Index

A

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)

branched_polymer() (pysoftk.topologies.branched.Bd method)

C

check_bond_order() (in module pysoftk.tools.utils_ob) check_proto() (pysoftk.topologies.ring.Rn 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)

copy_dir() (pysoftk.folder_manager.folder_creator.Fld method) core (pysoftk.topologies.branched.Bd attribute) count_plholder() (in module pysoftk.tools.utils_func) create() (pysoftk.folder_manager.folder_creator.Fld method) create_pol() (in module pysoftk.tools.utils_func) create_ring() (pysoftk.topologies.ring.Rn method)

D

Db (class in pysoftk.topologies.diblock)

diblock_copolymer() (pysoftk.topologies.diblock.Db method) draw_molecule() (pysoftk.torsional.torsional.Torsional method)

E

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)

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

H

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)

I

init_dir (pysoftk.htp_tools.calculator_htp.Htp attribute)

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) 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) merge_arms() (pysoftk.topologies.branched.Bd method) 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.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) 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)

O

Opt (class in pysoftk.linear_polymer.calculators)

P

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) 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_ring() (pysoftk.topologies.ring.Rn 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.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)

Rn (class in pysoftk.topologies.ring) Rnp (class in pysoftk.topologies.ranpol) rotor_opt() (in module pysoftk.tools.utils_ob)

S

seek_angles() (pysoftk.torsional.torsional.Torsional method) seek_files() (pysoftk.folder_manager.folder_creator.Fld 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) swap_hyd() (in module pysoftk.tools.utils_rdkit)

T

threshold (pysoftk.htp_tools.calculator_htp.Htp attribute)

Torsional (class in pysoftk.torsional.torsional) tuple_bonds() (in module pysoftk.tools.utils_func)

U

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

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) 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)