pysoftk package

Subpackages

• pysoftk.folder_manager package
  • Submodules
  • pysoftk.folder_manager.folder_creator module
    • Fld
      • Fld.copy_dir()
      • Fld.create()
      • Fld.file_to_dir()
      • Fld.fxd_name()
      • Fld.seek_files()
  • Module contents
• pysoftk.format_printers package
  • Submodules
  • pysoftk.format_printers.format_mol module
    • Cnv
      • Cnv.file_in_out()
    • Fmt
      • Fmt.format_print()
      • Fmt.mol_print()
      • Fmt.pdb_print()
      • Fmt.xyz_print()
  • Module contents
• pysoftk.htp_tools package
  • Submodules
  • pysoftk.htp_tools.calculator_htp module
    • Htp
      • Htp.ending
      • Htp.xtb_path
      • Htp.xyz_geom
      • Htp.init_dir
      • Htp.num_cores
      • Htp.threshold
      • Htp.htp_xtb_ff()
      • Htp.htp_xtb_gfn()
      • Htp.xtb_ff()
      • Htp.xtb_gfn()
  • Module contents
• pysoftk.linear_polymer package
  • Submodules
  • pysoftk.linear_polymer.calculators module
    • Opt
      • Opt.pyscf_semi()
    • Pyscf_print
      • Pyscf_print.xyz()
  • pysoftk.linear_polymer.linear_polymer module
    • Lp
      • Lp.atom
      • Lp.bond_conn()
      • Lp.copy_mol()
      • Lp.linear_polymer()
      • Lp.max_dist_mol()
      • Lp.mol
      • Lp.n_copies
      • Lp.polimerisation()
      • Lp.proto_polymer()
      • Lp.shift
      • Lp.x_shift()
  • pysoftk.linear_polymer.mol_conformer module
    • Mcon
      • Mcon.conformer()
      • Mcon.mol
      • Mcon.num_conf
  • pysoftk.linear_polymer.super_monomer module
    • Emb
      • Emb.etkdgv3()
    • Sm
      • Sm.atom
      • Sm.constructor()
      • Sm.mol_1
      • Sm.mol_2
      • Sm.mon_to_poly()
      • Sm.monomer()
  • Module contents
• pysoftk.pol_analysis package
  • Subpackages
    • pysoftk.pol_analysis.tools package
      • Submodules
      • pysoftk.pol_analysis.tools.clustering_prob_distribution_plot module
      • pysoftk.pol_analysis.tools.utils_mda module
      • pysoftk.pol_analysis.tools.utils_tools module
      • pysoftk.pol_analysis.tools.utils_tools_old module
      • Module contents
  • Submodules
  • pysoftk.pol_analysis.clustering module
    • SCP
      • SCP.contact_matrix()
      • SCP.spatial_clustering()
      • SCP.spatial_clustering_run()
    • timeit()
  • pysoftk.pol_analysis.contact_analysis module
    • contacts
      • contacts.contacts_calc()
      • contacts.run_contacts_calc()
    • timeit()
  • pysoftk.pol_analysis.ecc_micelle module
    • ecc
      • ecc.ecc_calc()
      • ecc.running_ecc()
  • pysoftk.pol_analysis.intrinsic_density_micelle module
    • intrinsic_density
      • intrinsic_density.box_volume()
      • intrinsic_density.intrinsic_density_not_normalized()
      • intrinsic_density.run_intrinsic_density()
    • timeit()
  • pysoftk.pol_analysis.intrinsic_density_water_micelle module
    • intrinsic_density_water
      • intrinsic_density_water.box_volume()
      • intrinsic_density_water.intrinsic_density_not_normalized()
      • intrinsic_density_water.run_intrinsic_density()
      • intrinsic_density_water.select_water_atoms()
    • timeit()
  • pysoftk.pol_analysis.make_micelle_whole module
    • micelle_whole
      • micelle_whole.count_dimensions()
      • micelle_whole.get_atom_name_list()
      • micelle_whole.get_polymer_positions()
      • micelle_whole.make_cluster_whole()
      • micelle_whole.obtain_largest_micelle_resids()
      • micelle_whole.obtain_snapshot()
      • micelle_whole.pbc_per_dimension()
      • micelle_whole.running_make_cluster_whole()
    • timeit()
  • pysoftk.pol_analysis.rgyr_micelle module
    • rgyr
      • rgyr.rgyr_calc()
      • rgyr.running_rgyr()
    • timeit()
  • pysoftk.pol_analysis.ring_ring module
    • RSA
      • RSA.GetRingSystems()
      • RSA.calc_angle()
      • RSA.find_several_rings_stacked()
      • RSA.get_polymer_resids()
      • RSA.nearest_neighbours()
      • RSA.number_pol()
      • RSA.pol_cutoff()
      • RSA.rings_stacking_dist()
      • RSA.run_rings_stacking_dist()
      • RSA.separate_rings()
      • RSA.stacking_analysis()
      • RSA.svd()
    • timeit()
  • pysoftk.pol_analysis.solvation module
    • solvation
      • solvation.hydration_calc()
      • solvation.solvation_calc_run()
    • timeit()
  • pysoftk.pol_analysis.spherical_density module
    • spherical_density
      • spherical_density.density_calc()
      • spherical_density.dist_com()
      • spherical_density.run_density_calc()
      • spherical_density.sph_histogram()
    • timeit()
  • pysoftk.pol_analysis.spherical_density_water module
    • spherical_density_water
      • spherical_density_water.density_calc()
      • spherical_density_water.dist_com()
      • spherical_density_water.run_density_calc()
      • spherical_density_water.sph_histogram()
    • timeit()
  • pysoftk.pol_analysis.umap_analysis module
    • timeit()
    • umap_analysis
      • umap_analysis.cluster_order_appearance()
      • umap_analysis.find_closest_point()
      • umap_analysis.get_array()
      • umap_analysis.get_average_rep_cluster()
      • umap_analysis.hdbscan_cluster()
      • umap_analysis.umap_run()
  • Module contents
• pysoftk.pysoftwhere package
  • Submodules
  • pysoftk.pysoftwhere.icsi module
    • icsi
  • Module contents
• pysoftk.tools package
  • Submodules
  • pysoftk.tools.utils_func module
    • atom_neigh()
    • count_plholder()
    • create_pol()
    • get_file_extension()
    • pattern_mol_seq()
    • pattern_recon()
    • pattern_repl()
    • tuple_bonds()
  • pysoftk.tools.utils_ob module
    • check_bond_order()
    • ff_ob_relaxation()
    • global_opt()
    • rotor_opt()
  • pysoftk.tools.utils_rdkit module
    • MMFF_rel()
    • UFF_rel()
    • etkdgv3_energies()
    • no_swap()
    • plc_holder()
    • remove_plcholder()
    • swap_hyd()
  • Module contents
• pysoftk.topologies package
  • Submodules
  • pysoftk.topologies.branched module
    • Bd
      • Bd.arm
      • Bd.atom
      • Bd.branched_polymer()
      • Bd.core
      • Bd.merge_arms()
  • pysoftk.topologies.diblock module
    • Db
      • Db.atom
      • Db.diblock_copolymer()
      • Db.ma
      • Db.mb
    • Pt
      • Pt.atom
      • Pt.mols
      • Pt.pattern
      • Pt.pattern_block_poly()
  • pysoftk.topologies.ranpol module
    • Rnp
      • Rnp.atom
      • Rnp.ma
      • Rnp.mb
      • Rnp.random_ab_copolymer()
      • Rnp.random_abc_copolymer()
  • pysoftk.topologies.ring module
    • Rn
      • Rn.atom
      • Rn.mol
      • Rn.pol_ring()
    • apply_force_field()
    • check_proto()
  • Module contents
• pysoftk.torsional package
  • Submodules
  • pysoftk.torsional.torsional module
    • Torsional
      • Torsional.draw_molecule()
      • Torsional.list_dhdl_atoms()
      • Torsional.mol_graph()
      • Torsional.mol_graph_neigh()
      • Torsional.plot_trs_ang()
      • Torsional.seek_angles()
      • Torsional.show_atom_number()
      • Torsional.validate_mol()
  • Module contents

Module contents