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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
initialize_positions.h
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1 /**
2  * \file initialize_positions.h
3  * \brief description
4  *
5  * Copyright 2007-2022 IMP Inventors. All rights reserved.
6  */
7 
8 #ifndef IMPNPCTRANSPORT_INITIALIZE_POSITIONS_H
9 #define IMPNPCTRANSPORT_INITIALIZE_POSITIONS_H
10 
11 #include "npctransport_config.h"
12 #include "SimulationData.h"
13 
14 IMPNPCTRANSPORT_BEGIN_NAMESPACE
15 IMPNPCTRANSPORTEXPORT
16 
17 /**
18  pre-optimize the positions of all diffusing particles in 'sd' whose
19  coordinates are optimizable, using only chain restraints, excluded
20  volumes and bounding box restraints (but not interaction
21  restraints).
22 
23  The initialization data is dumped to the RMF file `sd->get_rmf_file_name()`
24  using dump interval `sd->get_rmf_dump_interval_frames() * 100`, or every
25  frame in case that `debug` is true.
26 
27  @param sd the SimulationData object containing diffusing particles
28  @param extra_restraints a list of additional ad-hoc restraints that will be
29  used only throughout initialization
30  @param debug if true, the initialization will dump much more output (e.g.
31  every frame to RMF file)
32  @param short_init_factor a factor between >0 and 1 for decreasing
33  the number of optimization cycles at each
34  round
35  @param is_disable_randomize if true, do not initially randomize particle positions,
36  essentially performing an extended relaxation from
37  the starting coordinates
38  @param are_fgs_pre_initialized if true, do not try to pre-optimize FGs before adding diffusers
39  */
41 ( SimulationData *sd,
42  const RestraintsTemp &extra_restraints =
44  bool debug = false,
45  double short_init_factor = 1.0,
46  bool is_disable_randomize = false,
47  bool are_fgs_pre_initialized = false );
48 
49 
50 IMPNPCTRANSPORT_END_NAMESPACE
51 
52 #endif /* IMPNPCTRANSPORT_INITIALIZE_POSITIONS_H */
IMP::Vector< IMP::WeakPointer< Restraint > > RestraintsTemp
Definition: base_types.h:104
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
description