Index

A

apply_force_field() (in module pysoftk.topologies.ring) arm (pysoftk.topologies.branched.Bd attribute) atom (pysoftk.linear_polymer.linear_polymer.Lp attribute) (pysoftk.linear_polymer.super_monomer.Sm attribute) (pysoftk.topologies.branched.Bd attribute) (pysoftk.topologies.diblock.Db attribute) (pysoftk.topologies.diblock.Pt attribute) (pysoftk.topologies.ranpol.Rnp attribute) (pysoftk.topologies.ring.Rn attribute)

atom_neigh() (in module pysoftk.tools.utils_func)

B

Bd (class in pysoftk.topologies.branched) bond_conn() (pysoftk.linear_polymer.linear_polymer.Lp method)

box_volume() (pysoftk.pol_analysis.intrinsic_density_micelle.intrinsic_density method) (pysoftk.pol_analysis.intrinsic_density_water_micelle.intrinsic_density_water method) branched_polymer() (pysoftk.topologies.branched.Bd method)

C

calc_angle() (pysoftk.pol_analysis.ring_ring.RSA method) check_bond_order() (in module pysoftk.tools.utils_ob) check_proto() (in module pysoftk.topologies.ring) cluster_order_appearance() (pysoftk.pol_analysis.umap_analysis.umap_analysis method) Cnv (class in pysoftk.format_printers.format_mol) conformer() (pysoftk.linear_polymer.mol_conformer.Mcon method) constructor() (pysoftk.linear_polymer.super_monomer.Sm method) contact_matrix() (pysoftk.pol_analysis.clustering.SCP method) contacts (class in pysoftk.pol_analysis.contact_analysis) contacts_calc() (pysoftk.pol_analysis.contact_analysis.contacts method) coord_matrix_calc() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old)

copy_dir() (pysoftk.folder_manager.folder_creator.Fld method) copy_mol() (pysoftk.linear_polymer.linear_polymer.Lp method) core (pysoftk.topologies.branched.Bd attribute) count_dimensions() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) count_plholder() (in module pysoftk.tools.utils_func) create() (pysoftk.folder_manager.folder_creator.Fld method) create_binned_space() (in module pysoftk.pol_analysis.tools.utils_tools) create_network() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) create_pol() (in module pysoftk.tools.utils_func)

D

Db (class in pysoftk.topologies.diblock) density_calc() (pysoftk.pol_analysis.spherical_density.spherical_density method) (pysoftk.pol_analysis.spherical_density_water.spherical_density_water method) diblock_copolymer() (pysoftk.topologies.diblock.Db method)

dist_com() (pysoftk.pol_analysis.spherical_density.spherical_density method) (pysoftk.pol_analysis.spherical_density_water.spherical_density_water method) distance_matrix_calc() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) draw_molecule() (pysoftk.torsional.torsional.Torsional method)

E

ecc (class in pysoftk.pol_analysis.ecc_micelle) ecc_calc() (pysoftk.pol_analysis.ecc_micelle.ecc method) Emb (class in pysoftk.linear_polymer.super_monomer)

ending (pysoftk.htp_tools.calculator_htp.Htp attribute) etkdgv3() (pysoftk.linear_polymer.super_monomer.Emb method) etkdgv3_energies() (in module pysoftk.tools.utils_rdkit)

F

ff_ob_relaxation() (in module pysoftk.tools.utils_ob) file_in_out() (pysoftk.format_printers.format_mol.Cnv method) file_to_dir() (pysoftk.folder_manager.folder_creator.Fld method) find_closest_point() (pysoftk.pol_analysis.umap_analysis.umap_analysis method) find_several_rings_stacked() (pysoftk.pol_analysis.ring_ring.RSA method)

find_values() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) Fld (class in pysoftk.folder_manager.folder_creator) Fmt (class in pysoftk.format_printers.format_mol) format_print() (pysoftk.format_printers.format_mol.Fmt method) fxd_name() (pysoftk.folder_manager.folder_creator.Fld method)

G

get_array() (pysoftk.pol_analysis.umap_analysis.umap_analysis method) get_atom_name_list() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) get_average_rep_cluster() (pysoftk.pol_analysis.umap_analysis.umap_analysis method) get_file_extension() (in module pysoftk.tools.utils_func) get_frames() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) get_frames_hydr() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old)

get_index_pairs() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) get_mda_universe() (pysoftk.pol_analysis.tools.utils_mda.MDA_input method) get_polymer_positions() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) get_polymer_resids() (pysoftk.pol_analysis.ring_ring.RSA method) get_universe_per_frame() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) GetRingSystems() (pysoftk.pol_analysis.ring_ring.RSA method) global_opt() (in module pysoftk.tools.utils_ob)

H

hdbscan_cluster() (pysoftk.pol_analysis.umap_analysis.umap_analysis method) Htp (class in pysoftk.htp_tools.calculator_htp)

htp_xtb_ff() (pysoftk.htp_tools.calculator_htp.Htp method) htp_xtb_gfn() (pysoftk.htp_tools.calculator_htp.Htp method) hydration_calc() (pysoftk.pol_analysis.solvation.solvation method)

I

icsi (class in pysoftk.pysoftwhere.icsi) init_dir (pysoftk.htp_tools.calculator_htp.Htp attribute) intrinsic_density (class in pysoftk.pol_analysis.intrinsic_density_micelle)

intrinsic_density_not_normalized() (pysoftk.pol_analysis.intrinsic_density_micelle.intrinsic_density method) (pysoftk.pol_analysis.intrinsic_density_water_micelle.intrinsic_density_water method) intrinsic_density_water (class in pysoftk.pol_analysis.intrinsic_density_water_micelle)

L

linear_polymer() (pysoftk.linear_polymer.linear_polymer.Lp method)

list_dhdl_atoms() (pysoftk.torsional.torsional.Torsional method) Lp (class in pysoftk.linear_polymer.linear_polymer)

M

ma (pysoftk.topologies.diblock.Db attribute) (pysoftk.topologies.ranpol.Rnp attribute) make_cluster_whole() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) max_dist_mol() (pysoftk.linear_polymer.linear_polymer.Lp method) mb (pysoftk.topologies.diblock.Db attribute) (pysoftk.topologies.ranpol.Rnp attribute) Mcon (class in pysoftk.linear_polymer.mol_conformer) MDA_input (class in pysoftk.pol_analysis.tools.utils_mda) merge_arms() (pysoftk.topologies.branched.Bd method) micelle_whole (class in pysoftk.pol_analysis.make_micelle_whole) MMFF_rel() (in module pysoftk.tools.utils_rdkit) module pysoftk pysoftk.folder_manager pysoftk.folder_manager.folder_creator pysoftk.format_printers pysoftk.format_printers.format_mol pysoftk.htp_tools pysoftk.htp_tools.calculator_htp pysoftk.linear_polymer pysoftk.linear_polymer.calculators pysoftk.linear_polymer.linear_polymer pysoftk.linear_polymer.mol_conformer pysoftk.linear_polymer.super_monomer pysoftk.pol_analysis pysoftk.pol_analysis.clustering pysoftk.pol_analysis.contact_analysis pysoftk.pol_analysis.ecc_micelle pysoftk.pol_analysis.intrinsic_density_micelle pysoftk.pol_analysis.intrinsic_density_water_micelle pysoftk.pol_analysis.make_micelle_whole pysoftk.pol_analysis.rgyr_micelle pysoftk.pol_analysis.ring_ring pysoftk.pol_analysis.solvation pysoftk.pol_analysis.spherical_density pysoftk.pol_analysis.spherical_density_water pysoftk.pol_analysis.tools pysoftk.pol_analysis.tools.clustering_prob_distribution_plot pysoftk.pol_analysis.tools.utils_mda pysoftk.pol_analysis.tools.utils_tools pysoftk.pol_analysis.tools.utils_tools_old pysoftk.pol_analysis.umap_analysis pysoftk.pysoftwhere pysoftk.pysoftwhere.icsi pysoftk.tools pysoftk.tools.utils_func pysoftk.tools.utils_ob pysoftk.tools.utils_rdkit pysoftk.topologies pysoftk.topologies.branched pysoftk.topologies.diblock pysoftk.topologies.ranpol pysoftk.topologies.ring pysoftk.torsional pysoftk.torsional.torsional

mol (pysoftk.linear_polymer.linear_polymer.Lp attribute) (pysoftk.linear_polymer.mol_conformer.Mcon attribute) (pysoftk.topologies.ring.Rn attribute) mol_1 (pysoftk.linear_polymer.super_monomer.Sm attribute) mol_2 (pysoftk.linear_polymer.super_monomer.Sm attribute) mol_graph() (pysoftk.torsional.torsional.Torsional method) mol_graph_neigh() (pysoftk.torsional.torsional.Torsional method) mol_print() (pysoftk.format_printers.format_mol.Fmt method) mols (pysoftk.topologies.diblock.Pt attribute) mon_to_poly() (pysoftk.linear_polymer.super_monomer.Sm method) monomer() (pysoftk.linear_polymer.super_monomer.Sm method)

N

n_copies (pysoftk.linear_polymer.linear_polymer.Lp attribute) nearest_neighbours() (pysoftk.pol_analysis.ring_ring.RSA method) no_swap() (in module pysoftk.tools.utils_rdkit)

num_conf (pysoftk.linear_polymer.mol_conformer.Mcon attribute) num_cores (pysoftk.htp_tools.calculator_htp.Htp attribute) number_pol() (pysoftk.pol_analysis.ring_ring.RSA method)

O

obtain_largest_micelle_resids() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method)

obtain_snapshot() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) Opt (class in pysoftk.linear_polymer.calculators)

P

pair() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) pattern (pysoftk.topologies.diblock.Pt attribute) pattern_block_poly() (pysoftk.topologies.diblock.Pt method) pattern_mol_seq() (in module pysoftk.tools.utils_func) pattern_recon() (in module pysoftk.tools.utils_func) pattern_repl() (in module pysoftk.tools.utils_func) pbc_per_dimension() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) pdb_print() (pysoftk.format_printers.format_mol.Fmt method) plc_holder() (in module pysoftk.tools.utils_rdkit) plot_trs_ang() (pysoftk.torsional.torsional.Torsional method) pol_cutoff() (pysoftk.pol_analysis.ring_ring.RSA method) pol_ring() (pysoftk.topologies.ring.Rn method) polimerisation() (pysoftk.linear_polymer.linear_polymer.Lp method) proto_polymer() (pysoftk.linear_polymer.linear_polymer.Lp method) Pt (class in pysoftk.topologies.diblock) Pyscf_print (class in pysoftk.linear_polymer.calculators) pyscf_semi() (pysoftk.linear_polymer.calculators.Opt method) pysoftk module pysoftk.folder_manager module pysoftk.folder_manager.folder_creator module pysoftk.format_printers module pysoftk.format_printers.format_mol module pysoftk.htp_tools module pysoftk.htp_tools.calculator_htp module pysoftk.linear_polymer module pysoftk.linear_polymer.calculators module pysoftk.linear_polymer.linear_polymer module pysoftk.linear_polymer.mol_conformer module pysoftk.linear_polymer.super_monomer module pysoftk.pol_analysis module pysoftk.pol_analysis.clustering module pysoftk.pol_analysis.contact_analysis module pysoftk.pol_analysis.ecc_micelle module pysoftk.pol_analysis.intrinsic_density_micelle module

pysoftk.pol_analysis.intrinsic_density_water_micelle module pysoftk.pol_analysis.make_micelle_whole module pysoftk.pol_analysis.rgyr_micelle module pysoftk.pol_analysis.ring_ring module pysoftk.pol_analysis.solvation module pysoftk.pol_analysis.spherical_density module pysoftk.pol_analysis.spherical_density_water module pysoftk.pol_analysis.tools module 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 pysoftk.pol_analysis.umap_analysis module pysoftk.pysoftwhere module pysoftk.pysoftwhere.icsi module pysoftk.tools module pysoftk.tools.utils_func module pysoftk.tools.utils_ob module pysoftk.tools.utils_rdkit module pysoftk.topologies module pysoftk.topologies.branched module pysoftk.topologies.diblock module pysoftk.topologies.ranpol module pysoftk.topologies.ring module pysoftk.torsional module pysoftk.torsional.torsional module

R

random_ab_copolymer() (pysoftk.topologies.ranpol.Rnp method) random_abc_copolymer() (pysoftk.topologies.ranpol.Rnp method) remove_plcholder() (in module pysoftk.tools.utils_rdkit) rgyr (class in pysoftk.pol_analysis.rgyr_micelle) rgyr_calc() (pysoftk.pol_analysis.rgyr_micelle.rgyr method) rings_stacking_dist() (pysoftk.pol_analysis.ring_ring.RSA method) Rn (class in pysoftk.topologies.ring) Rnp (class in pysoftk.topologies.ranpol) rotor_opt() (in module pysoftk.tools.utils_ob)

RSA (class in pysoftk.pol_analysis.ring_ring) run_contacts_calc() (pysoftk.pol_analysis.contact_analysis.contacts method) run_density_calc() (pysoftk.pol_analysis.spherical_density.spherical_density method) (pysoftk.pol_analysis.spherical_density_water.spherical_density_water method) run_intrinsic_density() (pysoftk.pol_analysis.intrinsic_density_micelle.intrinsic_density method) (pysoftk.pol_analysis.intrinsic_density_water_micelle.intrinsic_density_water method) run_rings_stacking_dist() (pysoftk.pol_analysis.ring_ring.RSA method) running_ecc() (pysoftk.pol_analysis.ecc_micelle.ecc method) running_make_cluster_whole() (pysoftk.pol_analysis.make_micelle_whole.micelle_whole method) running_rgyr() (pysoftk.pol_analysis.rgyr_micelle.rgyr method)

S

SCP (class in pysoftk.pol_analysis.clustering) seek_angles() (pysoftk.torsional.torsional.Torsional method) seek_files() (pysoftk.folder_manager.folder_creator.Fld method) select_water_atoms() (pysoftk.pol_analysis.intrinsic_density_water_micelle.intrinsic_density_water method) selecting_atoms() (in module pysoftk.pol_analysis.tools.utils_tools) (in module pysoftk.pol_analysis.tools.utils_tools_old) selecting_atoms_density() (in module pysoftk.pol_analysis.tools.utils_tools) separate_rings() (pysoftk.pol_analysis.ring_ring.RSA method) shift (pysoftk.linear_polymer.linear_polymer.Lp attribute) show_atom_number() (pysoftk.torsional.torsional.Torsional method) Sm (class in pysoftk.linear_polymer.super_monomer)

solvation (class in pysoftk.pol_analysis.solvation) solvation_calc_run() (pysoftk.pol_analysis.solvation.solvation method) spatial_clustering() (pysoftk.pol_analysis.clustering.SCP method) spatial_clustering_run() (pysoftk.pol_analysis.clustering.SCP method) sph_histogram() (pysoftk.pol_analysis.spherical_density.spherical_density method) (pysoftk.pol_analysis.spherical_density_water.spherical_density_water method) spherical_density (class in pysoftk.pol_analysis.spherical_density) spherical_density_water (class in pysoftk.pol_analysis.spherical_density_water) stacking_analysis() (pysoftk.pol_analysis.ring_ring.RSA method) svd() (pysoftk.pol_analysis.ring_ring.RSA method) swap_hyd() (in module pysoftk.tools.utils_rdkit)

T

threshold (pysoftk.htp_tools.calculator_htp.Htp attribute) timeit() (in module pysoftk.pol_analysis.clustering) (in module pysoftk.pol_analysis.contact_analysis) (in module pysoftk.pol_analysis.intrinsic_density_micelle) (in module pysoftk.pol_analysis.intrinsic_density_water_micelle) (in module pysoftk.pol_analysis.make_micelle_whole) (in module pysoftk.pol_analysis.rgyr_micelle) (in module pysoftk.pol_analysis.ring_ring) (in module pysoftk.pol_analysis.solvation) (in module pysoftk.pol_analysis.spherical_density) (in module pysoftk.pol_analysis.spherical_density_water) (in module pysoftk.pol_analysis.umap_analysis)

Torsional (class in pysoftk.torsional.torsional) total_number_clusters() (in module pysoftk.pol_analysis.tools.clustering_prob_distribution_plot) tpr (pysoftk.pol_analysis.tools.utils_mda.MDA_input attribute) tuple_bonds() (in module pysoftk.tools.utils_func)

U

UFF_rel() (in module pysoftk.tools.utils_rdkit)

umap_analysis (class in pysoftk.pol_analysis.umap_analysis) umap_run() (pysoftk.pol_analysis.umap_analysis.umap_analysis method)

V

validate_mol() (pysoftk.torsional.torsional.Torsional method)

X

x_shift() (pysoftk.linear_polymer.linear_polymer.Lp method) xtb_ff() (pysoftk.htp_tools.calculator_htp.Htp static method) xtb_gfn() (pysoftk.htp_tools.calculator_htp.Htp static method) xtb_path (pysoftk.htp_tools.calculator_htp.Htp attribute)

xtc (pysoftk.pol_analysis.tools.utils_mda.MDA_input attribute) xyz() (pysoftk.linear_polymer.calculators.Pyscf_print method) xyz_geom (pysoftk.htp_tools.calculator_htp.Htp attribute) xyz_print() (pysoftk.format_printers.format_mol.Fmt method)