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/dports/science/py-rmf/rmf-1.3.1/swig/
H A DRMF.keys.i3 %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>;
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H A DRMF_HDF5.i72 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>;
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H A DRMF.i8 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 {
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H A DRMF.nullable.i8 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> > >;
/dports/science/rmf/rmf-1.3.1/swig/
H A DRMF.keys.i3 %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>;
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H A DRMF_HDF5.i72 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>;
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H A DRMF.i8 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 {
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H A DRMF.nullable.i8 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> > >;
/dports/science/py-rmf/rmf-1.3.1/test/
H A Dtest_file_level.py3 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")
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H A Dtest_children.py2 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))
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H A Dtest_low_level.py3 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(
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/dports/science/rmf/rmf-1.3.1/test/
H A Dtest_file_level.py3 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")
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H A Dtest_children.py2 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))
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/dports/science/py-rmf/rmf-1.3.1/benchmark/
H A Dbenchmark_rmf.cpp62 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()
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/dports/science/rmf/rmf-1.3.1/benchmark/
H A Dbenchmark_rmf.cpp62 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()
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/dports/science/py-rmf/rmf-1.3.1/bin/
H A Drmf_interpolate.cpp55 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);
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/dports/science/rmf/rmf-1.3.1/bin/
H A Drmf_interpolate.cpp55 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()
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/dports/science/py-rmf/rmf-1.3.1/examples/
H A Dmake_reference_frames.py5 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))
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H A Dalternatives.py9 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))
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/dports/science/rmf/rmf-1.3.1/examples/
H A Dmake_reference_frames.py5 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))
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H A Dalternatives.py9 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))
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/dports/science/py-rmf/rmf-1.3.1/src/backend/avro/
H A Dencode_decode.h445 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()
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/dports/science/rmf/rmf-1.3.1/src/backend/avro/
H A Dencode_decode.h445 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> >
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/dports/science/py-rmf/rmf-1.3.1/plugins/vmd/
H A DData.h37 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;
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/dports/science/rmf/rmf-1.3.1/plugins/vmd/
H A DData.h37 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;
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