reForge API

• reforge package
  • Subpackages
    • reforge.forge package
      • Submodules
      • reforge.forge.cgmap module
      • reforge.forge.forcefields module
      • reforge.forge.geometry module
      • reforge.forge.persistence_length module
      • reforge.forge.topology module
      • Module contents
    • reforge.martini package
      • Submodules
      • reforge.martini.getgo module
      • reforge.martini.martini_tools module
      • reforge.martini.martinize_nucleotides module
      • reforge.martini.martinize_rna module
      • Module contents
    • reforge.mdsystem package
      • Submodules
      • reforge.mdsystem.gmxmd module
      • reforge.mdsystem.mdsystem module
      • reforge.mdsystem.mmmd module
      • Module contents
    • reforge.rfgmath package
      • Submodules
      • reforge.rfgmath.legacy module
      • reforge.rfgmath.rcmath module
      • reforge.rfgmath.rpykernels module
      • reforge.rfgmath.rpymath module
      • Module contents
  • Submodules
  • reforge.cli module
    • run()
    • sbatch()
    • dojob()
    • gmx()
    • change_directory()
    • from_wdir()
    • gmx_editconf()
    • gmx_solvate()
    • gmx_make_ndx()
    • gmx_grompp()
    • gmx_mdrun()
    • gmx_trjconv()
    • gmx_rmsf()
    • gmx_rms()
    • gmx_rdf()
    • gmx_cluster()
    • gmx_extract_cluster()
    • gmx_covar()
    • gmx_anaeig()
    • gmx_make_edi()
    • args_to_str()
    • kwargs_to_str()
  • reforge.io module
    • read_positions()
    • read_velocities()
    • parse_covar_dat()
    • fname_filter()
    • filter_files()
    • pull_files()
    • pull_all_files()
    • xvg2npy()
    • pdb2system()
    • pdb2atomlist()
    • read_data()
    • read_xvg()
    • npy2csv()
    • save_1d_data()
    • save_2d_data()
  • reforge.itpio module
    • read_itp()
    • line2bond()
    • bond2line()
    • format_header()
    • format_sequence_section()
    • format_moleculetype_section()
    • format_atoms_section()
    • format_bonded_section()
    • format_posres_section()
    • write_itp()
    • make_in_terms()
    • make_cross_terms()
    • make_marnatini_itp()
    • make_ions_itp()
    • count_itp_atoms()
  • reforge.mdm module
    • fft_ccf()
    • ccf()
    • covariance_matrix()
    • calc_and_save_covmats()
    • calc_and_save_rmsf()
    • perturbation_matrix()
    • perturbation_matrix_iso()
    • td_perturbation_matrix()
    • dfi()
    • dci()
    • group_molecule_dci()
    • group_group_dci()
    • hessian()
    • inverse_matrix()
    • percentile()
  • reforge.pdbtools module
    • Atom
      • Atom.from_pdb_line()
      • Atom.to_pdb_line()
    • AtomList
      • AtomList.key_funcs
      • AtomList.records
      • AtomList.atids
      • AtomList.names
      • AtomList.alt_locs
      • AtomList.resnames
      • AtomList.chids
      • AtomList.resids
      • AtomList.icodes
      • AtomList.xs
      • AtomList.ys
      • AtomList.zs
      • AtomList.occupancies
      • AtomList.bfactors
      • AtomList.segids
      • AtomList.elements
      • AtomList.charges
      • AtomList.vecs
      • AtomList.residues
      • AtomList.chains
      • AtomList.segments
      • AtomList.renum()
      • AtomList.sort()
      • AtomList.mask()
      • AtomList.mask_out()
      • AtomList.renumber()
      • AtomList.remove_atoms()
      • AtomList.read_pdb()
      • AtomList.write_pdb()
      • AtomList.write_ndx()
    • AtomListCollection
      • AtomListCollection.records
      • AtomListCollection.atids
      • AtomListCollection.names
      • AtomListCollection.alt_locs
      • AtomListCollection.resnames
      • AtomListCollection.chids
      • AtomListCollection.resids
      • AtomListCollection.icodes
      • AtomListCollection.xs
      • AtomListCollection.ys
      • AtomListCollection.zs
      • AtomListCollection.occupancies
      • AtomListCollection.bfactors
      • AtomListCollection.segids
      • AtomListCollection.elements
      • AtomListCollection.charges
      • AtomListCollection.vecs
    • Residue
      • Residue.add_atom()
      • Residue.atoms
    • Chain
      • Chain.add_atom()
      • Chain.atoms
    • Model
      • Model.add_atom()
      • Model.atoms
      • Model.select_chains()
    • System
      • System.add_atom()
      • System.add_atoms()
      • System.atoms
      • System.residues()
      • System.chains()
      • System.write_pdb()
    • PDBParser
      • PDBParser.parse()
    • pdb2system()
    • pdb2atomlist()
    • sort_chains_atoms()
    • rename_chains_for_gromacs()
    • sort_pdb()
    • clean_pdb()
    • rename_chain_in_pdb()
    • rename_chain_and_histidines_in_pdb()
    • write_ndx()
    • update_bfactors()
    • sort_uld()
    • label_segments()
  • reforge.plotting module
    • init_figure()
    • make_hist()
    • make_plot()
    • make_errorbar()
    • make_heatmap()
    • plot_figure()
    • pull_data()
    • set_ax_parameters()
    • set_hm_parameters()
    • grid_labels()
    • plot_dfi()
    • plot_pdfi()
    • plot_rmsf()
    • plot_rmsd()
    • plot_dci()
    • plot_asym()
    • plot_pert()
    • plot_segment_dci()
    • plot_segment_asym()
    • response_1()
    • response_2()
    • response_2_2d()
    • response_force()
    • response()
    • make_1d_data()
    • make_2d_data()
    • make_heatmap_td()
    • make_plot_td()
    • make_plot_t_td()
    • make_plot_t_2d()
    • animate_1d()
    • animate_2d()
    • make_animation()
    • mkfigure()
    • make_1d_plots()
  • reforge.utils module
    • timeit()
    • memprofit()
    • cd()
    • clean_dir()
    • cuda_info()
    • cuda_detected()
  • Module contents