Index

_

__abstractmethods__ (aiida_amber.calculations.antechamber.AntechamberCalculation attribute) (aiida_amber.calculations.parmed.ParmedCalculation attribute) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation attribute) (aiida_amber.calculations.sander.SanderCalculation attribute) (aiida_amber.calculations.tleap.TleapCalculation attribute) (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) (aiida_amber.parsers.antechamber.AntechamberParser attribute) (aiida_amber.parsers.parmed.ParmedParser attribute) (aiida_amber.parsers.pdb4amber.Pdb4amberParser attribute) (aiida_amber.parsers.sander.SanderParser attribute) (aiida_amber.parsers.tleap.TleapParser attribute) __annotations__ (aiida_amber.calculations.antechamber.AntechamberCalculation attribute) (aiida_amber.calculations.parmed.ParmedCalculation attribute) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation attribute) (aiida_amber.calculations.sander.SanderCalculation attribute) (aiida_amber.calculations.tleap.TleapCalculation attribute) (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) (aiida_amber.parsers.antechamber.AntechamberParser attribute) (aiida_amber.parsers.parmed.ParmedParser attribute) (aiida_amber.parsers.pdb4amber.Pdb4amberParser attribute) (aiida_amber.parsers.sander.SanderParser attribute) (aiida_amber.parsers.tleap.TleapParser attribute) __firstlineno__ (aiida_amber.calculations.antechamber.AntechamberCalculation attribute) (aiida_amber.calculations.parmed.ParmedCalculation attribute) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation attribute) (aiida_amber.calculations.sander.SanderCalculation attribute) (aiida_amber.calculations.tleap.TleapCalculation attribute) (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) (aiida_amber.parsers.antechamber.AntechamberParser attribute) (aiida_amber.parsers.parmed.ParmedParser attribute) (aiida_amber.parsers.pdb4amber.Pdb4amberParser attribute) (aiida_amber.parsers.sander.SanderParser attribute) (aiida_amber.parsers.tleap.TleapParser attribute) __init__() (aiida_amber.data.antechamber.AntechamberParameters method) (aiida_amber.data.parmed.ParmedParameters method) (aiida_amber.data.pdb4amber.Pdb4amberParameters method) (aiida_amber.data.sander.SanderParameters method) (aiida_amber.data.tleap.TleapParameters method) (aiida_amber.parsers.antechamber.AntechamberParser method) (aiida_amber.parsers.parmed.ParmedParser method) (aiida_amber.parsers.pdb4amber.Pdb4amberParser method) (aiida_amber.parsers.sander.SanderParser method) (aiida_amber.parsers.tleap.TleapParser method) __module__ (aiida_amber.calculations.antechamber.AntechamberCalculation attribute) (aiida_amber.calculations.parmed.ParmedCalculation attribute) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation attribute) (aiida_amber.calculations.sander.SanderCalculation attribute) (aiida_amber.calculations.tleap.TleapCalculation attribute) (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) (aiida_amber.parsers.antechamber.AntechamberParser attribute) (aiida_amber.parsers.parmed.ParmedParser attribute) (aiida_amber.parsers.pdb4amber.Pdb4amberParser attribute) (aiida_amber.parsers.sander.SanderParser attribute) (aiida_amber.parsers.tleap.TleapParser attribute)

__parameters__ (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) __static_attributes__ (aiida_amber.calculations.antechamber.AntechamberCalculation attribute) (aiida_amber.calculations.parmed.ParmedCalculation attribute) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation attribute) (aiida_amber.calculations.sander.SanderCalculation attribute) (aiida_amber.calculations.tleap.TleapCalculation attribute) (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) (aiida_amber.parsers.antechamber.AntechamberParser attribute) (aiida_amber.parsers.parmed.ParmedParser attribute) (aiida_amber.parsers.pdb4amber.Pdb4amberParser attribute) (aiida_amber.parsers.sander.SanderParser attribute) (aiida_amber.parsers.tleap.TleapParser attribute) __str__() (aiida_amber.data.antechamber.AntechamberParameters method) (aiida_amber.data.parmed.ParmedParameters method) (aiida_amber.data.pdb4amber.Pdb4amberParameters method) (aiida_amber.data.sander.SanderParameters method) (aiida_amber.data.tleap.TleapParameters method) _abc_impl (aiida_amber.calculations.antechamber.AntechamberCalculation attribute) (aiida_amber.calculations.parmed.ParmedCalculation attribute) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation attribute) (aiida_amber.calculations.sander.SanderCalculation attribute) (aiida_amber.calculations.tleap.TleapCalculation attribute) (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute) (aiida_amber.parsers.antechamber.AntechamberParser attribute) (aiida_amber.parsers.parmed.ParmedParser attribute) (aiida_amber.parsers.pdb4amber.Pdb4amberParser attribute) (aiida_amber.parsers.sander.SanderParser attribute) (aiida_amber.parsers.tleap.TleapParser attribute) _logger (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute)

A

add_calculation_inputs() (in module aiida_amber.data.parmed_input) (in module aiida_amber.data.tleap_input) add_calculation_outputs() (in module aiida_amber.data.parmed_input) (in module aiida_amber.data.tleap_input) add_subdir_to_node() (in module aiida_amber.utils.node_utils) aiida_amber module aiida_amber.calculations module aiida_amber.calculations.antechamber module aiida_amber.calculations.parmed module aiida_amber.calculations.pdb4amber module aiida_amber.calculations.sander module aiida_amber.calculations.tleap module aiida_amber.cli module aiida_amber.cli.antechamber module aiida_amber.cli.parmed module aiida_amber.cli.pdb4amber module aiida_amber.cli.sander module aiida_amber.cli.tleap module aiida_amber.data module aiida_amber.data.antechamber module

aiida_amber.data.parmed module aiida_amber.data.parmed_input module aiida_amber.data.pdb4amber module aiida_amber.data.sander module aiida_amber.data.tleap module aiida_amber.data.tleap_input module aiida_amber.helpers module aiida_amber.parsers module aiida_amber.parsers.antechamber module aiida_amber.parsers.parmed module aiida_amber.parsers.pdb4amber module aiida_amber.parsers.sander module aiida_amber.parsers.tleap module aiida_amber.utils module aiida_amber.utils.node_utils module aiida_amber.utils.searchprevious module AntechamberCalculation (class in aiida_amber.calculations.antechamber) AntechamberParameters (class in aiida_amber.data.antechamber) AntechamberParser (class in aiida_amber.parsers.antechamber) append_prev_nodes() (in module aiida_amber.utils.searchprevious)

B

build_query() (in module aiida_amber.utils.searchprevious)

C

calculation_inputs_outputs (aiida_amber.data.parmed_input.ParmedInputData property) (aiida_amber.data.tleap_input.TleapInputData property) check_filepath() (in module aiida_amber.utils.node_utils) check_prev_process() (in module aiida_amber.utils.searchprevious)

cmdline_params() (aiida_amber.data.antechamber.AntechamberParameters method) (aiida_amber.data.parmed.ParmedParameters method) (aiida_amber.data.pdb4amber.Pdb4amberParameters method) (aiida_amber.data.sander.SanderParameters method) (aiida_amber.data.tleap.TleapParameters method)

D

define() (aiida_amber.calculations.antechamber.AntechamberCalculation class method) (aiida_amber.calculations.parmed.ParmedCalculation class method) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation class method) (aiida_amber.calculations.sander.SanderCalculation class method) (aiida_amber.calculations.tleap.TleapCalculation class method)

F

fields (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.parmed_input.ParmedInputData attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute) (aiida_amber.data.tleap_input.TleapInputData attribute)

find_previous_file_nodes() (in module aiida_amber.utils.searchprevious) format_link_label() (in module aiida_amber.utils.node_utils) (in module aiida_amber.utils.searchprevious)

G

get_code() (in module aiida_amber.helpers)

get_computer() (in module aiida_amber.helpers) get_path_to_executable() (in module aiida_amber.helpers)

I

inpfile_list (aiida_amber.data.parmed_input.ParmedInputData property) (aiida_amber.data.tleap_input.TleapInputData property)

L

launch() (in module aiida_amber.cli.antechamber) (in module aiida_amber.cli.parmed) (in module aiida_amber.cli.pdb4amber) (in module aiida_amber.cli.sander) (in module aiida_amber.cli.tleap)

link_previous_file_nodes() (in module aiida_amber.utils.searchprevious)

M

module aiida_amber aiida_amber.calculations aiida_amber.calculations.antechamber aiida_amber.calculations.parmed aiida_amber.calculations.pdb4amber aiida_amber.calculations.sander aiida_amber.calculations.tleap aiida_amber.cli aiida_amber.cli.antechamber aiida_amber.cli.parmed aiida_amber.cli.pdb4amber aiida_amber.cli.sander aiida_amber.cli.tleap aiida_amber.data aiida_amber.data.antechamber aiida_amber.data.parmed aiida_amber.data.parmed_input aiida_amber.data.pdb4amber aiida_amber.data.sander aiida_amber.data.tleap aiida_amber.data.tleap_input aiida_amber.helpers aiida_amber.parsers aiida_amber.parsers.antechamber aiida_amber.parsers.parmed aiida_amber.parsers.pdb4amber aiida_amber.parsers.sander aiida_amber.parsers.tleap aiida_amber.utils aiida_amber.utils.node_utils aiida_amber.utils.searchprevious

O

outfile_list (aiida_amber.data.parmed_input.ParmedInputData property) (aiida_amber.data.tleap_input.TleapInputData property)

P

ParmedCalculation (class in aiida_amber.calculations.parmed) ParmedInputData (class in aiida_amber.data.parmed_input) ParmedParameters (class in aiida_amber.data.parmed) ParmedParser (class in aiida_amber.parsers.parmed) parse() (aiida_amber.parsers.antechamber.AntechamberParser method) (aiida_amber.parsers.parmed.ParmedParser method) (aiida_amber.parsers.pdb4amber.Pdb4amberParser method) (aiida_amber.parsers.sander.SanderParser method) (aiida_amber.parsers.tleap.TleapParser method)

parse_parmed_input_file() (in module aiida_amber.data.parmed_input) parse_tleap_input_file() (in module aiida_amber.data.tleap_input) Pdb4amberCalculation (class in aiida_amber.calculations.pdb4amber) Pdb4amberParameters (class in aiida_amber.data.pdb4amber) Pdb4amberParser (class in aiida_amber.parsers.pdb4amber) prepare_for_submission() (aiida_amber.calculations.antechamber.AntechamberCalculation method) (aiida_amber.calculations.parmed.ParmedCalculation method) (aiida_amber.calculations.pdb4amber.Pdb4amberCalculation method) (aiida_amber.calculations.sander.SanderCalculation method) (aiida_amber.calculations.tleap.TleapCalculation method)

S

SanderCalculation (class in aiida_amber.calculations.sander) SanderParameters (class in aiida_amber.data.sander) SanderParser (class in aiida_amber.parsers.sander) save_command() (in module aiida_amber.utils.searchprevious) schema (aiida_amber.data.antechamber.AntechamberParameters attribute) (aiida_amber.data.parmed.ParmedParameters attribute) (aiida_amber.data.pdb4amber.Pdb4amberParameters attribute) (aiida_amber.data.sander.SanderParameters attribute) (aiida_amber.data.tleap.TleapParameters attribute)

set_file() (aiida_amber.data.parmed_input.ParmedInputData method) (aiida_amber.data.tleap_input.TleapInputData method) strip_path() (in module aiida_amber.utils.searchprevious)

T

TleapCalculation (class in aiida_amber.calculations.tleap) TleapInputData (class in aiida_amber.data.tleap_input)

TleapParameters (class in aiida_amber.data.tleap) TleapParser (class in aiida_amber.parsers.tleap)

V

validate() (aiida_amber.data.antechamber.AntechamberParameters method) (aiida_amber.data.parmed.ParmedParameters method) (aiida_amber.data.pdb4amber.Pdb4amberParameters method) (aiida_amber.data.sander.SanderParameters method) (aiida_amber.data.tleap.TleapParameters method)