Index

A

a_mapping (reforge.forge.forcefields.Martini30RNA attribute) add_atom() (reforge.pdbtools.Chain method) (reforge.pdbtools.Model method) (reforge.pdbtools.Residue method) (reforge.pdbtools.System method) add_atoms() (reforge.pdbtools.System method) add_bulk_ions() (reforge.mdsystem.gmxmd.GmxSystem method) alt_locs (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) alt_resnames (reforge.forge.forcefields.Martini30RNA attribute) anaeig() (reforge.mdsystem.gmxmd.GmxRun method) animate_1d() (in module reforge.plotting)

animate_2d() (in module reforge.plotting) append_to() (in module reforge.martini.martini_tools) args_to_str() (in module reforge.cli) atids (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) Atom (class in reforge.pdbtools) AtomList (class in reforge.pdbtools) AtomListCollection (class in reforge.pdbtools) atoms (reforge.pdbtools.Chain property) (reforge.pdbtools.Model property) (reforge.pdbtools.Residue property) (reforge.pdbtools.System property)

B

bb_mapping (reforge.forge.forcefields.Martini30RNA attribute) (reforge.forge.forcefields.Martini31Nucleic attribute) bfactors (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property)

bond2line() (in module reforge.itpio) BondList (class in reforge.forge.topology)

C

c_mapping (reforge.forge.forcefields.Martini30RNA attribute) calc_and_save_covmats() (in module reforge.mdm) calc_and_save_rmsf() (in module reforge.mdm) calc_angles() (in module reforge.forge.geometry) calc_bonds() (in module reforge.forge.geometry) calc_dihedrals() (in module reforge.forge.geometry) calcperturbMat() (in module reforge.rfgmath.legacy) calculate_hessian() (in module reforge.rfgmath.legacy) (in module reforge.rfgmath.rcmath) categorize() (reforge.forge.topology.BondList method) ccf() (in module reforge.mdm) (in module reforge.rfgmath.rpymath) cd() (in module reforge.utils) Chain (class in reforge.pdbtools) chains (reforge.mdsystem.mdsystem.MDSystem property) (reforge.pdbtools.AtomList property) chains() (reforge.pdbtools.System method) change_directory() (in module reforge.cli) charges (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) check_browser() (in module reforge.martini.getgo) check_browsers() (in module reforge.martini.getgo)

check_debian_package() (in module reforge.martini.getgo) check_geckodriver_installed() (in module reforge.martini.getgo) chids (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) clean_chains_gmx() (reforge.mdsystem.mdsystem.MDSystem method) clean_chains_mm() (reforge.mdsystem.mdsystem.MDSystem method) clean_dir() (in module reforge.utils) clean_pdb() (in module reforge.pdbtools) (reforge.mdsystem.mmmd.MmSystem method) clean_pdb_gmx() (reforge.mdsystem.mdsystem.MDSystem method) clean_pdb_mm() (reforge.mdsystem.mdsystem.MDSystem method) cluster() (reforge.mdsystem.gmxmd.GmxRun method) comms (reforge.forge.topology.BondList property) conns (reforge.forge.topology.BondList property) convert_tpr() (reforge.mdsystem.gmxmd.GmxRun method) count_itp_atoms() (in module reforge.itpio) count_resolved_ions() (reforge.mdsystem.mdsystem.MDSystem method) covar() (reforge.mdsystem.gmxmd.GmxRun method) covariance_matrix() (in module reforge.mdm) (in module reforge.rfgmath.rpymath) covmat() (in module reforge.rfgmath.rcmath) create_job_script() (in module reforge.cli)

D

dci() (in module reforge.mdm) (in module reforge.rfgmath.rpymath) describeNextReport() (reforge.mdsystem.mmmd.MmReporter method)

dfi() (in module reforge.mdm) dojob() (in module reforge.cli) dssp() (in module reforge.martini.martini_tools)

E

elastic_network() (reforge.forge.topology.Topology method) elements (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) em() (reforge.mdsystem.mmmd.MmRun method) empp() (reforge.mdsystem.gmxmd.GmxRun method)

eq() (reforge.mdsystem.mmmd.MmRun method) eqpp() (reforge.mdsystem.gmxmd.GmxRun method) extend() (reforge.mdsystem.mmmd.MmRun method) extract_cluster() (reforge.mdsystem.gmxmd.GmxRun method) extract_go_maps() (in module reforge.martini.getgo)

F

fft_ccf() (in module reforge.mdm) (in module reforge.rfgmath.rpymath) filter() (reforge.forge.topology.BondList method) filter_files() (in module reforge.io) find_resolved_ions() (reforge.mdsystem.mdsystem.MDSystem method) fix_go_map() (in module reforge.martini.martini_tools) fname_filter() (in module reforge.io) format_atoms_section() (in module reforge.itpio)

format_bonded_section() (in module reforge.itpio) format_header() (in module reforge.itpio) format_moleculetype_section() (in module reforge.itpio) format_posres_section() (in module reforge.itpio) format_sequence_section() (in module reforge.itpio) from_chain() (reforge.forge.topology.Topology method) from_pdb_line() (reforge.pdbtools.Atom class method) from_sequence() (reforge.forge.topology.Topology method) from_wdir() (in module reforge.cli)

G

g_mapping (reforge.forge.forcefields.Martini30RNA attribute) get_aa_bonds() (in module reforge.forge.geometry) get_angle() (in module reforge.forge.geometry) (in module reforge.forge.persistence_length) get_atoms_by_name() (in module reforge.forge.persistence_length) get_cg_bonds() (in module reforge.forge.geometry) get_coords() (in module reforge.forge.persistence_length) get_covmats() (reforge.mdsystem.mdsystem.MDRun method) get_dci() (reforge.mdsystem.mdsystem.MDRun method) get_dfi() (reforge.mdsystem.mdsystem.MDRun method) get_dihedral() (in module reforge.forge.geometry) get_distance() (in module reforge.forge.geometry) get_go() (in module reforge.martini.getgo) get_go_maps() (in module reforge.martini.getgo) (reforge.mdsystem.mdsystem.MDSystem method) get_group_dci() (reforge.mdsystem.mdsystem.MDRun method) get_logger() (in module reforge.utils) get_mean_sem() (reforge.mdsystem.mdsystem.MDSystem method) get_ntomp() (in module reforge.mdsystem.gmxmd) get_pertmats() (reforge.mdsystem.mdsystem.MDRun method)

get_resid() (in module reforge.forge.persistence_length) get_residues() (in module reforge.forge.persistence_length) get_rmsd_by_chain() (reforge.mdsystem.gmxmd.GmxRun method) get_rmsf_by_chain() (reforge.mdsystem.gmxmd.GmxRun method) get_std_reporters() (reforge.mdsystem.mmmd.MmRun method) get_structure_cif() (in module reforge.forge.persistence_length) get_structure_pdb() (in module reforge.forge.persistence_length) get_td_averages() (reforge.mdsystem.mdsystem.MDSystem method) gfft_ccf() (in module reforge.rfgmath.rpymath) gfft_ccf_auto() (in module reforge.rfgmath.rpymath) gfft_conv() (in module reforge.rfgmath.rpymath) gmx() (in module reforge.cli) (reforge.mdsystem.gmxmd.GmxRun method) (reforge.mdsystem.gmxmd.GmxSystem method) GmxRun (class in reforge.mdsystem.gmxmd) GmxSystem (class in reforge.mdsystem.gmxmd) grid_labels() (in module reforge.plotting) group_group_dci() (in module reforge.mdm) (in module reforge.rfgmath.rpymath) group_molecule_dci() (in module reforge.mdm) (in module reforge.rfgmath.rpymath)

H

hessian() (in module reforge.mdm) (in module reforge.rfgmath.rcmath)

hessian_cuda() (in module reforge.rfgmath.rpykernels) hu() (reforge.mdsystem.mmmd.MmRun method) hupp() (reforge.mdsystem.gmxmd.GmxRun method)

I

icodes (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) init_figure() (in module reforge.plotting) init_webdriver() (in module reforge.martini.getgo) initmd() (reforge.mdsystem.gmxmd.GmxSystem method) insert_membrane() (in module reforge.martini.martini_tools) (reforge.mdsystem.mdsystem.MDSystem method) install_webdriver() (in module reforge.martini.getgo)

inverse_matrix() (in module reforge.mdm) inverse_matrix_cpu() (in module reforge.rfgmath.rpymath) inverse_matrix_gpu() (in module reforge.rfgmath.rpymath) inverse_sparse_matrix_cpu() (in module reforge.rfgmath.rpymath) inverse_sparse_matrix_gpu() (in module reforge.rfgmath.rpymath) invert_hessian() (in module reforge.rfgmath.legacy) invert_matrix_gpu() (in module reforge.rfgmath.legacy) invert_symm_block_matrix_gpu() (in module reforge.rfgmath.legacy) itp_to_indata() (reforge.forge.forcefields.NucleicForceField static method)

K

key_funcs (reforge.pdbtools.AtomList attribute)

kwargs_to_str() (in module reforge.cli)

L

label_segments() (in module reforge.pdbtools)

line2bond() (in module reforge.itpio) lines() (reforge.forge.topology.Topology method)

M

main() (in module reforge.forge.persistence_length) (in module reforge.martini.martinize_rna) make_1d_data() (in module reforge.plotting) make_1d_plots() (in module reforge.plotting) make_2d_data() (in module reforge.plotting) make_animation() (in module reforge.plotting) make_box() (reforge.mdsystem.gmxmd.GmxSystem method) make_cg_structure() (reforge.mdsystem.gmxmd.GmxSystem method) make_cg_topology() (reforge.mdsystem.gmxmd.GmxSystem method) make_cross_terms() (in module reforge.itpio) make_edi() (reforge.mdsystem.gmxmd.GmxRun method) make_errorbar() (in module reforge.plotting) make_gro_file() (reforge.mdsystem.gmxmd.GmxSystem method) make_heatmap() (in module reforge.plotting) make_heatmap_td() (in module reforge.plotting) make_hist() (in module reforge.plotting) make_in_terms() (in module reforge.itpio) make_ions_itp() (in module reforge.itpio) make_marnatini_itp() (in module reforge.itpio) make_plot() (in module reforge.plotting) make_plot_t_2d() (in module reforge.plotting) make_plot_t_td() (in module reforge.plotting) make_plot_td() (in module reforge.plotting) make_system_ndx() (reforge.mdsystem.gmxmd.GmxSystem method) map_chain() (in module reforge.forge.cgmap) map_model() (in module reforge.forge.cgmap) map_residue() (in module reforge.forge.cgmap) mapping (reforge.forge.forcefields.Martini30RNA attribute) (reforge.forge.forcefields.Martini31Nucleic attribute) Martini30RNA (class in reforge.forge.forcefields) Martini31Nucleic (class in reforge.forge.forcefields) martinize_nucleotides() (reforge.mdsystem.mdsystem.MDSystem method) martinize_proteins_en() (reforge.mdsystem.mdsystem.MDSystem method) martinize_proteins_go() (reforge.mdsystem.mdsystem.MDSystem method) martinize_rna() (in module reforge.martini.martinize_rna) (reforge.mdsystem.mdsystem.MDSystem method) mask() (reforge.pdbtools.AtomList method) mask_out() (reforge.pdbtools.AtomList method) MDATDIR (reforge.mdsystem.mdsystem.MDSystem attribute) mdpp() (reforge.mdsystem.gmxmd.GmxRun method) MDRun (class in reforge.mdsystem.mdsystem)

mdrun() (reforge.mdsystem.gmxmd.GmxRun method) MDSystem (class in reforge.mdsystem.mdsystem) measures (reforge.forge.topology.BondList property) memprofit() (in module reforge.utils) merge_topologies() (in module reforge.martini.martinize_rna) (reforge.forge.topology.Topology static method) MITPDIR (reforge.mdsystem.mdsystem.MDSystem attribute) mkfigure() (in module reforge.plotting) MMDPDIR (reforge.mdsystem.gmxmd.GmxSystem attribute) MmReporter (class in reforge.mdsystem.mmmd) MmRun (class in reforge.mdsystem.mmmd) MmSystem (class in reforge.mdsystem.mmmd) Model (class in reforge.pdbtools) module reforge reforge.cli reforge.forge reforge.forge.cgmap reforge.forge.forcefields reforge.forge.geometry reforge.forge.persistence_length reforge.forge.topology reforge.io reforge.itpio reforge.martini reforge.martini.getgo reforge.martini.martini_tools reforge.martini.martinize_rna reforge.mdm reforge.mdsystem reforge.mdsystem.gmxmd reforge.mdsystem.mdsystem reforge.mdsystem.mmmd reforge.pdbtools reforge.plotting reforge.rfgmath reforge.rfgmath.legacy reforge.rfgmath.rcmath reforge.rfgmath.rpykernels reforge.rfgmath.rpymath reforge.utils move_o3() (in module reforge.forge.cgmap)

N

names (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) npy2csv() (in module reforge.io)

nsplit() (in module reforge.forge.forcefields) NUC_RESNAMES (reforge.mdsystem.mdsystem.MDSystem attribute) NucleicForceField (class in reforge.forge.forcefields)

O

occupancies (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property)

P

pad_matrix_if_odd() (in module reforge.rfgmath.legacy) parameters_by_resname() (reforge.forge.forcefields.NucleicForceField static method) params (reforge.forge.topology.BondList property) parse() (reforge.pdbtools.PDBParser method) parse_arguments() (in module reforge.martini.getgo) parse_covar_dat() (in module reforge.io) pcovmat() (in module reforge.rfgmath.rcmath) pdb2atomlist() (in module reforge.io) (in module reforge.pdbtools) pdb2system() (in module reforge.io) (in module reforge.pdbtools) PDBParser (class in reforge.pdbtools) percentile() (in module reforge.mdm) (in module reforge.rfgmath.rpymath) persistence_length() (in module reforge.forge.persistence_length) perturbation_matrix() (in module reforge.mdm) (in module reforge.rfgmath.rcmath) perturbation_matrix_cpu() (in module reforge.rfgmath.legacy) perturbation_matrix_cuda() (in module reforge.rfgmath.rpykernels) perturbation_matrix_iso() (in module reforge.mdm) (in module reforge.rfgmath.rcmath) perturbation_matrix_iso_par() (in module reforge.rfgmath.rcmath) perturbation_matrix_old() (in module reforge.rfgmath.legacy) (in module reforge.rfgmath.rcmath)

perturbation_matrix_par() (in module reforge.rfgmath.rcmath) pfft_ccf() (in module reforge.rfgmath.rpymath) plot_asym() (in module reforge.plotting) plot_dci() (in module reforge.plotting) plot_dfi() (in module reforge.plotting) plot_figure() (in module reforge.plotting) plot_pdfi() (in module reforge.plotting) plot_pert() (in module reforge.plotting) plot_rmsd() (in module reforge.plotting) plot_rmsf() (in module reforge.plotting) plot_segment_asym() (in module reforge.plotting) plot_segment_dci() (in module reforge.plotting) prepare_files() (reforge.mdsystem.gmxmd.GmxSystem method) (reforge.mdsystem.mdsystem.MDRun method) (reforge.mdsystem.mdsystem.MDSystem method) (reforge.mdsystem.mmmd.MmSystem method) process_atoms() (reforge.forge.topology.Topology method) process_bb_bonds() (reforge.forge.topology.Topology method) process_chain() (in module reforge.martini.martinize_rna) process_sc_bonds() (reforge.forge.topology.Topology method) pull_all_files() (in module reforge.io) pull_data() (in module reforge.plotting) pull_files() (in module reforge.io)

R

rdf() (reforge.mdsystem.gmxmd.GmxRun method) read_data() (in module reforge.io) read_itp() (in module reforge.itpio) (reforge.forge.forcefields.NucleicForceField static method) read_itps() (reforge.forge.forcefields.NucleicForceField static method) read_pdb() (reforge.pdbtools.AtomList method) read_positions() (in module reforge.io) read_positions_tmp() (in module reforge.io) read_velocities() (in module reforge.io) read_xvg() (in module reforge.io) records (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) reforge module reforge.cli module reforge.forge module reforge.forge.cgmap module reforge.forge.forcefields module reforge.forge.geometry module reforge.forge.persistence_length module reforge.forge.topology module reforge.io module reforge.itpio module reforge.martini module reforge.martini.getgo module reforge.martini.martini_tools module reforge.martini.martinize_rna module reforge.mdm module reforge.mdsystem module reforge.mdsystem.gmxmd module reforge.mdsystem.mdsystem module

reforge.mdsystem.mmmd module reforge.pdbtools module reforge.plotting module reforge.rfgmath module reforge.rfgmath.legacy module reforge.rfgmath.rcmath module reforge.rfgmath.rpykernels module reforge.rfgmath.rpymath module reforge.utils module remove_atoms() (reforge.pdbtools.AtomList method) rename_chain_and_histidines_in_pdb() (in module reforge.pdbtools) rename_chain_in_pdb() (in module reforge.pdbtools) rename_chains_for_gromacs() (in module reforge.pdbtools) renum() (reforge.pdbtools.AtomList method) renumber() (reforge.pdbtools.AtomList method) report() (reforge.mdsystem.mmmd.MmReporter method) resids (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) Residue (class in reforge.pdbtools) residues (reforge.pdbtools.AtomList property) residues() (reforge.pdbtools.System method) resnames (reforge.forge.forcefields.Martini30RNA attribute) (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) response() (in module reforge.plotting) response_1() (in module reforge.plotting) response_2() (in module reforge.plotting) response_2_2d() (in module reforge.plotting) response_force() (in module reforge.plotting) rmsd() (reforge.mdsystem.gmxmd.GmxRun method) rmsf() (reforge.mdsystem.gmxmd.GmxRun method) rotation_matrix_from_vectors() (in module reforge.forge.persistence_length) run() (in module reforge.cli) run_command() (in module reforge.cli) run_martinize_en() (in module reforge.martini.martini_tools) run_martinize_go() (in module reforge.martini.martini_tools) run_martinize_nucleotide() (in module reforge.martini.martini_tools) run_martinize_rna() (in module reforge.martini.martini_tools)

S

save_1d_data() (in module reforge.io) save_2d_data() (in module reforge.io) sbatch() (in module reforge.cli) sc_angles() (reforge.forge.forcefields.NucleicForceField method) sc_atoms() (reforge.forge.forcefields.Martini30RNA method) (reforge.forge.forcefields.Martini31Nucleic method) sc_blist() (reforge.forge.forcefields.NucleicForceField method) sc_bonds() (reforge.forge.forcefields.NucleicForceField method) sc_cons() (reforge.forge.forcefields.NucleicForceField method) sc_dihs() (reforge.forge.forcefields.NucleicForceField method) sc_excls() (reforge.forge.forcefields.NucleicForceField method) sc_pairs() (reforge.forge.forcefields.NucleicForceField method) sc_vs3s() (reforge.forge.forcefields.NucleicForceField method) segids (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property) segments (reforge.mdsystem.mdsystem.MDSystem property) (reforge.pdbtools.AtomList property)

select_chains() (reforge.pdbtools.Model method) set_ax_parameters() (in module reforge.plotting) set_hm_parameters() (in module reforge.plotting) sfft_ccf() (in module reforge.rfgmath.rpymath) sfft_cpsd() (in module reforge.rfgmath.rpymath) solvate() (reforge.mdsystem.gmxmd.GmxSystem method) sort() (reforge.pdbtools.AtomList method) sort_chains_atoms() (in module reforge.pdbtools) sort_for_gmx() (in module reforge.mdsystem.gmxmd) sort_input_pdb() (reforge.mdsystem.mdsystem.MDSystem method) sort_pdb() (in module reforge.pdbtools) sort_uld() (in module reforge.pdbtools) split_chains() (reforge.mdsystem.mdsystem.MDSystem method) split_matrix() (in module reforge.rfgmath.legacy) System (class in reforge.pdbtools)

T

td_perturbation_matrix() (in module reforge.mdm) (in module reforge.rfgmath.rcmath) td_perturbation_matrix_cpu() (in module reforge.rfgmath.legacy) td_perturbation_matrix_cuda() (in module reforge.rfgmath.rpykernels) td_perturbation_matrix_par() (in module reforge.rfgmath.rcmath)

test_rmats() (in module reforge.forge.persistence_length) timeit() (in module reforge.utils) to_pdb_line() (reforge.pdbtools.Atom method) Topology (class in reforge.forge.topology) trjconv() (reforge.mdsystem.gmxmd.GmxRun method)

U

u_mapping (reforge.forge.forcefields.Martini30RNA attribute)

update_bfactors() (in module reforge.pdbtools) update_non_standard_mapping() (reforge.forge.forcefields.NucleicForceField static method)

V

vecs (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property)

W

write_itp() (in module reforge.itpio) write_ndx() (in module reforge.pdbtools) (reforge.pdbtools.AtomList method)

write_pdb() (reforge.pdbtools.AtomList method) (reforge.pdbtools.System method) write_to_itp() (reforge.forge.topology.Topology method)

X

xs (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property)

xvg2npy() (in module reforge.io)

Y

ys (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property)

Z

zs (reforge.pdbtools.AtomList property) (reforge.pdbtools.AtomListCollection property)