pytraj
Python interface of cpptraj
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최종 버전 다운로드 (.zip)- python-package-conda.yml
- __init__.py
- base_setup.py
- build_config.py
- extension_builder.py
- platform_utils.py
- setup.py
- cpptraj.md
- pytraj.rst
- build_all.sh
- run_docker_build_conda_linux.sh
- run_docker_build_libcpptraj_linux.sh
- run_docker_build_wheels_linux.sh
- upload.sh
- after_success.sh
- coveralls
- install_ambertools.sh
- install_gfortran.sh
- install_test.sh
- pyflakes_check.sh
- run_tests.sh
- setup_env.sh
- test_pip_build.sh
- test_setup_command.py
- install_pytraj.sh
- setup_env.sh
- bld.bat
- build.sh
- meta.yaml
- README
- install_cpptraj.sh
- install_pytraj.sh
- README
- upload.sh
- DEVELOPMENT.md
- mkrelease
- README.md
- example_actionlist.py
- mdfrc
- mdfrc.prmtop
- nglview.png
- nglview_pytraj.gif
- nglview_pytraj_autoimage.png
- progress_bar.gif
- pytraj.gif
- __init__.py
- cpptraj.py
- mpi_load_batch.py
- mpi_molsurf.py
- mpi_pysander.py
- rmsd_mpi_example.py
- run_mpi_examples.sh
- serial_cal_molsurf_0_for_mpi_test.py
- example_density.py
- example_dihedral.py
- example_randomize_ions.py
- extract_temperature_traj_remd.py
- README.md
- example_Amber_to_CHARMM.py
- example_append_traj_and_write.py
- example_autocorrelation.py
- example_average_structure.py
- example_bfactors.py
- example_calculate_chi_angle.py
- example_center_of_geometry.py
- example_center_of_mass.py
- example_cpptraj_style.py
- example_distance.py
- example_distance_matrix.py
- example_dssp.py
- example_energy_decomposition.py
- example_fancy_indexing_traj.py
- example_get_atom_mass.py
- example_hydrogen_bonding.py
- example_kmeans_sklearn.py
- example_load_filelist.py
- example_load_pdb_as_trajectory.py
- example_load_pdb_from_rcsb.py
- example_load_trajectory_by_chunk.py
- example_mdtraj_to_pytraj.py
- example_minimum_distance.py
- example_multidihedral.py
- example_native_contacts.py
- example_nucleic_analysis.py
- example_out_of_core_calculation.py
- example_pairwise_rmsd.py
- example_pandas_DataFrame.py
- example_parallelize.py
- example_pca.py
- example_pca_sklearn_vs_cpptraj.py
- example_radgyr.py
- example_rmsd.py
- example_rmsd_2trajs.py
- example_rmsd_two_pars.py
- example_rotate_dihedral_and_energy_calc.py
- example_rotate_dihedral_for_movie.py
- example_save_traj_with_autoimage_and_rms.py
- example_selecting_atoms.py
- example_slice_to_get_z_coordinates.py
- example_split_and_write_trajectory.py
- example_strip_solvent.py
- example_superpose.py
- example_water_clustering.py
- example_write_force_to_trajectory.py
- example_write_parm.py
- example_write_pdb_options.py
- example_write_pdbs_for_movies.py
- example_write_traj.py
- example_write_traj_with_indices.py
- get_py_files.py
- progress_bar.gif
- pytraj_readme.ipynb
- README.md
- run_examples.py
- dask.txt
- jupyter-themes.txt
- magic.txt
- mdtraj.txt
- pandas.txt
- toolz.txt
- wurlitzer.txt
- pytraj.md
- README
- __init__.py
- base.py
- correlation.py
- diffusion.py
- energy.py
- geometry.py
- matrix.py
- pca.py
- rmsd.py
- spectroscopy.py
- structure.py
- topology_manipulation.py
- utilities.py
- visualization.py
- __init__.py
- actionlist.pxd
- actionlist.pyx
- c_action.pxd
- c_action.pyx
- __init__.py
- analysis_dict.py
- c_analysis.pxd
- c_analysis.pyx
- __init__.py
- base_holder.py
- dihedral_analysis.py
- dssp_analysis.py
- energy_analysis.py
- hbond_analysis.py
- matrix.py
- nmr.py
- nucleic_acid_analysis.py
- rmsd.py
- tica_analysis.py
- topology_analysis.py
- vector.py
- water.py
- __init__.py
- build.py
- __init__.py
- __init__.py
- box.pxd
- box.pyx
- c_core.pxd
- c_core.pyx
- c_dict.pxd
- c_dict.pyx
- c_options.pyx
- coordinfo.pxd
- coordinfo.pyx
- cpp_vector.pxd
- elements.py
- parameter_types.pxd
- parameter_types.pyx
- topology_objects.pxd
- topology_objects.pyx
- __init__.py
- cpp_algorithm.pxd
- cpp_vector.pxd
- __init__.py
- Ala3.crd
- Ala3.top
- __init__.py
- DPDP.nc
- DPDP.parm7
- __init__.py
- ala2.parm7
- rem.nc.000
- rem.nc.001
- rem.nc.002
- rem.nc.003
- __init__.py
- trpcage.pdb.gz
- __init__.py
- tz2.nc
- tz2.ortho.nc
- tz2.ortho.parm7
- tz2.parm7
- __init__.py
- datafiles.pxd
- datafiles.pyx
- load_samples.py
- README
- rna.pdb
- __init__.py
- array.py
- c_datasetlist.pxd
- c_datasetlist.pyx
- c_datasets.pxd
- c_datasets.pyx
- cast_dataset.pyx
- datasetlist.py
- __init__.py
- magic.py
- README
- wurlitzer.py
- __init__.py
- cpp_math.pxd
- cpp_math.pyx
- __init__.py
- base.py
- dataset.py
- mpi.py
- multiprocess.py
- __init__.py
- lazy.py
- qm.py
- TrajectoryBaseIterator.py
- transform.py
- __init__.py
- serialize.py
- __init__.py
- run_tests.py
- testing.py
- __init__.py
- topology.pxd
- topology.pyx
- __init__.py
- c_trajectory.pxd
- c_trajectory.pyx
- c_trajout.pxd
- c_trajout.pyx
- __init__.py
- frame.pxd
- frame.pyx
- frameiter.py
- shared_methods.py
- shared_trajectory.py
- stripped_trajectory.py
- trajectory.py
- trajectory_iterator.py
- oceans16.css
- circle.css
- progress-circle.js
- README.md
- __init__.py
- c_commands.py
- check_and_assert.py
- context.py
- convert.py
- cyutils.pyx
- decorators.py
- get_common_objects.py
- log
- misc.py
- progress.py
- Timer.py
- tools.py
- __init__.py
- view.py
- __init__.py
- all_actions.py
- all_actions_backup.py
- io.py
- unistd.h
- git_diff_amber_git_pytraj_github.sh
- git_fetch_pytraj_github.sh
- pull_from_pytraj_github.sh
- push_to_pytraj_github.sh
- push_to_pytraj_github_numpy_api.sh
- _fix_action.py
- check_list_headers.py
- codegen_all_enums.py
- codegen_enum.py
- codegen_pxd.py
- codegen_pyx.py
- codegen_typedef.py
- compare_files.py
- convert_property_to_old_style.py
- correct_method_names.py
- enum_to_dict.py
- find_action_and_analysis_commands.py
- find_class_name.py
- find_missing_cpptraj_action_names.py
- find_then_delete_files_having_keys.py
- fix_double_colons_for_Analysis.sh
- grep_class.sh
- grep_wrap.sh
- make_new_action_file.py
- PXD_template.dat
- PYX_template.dat
- rename_func_c_to_py.py
- util.py
- write_action_pxd.py
- write_action_pyx.py
- write_allanalyses.py
- write_analysis_pxd.py
- write_analysis_pyx.py
- cluster_.py
- mean_structure_.py
- pairwise_rmsd_.py
- rmsd_2trajs.py
- superpose_traj_on_disk.py
- topology_test.py
- write_traj.py
- change_name.py
- clean_cythonize_files.py
- clean_cythonize_files_git.py
- count_non_blank_lines.sh
- find_libcpptraj.py
- fix_rpath_pip_osx.py
- plot_dihedral.py
- replace_keyword.py
- pmap_speed.py
- README.md
- speed_get_coordinates.py
- timing_distance_actionlist.py
- timing_f_c_orders.py
- timing_iter.py
- timing_load_netcdf.py
- timing_molsurf.py
- timing_netcdf4_vs_pytraj_slicing.py
- timing_pickle_topology.py
- timing_pmap_.py
- timing_pmap_ired_vector_and_matrix.py
- timing_pmap_vs_mdtraj.py
- __init__.py
- acsii_art.py
- build_wheel.py
- check_openmp.py
- cythonize.py
- find_lib.py
- install_libcpptraj.py
- install_message.py
- six.py
- utils.py
- mdinfo
- mdout
- min.in
- min.r
- run.sh
- Ala3.crd
- Ala3.top
- strip.nc
- strip.prmtop
- GF2.log
- GF2.pdb
- 0readme
- system.prmtop
- trunc.nc
- pdb.gz
- short.dcd
- test.py
- BP.na.out
- BPstep.na.out
- Helix.na.out
- log
- rna_a_form_dup.pdb
- rna_a_form_dup_F2.pdb
- traj.in
- guv.H1.1.dx
- guv.O.1.dx
- saxs.save
- test.pdb
- Jcoupling.dat.save
- auxiliary.par
- bestpairs.pdb
- bp_helical.par
- bp_order.dat
- bp_step.par
- bpfile_tmp.dat
- cf_7methods.par
- col_chains.scr
- col_helices.scr
- hel_regions.pdb
- hstacking.pdb
- log
- poc_haxis.r3d
- ref_frames.dat
- rna.out
- rna.pdb
- rna_nab.pdb
- run_3dna.sh
- stacking.pdb
- auxiliary.par
- bestpairs.pdb
- bp_helical.par
- bp_order.dat
- bp_step.par
- bpfile_tmp.dat
- cf_7methods.par
- circ.out
- circ.pdb
- col_chains.scr
- col_helices.scr
- hel_regions.pdb
- hstacking.pdb
- ref_frames.dat
- run_3dna.sh
- stacking.pdb
- adh026.3.pdb
- adh026.3.top
- Atomic_G.pdb.nastruct
- BP.adh026.dat.save
- BPstep.adh026.dat.save
- G5.pdb
- Helix.adh026.dat.save
- nastruct.in
- RunTest.sh
- test.out
- ala2.99sb.mbondi2.parm7
- d1.crd.dat
- d1.crd.dat.save
- d1.ensemble.dat
- d1.ensemble.dat.save
- d1.nc.dat
- d1.nc.dat.save
- d1.offset.dat
- d1.offset.dat.save
- rem.crd.000
- rem.crd.001
- rem.crd.002
- rem.crd.003
- rem.nc.000
- rem.nc.001
- rem.nc.002
- rem.nc.003
- remd.in
- RunTest.sh
- temp0.crd.300.00
- temp0.crd.384.30
- temp0.crd.492.20
- temp0.crd.630.50
- test.out
- Test_Results.dat
- traj.in
- 0readme
- 1L2Y.pdb
- __init__.py
- A.pdb
- ala2.crazy_ext
- ala2.h5
- ala2_h5_faketop.top
- ala3.dcd
- ala3.psf
- avg.Tc5b.frame_2_to_8_skip_2.pdb
- avg.Tc5b.in
- avg.Tc5b.pdb
- CAres2_CAres10.Tc5b.dat
- cro.ac
- DOPC.parm7
- DOPC.rst7
- DPDP.nc
- DPDP.parm7
- dssp.Tc5b.dat
- dssp.Tc5b.dat.sum
- dssp.Tc5b.in
- esurf_vs_rmsd.dat
- find_dupes.py
- fit_to_1stframe.CA.Tc5b.x
- fit_to_1stframe.Tc5b.r
- fit_to_1stframe.Tc5b.x
- floBF-resp.chg
- HP36.top
- ired.in
- ired_reduced.in
- Karplus.txt
- log.openmp.1
- log.openmp.2
- log.openmp.4
- log.openmp.8
- m2-c1_f3.mol2
- mask.tz2.dat
- md1_prod.fit_to_first.Tc5b.x
- md1_prod.Tc5b.r
- polyAT.pdb
- ptraj_comp.in
- pycpptraj.in
- pycpptraj_2.in
- radgyr.Tc5b.dat
- README
- rmsd_allatoms.dat
- rmsd_allatoms_to_1st.Tc5b.dat
- rmsd_allatoms_to_1st.Tc5b.use_mass.dat
- rmsd_CA_to_nat_res3_18.dat
- rmsd_to_firstFrame_CA_allres.Tc5b.dat
- rotated_frame0.x60y120z50.Tc5b.r
- run_cpptraj_openmp.sh
- small_pbc.pdb
- stripAllButCA.Tc5b.x
- Tc5b.crd
- tc5b.matrix.in
- tc5b.matrix_CA.dat
- tc5b.multivector.in
- tc5b.myvec.out
- Tc5b.nat.crd
- Tc5b.nat.inpcrd
- tc5b.native_contacts.dat
- Tc5b.parm
- Tc5b.parm7
- tc5b.principal_dorotation.in
- Tc5b.principal_dorotation.rst7
- Tc5b.prmtop
- tc5b.rotate.in
- Tc5b.top
- tc5b.vector.0.in
- Tc5b.x
- test_multidihedral.dat
- test_openmp.Tc5b.n_threads_1.dat
- test_openmp.Tc5b.n_threads_2.dat
- test_openmp.Tc5b.n_threads_4.dat
- test_openmp.Tc5b.n_threads_8.dat
- tz2.autoimage.in
- tz2.autoimage.nc
- tz2.autoimage_with_fit.in
- tz2.autoimage_with_rmsfit.nc
- tz2.center.in
- tz2.center_mass.nc
- tz2.crd
- tz2.crd.gz
- tz2.in
- tz2.mask.in
- tz2.nc
- tz2.ortho.nc
- tz2.ortho.parm7
- tz2.ortho.rst7
- tz2.parm7
- tz2.pca.in
- tz2.pdb
- tz2.rst7
- tz2.truncoct.autoiamge.save.r
- tz2.truncoct.crd
- tz2.truncoct.nc
- tz2.truncoct.parm7
- vec.out
- eq1.x
- prmtop
- prmtop_an
- trxox.2.4ns.x
- min.r
- prmtop
- lysine.crd
- prmtop
- inpcrd
- prmtop
- __init__.py
- add-checkpoint.ipynb
- __init__.py
- add.ipynb
- load_antechamber.ipynb
- load_leap.ipynb
- make_structure.ipynb
- progress.ipynb
- progress_bar.ipynb
- stripped_trajectoryiterator.ipynb
- __init__.py
- README
- __init__.py
- test_leap_nab.py
- __init__.py
- test_analyze_matrix.py
- test_angle.py
- test_atom_map.py
- test_atomiccorr.py
- test_atomicfluct.py
- test_center_of_mass.py
- test_check_chirality.py
- test_check_structure.py
- test_checkoverlap.py
- test_closest.py
- test_closest_atom.py
- test_cluster.py
- test_compare_topology.py
- test_correlation.py
- test_count_in_voxel.py
- test_crank.py
- test_density.py
- test_diffusion.py
- test_dihedral.py
- test_dihedral_analysis.py
- test_dihedral_covariance_matrix.py
- test_dihedral_res.py
- test_dihedral_rms.py
- test_distance.py
- test_dssp.py
- test_ene_decomp.py
- test_fiximagedbonds.py
- test_gist.py
- test_grid.py
- test_hausdorff.py
- test_hbond.py
- test_infrared_spectrum.py
- test_ired.py
- test_jcoupling.py
- test_lie.py
- test_lipidscd.py
- test_lowestcurve.py
- test_matrix_analysis.py
- test_mean_structure.py
- test_mindist.py
- test_modes.py
- test_molsurf_and_surf.py
- test_multi_pucker.py
- test_multidihedral.py
- test_multivector.py
- test_nastruct.py
- test_nativecontacts.py
- test_order_parameters.py
- test_pairdist.py
- test_pca.py
- test_permute_dihedrals.py
- test_principal_dorotation.py
- test_projection.py
- test_pucker.py
- test_radgyr.py
- test_randomize_ions.py
- test_rdf.py
- test_replicate_cell.py
- test_rmsd.py
- test_rotate_dihedral.py
- test_rotation_matrix.py
- test_rotdif.py
- test_spam.py
- test_superpose.py
- test_ti.py
- test_tica_consolidated.py
- test_timecorr.py
- test_topology_analysis.py
- test_toroidal_diffusion.py
- test_vector_analysis.py
- test_velocity.py
- test_volmap.py
- test_volume.py
- test_watershell.py
- test_wavelet.py
- test_xtalsymm.py
- __init__.py
- test_cpptraj_dataset.py
- test_stack_dataset.py
- __init__.py
- test_dispatch_master.py
- test_super_dispatch.py
- __init__.py
- test_pmap_sander.py
- test_sander_energies.py
- __init__.py
- test_parmed_converter.py
- test_read_gaussian.py
- __init__.py
- test_are_instance.py
- test_array_to_resrange.py
- test_chain.py
- test_extra_coverage.py
- __init__.py
- test_fancy_indexing_Frame.py
- test_frame.py
- test_Frame_2.py
- test_Frame_3.py
- test_Frame_8.py
- test_Frame_9_mass.py
- test_Frame__array__.py
- test_Frame_append_xyz.py
- test_Frame_box.py
- test_Frame_construct_from_pointer.py
- test_Frame_load_xyz.py
- test_Frame_math.py
- test_Frame_swap_atoms.py
- test_Frame_xyz.py
- test_FrameArray_inherit.py
- test_FrameArray_update_xyz.py
- test_mix_tuple_list_frames.py
- __init__.py
- test_issue807_segfault_with_force.py
- test_issue876_pdb_PBC.py
- test_issue991_buffer_not_C_contiguous.py
- __init__.py
- test_convert.py
- test_io.py
- test_load_state.py
- test_read_data.py
- test_write_data.py
- test_write_pdb.py
- test_write_trajectory.py
- __init__.py
- test_chunk_iter.py
- test_chunk_iter_with_autoimage_rmsfit.py
- test_frame_iter_1.py
- test_frame_iter_3.py
- test_frame_iter_master_basic.py
- test_frame_iter_mutable_vs_unmutable.py
- test_frame_iter_with_autoimage.py
- test_frame_iter_with_mask.py
- test_iter_not_same_frame.py
- test_iter_traj_1.py
- test_iter_traj_2.py
- test_iterframe_indices.py
- test_iterframe_master.py
- test_iterload.py
- test_save_frameiter.py
- test_segfault_iterator.py
- __init__.py
- test_load_by_pattern.py
- test_load_charmm.py
- test_load_data_sample.py
- test_load_indices.py
- __init__.py
- test_math.py
- test_matrix3x3.py
- __init__.py
- test_mpi.py
- test_mpi_cpptraj_style.py
- test_mpi_hbond.py
- test_mpi_load_batch.py
- test_mpi_reference.py
- utils.py
- __init__.py
- test_pmap.py
- test_worker_state.py
- __init__.py
- load_batch_pmap_.py
- README
- run_openmp.sh
- speed_get_coordinates.py
- speed_iter.py
- __init__.py
- test_merge_coordinates.py
- test_merge_coordinates_frames.py
- test_merge_frames.py
- test_tools.py
- __init__.py
- test_Atom_basic.py
- test_AtomMask.py
- test_topology_objects.py
- __init__.py
- test_fancy_indexing.py
- test_iterframe.py
- test_stripped_trajectory.py
- test_trajectory.py
- test_trajectory_atommask.py
- test_trajectory_extensive_indexing.py
- test_trajectory_iterator.py
- test_trajectory_writer.py
- test_transform_trajectory_iterator.py
- __init__.py
- test_autoimage.py
- test_center.py
- test_image.py
- test_make_structure.py
- test_transform.py
- .coveragerc
- CMakeLists.txt
- Makefile
- README.md
- run_simple_test.py
- template_unittest.py
- test_actionlist.py
- test_crdframes.py
- test_createcrd.py
- test_cyutils.py
- test_distance_based_mask.py
- test_do.py
- test_docs.py
- test_force.py
- test_frame_indices_option.py
- test_known_bugs.py
- test_pickle.py
- test_pipeline.py
- test_progress_bar.py
- test_read_to_array.py
- test_reference.py
- test_run_mpi.py
- test_segfault.py
- test_slice_view.py
- test_timer.py
- test_to_cpptraj_mask.py
- test_topology.py
- test_unitcells.py
- test_unstrip.py
- test_visualization.py
- utils.py
- .gitignore
- .style.yapf
- changes.rst
- CMakeLists.txt
- conda-requirements.txt
- DEVELOPMENT.md
- docker.txt
- environment.yml
- Jenkinsfile
- MANIFEST.in
- pip-requirements.txt
- README.md
- run_tests.py
- setup.py
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