Index

A | B | C | D | E | F | G | I | J | M | N | P | R | S | T | W | Z

A

add_bond() (tools.build_template.PrepiAtom method)
addAtom() (tools.simulationobjects.Residue method)
alignhydrogens() (in module tools.convertwater)
angle() (in module tools.simulationobjects)
angle_atms() (in module tools.simulationobjects)
append() (tools.simulationobjects.TemplateFile method)
assign_paramobj() (tools.simulationobjects.TemplateFile method)
Atom (class in tools.simulationobjects)
AtomSet (class in tools.simulationobjects)

B

backward_bond() (tools.build_template.PrepiAtom method)
bar() (in module tools.calc_bar)
(in module tools.pms2pymbar)
build_template() (in module tools.build_template)

C

calc_density() (in module tools.calc_density)
calc_rmsd() (in module tools.calc_rmsd)
clear() (tools.generate_input.ProtoMSSimulation method)
clear_gcmcbox() (in module tools.clear_gcmcbox)
cluster_coords() (in module tools.calc_clusters)
color() (in module tools.simulationobjects)
convertwater() (in module tools.convertwater)
copy() (tools.simulationobjects.PDBFile method)
create_res() (in module tools.distribute_waters)

D

distribute_particles() (in module tools.distribute_waters)
divide_print() (in module tools.divide_pdb)
DualTopology (class in tools.generate_input)

E

EnergyResults (class in tools.simulationobjects)
Equilibration (class in tools.generate_input)
extract_energies() (in module tools.pms2pymbar)

F

find_box() (in module tools.simulationobjects)
find_equilibration() (in module tools.calc_series)
fit_pmf() (in module tools.calc_ti)
ForceFieldParameter (class in tools.simulationobjects)
format_help() (tools.simulationobjects.MyArgumentParser method)
from_residues() (tools.simulationobjects.PDBSet method)

G

GCMC (class in tools.generate_input)
generate_input() (in module tools.generate_input)
get_coords() (in module tools.calc_clusters)
get_params() (tools.simulationobjects.ParameterSet method)
getBox() (tools.simulationobjects.PDBFile method)
getCenter() (tools.simulationobjects.PDBFile method)
(tools.simulationobjects.Residue method)
getElement() (tools.simulationobjects.Atom method)

I

improper_dihedral() (tools.build_template.PrepiAtom method)
is_solvent() (in module tools.simulationobjects)
isAminoacid() (tools.simulationobjects.Residue method)

J

Jaws1 (class in tools.generate_input)
Jaws2 (class in tools.generate_input)

M

make_dummy() (in module tools.make_dummy)
make_gcmcbox() (in module tools.make_gcmcbox)
make_series() (tools.simulationobjects.ResultsFile method)
make_single() (in module tools.make_single)
make_zmat() (in module tools.build_template)
maximize_samples() (in module tools.calc_series)
mbar() (in module tools.pms2pymbar)
merge_pdbs() (in module tools.simulationobjects)
merge_templates() (in module tools.merge_templates)
MolTemplate (class in tools.simulationobjects)
moving() (in module tools.calc_series)
MyArgumentParser (class in tools.simulationobjects)

N

next_bond() (tools.build_template.PrepiAtom method)

P

Parameter (class in tools.simulationobjects)
ParameterSet (class in tools.simulationobjects)
parse() (tools.simulationobjects.AtomSet method)
(tools.simulationobjects.ForceFieldParameter method)
(tools.simulationobjects.SnapshotResults method)
(tools.simulationobjects.TemplateAtom method)
(tools.simulationobjects.TemplateConnectivity method)
(tools.simulationobjects.TemplateSoluteAtom method)
parse_files() (in module tools.calc_series)
parse_from() (tools.simulationobjects.MolTemplate method)
parse_line() (tools.simulationobjects.EnergyResults method)
parse_series() (in module tools.calc_series)
pdb2pms() (in module tools.convertatomnames)
PDBFile (class in tools.simulationobjects)
PDBSet (class in tools.simulationobjects)
plot_series() (in module tools.calc_series)
PrepiAtom (class in tools.build_template)
print_fullhelp() (tools.simulationobjects.MyArgumentParser method)
print_help() (tools.simulationobjects.MyArgumentParser method)
ProteinLigandSimulation (class in tools.generate_input)
ProtoMSSimulation (class in tools.generate_input)

R

read() (tools.build_template.PrepiAtom method)
(tools.simulationobjects.PDBFile method)
(tools.simulationobjects.PDBSet method)
(tools.simulationobjects.RestartFile method)
(tools.simulationobjects.ResultsFile method)
(tools.simulationobjects.TemplateFile method)
read_convfile() (in module tools.convertatomnames)
read_from() (tools.simulationobjects.PDBFile method)
readCommandFile() (tools.generate_input.ProtoMSSimulation method)
replica_path() (in module tools.calc_replicapath)
Residue (class in tools.simulationobjects)
RestartFile (class in tools.simulationobjects)
ResultsFile (class in tools.simulationobjects)
rotatesolute() (in module tools.convertwater)
rotatewat() (in module tools.convertwater)
rotmat_x() (in module tools.convertwater)
rotmat_y() (in module tools.convertwater)
rotmat_z() (in module tools.convertwater)
run() (tools.generate_input.ProtoMSSimulation method)
run_antechamber() (in module tools.ambertools)
run_parmchk() (in module tools.ambertools)
running() (in module tools.calc_series)

S

Sampling (class in tools.generate_input)
scoop() (in module tools.scoop)
set_jaws2_box() (in module tools.split_jawswater)
setChunk() (tools.generate_input.ProtoMSSimulation method)
setDump() (tools.generate_input.ProtoMSSimulation method)
setForceField() (tools.generate_input.ProtoMSSimulation method)
setParameter() (tools.generate_input.ProtoMSSimulation method)
setProtein() (tools.generate_input.ProtoMSSimulation method)
setSolute() (tools.generate_input.ProtoMSSimulation method)
setSolvent() (tools.generate_input.ProtoMSSimulation method)
setStream() (tools.generate_input.ProtoMSSimulation method)
setup_logger() (in module tools.simulationobjects)
SetupError
SingleTopology (class in tools.generate_input)
SnapshotResults (class in tools.simulationobjects)
solvate() (in module tools.solvate)
sort_bonds() (tools.build_template.PrepiAtom method)
split_waters() (in module tools.split_jawswater)
standard_filename() (in module tools.simulationobjects)
stat_inefficiency() (in module tools.calc_series)
summarize() (in module tools.make_single)

T

TemplateAtom (class in tools.simulationobjects)
TemplateConnectivity (class in tools.simulationobjects)
TemplateFile (class in tools.simulationobjects)
TemplateSoluteAtom (class in tools.simulationobjects)
ti() (in module tools.calc_ti)
tools (module)
tools.ambertools (module)
tools.build_template (module)
tools.calc_bar (module)
tools.calc_clusters (module)
tools.calc_density (module)
tools.calc_dg (module)
tools.calc_gcsingle (module)
tools.calc_replicapath (module)
tools.calc_rmsd (module)
tools.calc_series (module)
tools.calc_ti (module)
tools.clear_gcmcbox (module)
tools.convertatomnames (module)
tools.convertwater (module)
tools.distribute_waters (module)
tools.divide_pdb (module)
tools.generate_input (module)
tools.make_dummy (module)
tools.make_gcmcbox (module)
tools.make_single (module)
tools.merge_templates (module)
tools.pms2pymbar (module)
tools.scoop (module)
tools.simulationobjects (module)
tools.solvate (module)
tools.split_jawswater (module)

W

write() (tools.simulationobjects.PDBFile method)
(tools.simulationobjects.PDBSet method)
(tools.simulationobjects.TemplateFile method)
write_box() (in module tools.simulationobjects)
write_map() (in module tools.make_single)
write_series() (in module tools.calc_series)
write_to() (tools.simulationobjects.MolTemplate method)
write_zmat() (tools.simulationobjects.MolTemplate method)
writeCommandFile() (tools.generate_input.ProtoMSSimulation method)
writeDX() (in module tools.calc_density)

Z

zmat() (tools.simulationobjects.TemplateAtom method)
(tools.simulationobjects.TemplateSoluteAtom method)