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Gromacs_py
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A
add_atoms() (gromacs_py.gmx.topmol.TopMol method)
add_atomtypes() (gromacs_py.gmx.topsys.TopSys method)
add_atomtypes_2() (gromacs_py.gmx.topsys.TopSys method)
add_disulfide_bonds() (gromacs_py.gmx.gmxsys.GmxSys method)
add_intermol_restr_index() (gromacs_py.free_ener.FreeEner method)
add_intermolecular_restr() (gromacs_py.gmx.topsys.TopSys method)
add_ions() (gromacs_py.gmx.gmxsys.GmxSys method)
add_mdp() (gromacs_py.gmx.gmxsys.GmxSys method)
add_mol() (gromacs_py.gmx.topsys.TopSys method)
add_mol_itp() (gromacs_py.gmx.topsys.TopSys method)
add_ndx() (gromacs_py.gmx.gmxsys.GmxSys method)
add_posre() (gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.topsys.TopSys method)
add_top() (gromacs_py.gmx.gmxsys.GmxSys method)
add_tpr() (gromacs_py.gmx.gmxsys.GmxSys method)
align_ref_traj() (gromacs_py.free_ener.FreeEner method)
C
center_mol_box() (gromacs_py.gmx.gmxsys.GmxSys method)
change_mol_name() (gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.topsys.TopSys method)
change_mol_num() (gromacs_py.gmx.topsys.TopSys method)
charge() (gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.topsys.TopSys method)
compute_add_intermol_from_traj() (gromacs_py.free_ener.FreeEner method)
compute_convergence_alchemlyb() (gromacs_py.free_ener.FreeEner method)
compute_convergence_gbar() (gromacs_py.free_ener.FreeEner method)
compute_lambda_point() (gromacs_py.free_ener.FreeEner static method)
concat_coor() (gromacs_py.gmx.gmxsys.GmxSys static method)
concat_edr() (gromacs_py.gmx.gmxsys.GmxSys method)
concat_traj() (gromacs_py.gmx.gmxsys.GmxSys method)
conv_fac (gromacs_py.free_ener.FreeEner property)
convert_selection_to_index() (gromacs_py.gmx.gmxsys.GmxSys method)
convert_trj() (gromacs_py.gmx.gmxsys.GmxSys method)
coor_file (gromacs_py.gmx.gmxsys.GmxSys property)
copy_box() (gromacs_py.gmx.gmxsys.GmxSys method)
copy_dependancies() (gromacs_py.gmx.topsys.TopSys method)
copy_top_and_dependancies() (gromacs_py.gmx.topsys.TopSys method)
correct_charge_type() (gromacs_py.gmx.topmol.TopMol method)
create_box() (gromacs_py.gmx.gmxsys.GmxSys method)
create_itp_atomtype_ion_octa_dummy() (gromacs_py.gmx.gmxsys.GmxSys method)
create_itp_ion_octa_dummy() (gromacs_py.gmx.gmxsys.GmxSys method)
create_mdp() (gromacs_py.gmx.gmxsys.GmxSys method)
create_peptide() (gromacs_py.gmx.gmxsys.GmxSys method)
cyclic_peptide_top() (gromacs_py.gmx.gmxsys.GmxSys method)
D
delete_atom() (gromacs_py.gmx.topmol.TopMol method)
display() (gromacs_py.gmx.gmxsys.GmxSys method)
(gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.topsys.TopSys method)
display_history() (gromacs_py.gmx.gmxsys.GmxSys method)
E
edr (gromacs_py.gmx.gmxsys.GmxSys property)
em() (gromacs_py.gmx.gmxsys.GmxSys method)
em_2_steps() (gromacs_py.gmx.gmxsys.GmxSys method)
em_CG() (gromacs_py.gmx.gmxsys.GmxSys method)
em_equi_three_step_iter_error() (gromacs_py.gmx.gmxsys.GmxSys method)
equi_CG() (gromacs_py.gmx.gmxsys.GmxSys method)
equi_three_step() (gromacs_py.gmx.gmxsys.GmxSys method)
equilibrate_complex() (gromacs_py.free_ener.FreeEner method)
equilibrate_solvent_box() (gromacs_py.free_ener.FreeEner method)
extend_lambda_prod() (gromacs_py.free_ener.FreeEner method)
extend_sim() (gromacs_py.gmx.gmxsys.GmxSys method)
extract_log_dict() (in module gromacs_py.tools.monitor)
extract_mol_sys() (gromacs_py.gmx.gmxsys.GmxSys method)
F
FreeEner (class in gromacs_py.free_ener)
G
get_all_output() (gromacs_py.gmx.gmxsys.GmxSys method)
get_angle() (gromacs_py.gmx.gmxsys.GmxSys method)
get_bar() (gromacs_py.free_ener.FreeEner static method)
get_charge() (gromacs_py.gmx.topmol.TopMol method)
get_conv_fac() (gromacs_py.free_ener.FreeEner static method)
get_dist() (gromacs_py.gmx.gmxsys.GmxSys method)
get_ener() (gromacs_py.gmx.gmxsys.GmxSys method)
get_free_ener() (gromacs_py.free_ener.FreeEner method)
get_include_file_list() (gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.topsys.TopSys method)
get_include_no_posre_file_list() (gromacs_py.gmx.topsys.TopSys method)
get_index_dict() (gromacs_py.gmx.gmxsys.GmxSys method)
get_last_output() (gromacs_py.gmx.gmxsys.GmxSys method)
get_ligand_atoms() (gromacs_py.free_ener.FreeEner method)
get_mdp_dict() (gromacs_py.gmx.gmxsys.GmxSys method)
get_protein_atoms_from_res() (gromacs_py.free_ener.FreeEner method)
get_protein_atoms_from_rmsf() (gromacs_py.free_ener.FreeEner method)
get_res_num() (gromacs_py.gmx.topmol.TopMol method)
get_rmsd() (gromacs_py.gmx.gmxsys.GmxSys method)
get_rmsf() (gromacs_py.gmx.gmxsys.GmxSys method)
get_selection_index() (gromacs_py.gmx.topmol.TopMol method)
get_simulation_time() (gromacs_py.gmx.gmxsys.GmxSys method)
get_water_restr() (gromacs_py.free_ener.FreeEner method)
GmxSys (class in gromacs_py.gmx.gmxsys)
gromacs_py
module
gromacs_py.free_ener
module
gromacs_py.gmx
module
gromacs_py.gmx.gmxsys
module
gromacs_py.gmx.itp
module
gromacs_py.gmx.rtp
module
gromacs_py.gmx.topmol
module
gromacs_py.gmx.topsys
module
gromacs_py.test
module
gromacs_py.test.datafiles
module
gromacs_py.tools
module
gromacs_py.tools.monitor
module
I
insert_mol_sys() (gromacs_py.gmx.gmxsys.GmxSys method)
isnotebook() (in module gromacs_py.tools.monitor)
Itp (class in gromacs_py.gmx.itp)
L
log (gromacs_py.gmx.gmxsys.GmxSys property)
M
mdp (gromacs_py.gmx.gmxsys.GmxSys property)
module
gromacs_py
gromacs_py.free_ener
gromacs_py.gmx
gromacs_py.gmx.gmxsys
gromacs_py.gmx.itp
gromacs_py.gmx.rtp
gromacs_py.gmx.topmol
gromacs_py.gmx.topsys
gromacs_py.test
gromacs_py.test.datafiles
gromacs_py.tools
gromacs_py.tools.monitor
mol_num() (gromacs_py.gmx.topsys.TopSys method)
N
ndx (gromacs_py.gmx.gmxsys.GmxSys property)
O
octanol_box_from_SMILE() (gromacs_py.free_ener.FreeEner method)
P
plot_convergence() (gromacs_py.free_ener.FreeEner method)
plot_convergence_graph() (gromacs_py.free_ener.FreeEner method)
plot_intermol_restr() (gromacs_py.free_ener.FreeEner method)
prepare_complex_pdb() (gromacs_py.free_ener.FreeEner method)
prepare_top() (gromacs_py.gmx.gmxsys.GmxSys method)
prepare_top_ligand() (gromacs_py.gmx.gmxsys.GmxSys method)
print_log_file() (in module gromacs_py.tools.monitor)
prod_CG() (gromacs_py.gmx.gmxsys.GmxSys method)
production() (gromacs_py.gmx.gmxsys.GmxSys method)
progress_bar() (in module gromacs_py.tools.monitor)
prot_res_num() (gromacs_py.gmx.topsys.TopSys method)
R
read_file() (gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.rtp.Rtp method)
(gromacs_py.gmx.topsys.TopSys method)
read_xvg() (in module gromacs_py.tools.monitor)
remove_ion() (gromacs_py.gmx.topsys.TopSys method)
res_num() (gromacs_py.gmx.itp.Itp method)
Rtp (class in gromacs_py.gmx.rtp)
run() (gromacs_py.free_ener.FreeEner method)
run_md_sim() (gromacs_py.gmx.gmxsys.GmxSys method)
run_simulation() (gromacs_py.gmx.gmxsys.GmxSys method)
S
save_state() (gromacs_py.gmx.gmxsys.GmxSys method)
set_coor_aa_prot() (gromacs_py.gmx.gmxsys.GmxSys static method)
set_top_mol_name() (gromacs_py.gmx.itp.Itp method)
show_debug() (in module gromacs_py.gmx)
(in module gromacs_py.gmx.gmxsys)
(in module gromacs_py.gmx.topmol)
(in module gromacs_py.gmx.topsys)
show_intermol_restr() (gromacs_py.free_ener.FreeEner method)
show_log() (in module gromacs_py.free_ener)
(in module gromacs_py.gmx)
(in module gromacs_py.gmx.gmxsys)
(in module gromacs_py.gmx.itp)
(in module gromacs_py.gmx.topmol)
(in module gromacs_py.gmx.topsys)
simulation_plot() (in module gromacs_py.tools.monitor)
solvate_add_ions() (gromacs_py.gmx.gmxsys.GmxSys method)
solvate_box() (gromacs_py.gmx.gmxsys.GmxSys method)
switch_ion_octa_dummy() (gromacs_py.gmx.gmxsys.GmxSys method)
symmetry_correction() (gromacs_py.free_ener.FreeEner static method)
T
top_file (gromacs_py.gmx.gmxsys.GmxSys property)
TopMol (class in gromacs_py.gmx.topmol)
TopSys (class in gromacs_py.gmx.topsys)
tpr (gromacs_py.gmx.gmxsys.GmxSys property)
U
unit_graph (gromacs_py.free_ener.FreeEner property)
unit_name (gromacs_py.free_ener.FreeEner property)
V
view_coor() (gromacs_py.gmx.gmxsys.GmxSys method)
view_traj() (gromacs_py.gmx.gmxsys.GmxSys method)
W
water_box_from_SMILE() (gromacs_py.free_ener.FreeEner method)
write_file() (gromacs_py.gmx.itp.Itp method)
(gromacs_py.gmx.topmol.TopMol method)
(gromacs_py.gmx.topsys.TopSys method)
write_index_posre_file() (in module gromacs_py.gmx.itp)
X
xtc (gromacs_py.gmx.gmxsys.GmxSys property)
xvg (gromacs_py.gmx.gmxsys.GmxSys property)
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