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IMP Reference Guide  develop.97bab1d8fd,2021/09/21
The Integrative Modeling Platform
spb_main.h
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1 /**
2  * \file IMP/spb/spb_main.h
3  * \brief SPB MonteCarlo
4  *
5  * Copyright 2007-2021 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPSPB_SPB_MAIN_H
10 #define IMPSPB_SPB_MAIN_H
11 #include <IMP.h>
12 #include <map>
13 #include <string>
14 #include <IMP/spb/spb_config.h>
15 
16 IMPSPB_BEGIN_NAMESPACE
17 
18 // convert degrees to radians
19 double radians(double d);
20 inline double radians(double d) { return d * IMP::algebra::PI / 180.0; }
21 
22 struct MCParameters {
23  double tmin;
24  double tmax;
25  double dx;
26  double dang;
27  double dSigma0;
28  double dKda;
29  double dIda;
30  double dA;
31  double dSide;
32  double dR0;
33  double dpBl;
34  double wte_w0;
35  double wte_sigma;
36  double wte_gamma;
37  double wte_emin;
38  double wte_emax;
39  int nexc;
40  int nsteps;
41  int nwrite;
42  int nhot;
43  bool do_wte;
44  bool wte_restart;
45 };
46 
47 struct EM2DParameters {
48  double resolution;
49  double pixel_size;
50  std::string filename;
51  double SigmaMin;
52  double SigmaMax;
53 };
54 
55 struct FretParameters {
56  double R0Min;
57  double R0Max;
58  double KdaMin;
59  double KdaMax;
60  double Ida;
61  double IdaErr;
62  double Sigma0Min;
63  double Sigma0Max;
64  double pBlMin;
65  double pBlMax;
66  double KdaMin_new;
67  double KdaMax_new;
68  double Ida_new;
69  double IdaErr_new;
70  std::string filename;
71  std::string filename_new;
72 };
73 
74 struct ClusterParameters {
75  std::string trajfile;
76  std::string isdtrajfile;
77  std::string biasfile;
78  std::string weightfile;
79  std::string label;
80  int niter;
81  double cutoff;
82  bool weight;
83  bool identical;
84  bool symmetry;
85 };
86 
87 struct MapParameters {
88  std::string frames_list;
89  std::string label;
90  std::string ref_file;
91  std::string ref_isdfile;
92  double xmin;
93  double xmax;
94  double ymin;
95  double ymax;
96  double zmin;
97  double zmax;
98  double resolution;
99  int nbinx;
100  int nbiny;
101  int nbinz;
102 };
103 
104 struct SPBParameters {
105  MCParameters MC;
106  FretParameters Fret;
107  EM2DParameters EM2D;
108  ClusterParameters Cluster;
109  MapParameters Map;
110  double sideMin;
111  double sideMax;
112  double CP_thicknessMin;
113  double CP_thicknessMax;
114  double CP_IL2_gapMin;
115  double CP_IL2_gapMax;
116  double IL2_thickness;
117  double Spc29_diameter;
118  double Spc29_rgyr;
119  double kappa;
120  double kappa_vol;
121  double tilt;
122  double tilt_Spc42;
123  double resolution;
124 
125  double dist_Spc29_termMin;
126  double dist_Spc29_termMax;
127  double sigma0_dist;
128 
129  double dist_Spc42C_min;
130  double dist_Spc42C_max;
131  double sigma0_dist_spc42c;
132 
133  std::string cell_type;
134  int num_cells;
135  int num_copies;
136  algebra::Vector3Ds CP_centers;
137  algebra::Vector3Ds IL2_centers;
139  bool use_connectivity;
140  std::map<std::string, bool> protein_list;
141  bool add_fret;
142  bool add_new_fret;
143  bool add_y2h;
144  bool add_tilt;
145  bool add_GFP;
146  bool use_GFP_structure;
147  bool keep_GFP_layer;
148  bool GFP_exc_volume;
149  bool fix_GFP;
150  bool restraint_GFP;
151  std::map<std::string, std::string> file_list;
152  bool isd_restart;
153  std::string isd_restart_file;
154  bool add_IL2_layer;
155  bool restrain_distance_Spc29_termini;
156  bool restrain_distance_Spc42_Cterm;
157 };
158 
159 IMPSPB_END_NAMESPACE
160 
161 #endif /* IMPSPB_SPB_MAIN_H */
static const double PI
the constant pi
Vector< VectorD< 3 > > Vector3Ds
Definition: VectorD.h:423
Include all non-deprecated headers in IMP.
IMP::Vector< Transformation3D > Transformation3Ds