Index

A

aa_to_cg() (DNA3SPN2Parser static method) add_all_default_forces() (HPSModel method) (MOFFMRGModel method) add_contacts() (HPSModel method) (MOFFMRGModel method) (MpipiModel method) add_dh_elec() (HPSModel method) (MpipiModel method) add_dna_angles() (MOFFMRGModel method) add_dna_bonds() (MOFFMRGModel method) add_dna_fan_bonds() (MOFFMRGModel method) add_elec_switch() (MOFFMRGModel method) add_native_pairs() (MOFFMRGModel method)

add_plumed() (CGModel method) add_protein_angles() (MOFFMRGModel method) add_protein_bonds() (HPSModel method) (MOFFMRGModel method) (MpipiModel method) add_protein_dihedrals() (MOFFMRGModel method) add_reporters() (CGModel method) (TemperatureReplicaExchange method) add_rna_bonds() (MpipiModel method) align_protein() (in module openabc.utils.CA2AA) append_mol() (CGModel method) atomistic_pdb_to_ca_pdb() (in module openabc.utils.helper_functions) atomistic_pdb_to_nucleotide_pdb() (in module openabc.utils.helper_functions) atoms_to_pdb() (CGModel method)

B

build_straight_CA_chain() (in module openabc.utils.helper_functions)

build_straight_chain() (in module openabc.utils.helper_functions) build_x3dna_template() (DNA3SPN2Parser method)

C

CGModel (class in openabc.forcefields.cg_model) change_sequence() (DNA3SPN2Parser static method) combine_proteins() (in module openabc.utils.CA2AA)

compute_PE() (in module openabc.utils.helper_functions) compute_rg() (in module openabc.utils.helper_functions) create_system() (CGModel method)

D

DNA3SPN2Parser (class in openabc.forcefields.parsers.dna_3spn2_parser)

F

find_ca_pairs_from_atomistic_pdb() (in module openabc.utils.shadow_map) find_res_pairs_from_atomistic_pdb() (in module openabc.utils.shadow_map) fix_pdb() (in module openabc.utils.helper_functions) from_atomistic_pdb() (DNA3SPN2Parser class method) (HPSParser class method) (MOFFParser class method) (MpipiProteinParser class method) (MRGdsDNAParser class method) (SMOGParser class method)

from_sequence() (MpipiRNAParser class method)

G

get_bonded_neighbor_dict() (in module openabc.utils.shadow_map) get_chromatin_rigid_bodies() (in module openabc.utils.chromatin_helper_functions) get_neighbor_pairs_and_distances() (in module openabc.utils.shadow_map)

get_sequence() (DNA3SPN2Parser method) get_sequence_list() (DNA3SPN2Parser method) get_sequence_list_from_cg_atoms() (DNA3SPN2Parser static method) get_WC_paired_sequence() (in module openabc.utils.helper_functions)

H

HPSModel (class in openabc.forcefields.hps_model)

HPSParser (class in openabc.forcefields.parsers.hps_parser)

I

insert_molecules() (in module openabc.utils.insert)

insert_molecules_dataframe() (in module openabc.utils.insert)

L

light_is_blocked() (in module openabc.utils.shadow_map)

load_ca_pairs_from_gmx_top() (in module openabc.utils.shadow_map)

M

make_mol_whole() (in module openabc.utils.helper_functions) module openabc.forcefields.cg_model openabc.forcefields.hps_model openabc.forcefields.moff_mrg_model openabc.forcefields.mpipi_model openabc.forcefields.parsers.dna_3spn2_parser openabc.forcefields.parsers.hps_parser openabc.forcefields.parsers.moff_parser openabc.forcefields.parsers.mpipi_parsers openabc.forcefields.parsers.mrg_parser openabc.forcefields.parsers.smog_parser openabc.forcefields.smog_3spn2_model openabc.utils.CA2AA openabc.utils.chromatin_helper_functions openabc.utils.helper_functions openabc.utils.insert openabc.utils.replica_exchange openabc.utils.shadow_map openabc.utils.stride

MOFFMRGModel (class in openabc.forcefields.moff_mrg_model) MOFFParser (class in openabc.forcefields.parsers.moff_parser) move_atoms_to_closest_pbc_image() (in module openabc.utils.helper_functions) move_COM_to_box_center() (CGModel method) MpipiModel (class in openabc.forcefields.mpipi_model) MpipiProteinParser (class in openabc.forcefields.parsers.mpipi_parsers) MpipiRNAParser (class in openabc.forcefields.parsers.mpipi_parsers) MRGdsDNAParser (class in openabc.forcefields.parsers.mrg_parser) multiple_chains_CA2AA() (in module openabc.utils.CA2AA)

O

openabc.forcefields.cg_model module openabc.forcefields.hps_model module openabc.forcefields.moff_mrg_model module openabc.forcefields.mpipi_model module openabc.forcefields.parsers.dna_3spn2_parser module openabc.forcefields.parsers.hps_parser module openabc.forcefields.parsers.moff_parser module openabc.forcefields.parsers.mpipi_parsers module openabc.forcefields.parsers.mrg_parser module

openabc.forcefields.parsers.smog_parser module openabc.forcefields.smog_3spn2_model module openabc.utils.CA2AA module openabc.utils.chromatin_helper_functions module openabc.utils.helper_functions module openabc.utils.insert module openabc.utils.replica_exchange module openabc.utils.shadow_map module openabc.utils.stride module

P

parse_exclusions() (MOFFParser method) (MRGdsDNAParser method) (SMOGParser method) parse_mol() (DNA3SPN2Parser method) (HPSParser method) (MOFFParser method) (MpipiProteinParser method) (MpipiRNAParser method) (MRGdsDNAParser method) (SMOGParser method)

parse_pdb() (in module openabc.utils.helper_functions) parse_stride() (in module openabc.utils.stride)

R

remove_histone_tail_dihedrals() (in module openabc.utils.chromatin_helper_functions)

remove_histone_tail_native_pairs_and_exclusions() (in module openabc.utils.chromatin_helper_functions) run_replica_exchange() (TemperatureReplicaExchange method)

S

save_state() (CGModel method) save_system() (CGModel method) set_rigid_bodies() (CGModel method)

set_simulation() (CGModel method) single_chain_CA2AA() (in module openabc.utils.CA2AA) SMOGParser (class in openabc.forcefields.parsers.smog_parser) split_protein() (in module openabc.utils.CA2AA)

T

TemperatureReplicaExchange (class in openabc.utils.replica_exchange)

W

write_pdb() (in module openabc.utils.helper_functions)