9 #ifndef IMPMULTIFIT_SETTINGS_DATA_H
10 #define IMPMULTIFIT_SETTINGS_DATA_H
11 #include <IMP/multifit/multifit_config.h>
19 IMPMULTIFIT_BEGIN_NAMESPACE
31 transformations_fn_ =
"";
34 void set_name(
const std::string &name) { name_ = name; }
35 inline std::string get_name()
const {
return name_; }
36 inline std::string get_filename()
const {
return filename_; }
37 void set_filename(
const std::string &filename) { filename_ = filename; }
38 inline std::string get_surface_fn()
const {
return surface_fn_; }
39 void set_surface_fn(
const std::string &fn) { surface_fn_ = fn; }
40 void set_txt_ap_fn(
const std::string &pdb_ap_fn) { pdb_ap_fn_ = pdb_ap_fn; }
41 inline std::string get_txt_ap_fn()
const {
return pdb_ap_fn_; }
42 void set_txt_fine_ap_fn(
const std::string &pdb_ap_fn) {
43 pdb_fine_ap_fn_ = pdb_ap_fn;
45 inline std::string get_txt_fine_ap_fn()
const {
return pdb_fine_ap_fn_; }
46 void set_num_ap(
int num_ap) { num_ap_ = num_ap; }
47 inline int get_num_ap()
const {
return num_ap_; }
48 void set_num_fine_ap(
int num_ap) { num_fine_ap_ = num_ap; }
49 inline int get_num_fine_ap()
const {
return num_fine_ap_; }
50 void set_transformations_fn(std::string transformations_fn) {
51 transformations_fn_ = transformations_fn;
53 std::string get_transformations_fn()
const {
return transformations_fn_; }
54 void set_reference_fn(
const std::string &ref_fn) { reference_fn_ = ref_fn; }
55 std::string get_reference_fn()
const {
return reference_fn_; }
64 std::string filename_;
65 std::string surface_fn_;
66 std::string pdb_ap_fn_;
68 std::string pdb_fine_ap_fn_;
70 std::string transformations_fn_;
71 std::string reference_fn_;
84 coarse_over_sampled_ap_fn_ =
"";
86 fine_over_sampled_ap_fn_ =
"";
88 void set_dens_fn(
const std::string &dens_fn) { dens_fn_ = dens_fn; }
89 std::string get_dens_fn()
const {
return dens_fn_; }
90 void set_resolution(
float res) { resolution_ = res; }
92 float get_spacing()
const {
return spacing_; }
93 void set_spacing(
float spacing) { spacing_ = spacing; }
94 void set_threshold(
float t) { threshold_ = t; }
95 float get_threshold()
const {
return threshold_; }
98 std::string get_coarse_ap_fn()
const {
return coarse_ap_fn_; }
99 void set_coarse_ap_fn(
const std::string &new_fn) { coarse_ap_fn_ = new_fn; }
100 std::string get_coarse_over_sampled_ap_fn()
const {
101 return coarse_over_sampled_ap_fn_;
103 void set_coarse_over_sampled_ap_fn(
const std::string &new_fn) {
104 coarse_over_sampled_ap_fn_ = new_fn;
106 std::string get_fine_ap_fn()
const {
return fine_ap_fn_; }
107 void set_fine_ap_fn(
const std::string &new_fn) { fine_ap_fn_ = new_fn; }
108 std::string get_fine_over_sampled_ap_fn()
const {
109 return fine_over_sampled_ap_fn_;
111 void set_fine_over_sampled_ap_fn(
const std::string &new_fn) {
112 fine_over_sampled_ap_fn_ = new_fn;
123 std::string dens_fn_;
128 std::string coarse_ap_fn_;
129 std::string coarse_over_sampled_ap_fn_;
130 std::string fine_ap_fn_;
131 std::string fine_over_sampled_ap_fn_;
138 static void show_component_header_line(std::ostream &out = std::cout) {
139 out << get_component_header_line();
141 static std::string get_component_header_line() {
142 std::stringstream ss;
143 ss <<
"name|protein|surface|pdb_anchor_points|number of anchor points|"
144 <<
"fine pdb_anchor_points|number of fine anchor points|"
145 <<
"transformations|ref filename|" << std::endl;
148 static void show_density_header_line(std::ostream &out = std::cout) {
149 out << get_density_header_line();
151 static std::string get_density_header_line() {
152 std::stringstream ss;
153 ss <<
"map| resolution| spacing| threshold|x-origin| y-origin| z-origin|";
154 ss <<
"coarse anchor points|coarse over sampled anchor points|";
155 ss <<
"fine anchor points|fine over sampled anchor points|" << std::endl;
158 void set_assembly_filename(
const std::string &fn) { asmb_fn_ = fn; }
159 const char *get_assembly_filename()
const {
return asmb_fn_.c_str(); }
161 AssemblyHeader *get_assembly_header()
const {
return dens_data_; }
162 void set_data_path(
const std::string &fn) { data_path_ = fn; }
169 obj->set_was_used(
true);
174 std::string asmb_fn_;
175 std::string data_path_;
178 IMPMULTIFITEXPORT
SettingsData *read_settings(
const char *filename);
179 IMPMULTIFITEXPORT
void write_settings(
const char *filename,
181 IMPMULTIFIT_END_NAMESPACE
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Storage of a model, its restraints, constraints and particles.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
A more IMP-like version of the std::vector.
Macros to define containers of objects.
Common base class for heavy weight IMP objects.
A smart pointer to a ref-counted Object that is a class member.
Holds header data for optimization.
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing lists of object pointers.
A nullptr-initialized pointer to an IMP Object.
Object(std::string name)
Construct an object with the given name.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.