/dports/science/py-rmf/rmf-1.3.1/swig/ |
H A D | RMF.keys.i | 3 %template(IntKey) RMF::ID<RMF::IntTag >; 4 %template(FloatKey) RMF::ID<RMF::FloatTag>; 5 %template(StringKey) RMF::ID<RMF::StringTag>; 6 %template(Vector3Key) RMF::ID<RMF::Vector3Tag >; 7 %template(Vector4Key) RMF::ID<RMF::Vector4Tag>; 9 %template(IntsKey) RMF::ID<RMF::IntsTag >; 10 %template(FloatsKey) RMF::ID<RMF::FloatsTag>; 11 %template(StringsKey) RMF::ID<RMF::StringsTag>; 12 %template(Vector3sKey) RMF::ID<RMF::Vector3sTag >; 13 %template(Vector4sKey) RMF::ID<RMF::Vector4sTag>; [all …]
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H A D | RMF_HDF5.i | 72 namespace RMF { 78 namespace RMF { 94 %template(Ucname##DataSetAttributes1D) RMF::HDF5::MutableAttributes< RMF::HDF5::ConstDataSetD<RMF::… 95 %template(Ucname##DataSetAttributes2D) RMF::HDF5::MutableAttributes< RMF::HDF5::ConstDataSetD<RMF::… 96 %template(Ucname##DataSetAttributes3D) RMF::HDF5::MutableAttributes< RMF::HDF5::ConstDataSetD<RMF::… 100 %template(Ucname##DataSet1D) RMF::HDF5::DataSetD<RMF::HDF5::Ucname##Traits, 1>; 101 %template(Ucname##DataSet2D) RMF::HDF5::DataSetD<RMF::HDF5::Ucname##Traits, 2>; 102 %template(Ucname##DataSet3D) RMF::HDF5::DataSetD<RMF::HDF5::Ucname##Traits, 3>; 111 namespace RMF { 120 %template(_IntsTraitsBase) RMF::HDF5::SimplePluralTraits<RMF::HDF5::IntTraits>; [all …]
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H A D | RMF.i | 8 out << RMF::Showable(*self); in __str__() 13 out << RMF::Showable(*self); in __repr__() 58 %template(FrameID) RMF::ID<RMF::FrameTag>; 59 %template(NodeID) RMF::ID<RMF::NodeTag>; 60 %template(Category) RMF::ID<RMF::CategoryTag>; 61 %template(FrameIDs) std::vector<RMF::ID<RMF::FrameTag> >; 62 %template(NodeIDs) std::vector<RMF::ID<RMF::NodeTag> >; 63 %template(Categories) std::vector<RMF::ID<RMF::CategoryTag> >; 69 typedef RMF::Vector<3U> Vector3; 107 namespace RMF { [all …]
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H A D | RMF.nullable.i | 8 RMF_SWIG_SHOWABLE(RMF, Nullable); 12 %template(_NullableInt) RMF::Nullable<RMF::Int>; 13 %template(_NullableFloat) RMF::Nullable<RMF::Float>; 14 %template(_NullableString) RMF::Nullable<RMF::String>; 15 %template(_NullableVector3) RMF::Nullable<RMF::Vector<3U> >; 16 %template(_NullableVector4) RMF::Nullable<RMF::Vector<4U> >; 17 %template(_NullableInts) RMF::Nullable<RMF::Ints>; 18 %template(_NullableFloats) RMF::Nullable<RMF::Floats>; 19 %template(_NullableStrings) RMF::Nullable<RMF::Strings>; 20 %template(_NullableVector3s) RMF::Nullable<std::vector<RMF::Vector<3U> > >;
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/dports/science/rmf/rmf-1.3.1/swig/ |
H A D | RMF.keys.i | 3 %template(IntKey) RMF::ID<RMF::IntTag >; 4 %template(FloatKey) RMF::ID<RMF::FloatTag>; 5 %template(StringKey) RMF::ID<RMF::StringTag>; 6 %template(Vector3Key) RMF::ID<RMF::Vector3Tag >; 7 %template(Vector4Key) RMF::ID<RMF::Vector4Tag>; 9 %template(IntsKey) RMF::ID<RMF::IntsTag >; 10 %template(FloatsKey) RMF::ID<RMF::FloatsTag>; 11 %template(StringsKey) RMF::ID<RMF::StringsTag>; 12 %template(Vector3sKey) RMF::ID<RMF::Vector3sTag >; 13 %template(Vector4sKey) RMF::ID<RMF::Vector4sTag>; [all …]
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H A D | RMF_HDF5.i | 72 namespace RMF { 78 namespace RMF { 94 %template(Ucname##DataSetAttributes1D) RMF::HDF5::MutableAttributes< RMF::HDF5::ConstDataSetD<RMF::… 95 %template(Ucname##DataSetAttributes2D) RMF::HDF5::MutableAttributes< RMF::HDF5::ConstDataSetD<RMF::… 96 %template(Ucname##DataSetAttributes3D) RMF::HDF5::MutableAttributes< RMF::HDF5::ConstDataSetD<RMF::… 100 %template(Ucname##DataSet1D) RMF::HDF5::DataSetD<RMF::HDF5::Ucname##Traits, 1>; 101 %template(Ucname##DataSet2D) RMF::HDF5::DataSetD<RMF::HDF5::Ucname##Traits, 2>; 102 %template(Ucname##DataSet3D) RMF::HDF5::DataSetD<RMF::HDF5::Ucname##Traits, 3>; 111 namespace RMF { 120 %template(_IntsTraitsBase) RMF::HDF5::SimplePluralTraits<RMF::HDF5::IntTraits>; [all …]
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H A D | RMF.i | 8 out << RMF::Showable(*self); in __str__() 13 out << RMF::Showable(*self); in __repr__() 58 %template(FrameID) RMF::ID<RMF::FrameTag>; 59 %template(NodeID) RMF::ID<RMF::NodeTag>; 60 %template(Category) RMF::ID<RMF::CategoryTag>; 61 %template(FrameIDs) std::vector<RMF::ID<RMF::FrameTag> >; 62 %template(NodeIDs) std::vector<RMF::ID<RMF::NodeTag> >; 63 %template(Categories) std::vector<RMF::ID<RMF::CategoryTag> >; 69 typedef RMF::Vector<3U> Vector3; 107 namespace RMF { [all …]
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H A D | RMF.nullable.i | 8 RMF_SWIG_SHOWABLE(RMF, Nullable); 12 %template(_NullableInt) RMF::Nullable<RMF::Int>; 13 %template(_NullableFloat) RMF::Nullable<RMF::Float>; 14 %template(_NullableString) RMF::Nullable<RMF::String>; 15 %template(_NullableVector3) RMF::Nullable<RMF::Vector<3U> >; 16 %template(_NullableVector4) RMF::Nullable<RMF::Vector<4U> >; 17 %template(_NullableInts) RMF::Nullable<RMF::Ints>; 18 %template(_NullableFloats) RMF::Nullable<RMF::Floats>; 19 %template(_NullableStrings) RMF::Nullable<RMF::Strings>; 20 %template(_NullableVector3s) RMF::Nullable<std::vector<RMF::Vector<3U> > >;
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/dports/science/py-rmf/rmf-1.3.1/test/ |
H A D | test_file_level.py | 3 import RMF 16 for suffix in RMF.suffixes: 17 f = RMF.create_rmf_file( 23 f.add_frame("0", RMF.FRAME) 30 for suffix in RMF.suffixes: 32 f = RMF.create_rmf_file(path) 40 f.add_frame("1", RMF.FRAME) 62 for suffix in RMF.suffixes: 79 for suffix in RMF.suffixes: 80 RMF.set_log_level("trace") [all …]
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H A D | test_children.py | 2 import RMF 10 f = RMF.create_rmf_file(name) 17 self.assertIsInstance(ch, RMF.NodeHandle) 41 RMF.REPRESENTATION) 46 f = RMF.create_rmf_file(name) 61 outr = RMF.create_rmf_file(name2) 62 RMF.clone_file_info(inr, outr) 63 RMF.clone_hierarchy(inr, outr) 64 RMF.clone_static_frame(inr, outr) 65 inr.set_current_frame(RMF.FrameID(0)) [all …]
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H A D | test_low_level.py | 3 import RMF 7 I1 = RMF.HDF5.DataSetIndex1D 8 I2 = RMF.HDF5.DataSetIndex2D 9 I3 = RMF.HDF5.DataSetIndex3D 45 f = RMF.HDF5.create_file( 60 f = RMF.HDF5.create_file( 73 f = RMF.HDF5.open_file(RMF._get_temporary_file_path("test.hdf5")) 88 f = RMF.HDF5.create_file( 212 f = RMF.HDF5.open_file( 244 f = RMF.HDF5.open_file( [all …]
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/dports/science/rmf/rmf-1.3.1/test/ |
H A D | test_file_level.py | 3 import RMF 16 for suffix in RMF.suffixes: 17 f = RMF.create_rmf_file( 23 f.add_frame("0", RMF.FRAME) 30 for suffix in RMF.suffixes: 32 f = RMF.create_rmf_file(path) 40 f.add_frame("1", RMF.FRAME) 62 for suffix in RMF.suffixes: 79 for suffix in RMF.suffixes: 80 RMF.set_log_level("trace") [all …]
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H A D | test_children.py | 2 import RMF 10 f = RMF.create_rmf_file(name) 17 self.assertIsInstance(ch, RMF.NodeHandle) 41 RMF.REPRESENTATION) 46 f = RMF.create_rmf_file(name) 61 outr = RMF.create_rmf_file(name2) 62 RMF.clone_file_info(inr, outr) 63 RMF.clone_hierarchy(inr, outr) 64 RMF.clone_static_frame(inr, outr) 65 inr.set_current_frame(RMF.FrameID(0)) [all …]
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/dports/science/py-rmf/rmf-1.3.1/benchmark/ |
H A D | benchmark_rmf.cpp | 62 std::size_t create_residue(RMF::NodeHandle nh, RMF::decorator::AtomFactory af, in create_residue() 66 RMF::NodeHandle child = nh.add_child("CA", RMF::REPRESENTATION); in create_residue() 81 RMF::NodeHandle child = nh.add_child(oss.str(), RMF::REPRESENTATION); in create_chain() 99 RMF::NodeHandle child = n.add_child(oss.str(), RMF::REPRESENTATION); in create_hierarchy() 166 double load(RMF::FileConstHandle file, const RMF::NodeIDs& nodes) { in load() 183 RMF::NodeIDs atoms; in benchmark_create() 209 RMF::NodeIDs nodes; in benchmark_load() 244 RMF::FileHandle fh = RMF::create_rmf_file(name); in main() 261 RMF::FileHandle fh = RMF::create_rmf_file(name); in main() 274 RMF::FileHandle fh = RMF::create_rmf_buffer(buffer); in main() [all …]
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/dports/science/rmf/rmf-1.3.1/benchmark/ |
H A D | benchmark_rmf.cpp | 62 std::size_t create_residue(RMF::NodeHandle nh, RMF::decorator::AtomFactory af, in create_residue() 66 RMF::NodeHandle child = nh.add_child("CA", RMF::REPRESENTATION); in create_residue() 81 RMF::NodeHandle child = nh.add_child(oss.str(), RMF::REPRESENTATION); in create_chain() 99 RMF::NodeHandle child = n.add_child(oss.str(), RMF::REPRESENTATION); in create_hierarchy() 166 double load(RMF::FileConstHandle file, const RMF::NodeIDs& nodes) { in load() 183 RMF::NodeIDs atoms; in benchmark_create() 209 RMF::NodeIDs nodes; in benchmark_load() 244 RMF::FileHandle fh = RMF::create_rmf_file(name); in main() 261 RMF::FileHandle fh = RMF::create_rmf_file(name); in main() 274 RMF::FileHandle fh = RMF::create_rmf_buffer(buffer); in main() [all …]
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/dports/science/py-rmf/rmf-1.3.1/bin/ |
H A D | rmf_interpolate.cpp | 55 RMF::Vector3s result(3, RMF::Vector3()); \ in main() 72 RMF::decorator::BallFactory bcf0, RMF::decorator::BallFactory bcf1, in main() 73 RMF::decorator::BallFactory bf, RMF::decorator::ReferenceFrameFactory rfcf0, in main() 76 RMF::decorator::CylinderFactory ccf0, RMF::decorator::CylinderFactory ccf1, in main() 77 RMF::decorator::CylinderFactory cf, RMF::NodeConstHandle input0, in main() 78 RMF::NodeConstHandle input1, RMF::NodeHandle output) { in main() 160 RMF::FileConstHandle irh0 = RMF::open_rmf_file_read_only(input); 161 RMF::FileConstHandle irh1 = RMF::open_rmf_file_read_only(input); 162 RMF::FileHandle orh = RMF::create_rmf_file(output); 166 RMF::clone_hierarchy(irh0, orh); [all …]
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/dports/science/rmf/rmf-1.3.1/bin/ |
H A D | rmf_interpolate.cpp | 55 RMF::Vector3s result(3, RMF::Vector3()); \ 72 RMF::decorator::BallFactory bcf0, RMF::decorator::BallFactory bcf1, in interpolate_frame() 73 RMF::decorator::BallFactory bf, RMF::decorator::ReferenceFrameFactory rfcf0, in interpolate_frame() 76 RMF::decorator::CylinderFactory ccf0, RMF::decorator::CylinderFactory ccf1, in interpolate_frame() 77 RMF::decorator::CylinderFactory cf, RMF::NodeConstHandle input0, in interpolate_frame() 78 RMF::NodeConstHandle input1, RMF::NodeHandle output) { in interpolate_frame() 160 RMF::FileConstHandle irh0 = RMF::open_rmf_file_read_only(input); in main() 161 RMF::FileConstHandle irh1 = RMF::open_rmf_file_read_only(input); in main() 162 RMF::FileHandle orh = RMF::create_rmf_file(output); in main() 166 RMF::clone_hierarchy(irh0, orh); in main() [all …]
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/dports/science/py-rmf/rmf-1.3.1/examples/ |
H A D | make_reference_frames.py | 5 import RMF 9 fh = RMF.create_rmf_file(file_name) 10 fh.add_frame("root", RMF.FRAME) 15 segment_factory = RMF.SegmentFactory(fh) 16 color_factory = RMF.ColoredFactory(fh) 23 x = origin.add_child("x", RMF.GEOMETRY) 25 sx.set_coordinates_list([RMF.Vector3(0, 0, 0), RMF.Vector3(1, 0, 0)]) 27 cx.set_rgb_color(RMF.Vector3(1, 0, 0)) 30 sy.set_coordinates_list([RMF.Vector3(0, 0, 0), RMF.Vector3(0, 1, 0)]) 32 cy.set_rgb_color(RMF.Vector3(0, 1, 0)) [all …]
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H A D | alternatives.py | 9 import RMF 14 f = RMF.create_rmf_file(tfn) 15 f.add_frame("frame", RMF.FRAME) 20 pf = RMF.ParticleFactory(f) 21 gpf = RMF.GaussianParticleFactory(f) 22 rff = RMF.ReferenceFrameFactory(f) 54 center = RMF.Vector3( 73 af = RMF.AlternativesFactory(f) 80 RMF.show_hierarchy(n) 82 print("particles", RMF.get_resolutions(n, RMF.PARTICLE)) [all …]
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/dports/science/rmf/rmf-1.3.1/examples/ |
H A D | make_reference_frames.py | 5 import RMF 9 fh = RMF.create_rmf_file(file_name) 10 fh.add_frame("root", RMF.FRAME) 15 segment_factory = RMF.SegmentFactory(fh) 16 color_factory = RMF.ColoredFactory(fh) 23 x = origin.add_child("x", RMF.GEOMETRY) 25 sx.set_coordinates_list([RMF.Vector3(0, 0, 0), RMF.Vector3(1, 0, 0)]) 27 cx.set_rgb_color(RMF.Vector3(1, 0, 0)) 30 sy.set_coordinates_list([RMF.Vector3(0, 0, 0), RMF.Vector3(0, 1, 0)]) 32 cy.set_rgb_color(RMF.Vector3(0, 1, 0)) [all …]
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H A D | alternatives.py | 9 import RMF 14 f = RMF.create_rmf_file(tfn) 15 f.add_frame("frame", RMF.FRAME) 20 pf = RMF.ParticleFactory(f) 21 gpf = RMF.GaussianParticleFactory(f) 22 rff = RMF.ReferenceFrameFactory(f) 54 center = RMF.Vector3( 73 af = RMF.AlternativesFactory(f) 80 RMF.show_hierarchy(n) 82 print("particles", RMF.get_resolutions(n, RMF.PARTICLE)) [all …]
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/dports/science/py-rmf/rmf-1.3.1/src/backend/avro/ |
H A D | encode_decode.h | 445 RMF::internal::TypeData<RMF::Vector4sTraits> empty; in test_compare() 468 RMF::avro2::Skip<RMF::internal::TypeData<RMF::IntTraits> > int_data; in test_compare() 470 RMF::avro2::Skip<RMF::internal::TypeData<RMF::FloatTraits> > float_data; in test_compare() 472 RMF::avro2::Skip<RMF::internal::TypeData<RMF::StringTraits> > string_data; in test_compare() 474 RMF::avro2::Skip<RMF::internal::TypeData<RMF::Vector3Traits> > vector3_data; in test_compare() 476 RMF::avro2::Skip<RMF::internal::TypeData<RMF::Vector4Traits> > vector4_data; in test_compare() 478 RMF::avro2::Skip<RMF::internal::TypeData<RMF::IntsTraits> > ints_data; in test_compare() 480 RMF::avro2::Skip<RMF::internal::TypeData<RMF::FloatsTraits> > floats_data; in test_compare() 482 RMF::avro2::Skip<RMF::internal::TypeData<RMF::StringsTraits> > strings_data; in test_compare() 484 RMF::avro2::Skip<RMF::internal::TypeData<RMF::Vector3sTraits> > in test_compare() [all …]
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/dports/science/rmf/rmf-1.3.1/src/backend/avro/ |
H A D | encode_decode.h | 445 RMF::internal::TypeData<RMF::Vector4sTraits> empty; 468 RMF::avro2::Skip<RMF::internal::TypeData<RMF::IntTraits> > int_data; 470 RMF::avro2::Skip<RMF::internal::TypeData<RMF::FloatTraits> > float_data; 472 RMF::avro2::Skip<RMF::internal::TypeData<RMF::StringTraits> > string_data; 474 RMF::avro2::Skip<RMF::internal::TypeData<RMF::Vector3Traits> > vector3_data; 476 RMF::avro2::Skip<RMF::internal::TypeData<RMF::Vector4Traits> > vector4_data; 478 RMF::avro2::Skip<RMF::internal::TypeData<RMF::IntsTraits> > ints_data; 480 RMF::avro2::Skip<RMF::internal::TypeData<RMF::FloatsTraits> > floats_data; 482 RMF::avro2::Skip<RMF::internal::TypeData<RMF::StringsTraits> > strings_data; 484 RMF::avro2::Skip<RMF::internal::TypeData<RMF::Vector3sTraits> > [all …]
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/dports/science/py-rmf/rmf-1.3.1/plugins/vmd/ |
H A D | Data.h | 37 RMF::FileConstHandle file_; 38 RMF::decorator::AtomFactory af_; 40 RMF::decorator::ChainFactory chf_; 43 RMF::decorator::BallFactory bf_; 46 RMF::decorator::BondFactory bdf_; 47 RMF::decorator::ScoreFactory scf_; 49 RMF::decorator::DomainFactory df_; 51 RMF::decorator::CopyFactory cpf_; 52 RMF::decorator::TypedFactory tf_; 62 RMF::NodeID node_id; [all …]
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/dports/science/rmf/rmf-1.3.1/plugins/vmd/ |
H A D | Data.h | 37 RMF::FileConstHandle file_; 38 RMF::decorator::AtomFactory af_; 40 RMF::decorator::ChainFactory chf_; 43 RMF::decorator::BallFactory bf_; 46 RMF::decorator::BondFactory bdf_; 47 RMF::decorator::ScoreFactory scf_; 49 RMF::decorator::DomainFactory df_; 51 RMF::decorator::CopyFactory cpf_; 52 RMF::decorator::TypedFactory tf_; 62 RMF::NodeID node_id; [all …]
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