C024E12135A5F009192AB /* minscore.cc */, 931C024F12135A5F009192AB /* minscore.hpp */, 931C025012135A5F009192AB /* ostate.cc */, 931C025112135A5F009192AB /* ostate.hpp */, 931C025212135A5F009192AB /* restraint.cc */, 931C025312135A5F009192AB /* restraint.hpp */, 931C025412135A5F009192AB /* score.cc */, 931C025512135A5F009192AB /* score.hpp */, 931C025612135A5F009192AB /* set.cc */, 931C025712135A5F009192AB /* set.hpp */, 931C025812135A5F009192AB /* srestraint.cc */, 931C025912135A5F009192AB /* srestraint.hpp */, 931C025A12135A5F009192AB /* sstate.cc */, 931C025B12135A5F009192AB /* sstate.hpp */, 931C025C12135A5F009192AB /* state.cc */, 931C025D12135A5F009192AB /* state.hpp */, 931C025E12135A5F009192AB /* swig.i */, 931C025F12135A5F009192AB /* test.py */, 931C026012135A5F009192AB /* test_state.py */, ); path = container_templates; sourceTree = SOURCE_ROOT; }; 931C026812135A5F009192AB /* mac */ = { isa = PBXGroup; children = ( 931C026912135A5F009192AB /* Description.plist */, 931C026A12135A5F009192AB /* Info.plist */, 931C026B12135A5F009192AB /* make-package.sh */, ); path = mac; sourceTree = SOURCE_ROOT; }; 931C027112135A5F009192AB /* rpm */ = { isa = PBXGroup; children = ( 931C027212135A5F009192AB /* IMP.spec */, ); path = rpm; sourceTree = SOURCE_ROOT; }; 931C027612135A5F009192AB /* subversion */ = { isa = PBXGroup; children = ( 931C027712135A5F009192AB /* commit-email.pl */, 931C027812135A5F009192AB /* post-commit.template */, 931C027912135A5F009192AB /* pre-commit */, ); path = subversion; sourceTree = SOURCE_ROOT; }; 931C027B12135A5F009192AB /* w32 */ = { isa = PBXGroup; children = ( 931C027C12135A5F009192AB /* gen-w32instlist */, 931C027D12135A5F009192AB /* make-package.sh */, 931C027E12135A5F009192AB /* w32-install.nsi */, ); path = w32; sourceTree = SOURCE_ROOT; }; 931C027F12135A5F009192AB /* website */ = { isa = PBXGroup; children = ( 931C028012135A5F009192AB /* conf.inc.php */, 931C028112135A5F009192AB /* download-mac.txt */, 931C028212135A5F009192AB /* download-windows.txt */, 931C028312135A5F009192AB /* download.txt */, 931C028412135A5F009192AB /* footer.txt */, 931C028512135A5F009192AB /* get.php */, 931C028612135A5F009192AB /* get.php.in */, 931C028712135A5F009192AB /* goal.txt */, 931C028812135A5F009192AB /* groups.txt */, 931C028912135A5F009192AB /* hdevelopment.txt */, 931C028A12135A5F009192AB /* header.txt */, 931C028B12135A5F009192AB /* hresearch.txt */, 931C028C12135A5F009192AB /* images */, 931C029A12135A5F009192AB /* imp.css */, 931C029B12135A5F009192AB /* index.php */, 931C029C12135A5F009192AB /* make-get.php */, 931C029D12135A5F009192AB /* Makefile */, 931C029E12135A5F009192AB /* misc.inc.php */, 931C029F12135A5F009192AB /* mysql_connect.php.in */, 931C02A012135A5F009192AB /* news.txt */, 931C02A112135A5F009192AB /* site.inc.php */, ); name = website; path = ../website; sourceTree = SOURCE_ROOT; }; 931C028C12135A5F009192AB /* images */ = { isa = PBXGroup; children = ( 931C028D12135A5F009192AB /* CIPF.png */, 931C028E12135A5F009192AB /* download.png */, 931C028F12135A5F009192AB /* favicon.ico */, 931C029012135A5F009192AB /* greenline.png */, 931C029112135A5F009192AB /* groups.png */, 931C029212135A5F009192AB /* imp_blogo.png */, 931C029312135A5F009192AB /* imp_link.png */, 931C029412135A5F009192AB /* imp_logo.png */, 931C029512135A5F009192AB /* mail.gif */, 931C029612135A5F009192AB /* npc.png */, 931C029712135A5F009192AB /* rm.png */, 931C029812135A5F009192AB /* the_imp.png */, 931C029912135A5F009192AB /* ucsf.png */, ); name = images; path = ../website/images; sourceTree = SOURCE_ROOT; }; 931C02A212135A61009192AB /* Products */ = { isa = PBXGroup; children = ( ); name = Products; sourceTree = ""; }; 931CF94F12135A5C009192AB /* applications */ = { isa = PBXGroup; children = ( 931CF95012135A5C009192AB /* example */, 931CF95312135A5C009192AB /* saxs */, 931CF95F12135A5C009192AB /* SConscript */, 931CF96012135A5C009192AB /* spb */, ); name = applications; path = ../applications; sourceTree = SOURCE_ROOT; }; 931CF95012135A5C009192AB /* example */ = { isa = PBXGroup; children = ( 931CF95112135A5C009192AB /* example.cpp */, 931CF95212135A5C009192AB /* SConscript */, ); name = example; path = ../applications/example; sourceTree = SOURCE_ROOT; }; 931CF95312135A5C009192AB /* saxs */ = { isa = PBXGroup; children = ( 931CF95412135A5C009192AB /* foxs */, 931CF95512135A5C009192AB /* Gnuplot.cpp */, 931CF95612135A5C009192AB /* Gnuplot.h */, 931CF95712135A5C009192AB /* profile.cpp */, 931CF95812135A5C009192AB /* SConscript */, 931CF95912135A5C009192AB /* test */, ); name = saxs; path = ../applications/saxs; sourceTree = SOURCE_ROOT; }; 931CF95912135A5C009192AB /* test */ = { isa = PBXGroup; children = ( 931CF95A12135A5C009192AB /* input */, 931CF95D12135A5C009192AB /* SConscript */, 931CF95E12135A5C009192AB /* test_saxs.py */, ); name = test; path = ../applications/saxs/test; sourceTree = SOURCE_ROOT; }; 931CF95A12135A5C009192AB /* input */ = { isa = PBXGroup; children = ( 931CF95B12135A5C009192AB /* 6lyz.pdb */, 931CF95C12135A5C009192AB /* lyzexp.dat */, ); name = input; path = ../applications/saxs/test/input; sourceTree = SOURCE_ROOT; }; 931CF96012135A5C009192AB /* spb */ = { isa = PBXGroup; children = ( 931CF96112135A5C009192AB /* representation.py */, 931CF96212135A5C009192AB /* sampling.py */, ); name = spb; path = ../applications/spb; sourceTree = SOURCE_ROOT; }; 931CF96312135A5C009192AB /* doc */ = { isa = PBXGroup; children = ( 931CF96412135A5C009192AB /* angle.png */, 931CF96512135A5C009192AB /* atom.png */, 931CF96612135A5C009192AB /* bond.png */, 931CF96712135A5C009192AB /* centroid.png */, 931CF96812135A5C009192AB /* chain.png */, 931CF96912135A5C009192AB /* charged.png */, 931CF96A12135A5C009192AB /* connectivity.png */, 931CF96B12135A5C009192AB /* design_example.dox */, 931CF96C12135A5C009192AB /* developer_guide.dox */, 931CF96D12135A5C009192AB /* distance.png */, 931CF96E12135A5C009192AB /* docking.png */, 931CF96F12135A5C009192AB /* domain.png */, 931CF97012135A5C009192AB /* doxygen */, 931CF97812135A5C009192AB /* doxygen_markup.dox */, 931CF97912135A5C009192AB /* em.png */, 931CF97A12135A5C009192AB /* ev.png */, 931CF97B12135A5C009192AB /* fragment.png */, 931CF97C12135A5C009192AB /* hierarchy.png */, 931CF97D12135A5C009192AB /* history.dox */, 931CF97E12135A5C009192AB /* html */, 931CF99112135A5C009192AB /* IMP_Schema.png */, 931CF99212135A5C009192AB /* installation.dox */, 931CF99312135A5C009192AB /* introduction.dox */, 931CF99412135A5C009192AB /* maillists.dox */, 931CF99512135A5C009192AB /* main.dox */, 931CF99612135A5C009192AB /* mass.png */, 931CF99712135A5C009192AB /* protlig.png */, 931CF99812135A5C009192AB /* residue.png */, 931CF99912135A5C009192AB /* rigid.png */, 931CF99A12135A5C009192AB /* saxs.png */, 931CF99B12135A5C009192AB /* SConscript */, 931CF99C12135A5C009192AB /* sphere.png */, 931CF99D12135A5C009192AB /* spherecover.png */, 931CF99E12135A5C009192AB /* symmetry.png */, 931CF99F12135A5C009192AB /* torsion.png */, 931CF9A012135A5C009192AB /* volume.png */, 931CF9A112135A5C009192AB /* xyz.png */, ); name = doc; path = ../doc; sourceTree = SOURCE_ROOT; }; 931CF97012135A5C009192AB /* doxygen */ = { isa = PBXGroup; children = ( 931CF97212135A5C009192AB /* doxygen.conf-in */, 931CF97312135A5C009192AB /* doxypy.py */, 931CF97412135A5C009192AB /* footer.html */, 931CF97512135A5C009192AB /* layout.xml */, 931CF97612135A5C009192AB /* preprocess.py */, 931CF97712135A5C009192AB /* SConscript */, ); name = doxygen; path = ../doc/doxygen; sourceTree = SOURCE_ROOT; }; 931CF97E12135A5C009192AB /* html */ = { isa = PBXGroup; children = ( 931CF97F12135A5C009192AB /* bdfast.png */, 931CF98012135A5C009192AB /* bdrelease.png */, 931CF98112135A5C009192AB /* changingfast.png */, 931CF98212135A5C009192AB /* changingrelease.png */, 931CF98312135A5C009192AB /* colfast.png */, 931CF98412135A5C009192AB /* colrelease.png */, 931CF98512135A5C009192AB /* connectivityfast.png */, 931CF98612135A5C009192AB /* connectivityrelease.png */, 931CF98712135A5C009192AB /* containerfast.png */, 931CF98812135A5C009192AB /* containerrelease.png */, 931CF98912135A5C009192AB /* cpffast.png */, 931CF98A12135A5C009192AB /* cpfrelease.png */, 931CF98B12135A5C009192AB /* rigidfast.png */, 931CF98C12135A5C009192AB /* rigidrelease.png */, 931CF98D12135A5C009192AB /* rotationfast.png */, 931CF98E12135A5C009192AB /* rotationrelease.png */, 931CF98F12135A5C009192AB /* xyzfast.png */, 931CF99012135A5C009192AB /* xyzrelease.png */, ); name = html; path = ../doc/html; sourceTree = SOURCE_ROOT; }; 931CF9A212135A5C009192AB /* kernel */ = { isa = PBXGroup; children = ( 931CF9A312135A5C009192AB /* bin */, 931CF9A512135A5C009192AB /* data */, 931CF9A812135A5C009192AB /* doc */, 931CF9AC12135A5C009192AB /* examples */, 931CF9BF12135A5C009192AB /* include */, 931CFA1212135A5C009192AB /* pyext */, 931CFA2112135A5C009192AB /* SConscript */, 931CFA2212135A5C009192AB /* src */, 931CFA5912135A5C009192AB /* test */, ); name = kernel; path = ../kernel; sourceTree = SOURCE_ROOT; }; 931CF9A312135A5C009192AB /* bin */ = { isa = PBXGroup; children = ( 931CF9A412135A5C009192AB /* SConscript */, ); name = bin; path = ../kernel/bin; sourceTree = SOURCE_ROOT; }; 931CF9A512135A5C009192AB /* data */ = { isa = PBXGroup; children = ( 931CF9A612135A5C009192AB /* README */, 931CF9A712135A5C009192AB /* SConscript */, ); name = data; path = ../kernel/data; sourceTree = SOURCE_ROOT; }; 931CF9A812135A5C009192AB /* doc */ = { isa = PBXGroup; children = ( 931CF9A912135A5C009192AB /* generated */, 931CF9AB12135A5C009192AB /* SConscript */, ); 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name = src; path = ../modules/algebra/src; sourceTree = SOURCE_ROOT; }; 931CFAD712135A5C009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFAD812135A5C009192AB /* output_helpers.cpp */, 931CFAD912135A5C009192AB /* SConscript */, 931CFADA12135A5C009192AB /* utility.cpp */, ); name = internal; path = ../modules/algebra/src/internal; sourceTree = SOURCE_ROOT; }; 931CFAEC12135A5C009192AB /* test */ = { isa = PBXGroup; children = ( 931CFAED12135A5C009192AB /* SConscript */, 931CFAEE12135A5C009192AB /* test_bounding_box.py */, 931CFAEF12135A5C009192AB /* test_cone.py */, 931CFAF012135A5C009192AB /* test_cylinder.py */, 931CFAF112135A5C009192AB /* test_eigen_analysis.py */, 931CFAF212135A5C009192AB /* test_geom_alignment.py */, 931CFAF312135A5C009192AB /* test_grid.cpp */, 931CFAF412135A5C009192AB /* test_inverse.py */, 931CFAF512135A5C009192AB /* test_matrix2d.py */, 931CFAF612135A5C009192AB /* test_matrix3d.py */, 931CFAF712135A5C009192AB /* test_nearest_neighbor.py */, 931CFAF812135A5C009192AB /* test_plural.py */, 931CFAF912135A5C009192AB /* test_random_chain.py */, 931CFAFA12135A5C009192AB /* test_random_rotations.py */, 931CFAFB12135A5C009192AB /* test_regression_fit.py */, 931CFAFC12135A5C009192AB /* test_rigid_transformation.py */, 931CFAFD12135A5C009192AB /* test_rotation.py */, 931CFAFE12135A5C009192AB /* test_sphere.py */, 931CFAFF12135A5C009192AB /* test_sphere_cover.py */, 931CFB0012135A5C009192AB /* test_sphere_patch.py */, 931CFB0112135A5C009192AB /* test_spherical_coords.py */, 931CFB0212135A5C009192AB /* test_transformation.py */, 931CFB0312135A5C009192AB /* test_vector3d.py */, 931CFB0412135A5C009192AB /* test_vector4d.py */, 931CFB0512135A5C009192AB /* test_vector_on_box.py */, 931CFB0612135A5C009192AB /* test_xyz.py */, 931CFB0712135A5C009192AB /* test_zyz.py */, ); name = test; path = ../modules/algebra/test; sourceTree = SOURCE_ROOT; }; 931CFB0812135A5C009192AB /* atom */ = { isa = PBXGroup; children = ( 931CFB0912135A5C009192AB /* bin */, 931CFB0D12135A5C009192AB /* data */, 931CFB1412135A5C009192AB /* doc */, 931CFB1812135A5C009192AB /* examples */, 931CFB2912135A5C009192AB /* include */, 931CFB5F12135A5C009192AB /* pyext */, 931CFB6212135A5C009192AB /* SConscript */, 931CFB6312135A5C009192AB /* src */, 931CFB9212135A5C009192AB /* test */, ); name = atom; path = ../modules/atom; sourceTree = SOURCE_ROOT; }; 931CFB0912135A5C009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFB0A12135A5C009192AB /* protein_ligand_score */, 931CFB0B12135A5C009192AB /* protein_ligand_score.cpp */, 931CFB0C12135A5C009192AB /* SConscript */, ); name = bin; path = ../modules/atom/bin; sourceTree = SOURCE_ROOT; }; 931CFB0D12135A5C009192AB /* data */ = { isa = PBXGroup; children = ( 931CFB0E12135A5C009192AB /* par.lib */, 931CFB0F12135A5C009192AB /* protein_ligand_score.lib */, 931CFB1012135A5C009192AB /* radii.lib */, 931CFB1112135A5C009192AB /* SConscript */, 931CFB1212135A5C009192AB /* top.lib */, 931CFB1312135A5C009192AB /* top_heav.lib */, ); name = data; path = ../modules/atom/data; sourceTree = SOURCE_ROOT; }; 931CFB1412135A5C009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFB1512135A5C009192AB /* generated */, 931CFB1712135A5C009192AB /* SConscript */, ); name = doc; path = ../modules/atom/doc; sourceTree = SOURCE_ROOT; }; 931CFB1512135A5C009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFB1612135A5C009192AB /* overview.dox */, ); name = generated; path = ../modules/atom/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFB1812135A5C009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFB1912135A5C009192AB /* charmm_forcefield.py */, 931CFB1A12135A5C009192AB /* charmm_forcefield.readme */, 931CFB1B12135A5C009192AB /* create_protein_fragment.py */, 931CFB1C12135A5C009192AB /* create_protein_fragment.readme */, 931CFB1D12135A5C009192AB /* example_protein.pdb */, 931CFB1E12135A5C009192AB /* fragments */, 931CFB1F12135A5C009192AB /* generated */, 931CFB2412135A5C009192AB /* load_protein_restrain_bonds.py */, 931CFB2512135A5C009192AB /* load_protein_restrain_bonds.readme */, 931CFB2612135A5C009192AB /* molecular_hierarchy.py */, 931CFB2712135A5C009192AB /* molecular_hierarchy.readme */, 931CFB2812135A5C009192AB /* SConscript */, ); name = examples; path = ../modules/atom/examples; sourceTree = SOURCE_ROOT; }; 931CFB1E12135A5C009192AB /* fragments */ = { isa = PBXGroup; children = ( ); name = fragments; path = ../modules/atom/examples/fragments; sourceTree = SOURCE_ROOT; }; 931CFB1F12135A5C009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFB2012135A5C009192AB /* charmm_forcefield.py.html */, 931CFB2112135A5C009192AB /* examples.dox */, 931CFB2212135A5C009192AB /* load_protein_restrain_bonds.py.html */, 931CFB2312135A5C009192AB /* molecular_hierarchy.py.html */, ); name = generated; path = ../modules/atom/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFB2912135A5C009192AB /* include */ = { isa = PBXGroup; children = ( 931CFB2A12135A5C009192AB /* angle_decorators.h */, 931CFB2B12135A5C009192AB /* AngleSingletonScore.h */, 931CFB2C12135A5C009192AB /* Atom.h */, 931CFB2D12135A5C009192AB /* atom_macros.h */, 931CFB2E12135A5C009192AB /* bond_decorators.h */, 931CFB2F12135A5C009192AB /* bond_graph.h */, 931CFB3012135A5C009192AB /* BondedPairFilter.h */, 931CFB3112135A5C009192AB /* BondEndpointsRefiner.h */, 931CFB3212135A5C009192AB /* BondPairContainer.h */, 931CFB3312135A5C009192AB /* BondSingletonScore.h */, 931CFB3412135A5C009192AB /* BrownianDynamics.h */, 931CFB3512135A5C009192AB /* Chain.h */, 931CFB3612135A5C009192AB /* Charged.h */, 931CFB3712135A5C009192AB /* charmm_topology.h */, 931CFB3812135A5C009192AB /* CHARMMAtom.h */, 931CFB3912135A5C009192AB /* CHARMMParameters.h */, 931CFB3A12135A5C009192AB /* CoulombPairScore.h */, 931CFB3B12135A5C009192AB /* CoverBond.h */, 931CFB3C12135A5C009192AB /* Diffusion.h */, 931CFB3D12135A5C009192AB /* DihedralSingletonScore.h */, 931CFB3E12135A5C009192AB /* distance.h */, 931CFB3F12135A5C009192AB /* Domain.h */, 931CFB4012135A5C009192AB /* element.h */, 931CFB4112135A5C009192AB /* estimates.h */, 931CFB4212135A5C009192AB /* force_fields.h */, 931CFB4312135A5C009192AB /* ForceFieldParameters.h */, 931CFB4412135A5C009192AB /* Fragment.h */, 931CFB4512135A5C009192AB /* Hierarchy.h */, 931CFB4612135A5C009192AB /* hierarchy_tools.h */, 931CFB4712135A5C009192AB /* ImproperSingletonScore.h */, 931CFB4812135A5C009192AB /* internal */, 931CFB5212135A5C009192AB /* LennardJones.h */, 931CFB5312135A5C009192AB /* LennardJonesPairScore.h */, 931CFB5412135A5C009192AB /* Mass.h */, 931CFB5512135A5C009192AB /* mol2.h */, 931CFB5612135A5C009192AB /* MolecularDynamics.h */, 931CFB5712135A5C009192AB /* pdb.h */, 931CFB5812135A5C009192AB /* protein_ligand_score.h */, 931CFB5912135A5C009192AB /* Residue.h */, 931CFB5A12135A5C009192AB /* SConscript */, 931CFB5B12135A5C009192AB /* SimulationParameters.h */, 931CFB5C12135A5C009192AB /* smoothing_functions.h */, 931CFB5D12135A5C009192AB /* StereochemistryPairFilter.h */, 931CFB5E12135A5C009192AB /* VelocityScalingOptimizerState.h */, ); name = include; path = ../modules/atom/include; sourceTree = SOURCE_ROOT; }; 931CFB4812135A5C009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFB4912135A5C009192AB /* bond_graph_boost_functions.h */, 931CFB4A12135A5C009192AB /* bond_graph_functors.h */, 931CFB4B12135A5C009192AB /* bond_helpers.h */, 931CFB4C12135A5C009192AB /* charmm_helpers.h */, 931CFB4D12135A5C009192AB /* ExcludedPair.h */, 931CFB4E12135A5C009192AB /* mol2.h */, 931CFB4F12135A5C009192AB /* pdb.h */, 931CFB5012135A5C009192AB /* protein_ligand_internal_score.h */, 931CFB5112135A5C009192AB /* SConscript */, ); name = internal; path = ../modules/atom/include/internal; sourceTree = SOURCE_ROOT; }; 931CFB5F12135A5C009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFB6012135A5C009192AB /* SConscript */, 931CFB6112135A5C009192AB /* swig.i-in */, ); name = pyext; path = ../modules/atom/pyext; sourceTree = SOURCE_ROOT; }; 931CFB6312135A5C009192AB /* src */ = { isa = PBXGroup; children = ( 931CFB6412135A5C009192AB /* angle_decorators.cpp */, 931CFB6512135A5C009192AB /* AngleSingletonScore.cpp */, 931CFB6612135A5C009192AB /* Atom.cpp */, 931CFB6712135A5C009192AB /* bond_decorators.cpp */, 931CFB6812135A5C009192AB /* bond_graph.cpp */, 931CFB6912135A5C009192AB /* BondedPairFilter.cpp */, 931CFB6A12135A5C009192AB /* BondEndpointsRefiner.cpp */, 931CFB6B12135A5C009192AB /* BondPairContainer.cpp */, 931CFB6C12135A5C009192AB /* BondSingletonScore.cpp */, 931CFB6D12135A5C009192AB /* BrownianDynamics.cpp */, 931CFB6E12135A5C009192AB /* Chain.cpp */, 931CFB6F12135A5C009192AB /* Charged.cpp */, 931CFB7012135A5C009192AB /* charmm_topology.cpp */, 931CFB7112135A5C009192AB /* CHARMMAtom.cpp */, 931CFB7212135A5C009192AB /* CHARMMParameters.cpp */, 931CFB7312135A5C009192AB /* CoulombPairScore.cpp */, 931CFB7412135A5C009192AB /* CoverBond.cpp */, 931CFB7512135A5C009192AB /* Diffusion.cpp */, 931CFB7612135A5C009192AB /* DihedralSingletonScore.cpp */, 931CFB7712135A5C009192AB /* distance.cpp */, 931CFB7812135A5C009192AB /* Domain.cpp */, 931CFB7912135A5C009192AB /* element.cpp */, 931CFB7A12135A5C009192AB /* estimates.cpp */, 931CFB7B12135A5C009192AB /* force_fields.cpp */, 931CFB7C12135A5C009192AB /* ForceFieldParameters.cpp */, 931CFB7D12135A5C009192AB /* Fragment.cpp */, 931CFB7E12135A5C009192AB /* Hierarchy.cpp */, 931CFB7F12135A5C009192AB /* hierarchy_tools.cpp */, 931CFB8012135A5C009192AB /* ImproperSingletonScore.cpp */, 931CFB8112135A5C009192AB /* internal */, 931CFB8512135A5C009192AB /* LennardJones.cpp */, 931CFB8612135A5C009192AB /* LennardJonesPairScore.cpp */, 931CFB8712135A5C009192AB /* Mass.cpp */, 931CFB8812135A5C009192AB /* mol2.cpp */, 931CFB8912135A5C009192AB /* MolecularDynamics.cpp */, 931CFB8A12135A5C009192AB /* pdb.cpp */, 931CFB8B12135A5C009192AB /* protein_ligand_score.cpp */, 931CFB8C12135A5C009192AB /* Residue.cpp */, 931CFB8D12135A5C009192AB /* SConscript */, 931CFB8E12135A5C009192AB /* SimulationParameters.cpp */, 931CFB8F12135A5C009192AB /* smoothing_functions.cpp */, 931CFB9012135A5C009192AB /* StereochemistryPairFilter.cpp */, 931CFB9112135A5C009192AB /* VelocityScalingOptimizerState.cpp */, ); name = src; path = ../modules/atom/src; sourceTree = SOURCE_ROOT; }; 931CFB8112135A5C009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFB8212135A5C009192AB /* mol2.cpp */, 931CFB8312135A5C009192AB /* pdb.cpp */, 931CFB8412135A5C009192AB /* SConscript */, ); name = internal; path = ../modules/atom/src/internal; sourceTree = SOURCE_ROOT; }; 931CFB9212135A5C009192AB /* test */ = { isa = PBXGroup; children = ( 931CFB9312135A5C009192AB /* input */, 931CFBA512135A5C009192AB /* SConscript */, 931CFBA612135A5C009192AB /* test_bd.py */, 931CFBA712135A5C009192AB /* test_bd_singleton_score.py */, 931CFBA812135A5D009192AB /* test_bond_decorator_particle_pair_container.py */, 931CFBA912135A5D009192AB /* test_bond_refiner.py */, 931CFBAA12135A5D009192AB /* test_bonds.py */, 931CFBAB12135A5D009192AB /* test_charged_decorator.py */, 931CFBAC12135A5D009192AB /* test_charmm_atom.py */, 931CFBAD12135A5D009192AB /* test_charmm_parameters.py */, 931CFBAE12135A5D009192AB /* test_charmm_topology.py */, 931CFBAF12135A5D009192AB /* test_clone.py */, 931CFBB012135A5D009192AB /* test_coulomb.py */, 931CFBB112135A5D009192AB /* test_cover_bond.py */, 931CFBB212135A5D009192AB /* test_create_protein.py */, 931CFBB312135A5D009192AB /* test_distance.py */, 931CFBB412135A5D009192AB /* test_element.py */, 931CFBB512135A5D009192AB /* test_estimates.py */, 931CFBB612135A5D009192AB /* test_force_switch.py */, 931CFBB712135A5D009192AB /* test_fragment.py */, 931CFBB812135A5D009192AB /* test_get_residue.py */, 931CFBB912135A5D009192AB /* test_hierarchy.py */, 931CFBBA12135A5D009192AB /* test_lennard_jones_decorator.py */, 931CFBBB12135A5D009192AB /* test_lennard_jones_pair_score.py */, 931CFBBC12135A5D009192AB /* test_md_optimizer.py */, 931CFBBD12135A5D009192AB /* test_mol2.py */, 931CFBBE12135A5D009192AB /* test_pdb.py */, 931CFBBF12135A5D009192AB /* test_pdb_string.py */, 931CFBC012135A5D009192AB /* test_plural.py */, 931CFBC112135A5D009192AB /* test_protein_ligand_score.py */, 931CFBC212135A5D009192AB /* test_ref_optimizer_states.py */, 931CFBC312135A5D009192AB /* test_residue_type.py */, 931CFBC412135A5D009192AB /* test_rigid_alignment_with_rigid_bodies.py */, 931CFBC512135A5D009192AB /* test_rigid_alignment_with_rigid_bodies.py.bak */, 931CFBC612135A5D009192AB /* test_rmsd_and_no.py */, 931CFBC712135A5D009192AB /* test_simplify.py */, 931CFBC812135A5D009192AB /* test_stereo_pair_filter.py */, ); name = test; path = ../modules/atom/test; sourceTree = SOURCE_ROOT; }; 931CFB9312135A5C009192AB /* input */ = { isa = PBXGroup; children = ( 931CFB9412135A5C009192AB /* 1aon.pdb */, 931CFB9512135A5C009192AB /* 1d3d-ligands.mol2 */, 931CFB9612135A5C009192AB /* 1d3d-ligands.out1.mol2 */, 931CFB9712135A5C009192AB /* 1d3d-ligands.out2.mol2 */, 931CFB9812135A5C009192AB /* 1d3d-protein.pdb */, 931CFB9912135A5C009192AB /* 1DQK.pdb */, 931CFB9A12135A5C009192AB /* 1z5s_A.pdb */, 931CFB9B12135A5C009192AB /* 1z5s_C.pdb */, 931CFB9C12135A5C009192AB /* elements.pdb */, 931CFB9D12135A5C009192AB /* hydrogen.pdb */, 931CFB9E12135A5C009192AB /* input.pdb */, 931CFB9F12135A5C009192AB /* mini.pdb */, 931CFBA012135A5C009192AB /* notapdb.pdb */, 931CFBA112135A5C009192AB /* problem_lines.pdb */, 931CFBA212135A5C009192AB /* protein_water.pdb */, 931CFBA312135A5C009192AB /* regression_0.pdb */, 931CFBA412135A5C009192AB /* single_dna.pdb */, ); name = input; path = ../modules/atom/test/input; sourceTree = SOURCE_ROOT; }; 931CFBC912135A5D009192AB /* benchmark */ = { isa = PBXGroup; children = ( 931CFBCA12135A5D009192AB /* bin */, 931CFBE412135A5D009192AB /* data */, 931CFBEA12135A5D009192AB /* doc */, 931CFC0212135A5D009192AB /* examples */, 931CFC0612135A5D009192AB /* include */, 931CFC0D12135A5D009192AB /* pyext */, 931CFC1212135A5D009192AB /* README */, 931CFC1312135A5D009192AB /* SConscript */, 931CFC1412135A5D009192AB /* src */, 931CFC1A12135A5D009192AB /* test */, ); name = benchmark; path = ../modules/benchmark; sourceTree = SOURCE_ROOT; }; 931CFBCA12135A5D009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFBCB12135A5D009192AB /* benchmark_brownian */, 931CFBCC12135A5D009192AB /* benchmark_brownian.cpp */, 931CFBCD12135A5D009192AB /* benchmark_close_pairs_finders */, 931CFBCE12135A5D009192AB /* benchmark_close_pairs_finders.cpp */, 931CFBCF12135A5D009192AB /* benchmark_connectivity */, 931CFBD012135A5D009192AB /* benchmark_connectivity.cpp */, 931CFBD112135A5D009192AB /* benchmark_density.cpp */, 931CFBD212135A5D009192AB /* benchmark_domino2.cpp */, 931CFBD312135A5D009192AB /* benchmark_domino2_2.cpp */, 931CFBD412135A5D009192AB /* benchmark_evaluate */, 931CFBD512135A5D009192AB /* benchmark_evaluate.cpp */, 931CFBD612135A5D009192AB /* benchmark_incremental */, 931CFBD712135A5D009192AB /* benchmark_incremental.cpp */, 931CFBD812135A5D009192AB /* benchmark_knn.cpp */, 931CFBD912135A5D009192AB /* benchmark_random_collisions */, 931CFBDA12135A5D009192AB /* benchmark_random_collisions.cpp */, 931CFBDB12135A5D009192AB /* benchmark_refiners */, 931CFBDC12135A5D009192AB /* benchmark_refiners.cpp */, 931CFBDD12135A5D009192AB /* benchmark_rigid_collisons */, 931CFBDE12135A5D009192AB /* benchmark_rigid_collisons.cpp */, 931CFBDF12135A5D009192AB /* benchmark_rotate */, 931CFBE012135A5D009192AB /* benchmark_rotate.cpp */, 931CFBE112135A5D009192AB /* benchmark_xyz_access */, 931CFBE212135A5D009192AB /* benchmark_xyz_access.cpp */, 931CFBE312135A5D009192AB /* SConscript */, ); name = bin; path = ../modules/benchmark/bin; sourceTree = SOURCE_ROOT; }; 931CFBE412135A5D009192AB /* data */ = { isa = PBXGroup; children = ( 931CFBE512135A5D009192AB /* huge_protein.pdb */, 931CFBE612135A5D009192AB /* large_protein.pdb */, 931CFBE712135A5D009192AB /* medium_protein.pdb */, 931CFBE812135A5D009192AB /* SConscript */, 931CFBE912135A5D009192AB /* small_protein.pdb */, ); name = data; path = ../modules/benchmark/data; sourceTree = SOURCE_ROOT; }; 931CFBEA12135A5D009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFBEB12135A5D009192AB /* baselines.py */, 931CFBEC12135A5D009192AB /* bdfast.png */, 931CFBED12135A5D009192AB /* bdrelease.png */, 931CFBEE12135A5D009192AB /* benchmark_results.csv */, 931CFBEF12135A5D009192AB /* changingfast.png */, 931CFBF012135A5D009192AB /* changingrelease.png */, 931CFBF112135A5D009192AB /* colfast.png */, 931CFBF212135A5D009192AB /* colrelease.png */, 931CFBF312135A5D009192AB /* connectivityfast.png */, 931CFBF412135A5D009192AB /* connectivityrelease.png */, 931CFBF512135A5D009192AB /* containerfast.png */, 931CFBF612135A5D009192AB /* containerrelease.png */, 931CFBF712135A5D009192AB /* cpffast.png */, 931CFBF812135A5D009192AB /* cpfrelease.png */, 931CFBF912135A5D009192AB /* generated */, 931CFBFB12135A5D009192AB /* rigidfast.png */, 931CFBFC12135A5D009192AB /* rigidrelease.png */, 931CFBFD12135A5D009192AB /* rotationfast.png */, 931CFBFE12135A5D009192AB /* rotationrelease.png */, 931CFBFF12135A5D009192AB /* SConscript */, 931CFC0012135A5D009192AB /* xyzfast.png */, 931CFC0112135A5D009192AB /* xyzrelease.png */, ); name = doc; path = ../modules/benchmark/doc; sourceTree = SOURCE_ROOT; }; 931CFBF912135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFBFA12135A5D009192AB /* overview.dox */, ); name = generated; path = ../modules/benchmark/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFC0212135A5D009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFC0312135A5D009192AB /* generated */, 931CFC0512135A5D009192AB /* SConscript */, ); name = examples; path = ../modules/benchmark/examples; sourceTree = SOURCE_ROOT; }; 931CFC0312135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFC0412135A5D009192AB /* examples.dox */, ); name = generated; path = ../modules/benchmark/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFC0612135A5D009192AB /* include */ = { isa = PBXGroup; children = ( 931CFC0712135A5D009192AB /* benchmark_macros.h */, 931CFC0812135A5D009192AB /* hidden_keys.h */, 931CFC0912135A5D009192AB /* internal */, 931CFC0B12135A5D009192AB /* SConscript */, 931CFC0C12135A5D009192AB /* utility.h */, ); name = include; path = ../modules/benchmark/include; sourceTree = SOURCE_ROOT; }; 931CFC0912135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFC0A12135A5D009192AB /* SConscript */, ); name = internal; path = ../modules/benchmark/include/internal; sourceTree = SOURCE_ROOT; }; 931CFC0D12135A5D009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFC0E12135A5D009192AB /* benchmark */, 931CFC1012135A5D009192AB /* SConscript */, 931CFC1112135A5D009192AB /* swig.i-in */, ); name = pyext; path = ../modules/benchmark/pyext; sourceTree = SOURCE_ROOT; }; 931CFC0E12135A5D009192AB /* benchmark */ = { isa = PBXGroup; children = ( 931CFC0F12135A5D009192AB /* randomize.py */, ); name = benchmark; path = ../modules/benchmark/pyext/benchmark; sourceTree = SOURCE_ROOT; }; 931CFC1412135A5D009192AB /* src */ = { isa = PBXGroup; children = ( 931CFC1512135A5D009192AB /* hidden_keys.cpp */, 931CFC1612135A5D009192AB /* internal */, 931CFC1812135A5D009192AB /* SConscript */, 931CFC1912135A5D009192AB /* utility.cpp */, ); name = src; path = ../modules/benchmark/src; sourceTree = SOURCE_ROOT; }; 931CFC1612135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFC1712135A5D009192AB /* SConscript */, ); name = internal; path = ../modules/benchmark/src/internal; sourceTree = SOURCE_ROOT; }; 931CFC1A12135A5D009192AB /* test */ = { isa = PBXGroup; children = ( 931CFC1B12135A5D009192AB /* restraints */, 931CFC1C12135A5D009192AB /* SConscript */, ); name = test; path = ../modules/benchmark/test; sourceTree = SOURCE_ROOT; }; 931CFC1B12135A5D009192AB /* restraints */ = { isa = PBXGroup; children = ( ); name = restraints; path = ../modules/benchmark/test/restraints; sourceTree = SOURCE_ROOT; }; 931CFC1D12135A5D009192AB /* container */ = { isa = PBXGroup; children = ( 931CFC1E12135A5D009192AB /* bin */, 931CFC2012135A5D009192AB /* data */, 931CFC2212135A5D009192AB /* doc */, 931CFC2612135A5D009192AB /* examples */, 931CFC3612135A5D009192AB /* include */, 931CFC6712135A5D009192AB /* pyext */, 931CFC6B12135A5D009192AB /* README */, 931CFC6C12135A5D009192AB /* SConscript */, 931CFC6D12135A5D009192AB /* src */, 931CFC9E12135A5D009192AB /* test */, ); name = container; path = ../modules/container; sourceTree = SOURCE_ROOT; }; 931CFC1E12135A5D009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFC1F12135A5D009192AB /* SConscript */, ); name = bin; path = ../modules/container/bin; sourceTree = SOURCE_ROOT; }; 931CFC2012135A5D009192AB /* data */ = { isa = PBXGroup; children = ( 931CFC2112135A5D009192AB /* SConscript */, ); name = data; path = ../modules/container/data; sourceTree = SOURCE_ROOT; }; 931CFC2212135A5D009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFC2312135A5D009192AB /* generated */, 931CFC2512135A5D009192AB /* SConscript */, ); name = doc; path = ../modules/container/doc; sourceTree = SOURCE_ROOT; }; 931CFC2312135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFC2412135A5D009192AB /* overview.dox */, ); name = generated; path = ../modules/container/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFC2612135A5D009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFC2712135A5D009192AB /* bipartite_nonbonded_interactions.py */, 931CFC2812135A5D009192AB /* bipartite_nonbonded_interactions.readme */, 931CFC2912135A5D009192AB /* connectivity.py */, 931CFC2A12135A5D009192AB /* connectivity.readme */, 931CFC2B12135A5D009192AB /* generated */, 931CFC3112135A5D009192AB /* nonbonded_interactions.py */, 931CFC3212135A5D009192AB /* nonbonded_interactions.readme */, 931CFC3312135A5D009192AB /* restrain_in_sphere.py */, 931CFC3412135A5D009192AB /* restrain_in_sphere.readme */, 931CFC3512135A5D009192AB /* SConscript */, ); name = examples; path = ../modules/container/examples; sourceTree = SOURCE_ROOT; }; 931CFC2B12135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFC2C12135A5D009192AB /* bipartite_nonbonded_interactions.py.html */, 931CFC2D12135A5D009192AB /* connectivity.py.html */, 931CFC2E12135A5D009192AB /* examples.dox */, 931CFC2F12135A5D009192AB /* nonbonded_interactions.py.html */, 931CFC3012135A5D009192AB /* restrain_in_sphere.py.html */, ); name = generated; path = ../modules/container/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFC3612135A5D009192AB /* include */ = { isa = PBXGroup; children = ( 931CFC3712135A5D009192AB /* AllBipartitePairContainer.h */, 931CFC3812135A5D009192AB /* AllPairContainer.h */, 931CFC3912135A5D009192AB /* CloseBipartitePairContainer.h */, 931CFC3A12135A5D009192AB /* ClosePairContainer.h */, 931CFC3B12135A5D009192AB /* ConnectingPairContainer.h */, 931CFC3C12135A5D009192AB /* InContainerPairFilter.h */, 931CFC3D12135A5D009192AB /* InContainerQuadFilter.h */, 931CFC3E12135A5D009192AB /* InContainerSingletonFilter.h */, 931CFC3F12135A5D009192AB /* InContainerTripletFilter.h */, 931CFC4012135A5D009192AB /* internal */, 931CFC4212135A5D009192AB /* ListPairContainer.h */, 931CFC4312135A5D009192AB /* ListQuadContainer.h */, 931CFC4412135A5D009192AB /* ListSingletonContainer.h */, 931CFC4512135A5D009192AB /* ListTripletContainer.h */, 931CFC4612135A5D009192AB /* MaximumPairRestraint.h */, 931CFC4712135A5D009192AB /* MaximumPairScore.h */, 931CFC4812135A5D009192AB /* MaximumQuadRestraint.h */, 931CFC4912135A5D009192AB /* MaximumQuadScore.h */, 931CFC4A12135A5D009192AB /* MaximumSingletonRestraint.h */, 931CFC4B12135A5D009192AB /* MaximumSingletonScore.h */, 931CFC4C12135A5D009192AB /* MaximumTripletRestraint.h */, 931CFC4D12135A5D009192AB /* MaximumTripletScore.h */, 931CFC4E12135A5D009192AB /* MinimumPairRestraint.h */, 931CFC4F12135A5D009192AB /* MinimumPairScore.h */, 931CFC5012135A5D009192AB /* MinimumQuadRestraint.h */, 931CFC5112135A5D009192AB /* MinimumQuadScore.h */, 931CFC5212135A5D009192AB /* MinimumSingletonRestraint.h */, 931CFC5312135A5D009192AB /* MinimumSingletonScore.h */, 931CFC5412135A5D009192AB /* MinimumTripletRestraint.h */, 931CFC5512135A5D009192AB /* MinimumTripletScore.h */, 931CFC5612135A5D009192AB /* PairContainerSet.h */, 931CFC5712135A5D009192AB /* PairsConstraint.h */, 931CFC5812135A5D009192AB /* PairsOptimizerState.h */, 931CFC5912135A5D009192AB /* PairsRestraint.h */, 931CFC5A12135A5D009192AB /* QuadContainerSet.h */, 931CFC5B12135A5D009192AB /* QuadsConstraint.h */, 931CFC5C12135A5D009192AB /* QuadsOptimizerState.h */, 931CFC5D12135A5D009192AB /* QuadsRestraint.h */, 931CFC5E12135A5D009192AB /* SConscript */, 931CFC5F12135A5D009192AB /* SingletonContainerSet.h */, 931CFC6012135A5D009192AB /* SingletonsConstraint.h */, 931CFC6112135A5D009192AB /* SingletonsOptimizerState.h */, 931CFC6212135A5D009192AB /* SingletonsRestraint.h */, 931CFC6312135A5D009192AB /* TripletContainerSet.h */, 931CFC6412135A5D009192AB /* TripletsConstraint.h */, 931CFC6512135A5D009192AB /* TripletsOptimizerState.h */, 931CFC6612135A5D009192AB /* TripletsRestraint.h */, ); name = include; path = ../modules/container/include; sourceTree = SOURCE_ROOT; }; 931CFC4012135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFC4112135A5D009192AB /* SConscript */, ); name = internal; path = ../modules/container/include/internal; sourceTree = SOURCE_ROOT; }; 931CFC6712135A5D009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFC6812135A5D009192AB /* SConscript */, 931CFC6912135A5D009192AB /* src */, 931CFC6A12135A5D009192AB /* swig.i-in */, ); name = pyext; path = ../modules/container/pyext; sourceTree = SOURCE_ROOT; }; 931CFC6912135A5D009192AB /* src */ = { isa = PBXGroup; children = ( ); name = src; path = ../modules/container/pyext/src; sourceTree = SOURCE_ROOT; }; 931CFC6D12135A5D009192AB /* src */ = { isa = PBXGroup; children = ( 931CFC6E12135A5D009192AB /* AllBipartitePairContainer.cpp */, 931CFC6F12135A5D009192AB /* AllPairContainer.cpp */, 931CFC7012135A5D009192AB /* CloseBipartitePairContainer.cpp */, 931CFC7112135A5D009192AB /* ClosePairContainer.cpp */, 931CFC7212135A5D009192AB /* ConnectingPairContainer.cpp */, 931CFC7312135A5D009192AB /* InContainerPairFilter.cpp */, 931CFC7412135A5D009192AB /* InContainerQuadFilter.cpp */, 931CFC7512135A5D009192AB /* InContainerSingletonFilter.cpp */, 931CFC7612135A5D009192AB /* InContainerTripletFilter.cpp */, 931CFC7712135A5D009192AB /* internal */, 931CFC7912135A5D009192AB /* ListPairContainer.cpp */, 931CFC7A12135A5D009192AB /* ListQuadContainer.cpp */, 931CFC7B12135A5D009192AB /* ListSingletonContainer.cpp */, 931CFC7C12135A5D009192AB /* ListTripletContainer.cpp */, 931CFC7D12135A5D009192AB /* MaximumPairRestraint.cpp */, 931CFC7E12135A5D009192AB /* MaximumPairScore.cpp */, 931CFC7F12135A5D009192AB /* MaximumQuadRestraint.cpp */, 931CFC8012135A5D009192AB /* MaximumQuadScore.cpp */, 931CFC8112135A5D009192AB /* MaximumSingletonRestraint.cpp */, 931CFC8212135A5D009192AB /* MaximumSingletonScore.cpp */, 931CFC8312135A5D009192AB /* MaximumTripletRestraint.cpp */, 931CFC8412135A5D009192AB /* MaximumTripletScore.cpp */, 931CFC8512135A5D009192AB /* MinimumPairRestraint.cpp */, 931CFC8612135A5D009192AB /* MinimumPairScore.cpp */, 931CFC8712135A5D009192AB /* MinimumQuadRestraint.cpp */, 931CFC8812135A5D009192AB /* MinimumQuadScore.cpp */, 931CFC8912135A5D009192AB /* MinimumSingletonRestraint.cpp */, 931CFC8A12135A5D009192AB /* MinimumSingletonScore.cpp */, 931CFC8B12135A5D009192AB /* MinimumTripletRestraint.cpp */, 931CFC8C12135A5D009192AB /* MinimumTripletScore.cpp */, 931CFC8D12135A5D009192AB /* PairContainerSet.cpp */, 931CFC8E12135A5D009192AB /* PairsConstraint.cpp */, 931CFC8F12135A5D009192AB /* PairsOptimizerState.cpp */, 931CFC9012135A5D009192AB /* PairsRestraint.cpp */, 931CFC9112135A5D009192AB /* QuadContainerSet.cpp */, 931CFC9212135A5D009192AB /* QuadsConstraint.cpp */, 931CFC9312135A5D009192AB /* QuadsOptimizerState.cpp */, 931CFC9412135A5D009192AB /* QuadsRestraint.cpp */, 931CFC9512135A5D009192AB /* SConscript */, 931CFC9612135A5D009192AB /* SingletonContainerSet.cpp */, 931CFC9712135A5D009192AB /* SingletonsConstraint.cpp */, 931CFC9812135A5D009192AB /* SingletonsOptimizerState.cpp */, 931CFC9912135A5D009192AB /* SingletonsRestraint.cpp */, 931CFC9A12135A5D009192AB /* TripletContainerSet.cpp */, 931CFC9B12135A5D009192AB /* TripletsConstraint.cpp */, 931CFC9C12135A5D009192AB /* TripletsOptimizerState.cpp */, 931CFC9D12135A5D009192AB /* TripletsRestraint.cpp */, ); name = src; path = ../modules/container/src; sourceTree = SOURCE_ROOT; }; 931CFC7712135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFC7812135A5D009192AB /* SConscript */, ); name = internal; path = ../modules/container/src/internal; sourceTree = SOURCE_ROOT; }; 931CFC9E12135A5D009192AB /* test */ = { isa = PBXGroup; children = ( 931CFC9F12135A5D009192AB /* SConscript */, 931CFCA012135A5D009192AB /* test_all_pairs.py */, 931CFCA112135A5D009192AB /* test_close_bipartite_pairs_score_state.py */, 931CFCA212135A5D009192AB /* test_close_pairs_score_state.py */, 931CFCA312135A5D009192AB /* test_connectivity_container.py */, 931CFCA412135A5D009192AB /* test_list.py */, 931CFCA512135A5D009192AB /* test_Particle_restraint.py */, 931CFCA612135A5D009192AB /* test_Particle_state.py */, 931CFCA712135A5D009192AB /* test_ParticlePair_restraint.py */, 931CFCA812135A5D009192AB /* test_ParticlePair_state.py */, 931CFCA912135A5D009192AB /* test_ParticleQuad_restraint.py */, 931CFCAA12135A5D009192AB /* test_ParticleQuad_state.py */, 931CFCAB12135A5D009192AB /* test_ParticleTriplet_restraint.py */, 931CFCAC12135A5D009192AB /* test_ParticleTriplet_state.py */, 931CFCAD12135A5D009192AB /* test_plural.py */, 931CFCAE12135A5D009192AB /* test_removes.py */, ); name = test; path = ../modules/container/test; sourceTree = SOURCE_ROOT; }; 931CFCAF12135A5D009192AB /* core */ = { isa = PBXGroup; children = ( 931CFCB012135A5D009192AB /* bin */, 931CFCB212135A5D009192AB /* data */, 931CFCB412135A5D009192AB /* doc */, 931CFCB812135A5D009192AB /* examples */, 931CFCE012135A5D009192AB /* include */, 931CFD4512135A5D009192AB /* pyext */, 931CFD4812135A5D009192AB /* SConscript */, 931CFD4912135A5D009192AB /* src */, 931CFD9E12135A5D009192AB /* test */, ); name = core; path = ../modules/core; sourceTree = SOURCE_ROOT; }; 931CFCB012135A5D009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFCB112135A5D009192AB /* SConscript */, ); name = bin; path = ../modules/core/bin; sourceTree = SOURCE_ROOT; }; 931CFCB212135A5D009192AB /* data */ = { isa = PBXGroup; children = ( 931CFCB312135A5D009192AB /* SConscript */, ); name = data; path = ../modules/core/data; sourceTree = SOURCE_ROOT; }; 931CFCB412135A5D009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFCB512135A5D009192AB /* generated */, 931CFCB712135A5D009192AB /* SConscript */, ); name = doc; path = ../modules/core/doc; sourceTree = SOURCE_ROOT; }; 931CFCB512135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFCB612135A5D009192AB /* overview.dox */, ); name = generated; path = ../modules/core/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFCB812135A5D009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFCB912135A5D009192AB /* connectivity_restraint.py */, 931CFCBA12135A5D009192AB /* connectivity_restraint.readme */, 931CFCBB12135A5D009192AB /* cover_particles.py */, 931CFCBC12135A5D009192AB /* cover_particles.readme */, 931CFCBD12135A5D009192AB /* example_protein.pdb */, 931CFCBE12135A5D009192AB /* excluded_volume.py */, 931CFCBF12135A5D009192AB /* excluded_volume.readme */, 931CFCC012135A5D009192AB /* fragments */, 931CFCC812135A5D009192AB /* generated */, 931CFCD312135A5D009192AB /* pair_restraint.py */, 931CFCD412135A5D009192AB /* pair_restraint.readme */, 931CFCD512135A5D009192AB /* restrain_diameter.py */, 931CFCD612135A5D009192AB /* restrain_diameter.readme */, 931CFCD712135A5D009192AB /* rigid_bodies.py */, 931CFCD812135A5D009192AB /* rigid_bodies.readme */, 931CFCD912135A5D009192AB /* rigid_collisions.py */, 931CFCDA12135A5D009192AB /* rigid_collisions.readme */, 931CFCDB12135A5D009192AB /* SConscript */, 931CFCDC12135A5D009192AB /* XYZ_Decorator.py */, 931CFCDD12135A5D009192AB /* XYZ_Decorator.readme */, 931CFCDE12135A5D009192AB /* XYZR_Decorator.py */, 931CFCDF12135A5D009192AB /* XYZR_Decorator.readme */, ); name = examples; path = ../modules/core/examples; sourceTree = SOURCE_ROOT; }; 931CFCC012135A5D009192AB /* fragments */ = { isa = PBXGroup; children = ( 931CFCC112135A5D009192AB /* custom_hierarchy.py */, 931CFCC212135A5D009192AB /* custom_hierarchy.readme */, 931CFCC312135A5D009192AB /* generated */, 931CFCC612135A5D009192AB /* randomize_rigid_body.py */, 931CFCC712135A5D009192AB /* randomize_rigid_body.readme */, ); name = fragments; path = ../modules/core/examples/fragments; sourceTree = SOURCE_ROOT; }; 931CFCC312135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFCC412135A5D009192AB /* custom_hierarchy.py.html */, 931CFCC512135A5D009192AB /* randomize_rigid_body.py.html */, ); name = generated; path = ../modules/core/examples/fragments/generated; sourceTree = SOURCE_ROOT; }; 931CFCC812135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFCC912135A5D009192AB /* connectivity_restraint.py.html */, 931CFCCA12135A5D009192AB /* cover_particles.py.html */, 931CFCCB12135A5D009192AB /* examples.dox */, 931CFCCC12135A5D009192AB /* excluded_volume.py.html */, 931CFCCD12135A5D009192AB /* pair_restraint.py.html */, 931CFCCE12135A5D009192AB /* restrain_diameter.py.html */, 931CFCCF12135A5D009192AB /* rigid_bodies.py.html */, 931CFCD012135A5D009192AB /* rigid_collisions.py.html */, 931CFCD112135A5D009192AB /* XYZ_Decorator.py.html */, 931CFCD212135A5D009192AB /* XYZR_Decorator.py.html */, ); name = generated; path = ../modules/core/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFCE012135A5D009192AB /* include */ = { isa = PBXGroup; children = ( 931CFCE112135A5D009192AB /* AngleRestraint.h */, 931CFCE212135A5D009192AB /* AngleTripletScore.h */, 931CFCE312135A5D009192AB /* AttributeSingletonScore.h */, 931CFCE412135A5D009192AB /* BallMover.h */, 931CFCE512135A5D009192AB /* BoundingBox3DSingletonScore.h */, 931CFCE612135A5D009192AB /* BoxSweepClosePairsFinder.h */, 931CFCE712135A5D009192AB /* CentroidOfRefined.h */, 931CFCE812135A5D009192AB /* ChecksScoreState.h */, 931CFCE912135A5D009192AB /* ChildrenRefiner.h */, 931CFCEA12135A5D009192AB /* ClosedCubicSpline.h */, 931CFCEB12135A5D009192AB /* ClosePairsFinder.h */, 931CFCEC12135A5D009192AB /* ClosePairsPairScore.h */, 931CFCED12135A5D009192AB /* ConjugateGradients.h */, 931CFCEE12135A5D009192AB /* ConnectivityRestraint.h */, 931CFCEF12135A5D009192AB /* ConstantRestraint.h */, 931CFCF012135A5D009192AB /* core_macros.h */, 931CFCF112135A5D009192AB /* Cosine.h */, 931CFCF212135A5D009192AB /* CoverRefined.h */, 931CFCF312135A5D009192AB /* DerivativesFromRefined.h */, 931CFCF412135A5D009192AB /* DerivativesToRefined.h */, 931CFCF512135A5D009192AB /* DiameterRestraint.h */, 931CFCF612135A5D009192AB /* DihedralRestraint.h */, 931CFCF712135A5D009192AB /* DistancePairScore.h */, 931CFCF812135A5D009192AB /* DistanceRestraint.h */, 931CFCF912135A5D009192AB /* DistanceToSingletonScore.h */, 931CFCFA12135A5D009192AB /* ExcludedVolumeRestraint.h */, 931CFCFB12135A5D009192AB /* FixedRefiner.h */, 931CFCFC12135A5D009192AB /* GridClosePairsFinder.h */, 931CFCFD12135A5D009192AB /* Harmonic.h */, 931CFCFE12135A5D009192AB /* HarmonicLowerBound.h */, 931CFCFF12135A5D009192AB /* HarmonicUpperBound.h */, 931CFD0012135A5D009192AB /* HarmonicWell.h */, 931CFD0112135A5D009192AB /* Hierarchy.h */, 931CFD0212135A5D009192AB /* IncrementalBallMover.h */, 931CFD0312135A5D009192AB /* internal */, 931CFD2112135A5D009192AB /* LeavesRefiner.h */, 931CFD2212135A5D009192AB /* Linear.h */, 931CFD2312135A5D009192AB /* MCCGSampler.h */, 931CFD2412135A5D009192AB /* MonteCarlo.h */, 931CFD2512135A5D009192AB /* Mover.h */, 931CFD2612135A5D009192AB /* MoverBase.h */, 931CFD2712135A5D009192AB /* NearestNeighborsClosePairsFinder.h */, 931CFD2812135A5D009192AB /* NormalMover.h */, 931CFD2912135A5D009192AB /* OpenCubicSpline.h */, 931CFD2A12135A5D009192AB /* PairConstraint.h */, 931CFD2B12135A5D009192AB /* PairRestraint.h */, 931CFD2C12135A5D009192AB /* QuadConstraint.h */, 931CFD2D12135A5D009192AB /* QuadraticClosePairsFinder.h */, 931CFD2E12135A5D009192AB /* QuadRestraint.h */, 931CFD2F12135A5D009192AB /* RefinedPairsPairScore.h */, 931CFD3012135A5D009192AB /* rigid_bodies.h */, 931CFD3112135A5D009192AB /* RigidBodyDistancePairScore.h */, 931CFD3212135A5D009192AB /* RigidBodyMover.h */, 931CFD3312135A5D009192AB /* RigidClosePairsFinder.h */, 931CFD3412135A5D009192AB /* SConscript */, 931CFD3512135A5D009192AB /* SingletonConstraint.h */, 931CFD3612135A5D009192AB /* SingletonRestraint.h */, 931CFD3712135A5D009192AB /* SphereDistancePairScore.h */, 931CFD3812135A5D009192AB /* SteepestDescent.h */, 931CFD3912135A5D009192AB /* TableRefiner.h */, 931CFD3A12135A5D009192AB /* Transform.h */, 931CFD3B12135A5D009192AB /* TransformedDistancePairScore.h */, 931CFD3C12135A5D009192AB /* TripletConstraint.h */, 931CFD3D12135A5D009192AB /* TripletRestraint.h */, 931CFD3E12135A5D009192AB /* TruncatedHarmonic.h */, 931CFD3F12135A5D009192AB /* TypedPairScore.h */, 931CFD4012135A5D009192AB /* utility.h */, 931CFD4112135A5D009192AB /* VolumeRestraint.h */, 931CFD4212135A5D009192AB /* WriteModelOptimizerState.h */, 931CFD4312135A5D009192AB /* XYZ.h */, 931CFD4412135A5D009192AB /* XYZR.h */, ); 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name = internal; path = ../modules/core/include/internal; sourceTree = SOURCE_ROOT; }; 931CFD4512135A5D009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFD4612135A5D009192AB /* SConscript */, 931CFD4712135A5D009192AB /* swig.i-in */, ); name = pyext; path = ../modules/core/pyext; sourceTree = SOURCE_ROOT; }; 931CFD4912135A5D009192AB /* src */ = { isa = PBXGroup; children = ( 931CFD4A12135A5D009192AB /* AngleRestraint.cpp */, 931CFD4B12135A5D009192AB /* AngleTripletScore.cpp */, 931CFD4C12135A5D009192AB /* AttributeSingletonScore.cpp */, 931CFD4D12135A5D009192AB /* BallMover.cpp */, 931CFD4E12135A5D009192AB /* BoundingBox3DSingletonScore.cpp */, 931CFD4F12135A5D009192AB /* BoxSweepClosePairsFinder.cpp */, 931CFD5012135A5D009192AB /* CentroidOfRefined.cpp */, 931CFD5112135A5D009192AB /* ChecksScoreState.cpp */, 931CFD5212135A5D009192AB /* ChildrenRefiner.cpp */, 931CFD5312135A5D009192AB /* ClosedCubicSpline.cpp */, 931CFD5412135A5D009192AB /* ClosePairsFinder.cpp */, 931CFD5512135A5D009192AB /* ClosePairsPairScore.cpp */, 931CFD5612135A5D009192AB /* ConjugateGradients.cpp */, 931CFD5712135A5D009192AB /* ConnectivityRestraint.cpp */, 931CFD5812135A5D009192AB /* ConstantRestraint.cpp */, 931CFD5912135A5D009192AB /* Cosine.cpp */, 931CFD5A12135A5D009192AB /* CoverRefined.cpp */, 931CFD5B12135A5D009192AB /* DerivativesFromRefined.cpp */, 931CFD5C12135A5D009192AB /* DerivativesToRefined.cpp */, 931CFD5D12135A5D009192AB /* DiameterRestraint.cpp */, 931CFD5E12135A5D009192AB /* DihedralRestraint.cpp */, 931CFD5F12135A5D009192AB /* DistancePairScore.cpp */, 931CFD6012135A5D009192AB /* DistanceRestraint.cpp */, 931CFD6112135A5D009192AB /* DistanceToSingletonScore.cpp */, 931CFD6212135A5D009192AB /* ExcludedVolumeRestraint.cpp */, 931CFD6312135A5D009192AB /* FixedRefiner.cpp */, 931CFD6412135A5D009192AB /* GridClosePairsFinder.cpp */, 931CFD6512135A5D009192AB /* Hierarchy.cpp */, 931CFD6612135A5D009192AB /* IncrementalBallMover.cpp */, 931CFD6712135A5D009192AB /* internal */, 931CFD7D12135A5D009192AB /* LeavesRefiner.cpp */, 931CFD7E12135A5D009192AB /* MCCGSampler.cpp */, 931CFD7F12135A5D009192AB /* MonteCarlo.cpp */, 931CFD8012135A5D009192AB /* MoverBase.cpp */, 931CFD8112135A5D009192AB /* NearestNeighborsClosePairsFinder.cpp */, 931CFD8212135A5D009192AB /* NormalMover.cpp */, 931CFD8312135A5D009192AB /* OpenCubicSpline.cpp */, 931CFD8412135A5D009192AB /* PairConstraint.cpp */, 931CFD8512135A5D009192AB /* PairRestraint.cpp */, 931CFD8612135A5D009192AB /* QuadConstraint.cpp */, 931CFD8712135A5D009192AB /* QuadraticClosePairsFinder.cpp */, 931CFD8812135A5D009192AB /* QuadRestraint.cpp */, 931CFD8912135A5D009192AB /* RefinedPairsPairScore.cpp */, 931CFD8A12135A5D009192AB /* rigid_bodies.cpp */, 931CFD8B12135A5D009192AB /* RigidBodyDistancePairScore.cpp */, 931CFD8C12135A5D009192AB /* RigidBodyMover.cpp */, 931CFD8D12135A5D009192AB /* RigidClosePairsFinder.cpp */, 931CFD8E12135A5D009192AB /* SConscript */, 931CFD8F12135A5D009192AB /* SingletonConstraint.cpp */, 931CFD9012135A5D009192AB /* SingletonRestraint.cpp */, 931CFD9112135A5D009192AB /* SphereDistancePairScore.cpp */, 931CFD9212135A5D009192AB /* SteepestDescent.cpp */, 931CFD9312135A5D009192AB /* TableRefiner.cpp */, 931CFD9412135A5D009192AB /* Transform.cpp */, 931CFD9512135A5D009192AB /* TransformedDistancePairScore.cpp */, 931CFD9612135A5D009192AB /* TripletConstraint.cpp */, 931CFD9712135A5D009192AB /* TripletRestraint.cpp */, 931CFD9812135A5D009192AB /* TypedPairScore.cpp */, 931CFD9912135A5D009192AB /* utility.cpp */, 931CFD9A12135A5D009192AB /* VolumeRestraint.cpp */, 931CFD9B12135A5D009192AB /* WriteModelOptimizerState.cpp */, 931CFD9C12135A5D009192AB /* XYZ.cpp */, 931CFD9D12135A5D009192AB /* XYZR.cpp */, ); name = src; path = ../modules/core/src; sourceTree = SOURCE_ROOT; }; 931CFD6712135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFD6812135A5D009192AB /* ArrayOnAttributesHelper.cpp */, 931CFD6912135A5D009192AB /* CoreClosePairContainer.cpp */, 931CFD6A12135A5D009192AB /* CoreListPairContainer.cpp */, 931CFD6B12135A5D009192AB /* CoreListQuadContainer.cpp */, 931CFD6C12135A5D009192AB /* CoreListSingletonContainer.cpp */, 931CFD6D12135A5D009192AB /* CoreListTripletContainer.cpp */, 931CFD6E12135A5D009192AB /* CorePairsRestraint.cpp */, 931CFD6F12135A5D009192AB /* CoreQuadsRestraint.cpp */, 931CFD7012135A5D009192AB /* CoreSingletonsRestraint.cpp */, 931CFD7112135A5D009192AB /* CoreTripletsRestraint.cpp */, 931CFD7212135A5D009192AB /* DifferenceSingletonContainer.cpp */, 931CFD7312135A5D009192AB /* evaluate_distance_pair_score.cpp */, 931CFD7412135A5D009192AB /* graph_base.cpp */, 931CFD7512135A5D009192AB /* MovedSingletonContainer.cpp */, 931CFD7612135A5D009192AB /* pair_helpers.cpp */, 931CFD7712135A5D009192AB /* ParticleGrid.cpp */, 931CFD7812135A5D009192AB /* quad_helpers.cpp */, 931CFD7912135A5D009192AB /* rigid_body_tree.cpp */, 931CFD7A12135A5D009192AB /* SConscript */, 931CFD7B12135A5D009192AB /* singleton_helpers.cpp */, 931CFD7C12135A5D009192AB /* triplet_helpers.cpp */, ); name = internal; path = ../modules/core/src/internal; sourceTree = SOURCE_ROOT; }; 931CFD9E12135A5D009192AB /* test */ = { isa = PBXGroup; children = ( 931CFD9F12135A5D009192AB /* input */, 931CFDA312135A5D009192AB /* SConscript */, 931CFDA412135A5D009192AB /* test_angle.py */, 931CFDA512135A5D009192AB /* test_box.py */, 931CFDA612135A5D009192AB /* test_centroid.py */, 931CFDA712135A5D009192AB /* test_cg_optimizer.py */, 931CFDA812135A5D009192AB /* test_children.py */, 931CFDA912135A5D009192AB /* test_close_pair_finders.py */, 931CFDAA12135A5D009192AB /* test_close_pairs_ps.py */, 931CFDAB12135A5D009192AB /* test_connectivity.py */, 931CFDAC12135A5D009192AB /* test_cosine.py */, 931CFDAD12135A5D009192AB /* test_cover.py */, 931CFDAE12135A5D009192AB /* test_cover_refiner.py */, 931CFDAF12135A5D009192AB /* test_destroy_rigid_body.py */, 931CFDB012135A5D009192AB /* test_destroy_rigid_body.py.bak */, 931CFDB112135A5D009192AB /* test_diameter.py */, 931CFDB212135A5D009192AB /* test_dihedral.py */, 931CFDB312135A5D009192AB /* test_distance.py */, 931CFDB412135A5D009192AB /* test_ev_restraint.py */, 931CFDB512135A5D009192AB /* test_harmonic.py */, 931CFDB612135A5D009192AB /* test_hierarchy.py */, 931CFDB712135A5D009192AB /* test_linear.py */, 931CFDB812135A5D009192AB /* test_mc.py */, 931CFDB912135A5D009192AB /* test_mc_rigid_bodies.py */, 931CFDBA12135A5D009192AB /* test_mccg.py */, 931CFDBB12135A5D009192AB /* test_particles.py */, 931CFDBC12135A5D009192AB /* test_plural.py */, 931CFDBD12135A5D009192AB /* test_refined_pairs_ps.py */, 931CFDBE12135A5D009192AB /* test_rigid_bodies.py */, 931CFDBF12135A5D009192AB /* test_rigid_distance.py */, 931CFDC012135A5D009192AB /* test_sd_optimizer.py */, 931CFDC112135A5D009192AB /* test_splines.py */, 931CFDC212135A5D009192AB /* test_table.py */, 931CFDC312135A5D009192AB /* test_to_from_refined.py */, 931CFDC412135A5D009192AB /* test_transform.py */, 931CFDC512135A5D009192AB /* test_transform_particles.py */, 931CFDC612135A5D009192AB /* test_truncated_harmonic.py */, 931CFDC712135A5D009192AB /* test_typed_pair_score.py */, 931CFDC812135A5D009192AB /* test_volume.py */, 931CFDC912135A5D009192AB /* test_xyzr.py */, ); name = test; path = ../modules/core/test; sourceTree = SOURCE_ROOT; }; 931CFD9F12135A5D009192AB /* input */ = { isa = PBXGroup; children = ( 931CFDA012135A5D009192AB /* 1z5s_A.pdb */, 931CFDA112135A5D009192AB /* 1z5s_C.pdb */, 931CFDA212135A5D009192AB /* input.pdb */, ); name = input; path = ../modules/core/test/input; sourceTree = SOURCE_ROOT; }; 931CFDCA12135A5D009192AB /* display */ = { isa = PBXGroup; children = ( 931CFDCB12135A5D009192AB /* bin */, 931CFDCD12135A5D009192AB /* data */, 931CFDCF12135A5D009192AB /* doc */, 931CFDD312135A5D009192AB /* examples */, 931CFDDF12135A5D009192AB /* include */, 931CFDF312135A5D009192AB /* pyext */, 931CFDF712135A5D009192AB /* SConscript */, 931CFDF812135A5D009192AB /* src */, 931CFE0B12135A5D009192AB /* test */, ); name = display; path = ../modules/display; sourceTree = SOURCE_ROOT; }; 931CFDCB12135A5D009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFDCC12135A5D009192AB /* SConscript */, ); name = bin; path = ../modules/display/bin; sourceTree = SOURCE_ROOT; }; 931CFDCD12135A5D009192AB /* data */ = { isa = PBXGroup; children = ( 931CFDCE12135A5D009192AB /* SConscript */, ); name = data; path = ../modules/display/data; sourceTree = SOURCE_ROOT; }; 931CFDCF12135A5D009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFDD012135A5D009192AB /* generated */, 931CFDD212135A5D009192AB /* SConscript */, ); name = doc; path = ../modules/display/doc; sourceTree = SOURCE_ROOT; }; 931CFDD012135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFDD112135A5D009192AB /* overview.dox */, ); name = generated; path = ../modules/display/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFDD312135A5D009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFDD412135A5D009192AB /* display_log.py */, 931CFDD512135A5D009192AB /* display_log.readme */, 931CFDD612135A5D009192AB /* fragments */, 931CFDDB12135A5D009192AB /* generated */, 931CFDDE12135A5D009192AB /* SConscript */, ); name = examples; path = ../modules/display/examples; sourceTree = SOURCE_ROOT; }; 931CFDD612135A5D009192AB /* fragments */ = { isa = PBXGroup; children = ( 931CFDD712135A5D009192AB /* generated */, 931CFDD912135A5D009192AB /* show_spheres.py */, 931CFDDA12135A5D009192AB /* show_spheres.readme */, ); name = fragments; path = ../modules/display/examples/fragments; sourceTree = SOURCE_ROOT; }; 931CFDD712135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFDD812135A5D009192AB /* show_spheres.py.html */, ); name = generated; path = ../modules/display/examples/fragments/generated; sourceTree = SOURCE_ROOT; }; 931CFDDB12135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFDDC12135A5D009192AB /* display_log.py.html */, 931CFDDD12135A5D009192AB /* examples.dox */, ); name = generated; path = ../modules/display/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFDDF12135A5D009192AB /* include */ = { isa = PBXGroup; children = ( 931CFDE012135A5D009192AB /* BildWriter.h */, 931CFDE112135A5D009192AB /* ChimeraWriter.h */, 931CFDE212135A5D009192AB /* CMMWriter.h */, 931CFDE312135A5D009192AB /* Color.h */, 931CFDE412135A5D009192AB /* Colored.h */, 931CFDE512135A5D009192AB /* display_macros.h */, 931CFDE612135A5D009192AB /* FilterGeometry.h */, 931CFDE712135A5D009192AB /* geometry.h */, 931CFDE812135A5D009192AB /* GeometryProcessor.h */, 931CFDE912135A5D009192AB /* internal */, 931CFDED12135A5D009192AB /* LogOptimizerState.h */, 931CFDEE12135A5D009192AB /* particle_geometry.h */, 931CFDEF12135A5D009192AB /* PDBOptimizerState.h */, 931CFDF012135A5D009192AB /* PymolWriter.h */, 931CFDF112135A5D009192AB /* SConscript */, 931CFDF212135A5D009192AB /* Writer.h */, ); name = include; path = ../modules/display/include; sourceTree = SOURCE_ROOT; }; 931CFDE912135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFDEA12135A5D009192AB /* SConscript */, 931CFDEB12135A5D009192AB /* utility.h */, 931CFDEC12135A5D009192AB /* writers.h */, ); name = internal; path = ../modules/display/include/internal; sourceTree = SOURCE_ROOT; }; 931CFDF312135A5D009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFDF412135A5D009192AB /* display */, 931CFDF512135A5D009192AB /* SConscript */, 931CFDF612135A5D009192AB /* swig.i-in */, ); name = pyext; path = ../modules/display/pyext; sourceTree = SOURCE_ROOT; }; 931CFDF412135A5D009192AB /* display */ = { isa = PBXGroup; children = ( ); name = display; path = ../modules/display/pyext/display; sourceTree = SOURCE_ROOT; }; 931CFDF812135A5D009192AB /* src */ = { isa = PBXGroup; children = ( 931CFDF912135A5D009192AB /* BildWriter.cpp */, 931CFDFA12135A5D009192AB /* ChimeraWriter.cpp */, 931CFDFB12135A5D009192AB /* CMMWriter.cpp */, 931CFDFC12135A5D009192AB /* Color.cpp */, 931CFDFD12135A5D009192AB /* Colored.cpp */, 931CFDFE12135A5D009192AB /* FilterGeometry.cpp */, 931CFDFF12135A5D009192AB /* geometry.cpp */, 931CFE0012135A5D009192AB /* GeometryProcessor.cpp */, 931CFE0112135A5D009192AB /* internal */, 931CFE0512135A5D009192AB /* LogOptimizerState.cpp */, 931CFE0612135A5D009192AB /* particle_geometry.cpp */, 931CFE0712135A5D009192AB /* PDBOptimizerState.cpp */, 931CFE0812135A5D009192AB /* PymolWriter.cpp */, 931CFE0912135A5D009192AB /* SConscript */, 931CFE0A12135A5D009192AB /* Writer.cpp */, ); name = src; path = ../modules/display/src; sourceTree = SOURCE_ROOT; }; 931CFE0112135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFE0212135A5D009192AB /* SConscript */, 931CFE0312135A5D009192AB /* utility.cpp */, 931CFE0412135A5D009192AB /* writers.cpp */, ); name = internal; path = ../modules/display/src/internal; sourceTree = SOURCE_ROOT; }; 931CFE0B12135A5D009192AB /* test */ = { isa = PBXGroup; children = ( 931CFE0C12135A5D009192AB /* SConscript */, 931CFE0D12135A5D009192AB /* test_create_writer.py */, 931CFE0E12135A5D009192AB /* test_deriv.py */, 931CFE0F12135A5D009192AB /* test_log.py */, 931CFE1012135A5D009192AB /* test_polygon.py */, 931CFE1112135A5D009192AB /* test_polygon.py.bak */, 931CFE1212135A5D009192AB /* test_writers.py */, ); name = test; path = ../modules/display/test; sourceTree = SOURCE_ROOT; }; 931CFE1312135A5D009192AB /* domino */ = { isa = PBXGroup; children = ( 931CFE1412135A5D009192AB /* bin */, 931CFE1612135A5D009192AB /* data */, 931CFE1812135A5D009192AB /* doc */, 931CFE1C12135A5D009192AB /* examples */, 931CFE2F12135A5D009192AB /* include */, 931CFE4E12135A5D009192AB /* pyext */, 931CFE5412135A5D009192AB /* SConscript */, 931CFE5512135A5D009192AB /* src */, 931CFE6F12135A5D009192AB /* test */, ); name = domino; path = ../modules/domino; sourceTree = SOURCE_ROOT; }; 931CFE1412135A5D009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFE1512135A5D009192AB /* SConscript */, ); name = bin; path = ../modules/domino/bin; sourceTree = SOURCE_ROOT; }; 931CFE1612135A5D009192AB /* data */ = { isa = PBXGroup; children = ( 931CFE1712135A5D009192AB /* SConscript */, ); name = data; path = ../modules/domino/data; sourceTree = SOURCE_ROOT; }; 931CFE1812135A5D009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFE1912135A5D009192AB /* generated */, 931CFE1B12135A5D009192AB /* SConscript */, ); name = doc; path = ../modules/domino/doc; sourceTree = SOURCE_ROOT; }; 931CFE1912135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFE1A12135A5D009192AB /* overview.dox */, ); name = generated; path = ../modules/domino/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFE1C12135A5D009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFE1D12135A5D009192AB /* 1z5s.jt */, 931CFE1E12135A5D009192AB /* 1z5s_A.pdb */, 931CFE1F12135A5D009192AB /* 1z5s_A_1.pdb */, 931CFE2012135A5D009192AB /* 1z5s_B.pdb */, 931CFE2112135A5D009192AB /* 1z5s_C.pdb */, 931CFE2212135A5D009192AB /* 1z5s_D.pdb */, 931CFE2312135A5D009192AB /* four_proteins_optimization.py */, 931CFE2412135A5D009192AB /* four_proteins_optimization.readme */, 931CFE2512135A5D009192AB /* generated */, 931CFE2912135A5D009192AB /* README */, 931CFE2A12135A5D009192AB /* SConscript */, 931CFE2B12135A5D009192AB /* six_particles.jt */, 931CFE2C12135A5D009192AB /* six_particles.restraints */, 931CFE2D12135A5D009192AB /* six_particles_optimization.py */, 931CFE2E12135A5D009192AB /* six_particles_optimization.readme */, ); name = examples; path = ../modules/domino/examples; sourceTree = SOURCE_ROOT; }; 931CFE2512135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFE2612135A5D009192AB /* examples.dox */, 931CFE2712135A5D009192AB /* four_proteins_optimization.py.html */, 931CFE2812135A5D009192AB /* six_particles_optimization.py.html */, ); name = generated; path = ../modules/domino/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFE2F12135A5D009192AB /* include */ = { isa = PBXGroup; children = ( 931CFE3012135A5D009192AB /* boost */, 931CFE3312135A5D009192AB /* CartesianProductSampler.h */, 931CFE3412135A5D009192AB /* CombState.h */, 931CFE3512135A5D009192AB /* DiscreteSampler.h */, 931CFE3612135A5D009192AB /* DiscreteSet.h */, 931CFE3712135A5D009192AB /* DominoOptimizer.h */, 931CFE3812135A5D009192AB /* internal */, 931CFE3A12135A5D009192AB /* JEdge.h */, 931CFE3B12135A5D009192AB /* JNode.h */, 931CFE3C12135A5D009192AB /* JunctionTree.h */, 931CFE3D12135A5D009192AB /* MappedDiscreteSet.h */, 931CFE3E12135A5D009192AB /* PermutationSampler.h */, 931CFE3F12135A5D009192AB /* RestraintEvaluator.h */, 931CFE4012135A5D009192AB /* RestraintEvaluatorFromFile.h */, 931CFE4112135A5D009192AB /* RestraintEvaluatorI.h */, 931CFE4212135A5D009192AB /* RestraintGraph.h */, 931CFE4312135A5D009192AB /* SConscript */, 931CFE4412135A5D009192AB /* SimpleDiscreteRestraint.h */, 931CFE4512135A5D009192AB /* SimpleDiscreteSampler.h */, 931CFE4612135A5D009192AB /* SimpleDiscreteSpace.h */, 931CFE4712135A5D009192AB /* SymmetrySampler.h */, 931CFE4812135A5D009192AB /* Transformation.h */, 931CFE4912135A5D009192AB /* TransformationCartesianProductSampler.h */, 931CFE4A12135A5D009192AB /* TransformationDiscreteSet.h */, 931CFE4B12135A5D009192AB /* TransformationMappedDiscreteSet.h */, 931CFE4C12135A5D009192AB /* TransformationPermutationSampler.h */, 931CFE4D12135A5D009192AB /* TransformationUtils.h */, ); name = include; path = ../modules/domino/include; sourceTree = SOURCE_ROOT; }; 931CFE3012135A5D009192AB /* boost */ = { isa = PBXGroup; children = ( 931CFE3112135A5D009192AB /* combination.hpp */, 931CFE3212135A5D009192AB /* SConscript */, ); name = boost; path = ../modules/domino/include/boost; sourceTree = SOURCE_ROOT; }; 931CFE3812135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFE3912135A5D009192AB /* SConscript */, ); name = internal; path = ../modules/domino/include/internal; sourceTree = SOURCE_ROOT; }; 931CFE4E12135A5D009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFE4F12135A5D009192AB /* interaction_graph.py */, 931CFE5012135A5D009192AB /* junction_tree_from_pair_list.py */, 931CFE5112135A5D009192AB /* SConscript */, 931CFE5212135A5D009192AB /* swig.i-in */, 931CFE5312135A5D009192AB /* swig.i.in */, ); name = pyext; path = ../modules/domino/pyext; sourceTree = SOURCE_ROOT; }; 931CFE5512135A5D009192AB /* src */ = { isa = PBXGroup; children = ( 931CFE5612135A5D009192AB /* CartesianProductSampler.cpp */, 931CFE5712135A5D009192AB /* CombState.cpp */, 931CFE5812135A5D009192AB /* DiscreteSet.cpp */, 931CFE5912135A5D009192AB /* DominoOptimizer.cpp */, 931CFE5A12135A5D009192AB /* internal */, 931CFE5C12135A5D009192AB /* JEdge.cpp */, 931CFE5D12135A5D009192AB /* JNode.cpp */, 931CFE5E12135A5D009192AB /* JunctionTree.cpp */, 931CFE5F12135A5D009192AB /* MappedDiscreteSet.cpp */, 931CFE6012135A5D009192AB /* PermutationSampler.cpp */, 931CFE6112135A5D009192AB /* RestraintEvaluator.cpp */, 931CFE6212135A5D009192AB /* RestraintEvaluatorFromFile.cpp */, 931CFE6312135A5D009192AB /* RestraintGraph.cpp */, 931CFE6412135A5D009192AB /* SConscript */, 931CFE6512135A5D009192AB /* SimpleDiscreteRestraint.cpp */, 931CFE6612135A5D009192AB /* SimpleDiscreteSampler.cpp */, 931CFE6712135A5D009192AB /* SimpleDiscreteSpace.cpp */, 931CFE6812135A5D009192AB /* SymmetrySampler.cpp */, 931CFE6912135A5D009192AB /* Transformation.cpp */, 931CFE6A12135A5D009192AB /* TransformationCartesianProductSampler.cpp */, 931CFE6B12135A5D009192AB /* TransformationDiscreteSet.cpp */, 931CFE6C12135A5D009192AB /* TransformationMappedDiscreteSet.cpp */, 931CFE6D12135A5D009192AB /* TransformationPermutationSampler.cpp */, 931CFE6E12135A5D009192AB /* TransformationUtils.cpp */, ); name = src; path = ../modules/domino/src; sourceTree = SOURCE_ROOT; }; 931CFE5A12135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFE5B12135A5D009192AB /* SConscript */, ); name = internal; path = ../modules/domino/src/internal; sourceTree = SOURCE_ROOT; }; 931CFE6F12135A5D009192AB /* test */ = { isa = PBXGroup; children = ( 931CFE7012135A5D009192AB /* annotation_enumeration.py */, 931CFE7112135A5D009192AB /* input */, 931CFE8F12135A5D009192AB /* my_helpers.py */, 931CFE9012135A5D009192AB /* my_optimizer.py */, 931CFE9112135A5D009192AB /* SConscript */, 931CFE9212135A5D009192AB /* test_cartesian_product_sampler.py */, 931CFE9312135A5D009192AB /* test_global_minimum_1.py */, 931CFE9412135A5D009192AB /* test_global_minimum_2.py */, 931CFE9512135A5D009192AB /* test_global_minimum_3.py */, 931CFE9612135A5D009192AB /* test_hierarchy_cartesian.py */, 931CFE9712135A5D009192AB /* test_permutation_sampler.py */, 931CFE9812135A5D009192AB /* test_restraint_evaluator_from_file.py */, 931CFE9912135A5D009192AB /* test_restraints.py */, 931CFE9A12135A5D009192AB /* test_restraints_from_file.py */, 931CFE9B12135A5D009192AB /* test_symmetry_sampler.py */, 931CFE9C12135A5D009192AB /* test_transformation_utils.py */, ); name = test; path = ../modules/domino/test; sourceTree = SOURCE_ROOT; }; 931CFE7112135A5D009192AB /* input */ = { isa = PBXGroup; children = ( 931CFE7212135A5D009192AB /* 1z5s.jt */, 931CFE7312135A5D009192AB /* 1z5s_A.pdb */, 931CFE7412135A5D009192AB /* 1z5s_B.pdb */, 931CFE7512135A5D009192AB /* 1z5s_C.pdb */, 931CFE7612135A5D009192AB /* 1z5s_D.pdb */, 931CFE7712135A5D009192AB /* comb_0_1.txt */, 931CFE7812135A5D009192AB /* comb_0_3.txt */, 931CFE7912135A5D009192AB /* comb_1_4.txt */, 931CFE7A12135A5D009192AB /* comb_2_6.txt */, 931CFE7B12135A5D009192AB /* comb_2_7.txt */, 931CFE7C12135A5D009192AB /* comb_3_4.txt */, 931CFE7D12135A5D009192AB /* comb_4_5.txt */, 931CFE7E12135A5D009192AB /* comb_4_6.txt */, 931CFE7F12135A5D009192AB /* comb_6_7.txt */, 931CFE8012135A5D009192AB /* hierarchy_jt.txt */, 931CFE8112135A5D009192AB /* permutation_test_jt.txt */, 931CFE8212135A5D009192AB /* prot1.pdb */, 931CFE8312135A5D009192AB /* prot2.pdb */, 931CFE8412135A5D009192AB /* prot3.pdb */, 931CFE8512135A5D009192AB /* simple_interaction2.xml */, 931CFE8612135A5D009192AB /* simple_jt1.txt */, 931CFE8712135A5D009192AB /* simple_jt1_restraints.txt */, 931CFE8812135A5D009192AB /* simple_jt1_restraints.xml */, 931CFE8912135A5D009192AB /* simple_jt2.txt */, 931CFE8A12135A5D009192AB /* simple_jt2_restraints.txt */, 931CFE8B12135A5D009192AB /* simple_jt3.txt */, 931CFE8C12135A5D009192AB /* symm1.pdb */, 931CFE8D12135A5D009192AB /* symm2.pdb */, 931CFE8E12135A5D009192AB /* symm3.pdb */, ); name = input; path = ../modules/domino/test/input; sourceTree = SOURCE_ROOT; }; 931CFE9D12135A5D009192AB /* domino2 */ = { isa = PBXGroup; children = ( 931CFE9E12135A5D009192AB /* bin */, 931CFEA012135A5D009192AB /* data */, 931CFEA212135A5D009192AB /* doc */, 931CFEA412135A5D009192AB /* examples */, 931CFEB512135A5D009192AB /* include */, 931CFEC912135A5E009192AB /* proof_of_concept.cpp */, 931CFECA12135A5E009192AB /* pyext */, 931CFED012135A5E009192AB /* README */, 931CFED112135A5E009192AB /* SConscript */, 931CFED212135A5E009192AB /* src */, 931CFEE312135A5E009192AB /* test */, ); name = domino2; path = ../modules/domino2; sourceTree = SOURCE_ROOT; }; 931CFE9E12135A5D009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFE9F12135A5D009192AB /* SConscript */, ); name = bin; path = ../modules/domino2/bin; sourceTree = SOURCE_ROOT; }; 931CFEA012135A5D009192AB /* data */ = { isa = PBXGroup; children = ( 931CFEA112135A5D009192AB /* SConscript */, ); name = data; path = ../modules/domino2/data; sourceTree = SOURCE_ROOT; }; 931CFEA212135A5D009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFEA312135A5D009192AB /* SConscript */, ); name = doc; path = ../modules/domino2/doc; sourceTree = SOURCE_ROOT; }; 931CFEA412135A5D009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFEA512135A5D009192AB /* domino_approach.py */, 931CFEA612135A5D009192AB /* domino_approach.readme */, 931CFEA712135A5D009192AB /* generated */, 931CFEAA12135A5D009192AB /* SConscript */, 931CFEAB12135A5D009192AB /* six_particles_optimization. */, 931CFEAC12135A5D009192AB /* six_particles_optimization.py */, 931CFEAD12135A5D009192AB /* six_particles_optimization.py.bak */, 931CFEAE12135A5D009192AB /* six_particles_optimization.readme */, 931CFEAF12135A5D009192AB /* spb_data.py */, 931CFEB012135A5D009192AB /* spb_data.readme */, 931CFEB112135A5D009192AB /* spb_fret.py */, 931CFEB212135A5D009192AB /* spb_fret.readme */, 931CFEB312135A5D009192AB /* spb_tools.py */, 931CFEB412135A5D009192AB /* spb_tools.readme */, ); name = examples; path = ../modules/domino2/examples; sourceTree = SOURCE_ROOT; }; 931CFEA712135A5D009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFEA812135A5D009192AB /* examples.dox */, 931CFEA912135A5D009192AB /* six_particles_optimization.py.html */, ); name = generated; path = ../modules/domino2/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFEB512135A5D009192AB /* include */ = { isa = PBXGroup; children = ( 931CFEB612135A5D009192AB /* analysis.h */, 931CFEB712135A5D009192AB /* BranchAndBoundSampler.h */, 931CFEB812135A5D009192AB /* DiscreteSampler.h */, 931CFEB912135A5D009192AB /* domino2_macros.h */, 931CFEBA12135A5D009192AB /* DominoSampler.h */, 931CFEBB12135A5D009192AB /* internal */, 931CFEC012135A5E009192AB /* particle_states.h */, 931CFEC112135A5E009192AB /* SConscript */, 931CFEC212135A5E009192AB /* Subset.h */, 931CFEC312135A5E009192AB /* subset_evaluators.h */, 931CFEC412135A5E009192AB /* subset_filters.h */, 931CFEC512135A5E009192AB /* subset_graphs.h */, 931CFEC612135A5E009192AB /* subset_states.h */, 931CFEC712135A5E009192AB /* SubsetState.h */, 931CFEC812135A5E009192AB /* utility.h */, ); name = include; path = ../modules/domino2/include; sourceTree = SOURCE_ROOT; }; 931CFEBB12135A5D009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFEBC12135A5D009192AB /* inference.h */, 931CFEBD12135A5D009192AB /* maximal_cliques.h */, 931CFEBE12135A5D009192AB /* restraint_evaluator.h */, 931CFEBF12135A5E009192AB /* SConscript */, ); name = internal; path = ../modules/domino2/include/internal; sourceTree = SOURCE_ROOT; }; 931CFECA12135A5E009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFECB12135A5E009192AB /* SConscript */, 931CFECC12135A5E009192AB /* src */, 931CFECF12135A5E009192AB /* swig.i-in */, ); name = pyext; path = ../modules/domino2/pyext; sourceTree = SOURCE_ROOT; }; 931CFECC12135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931CFECD12135A5E009192AB /* _interaction_graph.py */, 931CFECE12135A5E009192AB /* randomize.py */, ); name = src; path = ../modules/domino2/pyext/src; sourceTree = SOURCE_ROOT; }; 931CFED212135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931CFED312135A5E009192AB /* analysis.cpp */, 931CFED412135A5E009192AB /* BranchAndBoundSampler.cpp */, 931CFED512135A5E009192AB /* DiscreteSampler.cpp */, 931CFED612135A5E009192AB /* DominoSampler.cpp */, 931CFED712135A5E009192AB /* internal */, 931CFEDB12135A5E009192AB /* particle_states.cpp */, 931CFEDC12135A5E009192AB /* SConscript */, 931CFEDD12135A5E009192AB /* Subset.cpp */, 931CFEDE12135A5E009192AB /* subset_evaluators.cpp */, 931CFEDF12135A5E009192AB /* subset_filters.cpp */, 931CFEE012135A5E009192AB /* subset_graphs.cpp */, 931CFEE112135A5E009192AB /* subset_states.cpp */, 931CFEE212135A5E009192AB /* utility.cpp */, ); name = src; path = ../modules/domino2/src; sourceTree = SOURCE_ROOT; }; 931CFED712135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFED812135A5E009192AB /* inference.cpp */, 931CFED912135A5E009192AB /* restraint_evaluator.cpp */, 931CFEDA12135A5E009192AB /* SConscript */, ); name = internal; path = ../modules/domino2/src/internal; sourceTree = SOURCE_ROOT; }; 931CFEE312135A5E009192AB /* test */ = { isa = PBXGroup; children = ( 931CFEE412135A5E009192AB /* input */, 931CFEE612135A5E009192AB /* SConscript */, 931CFEE712135A5E009192AB /* test_bandb_sampler.py */, 931CFEE812135A5E009192AB /* test_caching_sampling.py */, 931CFEE912135A5E009192AB /* test_cluster.py */, 931CFEEA12135A5E009192AB /* test_default_subset_states.py */, 931CFEEB12135A5E009192AB /* test_default_subset_states_with_filtering.py */, 931CFEEC12135A5E009192AB /* test_interaction_graph.py */, 931CFEED12135A5E009192AB /* test_junction_tree.py */, 931CFEEE12135A5E009192AB /* test_optimize_model.py */, 931CFEEF12135A5E009192AB /* test_sampling.py */, 931CFEF012135A5E009192AB /* test_six_particle_like.py */, 931CFEF112135A5E009192AB /* test_six_particle_like.py.bak */, 931CFEF212135A5E009192AB /* test_static_container.py */, ); name = test; path = ../modules/domino2/test; sourceTree = SOURCE_ROOT; }; 931CFEE412135A5E009192AB /* input */ = { isa = PBXGroup; children = ( 931CFEE512135A5E009192AB /* small_protein.pdb */, ); name = input; path = ../modules/domino2/test/input; sourceTree = SOURCE_ROOT; }; 931CFEF312135A5E009192AB /* em */ = { isa = PBXGroup; children = ( 931CFEF412135A5E009192AB /* bin */, 931CFEF612135A5E009192AB /* data */, 931CFEF812135A5E009192AB /* doc */, 931CFEFC12135A5E009192AB /* examples */, 931CFF0E12135A5E009192AB /* include */, 931CFF2E12135A5E009192AB /* pyext */, 931CFF3112135A5E009192AB /* SConscript */, 931CFF3212135A5E009192AB /* src */, 931CFF4C12135A5E009192AB /* test */, ); name = em; path = ../modules/em; sourceTree = SOURCE_ROOT; }; 931CFEF412135A5E009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFEF512135A5E009192AB /* SConscript */, ); name = bin; path = ../modules/em/bin; sourceTree = SOURCE_ROOT; }; 931CFEF612135A5E009192AB /* data */ = { isa = PBXGroup; children = ( 931CFEF712135A5E009192AB /* SConscript */, ); name = data; path = ../modules/em/data; sourceTree = SOURCE_ROOT; }; 931CFEF812135A5E009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFEF912135A5E009192AB /* generated */, 931CFEFB12135A5E009192AB /* SConscript */, ); name = doc; path = ../modules/em/doc; sourceTree = SOURCE_ROOT; }; 931CFEF912135A5E009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFEFA12135A5E009192AB /* overview.dox */, ); name = generated; path = ../modules/em/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFEFC12135A5E009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFEFD12135A5E009192AB /* fit_input.mrc */, 931CFEFE12135A5E009192AB /* fit_restraint.py */, 931CFEFF12135A5E009192AB /* fit_restraint.readme */, 931CFF0012135A5E009192AB /* generate_density_map_of_fixed_dimension.py */, 931CFF0112135A5E009192AB /* generate_density_map_of_fixed_dimension.readme */, 931CFF0212135A5E009192AB /* generated */, 931CFF0712135A5E009192AB /* input.mrc */, 931CFF0812135A5E009192AB /* input.pdb */, 931CFF0912135A5E009192AB /* local_fitting.py */, 931CFF0A12135A5E009192AB /* local_fitting.readme */, 931CFF0B12135A5E009192AB /* pdb2density.py */, 931CFF0C12135A5E009192AB /* pdb2density.readme */, 931CFF0D12135A5E009192AB /* SConscript */, ); name = examples; path = ../modules/em/examples; sourceTree = SOURCE_ROOT; }; 931CFF0212135A5E009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFF0312135A5E009192AB /* examples.dox */, 931CFF0412135A5E009192AB /* fit_restraint.py.html */, 931CFF0512135A5E009192AB /* local_fitting.py.html */, 931CFF0612135A5E009192AB /* pdb2density.py.html */, ); name = generated; path = ../modules/em/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFF0E12135A5E009192AB /* include */ = { isa = PBXGroup; children = ( 931CFF0F12135A5E009192AB /* CoarseCC.h */, 931CFF1012135A5E009192AB /* CoarseCCatIntervals.h */, 931CFF1112135A5E009192AB /* CoarseConvolution.h */, 931CFF1212135A5E009192AB /* converters.h */, 931CFF1312135A5E009192AB /* def.h */, 931CFF1412135A5E009192AB /* DensityHeader.h */, 931CFF1512135A5E009192AB /* DensityMap.h */, 931CFF1612135A5E009192AB /* EMReaderWriter.h */, 931CFF1712135A5E009192AB /* envelope_penetration.h */, 931CFF1812135A5E009192AB /* exp.h */, 931CFF1912135A5E009192AB /* filters.h */, 931CFF1A12135A5E009192AB /* FitRestraint.h */, 931CFF1B12135A5E009192AB /* header_converters.h */, 931CFF1C12135A5E009192AB /* Image.h */, 931CFF1D12135A5E009192AB /* ImageHeader.h */, 931CFF1E12135A5E009192AB /* ImageReaderWriter.h */, 931CFF1F12135A5E009192AB /* internal */, 931CFF2112135A5E009192AB /* KernelParameters.h */, 931CFF2212135A5E009192AB /* MapReaderWriter.h */, 931CFF2312135A5E009192AB /* MRCReaderWriter.h */, 931CFF2412135A5E009192AB /* noise.h */, 931CFF2512135A5E009192AB /* rigid_fitting.h */, 931CFF2612135A5E009192AB /* RigidBodiesFitRestraint.h */, 931CFF2712135A5E009192AB /* SampledDensityMap.h */, 931CFF2812135A5E009192AB /* SConscript */, 931CFF2912135A5E009192AB /* SpiderHeader.h */, 931CFF2A12135A5E009192AB /* SpiderReaderWriter.h */, 931CFF2B12135A5E009192AB /* SurfaceShellDensityMap.h */, 931CFF2C12135A5E009192AB /* Voxel.h */, 931CFF2D12135A5E009192AB /* XplorReaderWriter.h */, ); name = include; path = ../modules/em/include; sourceTree = SOURCE_ROOT; }; 931CFF1F12135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFF2012135A5E009192AB /* SConscript */, ); name = internal; path = ../modules/em/include/internal; sourceTree = SOURCE_ROOT; }; 931CFF2E12135A5E009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFF2F12135A5E009192AB /* SConscript */, 931CFF3012135A5E009192AB /* swig.i-in */, ); name = pyext; path = ../modules/em/pyext; sourceTree = SOURCE_ROOT; }; 931CFF3212135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931CFF3312135A5E009192AB /* CoarseCC.cpp */, 931CFF3412135A5E009192AB /* CoarseCCatIntervals.cpp */, 931CFF3512135A5E009192AB /* CoarseConvolution.cpp */, 931CFF3612135A5E009192AB /* converters.cpp */, 931CFF3712135A5E009192AB /* DensityHeader.cpp */, 931CFF3812135A5E009192AB /* DensityMap.cpp */, 931CFF3912135A5E009192AB /* EMReaderWriter.cpp */, 931CFF3A12135A5E009192AB /* envelope_penetration.cpp */, 931CFF3B12135A5E009192AB /* filters.cpp */, 931CFF3C12135A5E009192AB /* FitRestraint.cpp */, 931CFF3D12135A5E009192AB /* header_converters.cpp */, 931CFF3E12135A5E009192AB /* Image.cpp */, 931CFF3F12135A5E009192AB /* ImageHeader.cpp */, 931CFF4012135A5E009192AB /* internal */, 931CFF4212135A5E009192AB /* KernelParameters.cpp */, 931CFF4312135A5E009192AB /* MRCReaderWriter.cpp */, 931CFF4412135A5E009192AB /* rigid_fitting.cpp */, 931CFF4512135A5E009192AB /* RigidBodiesFitRestraint.cpp */, 931CFF4612135A5E009192AB /* SampledDensityMap.cpp */, 931CFF4712135A5E009192AB /* SConscript */, 931CFF4812135A5E009192AB /* SpiderReaderWriter.cpp */, 931CFF4912135A5E009192AB /* SurfaceShellDensityMap.cpp */, 931CFF4A12135A5E009192AB /* Voxel.cpp */, 931CFF4B12135A5E009192AB /* XplorReaderWriter.cpp */, ); name = src; path = ../modules/em/src; sourceTree = SOURCE_ROOT; }; 931CFF4012135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( 931CFF4112135A5E009192AB /* SConscript */, ); name = internal; path = ../modules/em/src/internal; sourceTree = SOURCE_ROOT; }; 931CFF4C12135A5E009192AB /* test */ = { isa = PBXGroup; children = ( 931CFF4D12135A5E009192AB /* atoms_provider */, 931CFF4E12135A5E009192AB /* broken_test_fitting_of_rigid_bodies.py */, 931CFF4F12135A5E009192AB /* input */, 931CFF6A12135A5E009192AB /* keren_test.py */, 931CFF6B12135A5E009192AB /* SConscript */, 931CFF6C12135A5E009192AB /* test_add_map2map */, 931CFF6E12135A5E009192AB /* test_bounding_box.py */, 931CFF6F12135A5E009192AB /* test_calc_cc */, 931CFF7212135A5E009192AB /* test_coverters.py */, 931CFF7312135A5E009192AB /* test_density2particles.py */, 931CFF7412135A5E009192AB /* test_derivs.py */, 931CFF7512135A5E009192AB /* test_em_fit.py */, 931CFF7612135A5E009192AB /* test_fitting_grid_search_pdb.py */, 931CFF7712135A5E009192AB /* test_get_density.py */, 931CFF7812135A5E009192AB /* test_kernel_parameters.py */, 931CFF7912135A5E009192AB /* test_map_header.py */, 931CFF7A12135A5E009192AB /* test_module.py */, 931CFF7B12135A5E009192AB /* test_origin_spacing.py */, 931CFF7C12135A5E009192AB /* test_pad_margin.py */, 931CFF7D12135A5E009192AB /* test_protein_fit_at_different_resolutions.py */, 931CFF7E12135A5E009192AB /* test_read_write_maps */, 931CFF8012135A5E009192AB /* test_refcount.py */, 931CFF8112135A5E009192AB /* test_resample.py */, 931CFF8212135A5E009192AB /* test_resample_by_rigid_bodies.py */, 931CFF8312135A5E009192AB /* test_rigid_cc_score_by_grid_rotation.py */, 931CFF8412135A5E009192AB /* test_rigid_fitting_by_grid_rotation.py */, 931CFF8512135A5E009192AB /* test_sample_particles */, 931CFF8712135A5E009192AB /* test_sample_particles.py */, 931CFF8812135A5E009192AB /* test_surface */, 931CFF8B12135A5E009192AB /* test_surface_sample_particles.py */, 931CFF8C12135A5E009192AB /* test_surface_sample_protein.py */, 931CFF8D12135A5E009192AB /* test_transform.py */, 931CFF8E12135A5E009192AB /* test_volumes_and_images.py */, ); name = test; path = ../modules/em/test; sourceTree = SOURCE_ROOT; }; 931CFF4D12135A5E009192AB /* atoms_provider */ = { isa = PBXGroup; children = ( ); name = atoms_provider; path = ../modules/em/test/atoms_provider; sourceTree = SOURCE_ROOT; }; 931CFF4F12135A5E009192AB /* input */ = { isa = PBXGroup; children = ( 931CFF5012135A5E009192AB /* 1ab4A02.pdb */, 931CFF5112135A5E009192AB /* 1arsA01.pdb */, 931CFF5212135A5E009192AB /* 1atiB01.pdb */, 931CFF5312135A5E009192AB /* 1f7dA00.pdb */, 931CFF5412135A5E009192AB /* 1f7dA00_8.mrc */, 931CFF5512135A5E009192AB /* 1tdx.pdb */, 931CFF5612135A5E009192AB /* 1tdx_sampled.mrc */, 931CFF5712135A5E009192AB /* 1z5s.mrc */, 931CFF5812135A5E009192AB /* 1z5s.pdb */, 931CFF5912135A5E009192AB /* 1z5s_10.imp.mrc */, 931CFF5A12135A5E009192AB /* 1z5s_10.mrc */, 931CFF5B12135A5E009192AB /* 1z5s_15.imp.mrc */, 931CFF5C12135A5E009192AB /* 1z5s_20.imp.mrc */, 931CFF5D12135A5E009192AB /* 1z5s_5.imp.mrc */, 931CFF5E12135A5E009192AB /* 1z5s_A.pdb */, 931CFF5F12135A5E009192AB /* 1z5s_C.pdb */, 931CFF6012135A5E009192AB /* 1z5s_C_wrong.pdb */, 931CFF6112135A5E009192AB /* cube.em */, 931CFF6212135A5E009192AB /* d1q3sa1.pdb */, 931CFF6312135A5E009192AB /* flipY-nup84-0.spi */, 931CFF6412135A5E009192AB /* image.xmp */, 931CFF6512135A5E009192AB /* in.em */, 931CFF6612135A5E009192AB /* in.mrc */, 931CFF6712135A5E009192AB /* input1.pdb */, 931CFF6812135A5E009192AB /* media_mon_iter3.xmp */, 931CFF6912135A5E009192AB /* three_particles_in.em */, ); name = input; path = ../modules/em/test/input; sourceTree = SOURCE_ROOT; }; 931CFF6C12135A5E009192AB /* test_add_map2map */ = { isa = PBXGroup; children = ( 931CFF6D12135A5E009192AB /* test_add_map2map.py */, ); name = test_add_map2map; path = ../modules/em/test/test_add_map2map; sourceTree = SOURCE_ROOT; }; 931CFF6F12135A5E009192AB /* test_calc_cc */ = { isa = PBXGroup; children = ( 931CFF7012135A5E009192AB /* test_calc_cc.py */, 931CFF7112135A5E009192AB /* test_correlation.py */, ); name = test_calc_cc; path = ../modules/em/test/test_calc_cc; sourceTree = SOURCE_ROOT; }; 931CFF7E12135A5E009192AB /* test_read_write_maps */ = { isa = PBXGroup; children = ( 931CFF7F12135A5E009192AB /* test_read_write_map.py */, ); name = test_read_write_maps; path = ../modules/em/test/test_read_write_maps; sourceTree = SOURCE_ROOT; }; 931CFF8512135A5E009192AB /* test_sample_particles */ = { isa = PBXGroup; children = ( 931CFF8612135A5E009192AB /* test_sample_particles.py */, ); name = test_sample_particles; path = ../modules/em/test/test_sample_particles; sourceTree = SOURCE_ROOT; }; 931CFF8812135A5E009192AB /* test_surface */ = { isa = PBXGroup; children = ( 931CFF8912135A5E009192AB /* test_geo_score.py */, 931CFF8A12135A5E009192AB /* test_pad.py */, ); name = test_surface; path = ../modules/em/test/test_surface; sourceTree = SOURCE_ROOT; }; 931CFF8F12135A5E009192AB /* example */ = { isa = PBXGroup; children = ( 931CFF9012135A5E009192AB /* bin */, 931CFF9412135A5E009192AB /* data */, 931CFF9612135A5E009192AB /* doc */, 931CFF9A12135A5E009192AB /* examples */, 931CFFA512135A5E009192AB /* include */, 931CFFAF12135A5E009192AB /* pyext */, 931CFFB412135A5E009192AB /* README */, 931CFFB512135A5E009192AB /* SConscript */, 931CFFB612135A5E009192AB /* src */, 931CFFBE12135A5E009192AB /* test */, ); name = example; path = ../modules/example; sourceTree = SOURCE_ROOT; }; 931CFF9012135A5E009192AB /* bin */ = { isa = PBXGroup; children = ( 931CFF9112135A5E009192AB /* examples_program */, 931CFF9212135A5E009192AB /* examples_program.cpp */, 931CFF9312135A5E009192AB /* SConscript */, ); name = bin; path = ../modules/example/bin; sourceTree = SOURCE_ROOT; }; 931CFF9412135A5E009192AB /* data */ = { isa = PBXGroup; children = ( 931CFF9512135A5E009192AB /* SConscript */, ); name = data; path = ../modules/example/data; sourceTree = SOURCE_ROOT; }; 931CFF9612135A5E009192AB /* doc */ = { isa = PBXGroup; children = ( 931CFF9712135A5E009192AB /* generated */, 931CFF9912135A5E009192AB /* SConscript */, ); name = doc; path = ../modules/example/doc; sourceTree = SOURCE_ROOT; }; 931CFF9712135A5E009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFF9812135A5E009192AB /* overview.dox */, ); name = generated; path = ../modules/example/doc/generated; sourceTree = SOURCE_ROOT; }; 931CFF9A12135A5E009192AB /* examples */ = { isa = PBXGroup; children = ( 931CFF9B12135A5E009192AB /* generated */, 931CFF9E12135A5E009192AB /* range_restriction.py */, 931CFF9F12135A5E009192AB /* range_restriction.readme */, 931CFFA012135A5E009192AB /* SConscript */, 931CFFA112135A5E009192AB /* using_imp.py */, 931CFFA212135A5E009192AB /* using_imp.readme */, 931CFFA312135A5E009192AB /* using_imp_tools.py */, 931CFFA412135A5E009192AB /* using_imp_tools.readme */, ); name = examples; path = ../modules/example/examples; sourceTree = SOURCE_ROOT; }; 931CFF9B12135A5E009192AB /* generated */ = { isa = PBXGroup; children = ( 931CFF9C12135A5E009192AB /* examples.dox */, 931CFF9D12135A5E009192AB /* range_restriction.py.html */, ); name = generated; path = ../modules/example/examples/generated; sourceTree = SOURCE_ROOT; }; 931CFFA512135A5E009192AB /* include */ = { isa = PBXGroup; children = ( 931CFFA612135A5E009192AB /* ExampleComplexRestraint.h */, 931CFFA712135A5E009192AB /* ExampleDecorator.h */, 931CFFA812135A5E009192AB /* ExampleRefCounted.h */, 931CFFA912135A5E009192AB /* ExampleRestraint.h */, 931CFFAA12135A5E009192AB /* ExampleSingletonModifier.h */, 931CFFAB12135A5E009192AB /* ExampleTemplateClass.h */, 931CFFAC12135A5E009192AB /* ExampleUnaryFunction.h */, 931CFFAD12135A5E009192AB /* internal */, 931CFFAE12135A5E009192AB /* SConscript */, ); name = include; path = ../modules/example/include; sourceTree = SOURCE_ROOT; }; 931CFFAD12135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/example/include/internal; sourceTree = SOURCE_ROOT; }; 931CFFAF12135A5E009192AB /* pyext */ = { isa = PBXGroup; children = ( 931CFFB012135A5E009192AB /* SConscript */, 931CFFB112135A5E009192AB /* src */, 931CFFB312135A5E009192AB /* swig.i-in */, ); name = pyext; path = ../modules/example/pyext; sourceTree = SOURCE_ROOT; }; 931CFFB112135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931CFFB212135A5E009192AB /* randomize.py */, ); name = src; path = ../modules/example/pyext/src; sourceTree = SOURCE_ROOT; }; 931CFFB612135A5E009192AB /* src */ = { isa = PBXGroup; children = ( 931CFFB712135A5E009192AB /* ExampleComplexRestraint.cpp */, 931CFFB812135A5E009192AB /* ExampleDecorator.cpp */, 931CFFB912135A5E009192AB /* ExampleRefCounted.cpp */, 931CFFBA12135A5E009192AB /* ExampleRestraint.cpp */, 931CFFBB12135A5E009192AB /* ExampleSingletonModifier.cpp */, 931CFFBC12135A5E009192AB /* internal */, 931CFFBD12135A5E009192AB /* SConscript */, ); name = src; path = ../modules/example/src; sourceTree = SOURCE_ROOT; }; 931CFFBC12135A5E009192AB /* internal */ = { isa = PBXGroup; children = ( ); name = internal; path = ../modules/example/src/internal; sourceTree = SOURCE_ROOT; }; 931CFFBE12135A5E009192AB /* test */ = { isa = PBXGroup; children = ( 931CFFBF12135A5E009192AB /* SConscript */, 931CFFC012135A5E009192AB /* test_modifier.py */, ); name = test; path = ../modules/example/test; sourceTree = SOURCE_ROOT; }; 931CFFC112135A5E009192AB /* gsl */ = { isa = PBXGroup; children = ( 931CFFC212135A5E009192AB /* bin */, 931CFFC412135A5E009192AB /* data */, 931CFFC612135A5E009192AB /* doc */, 931CFFCA12135A5E009192AB /* examples */, 931CFFD112135A5E009192AB /* include */, 931CFFD912135A5E009192AB /* pyext */, 931CFFDD12135A5E009192AB /* README */, 931CFFDE12135A5E009192AB /* SConscript */, 931CFFDF12135A5E009192AB /* src */, 931CFFE712135A5E009192AB /* test */, ); name = gsl; path = ../modules/gsl; sourceTree = SOURCE_ROOT; }; 931CFFC212135A5E009192AB /* bin */ = { isa = PBXGroup; 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