Index

A

add_connection_group() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) add_connection_group_symm() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) add_R_group() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) align_to() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) angle() (in module pycofbuilder.tools) angle_tol (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) as_dict() (pycofbuilder.cjson.ChemJSON method) as_string() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method)

atom_pos (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) atom_types (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) atomic_labels (pycofbuilder.cjson.ChemJSON attribute) atomic_numbers (pycofbuilder.cjson.ChemJSON attribute) atomic_types (pycofbuilder.cjson.ChemJSON attribute) available_2D_topologies (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) available_3D_topologies (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) available_stacking (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) available_topologies (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

B

BuildingBlock (class in pycofbuilder) (class in pycofbuilder.building_block)

C

calculate_size() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) calculate_UnitCells() (in module pycofbuilder.tools) cartesian_positions (pycofbuilder.cjson.ChemJSON attribute) cell_matrix (pycofbuilder.cjson.ChemJSON attribute) cell_parameters (pycofbuilder.cjson.ChemJSON attribute) cell_to_cellpar() (in module pycofbuilder.tools) cell_to_ibrav() (in module pycofbuilder.tools) cellpar_to_cell() (in module pycofbuilder.tools) cellpar_to_lammpsbox() (in module pycofbuilder.tools) centralize() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) change_X_atoms() (in module pycofbuilder.tools) charge (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) check_existence() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) check_name_concistency() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) ChemJSON (class in pycofbuilder.cjson) chirality (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) classify_unit_cell() (in module pycofbuilder.tools) closest_atom() (in module pycofbuilder.tools) closest_atom_struc() (in module pycofbuilder.tools) composition (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) convert_cif_2_qe() (in module pycofbuilder.io_tools) convert_cif_2_xyz() (in module pycofbuilder.io_tools) convert_gjf_2_xyz() (in module pycofbuilder.io_tools) convert_json_2_cif() (in module pycofbuilder.io_tools)

convert_xyz_2_gjf() (in module pycofbuilder.io_tools) copy() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) create_BB_structure() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) create_bor_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_CellBox() (in module pycofbuilder.tools) create_COF_json() (in module pycofbuilder.io_tools) create_dia_a_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_dia_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_empty_CJSON() (in module pycofbuilder.io_tools) create_fxt_a_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_fxt_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_hcb_a_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_hcb_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_hxl_a_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_kgd_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_sql_a_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_sql_structure() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) create_structure_CJSON() (in module pycofbuilder.io_tools)

D

dimention (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

dist_threshold (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

E

elements_dict() (in module pycofbuilder.tools)

equal_value() (in module pycofbuilder.tools)

F

file_name (pycofbuilder.cjson.ChemJSON attribute) find_index() (in module pycofbuilder.tools) formula (pycofbuilder.cjson.ChemJSON attribute) formula_from_atom_list() (in module pycofbuilder.tools) fractional_positions (pycofbuilder.cjson.ChemJSON attribute) Framework (class in pycofbuilder) (class in pycofbuilder.framework) from_building_blocks() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method)

from_cif() (pycofbuilder.cjson.ChemJSON method) from_cjson() (pycofbuilder.cjson.ChemJSON method) from_file() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) from_gjf() (pycofbuilder.cjson.ChemJSON method) from_name() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) from_xyz() (pycofbuilder.cjson.ChemJSON method)

G

generate_mol_dict() (in module pycofbuilder.io_tools) get_available_conector() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) get_available_core() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) get_available_R() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) get_available_topologies() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) get_bond_atom() (in module pycofbuilder.tools) get_bonds() (in module pycofbuilder.tools) get_buildingblock_list() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method)

get_cartesian_to_fractional_matrix() (in module pycofbuilder.tools) get_fractional_to_cartesian_matrix() (in module pycofbuilder.tools) get_framework_symm_text() (in module pycofbuilder.tools) get_kgrid() (in module pycofbuilder.tools) get_n_atoms() (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) get_Q_points() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) get_R_points() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) get_reciprocal_vectors() (in module pycofbuilder.tools) get_X_points() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method)

I

ibrav_to_cell() (in module pycofbuilder.tools)

is_bonded() (in module pycofbuilder.tools)

L

lattice (pycofbuilder.Framework attribute), [1] (pycofbuilder.framework.Framework attribute), [1] lattice_sgs (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

lib_bb (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) lib_path (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

M

mass (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) module pycofbuilder pycofbuilder.building_block pycofbuilder.cjson pycofbuilder.framework pycofbuilder.io_tools pycofbuilder.tools

multiplicity (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

N

n_atoms() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method)

name (pycofbuilder.cjson.ChemJSON attribute) (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

O

out_dir (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

P

partial_charges (pycofbuilder.cjson.ChemJSON attribute) print_command() (in module pycofbuilder.tools) print_framework_name() (in module pycofbuilder.tools) print_structure() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) properties (pycofbuilder.cjson.ChemJSON attribute) pycofbuilder module pycofbuilder.building_block module

pycofbuilder.cjson module pycofbuilder.framework module pycofbuilder.io_tools module pycofbuilder.tools module

R

read_cif() (in module pycofbuilder.io_tools) read_gjf() (in module pycofbuilder.io_tools) read_json() (in module pycofbuilder.io_tools) read_pdb() (in module pycofbuilder.io_tools) read_xyz() (in module pycofbuilder.io_tools) remove_X() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method)

replace_X() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) rmsd() (in module pycofbuilder.tools) rotate_around() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) rotate_to_xy_plane() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) rotation_matrix_from_vectors() (in module pycofbuilder.tools)

S

save() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) (pycofbuilder.Framework method) (pycofbuilder.framework.Framework method) save_bb (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) save_chemjson() (in module pycofbuilder.io_tools) save_cif() (in module pycofbuilder.io_tools) save_csv() (in module pycofbuilder.io_tools) save_gjf() (in module pycofbuilder.io_tools) save_pdb() (in module pycofbuilder.io_tools) save_pqr() (in module pycofbuilder.io_tools) save_qe() (in module pycofbuilder.io_tools) save_turbomole() (in module pycofbuilder.io_tools) save_vasp() (in module pycofbuilder.io_tools) save_xsf() (in module pycofbuilder.io_tools) save_xyz() (in module pycofbuilder.io_tools) set_atomic_numbers() (pycofbuilder.cjson.ChemJSON method) set_atomic_types() (pycofbuilder.cjson.ChemJSON method)

set_cartesian_positions() (pycofbuilder.cjson.ChemJSON method) set_cell_matrix() (pycofbuilder.cjson.ChemJSON method) set_cell_parameters() (pycofbuilder.cjson.ChemJSON method) set_fractional_positions() (pycofbuilder.cjson.ChemJSON method) set_properties() (pycofbuilder.cjson.ChemJSON method) set_results() (pycofbuilder.cjson.ChemJSON method) shift() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) smiles_to_xsmiles() (in module pycofbuilder.tools) space_group (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) space_group_n (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) stacking (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute) structure_as_string() (pycofbuilder.building_block.BuildingBlock method) (pycofbuilder.BuildingBlock method) symm_tol (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

T

topology (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

U

unit_vector() (in module pycofbuilder.tools)

V

verbosity (pycofbuilder.Framework attribute) (pycofbuilder.framework.Framework attribute)

W

write_cjson() (pycofbuilder.cjson.ChemJSON method)

write_json() (in module pycofbuilder.io_tools)