9 #ifndef IMPMULTIFIT_PROTEIN_ANCHORS_MAPPING_READER_H
10 #define IMPMULTIFIT_PROTEIN_ANCHORS_MAPPING_READER_H
12 #include <IMP/multifit/multifit_config.h>
18 IMPMULTIFIT_BEGIN_NAMESPACE
27 inline std::string get_anchors_filename()
const {
return anchors_fn_; }
28 void set_anchors_filename(
const std::string &fn) { anchors_fn_ = fn; }
30 void add_protein(
const multifit::ProteinRecordData &rec) {
33 IntsList get_paths_for_protein(
const std::string &prot_name)
const {
35 "Protein:" << prot_name <<
" is not found");
36 return paths_map_.find(prot_name)->second;
38 void set_paths_filename_for_protein(
const std::string &prot_name,
39 const std::string &paths_filename) {
40 IMP_USAGE_CHECK(paths_filename_.find(prot_name) == paths_filename_.end(),
41 "Protein:" << prot_name <<
" is already set");
42 paths_filename_[prot_name] = paths_filename;
44 std::string get_paths_filename_for_protein(
const std::string &prot_name)
46 IMP_USAGE_CHECK(paths_filename_.find(prot_name) != paths_filename_.end(),
47 "Protein:" << prot_name <<
" is not found");
48 return paths_filename_.find(prot_name)->second;
50 void set_paths_for_protein(
const std::string &prot_name,
IntsList paths) {
52 "Protein:" << prot_name <<
" is already set");
53 paths_map_[prot_name] = paths;
56 void show(std::ostream &s = std::cout)
const;
59 std::map<std::string, IntsList> paths_map_;
60 std::map<std::string, std::string> paths_filename_;
63 std::string anchors_fn_;
70 int max_paths = INT_MAX);
72 void write_protein_anchors_mapping(
73 const std::string &anchors_prot_map_fn,
const std::string &anchors_fn,
74 const std::vector<std::pair<String, String> > &prot_paths);
78 void write_protein_anchors_mapping(
const std::string &anchors_prot_map_fn,
91 IMPMULTIFIT_END_NAMESPACE
handles reading of proteomics data
Storage of proteomics data.
Storage of anchors (points and edges)
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
multifit::SettingsData * get_partial_assembly_setting_data(multifit::SettingsData *prots_sd, const Strings &prot_names)
Get the assembly data for a few of the proteins.
int add_protein(std::string name, int start_res, int end_res, const std::string &mol_fn, const std::string &surface_fn, const std::string &ref_fn)
stored multifit settings data
#define IMP_VALUES(Name, PluralName)
Define the type for storing sets of values.
A smart pointer to a ref-counted Object that is a class member.
Holds header data for optimization.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
#define IMP_USAGE_CHECK(expr, message)
A runtime test for incorrect usage of a class or method.
Sample best solutions using Domino.
handles reading of anchors data