Index

_

__init__() (pyCADD.Dynamic.common.Analyzer method) (pyCADD.Dynamic.common.Processor method) (pyCADD.Dynamic.common.Simulator method) (pyCADD.Dynamic.core.BaseProcess method) (pyCADD.Dynamic.core.MDProcess method) (pyCADD.Dynamic.core.MinimizeProcess method) (pyCADD.Dynamic.core.NPTProcess method) (pyCADD.Dynamic.core.NVTProcess method) (pyCADD.Dynamic.template.AnalysisConstructor method) (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) (pyCADD.Dynamic.template.LeapConstructor method) (pyCADD.Dynamic.template.LeapInput method) (pyCADD.Dynamic.template.MinimizeInput method) (pyCADD.Dynamic.template.MMGBSAInput method) (pyCADD.Dynamic.template.MultiConstructorManager method) (pyCADD.Dynamic.template.NPTInput method) (pyCADD.Dynamic.template.NVTInput method) (pyCADD.Dynamic.template.RestrainedMinimizeInput method) (pyCADD.Dynamic.template.SimulationConstructor method)

_state_dict (pyCADD.Dynamic.template.BaseConstructor attribute) _state_keys (pyCADD.Dynamic.template.BaseConstructor attribute) _type (pyCADD.Dynamic.template.AnalysisConstructor attribute)

A

add_attr() (pyCADD.Dynamic.template.BaseConstructor method) add_constructor() (pyCADD.Dynamic.template.MultiConstructorManager method) add_decomp() (pyCADD.Dynamic.template.MMGBSAInput method) add_gb() (pyCADD.Dynamic.template.MMGBSAInput method) add_general() (pyCADD.Dynamic.template.MMGBSAInput method) add_heat() (pyCADD.Dynamic.template.HeatInput method) add_heat_process() (pyCADD.Dynamic.common.Processor method) add_minimize_process() (pyCADD.Dynamic.common.Processor method)

add_nmode() (pyCADD.Dynamic.template.MMGBSAInput method) add_npt_process() (pyCADD.Dynamic.common.Processor method) add_nvt() (pyCADD.Dynamic.template.HeatInput method) add_nvt_process() (pyCADD.Dynamic.common.Processor method) add_pb() (pyCADD.Dynamic.template.MMGBSAInput method) add_process() (pyCADD.Dynamic.common.Processor method) AnalysisConstructor (class in pyCADD.Dynamic.template) Analyzer (class in pyCADD.Dynamic.common) apo (pyCADD.Dynamic.common.Processor attribute)

B

base_template (pyCADD.Dynamic.template.LeapConstructor property)

BaseConstructor (class in pyCADD.Dynamic.template) BaseProcess (class in pyCADD.Dynamic.core)

C

calc_am1bcc() (in module pyCADD.Dynamic.utils) calc_hbond() (pyCADD.Dynamic.common.Analyzer method) calc_rmsd() (pyCADD.Dynamic.common.Analyzer method) calc_rmsf() (pyCADD.Dynamic.common.Analyzer method) cfg (pyCADD.Dynamic.core.BaseProcess attribute) cmd (pyCADD.Dynamic.core.MDProcess attribute) com_topfile (pyCADD.Dynamic.common.Processor attribute) comsolvate_crdfile (pyCADD.Dynamic.common.Processor attribute) (pyCADD.Dynamic.common.Simulator attribute) comsolvate_pdbfile (pyCADD.Dynamic.common.Processor attribute)

comsolvate_topfile (pyCADD.Dynamic.common.Processor attribute) (pyCADD.Dynamic.common.Simulator attribute) constructor_list (pyCADD.Dynamic.template.MultiConstructorManager attribute) control_cfg (pyCADD.Dynamic.core.MDProcess attribute) create_energy_inputfile() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Analyzer method) create_heat_input() (pyCADD.Dynamic.common.Processor method) create_minimize_input() (pyCADD.Dynamic.common.Processor method) create_npt_input() (pyCADD.Dynamic.common.Processor method) create_nvt_input() (pyCADD.Dynamic.common.Processor method) cuda_device (pyCADD.Dynamic.common.Simulator attribute)

D

del_attr() (pyCADD.Dynamic.template.BaseConstructor method)

del_constructor() (pyCADD.Dynamic.template.MultiConstructorManager method)

E

extract_frame() (pyCADD.Dynamic.common.Analyzer method)

extract_frames() (pyCADD.Dynamic.common.Analyzer method) extract_lowest_energy_st() (pyCADD.Dynamic.common.Analyzer method)

F

frcmod_file (pyCADD.Dynamic.common.Processor attribute)

G

general_dict (pyCADD.Dynamic.template.MMGBSAInput attribute) get_attr() (pyCADD.Dynamic.template.BaseConstructor method)

get_state_dict() (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) get_water_resnum() (pyCADD.Dynamic.common.Processor method)

H

HEAT_TEMPLATE (pyCADD.Dynamic.template.HeatInput attribute), [1]

HeatInput (class in pyCADD.Dynamic.template)

I

inpcrd_file (pyCADD.Dynamic.core.MDProcess attribute) input_file (pyCADD.Dynamic.core.BaseProcess attribute) is_empty() (pyCADD.Dynamic.template.MultiConstructorManager method) is_minimize (pyCADD.Dynamic.core.MDProcess attribute)

is_production (pyCADD.Dynamic.core.MDProcess attribute) (pyCADD.Dynamic.core.NPTProcess attribute) (pyCADD.Dynamic.core.NVTProcess attribute) is_restrained (pyCADD.Dynamic.core.MDProcess attribute)

L

leap_prepare() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Processor method) LeapConstructor (class in pyCADD.Dynamic.template) LeapInput (class in pyCADD.Dynamic.template) lig_topfile (pyCADD.Dynamic.common.Processor attribute)

load_frcmod_file() (pyCADD.Dynamic.common.Processor method) load_mdout() (pyCADD.Dynamic.common.Analyzer method) load_processed_molfile() (pyCADD.Dynamic.common.Processor method) load_processed_profile() (pyCADD.Dynamic.common.Processor method) load_topfile() (pyCADD.Dynamic.common.Analyzer method) load_traj() (pyCADD.Dynamic.common.Analyzer method)

M

manager (pyCADD.Dynamic.template.HeatInput attribute) (pyCADD.Dynamic.template.MMGBSAInput attribute) md_prepare() (in module pyCADD.Dynamic.cli) md_process_list (pyCADD.Dynamic.common.Processor attribute) (pyCADD.Dynamic.common.Simulator attribute) md_simulate() (in module pyCADD.Dynamic.cli) md_workflow() (in module pyCADD.Dynamic.cli) mdcrd_file_path (pyCADD.Dynamic.core.MDProcess attribute) mdout_file_path (pyCADD.Dynamic.core.MDProcess attribute) MDProcess (class in pyCADD.Dynamic.core) mdrst_file_path (pyCADD.Dynamic.core.MDProcess attribute) MinimizeInput (class in pyCADD.Dynamic.template) MinimizeProcess (class in pyCADD.Dynamic.core)

MMGBSAInput (class in pyCADD.Dynamic.template) module pyCADD.Dynamic pyCADD.Dynamic.analysis pyCADD.Dynamic.cli pyCADD.Dynamic.common pyCADD.Dynamic.constant pyCADD.Dynamic.core pyCADD.Dynamic.template pyCADD.Dynamic.utils mol2_file (pyCADD.Dynamic.common.Processor attribute) molecule_prepare() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Processor method) MultiConstructorManager (class in pyCADD.Dynamic.template)

N

NPTInput (class in pyCADD.Dynamic.template) NPTProcess (class in pyCADD.Dynamic.core)

NVTInput (class in pyCADD.Dynamic.template) NVTProcess (class in pyCADD.Dynamic.core)

P

pro_file (pyCADD.Dynamic.common.Processor attribute) pro_topfile (pyCADD.Dynamic.common.Processor attribute) process_name (pyCADD.Dynamic.core.BaseProcess attribute) Processor (class in pyCADD.Dynamic.common) processor (pyCADD.Dynamic.common.Simulator attribute) protein_prepare() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Processor method) pyCADD.Dynamic module pyCADD.Dynamic.analysis module

pyCADD.Dynamic.cli module pyCADD.Dynamic.common module pyCADD.Dynamic.constant module pyCADD.Dynamic.core module pyCADD.Dynamic.template module pyCADD.Dynamic.utils module

R

RestrainedMinimizeInput (class in pyCADD.Dynamic.template) run() (pyCADD.Dynamic.core.BaseProcess method) (pyCADD.Dynamic.core.MDProcess method) run_energy_calc() (pyCADD.Dynamic.common.Analyzer method)

run_energy_calculation() (in module pyCADD.Dynamic.core) run_parmchk2() (in module pyCADD.Dynamic.utils) run_simulation() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Simulator method)

S

save() (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) (pyCADD.Dynamic.template.MMGBSAInput method) (pyCADD.Dynamic.template.MultiConstructorManager method) set_attr() (pyCADD.Dynamic.template.BaseConstructor method) set_cuda_device() (pyCADD.Dynamic.common.Simulator method)

set_prepared_file() (pyCADD.Dynamic.common.Processor method) show_cuda_device() (pyCADD.Dynamic.common.Simulator method) SimulationConstructor (class in pyCADD.Dynamic.template) Simulator (class in pyCADD.Dynamic.common) stage_1_dict (pyCADD.Dynamic.template.HeatInput attribute) stage_2_dict (pyCADD.Dynamic.template.HeatInput attribute) step_size (pyCADD.Dynamic.core.MDProcess attribute)

T

title (pyCADD.Dynamic.template.AnalysisConstructor attribute) to_dict() (pyCADD.Dynamic.template.BaseConstructor method) to_str() (pyCADD.Dynamic.template.BaseConstructor method) to_string() (pyCADD.Dynamic.template.AnalysisConstructor method) (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) (pyCADD.Dynamic.template.LeapConstructor method) (pyCADD.Dynamic.template.MMGBSAInput method) (pyCADD.Dynamic.template.MultiConstructorManager method) (pyCADD.Dynamic.template.SimulationConstructor method)

top_file (pyCADD.Dynamic.common.Analyzer attribute) top_file_path (pyCADD.Dynamic.common.Analyzer attribute) topology_file (pyCADD.Dynamic.core.MDProcess attribute) total_step (pyCADD.Dynamic.core.MDProcess attribute) trace_angle() (pyCADD.Dynamic.common.Analyzer method) trace_distance() (pyCADD.Dynamic.common.Analyzer method) traj (pyCADD.Dynamic.common.Analyzer attribute) traj_file (pyCADD.Dynamic.common.Analyzer attribute) traj_file_path (pyCADD.Dynamic.common.Analyzer attribute)

W

work_dir (pyCADD.Dynamic.common.Processor attribute)