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IMP Reference Guide
2.22.0
The Integrative Modeling Platform
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#include <IMP/saxs/Profile.h>
Inheritance diagram for IMP::saxs::Profile:Basic profile class, can be initialized from the input file (experimental or theoretical) or computed from a set of Model Particles (theoretical)
Public Member Functions | |
| Profile (const std::string &file_name, bool fit_file=false, double max_q=0.0, int units=1) | |
| init from file More... | |
| Profile (double qmin=0.0, double qmax=0.5, double delta=0.005) | |
| init for theoretical profile More... | |
| void | add (const Profile *other_profile, double weight=1.0) |
| add another profile - useful for rigid bodies More... | |
| void | add (const Vector< Profile * > &profiles, const Vector< double > &weights=Vector< double >()) |
| add other profiles - useful for weighted ensembles More... | |
| void | add_errors () |
| add simulated error More... | |
| void | add_noise (double percentage=0.03) |
| add simulated noise More... | |
| void | add_partial_profiles (const Profile *other_profile, double weight=1.0) |
| add partial profiles More... | |
| void | add_partial_profiles (const Vector< Profile * > &profiles, const Vector< double > &weights=Vector< double >()) |
| add other partial profiles More... | |
| void | background_adjust (double start_q) |
| background adjustment option More... | |
| double | calculate_I0 (const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS) |
| calculate Intensity at zero (= squared number of electrons) More... | |
| void | calculate_profile (const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=false) |
| computes theoretical profile More... | |
| void | calculate_profile (const Particles &particles1, const Particles &particles2, FormFactorType ff_type=HEAVY_ATOMS) |
| void | calculate_profile_constant_form_factor (const Particles &particles, double form_factor=1.0) |
| calculate profile for any type of Particles that have coordinates More... | |
| void | calculate_profile_partial (const Particles &particles, const Vector< double > &surface=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS) |
| compute profile for fitting with hydration layer and excluded volume More... | |
| void | calculate_profile_partial (const Particles &particles1, const Particles &particles2, const Vector< double > &surface1=Vector< double >(), const Vector< double > &surface2=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS) |
| compute profile for fitting with hydration layer and excluded volume More... | |
| void | calculate_profile_reciprocal_partial (const Particles &particles, const Vector< double > &surface=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS) |
| void | calculate_profile_symmetric (const Particles &particles, unsigned int n, FormFactorType ff_type=HEAVY_ATOMS) |
| void | copy_errors (const Profile *exp_profile) |
| void | distribution_2_profile (const RadialDistributionFunction &r_dist) |
| convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr) More... | |
| void | downsample (Profile *downsampled_profile, unsigned int point_number) const |
| downsample the profile to a given number of points More... | |
| double | get_average_radius () const |
| double | get_delta_q () const |
| return sampling resolution More... | |
| double | get_error (unsigned int i) const |
| const Eigen::VectorXf & | get_errors () const |
| unsigned int | get_id () const |
| const Eigen::VectorXf & | get_intensities () const |
| double | get_intensity (unsigned int i) const |
| double | get_max_q () const |
| return maximal sampling point More... | |
| double | get_min_q () const |
| return minimal sampling point More... | |
| std::string | get_name () const |
| double | get_q (unsigned int i) const |
| const Eigen::VectorXf & | get_qs () const |
| virtual std::string | get_type_name () const override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| double | get_weight (unsigned int i) const |
| bool | is_partial_profile () const |
| bool | is_uniform_sampling () const |
| checks the sampling of experimental profile More... | |
| double | mean_intensity () const |
| calculate mean intensity More... | |
| void | offset (double c) |
| offset profile by c, I(q) = I(q) - c More... | |
| void | profile_2_distribution (RadialDistributionFunction &rd, double max_distance) const |
| convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)*qr*sin(qr)) More... | |
| double | radius_of_gyration (double end_q_rg=1.3) const |
| compute radius of gyration with Guinier approximation More... | |
| void | read_partial_profiles (const std::string &file_name) |
| read a partial profile from file (7 columns) More... | |
| void | read_SAXS_file (const std::string &file_name, bool fit_file=false, double max_q=0.0, int units=1) |
| reads SAXS profile from file More... | |
| void | resample (const Profile *exp_profile, Profile *resampled_profile) const |
| return a profile that is sampled on the q values of the exp_profile More... | |
| void | scale (double c) |
| scale More... | |
| void | set_average_radius (double r) |
| void | set_average_volume (double v) |
| void | set_beam_profile (std::string beam_profile_file) |
| void | set_errors (const Eigen::VectorXf &e) |
| void | set_ff_table (FormFactorTable *ff_table) |
| required for reciprocal space calculation More... | |
| void | set_id (unsigned int id) |
| void | set_intensities (const Eigen::VectorXf &i) |
| void | set_intensity (unsigned int i, double iq) |
| void | set_name (std::string name) |
| void | set_qs (const Eigen::VectorXf &q) |
| unsigned int | size () const |
| return number of entries in SAXS profile More... | |
| void | sum_partial_profiles (double c1, double c2, bool check_cashed=true) |
| computes full profile for given fitting parameters More... | |
| void | write_partial_profiles (const std::string &file_name) const |
| write a partial profile to file More... | |
| void | write_SAXS_file (const std::string &file_name, double max_q=0.0) const |
| print to file More... | |
| Public Member Functions inherited from IMP::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Static Public Attributes | |
| static const double | modulation_function_parameter_ |
Protected Member Functions | |
| void | init (unsigned int size=0, unsigned int partial_profiles_size=0) |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
Protected Attributes | |
| double | average_radius_ |
| double | average_volume_ |
| Pointer< Profile > | beam_profile_ |
| double | c1_ |
| double | c2_ |
| double | delta_q_ |
| Eigen::VectorXf | error_ |
| bool | experimental_ |
| FormFactorTable * | ff_table_ |
| unsigned int | id_ |
| Eigen::VectorXf | intensity_ |
| double | max_q_ |
| double | min_q_ |
| std::string | name_ |
| std::vector< Eigen::VectorXf > | partial_profiles_ |
| Eigen::VectorXf | q_ |
| std::map< double, unsigned int > | q_mapping_ |
| IMP::saxs::Profile::Profile | ( | const std::string & | file_name, |
| bool | fit_file = false, |
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| double | max_q = 0.0, |
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| int | units = 1 |
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| ) |
init from file
| [in] | file_name | profile file name |
| [in] | fit_file | if true, intensities are read from column 3 |
| [in] | max_q | read till maximal q value = max_q, or all if max_q<=0 |
| [in] | units | gets 1, 2, or 3 for unknown q units, 1/A, or 1/nm |
| IMP::saxs::Profile::Profile | ( | double | qmin = 0.0, |
| double | qmax = 0.5, |
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| double | delta = 0.005 |
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| ) |
init for theoretical profile
| void IMP::saxs::Profile::add | ( | const Profile * | other_profile, |
| double | weight = 1.0 |
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| ) |
add another profile - useful for rigid bodies
| void IMP::saxs::Profile::add | ( | const Vector< Profile * > & | profiles, |
| const Vector< double > & | weights = Vector< double >() |
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| ) |
add other profiles - useful for weighted ensembles
| void IMP::saxs::Profile::add_errors | ( | ) |
add simulated error
| void IMP::saxs::Profile::add_noise | ( | double | percentage = 0.03 | ) |
add simulated noise
| void IMP::saxs::Profile::add_partial_profiles | ( | const Profile * | other_profile, |
| double | weight = 1.0 |
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| ) |
add partial profiles
| void IMP::saxs::Profile::add_partial_profiles | ( | const Vector< Profile * > & | profiles, |
| const Vector< double > & | weights = Vector< double >() |
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| ) |
add other partial profiles
| void IMP::saxs::Profile::background_adjust | ( | double | start_q | ) |
background adjustment option
| double IMP::saxs::Profile::calculate_I0 | ( | const Particles & | particles, |
| FormFactorType | ff_type = HEAVY_ATOMS |
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| ) |
calculate Intensity at zero (= squared number of electrons)
| void IMP::saxs::Profile::calculate_profile | ( | const Particles & | particles, |
| FormFactorType | ff_type = HEAVY_ATOMS, |
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| bool | reciprocal = false |
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| ) |
| void IMP::saxs::Profile::calculate_profile | ( | const Particles & | particles1, |
| const Particles & | particles2, | ||
| FormFactorType | ff_type = HEAVY_ATOMS |
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| ) |
| void IMP::saxs::Profile::calculate_profile_constant_form_factor | ( | const Particles & | particles, |
| double | form_factor = 1.0 |
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| ) |
calculate profile for any type of Particles that have coordinates
| void IMP::saxs::Profile::calculate_profile_partial | ( | const Particles & | particles, |
| const Vector< double > & | surface = Vector< double >(), |
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| FormFactorType | ff_type = HEAVY_ATOMS |
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| ) |
compute profile for fitting with hydration layer and excluded volume
A partial profile is a pre-computed profile, where intensities are split into 6 parts that can be summed up into a regular profile given a pair of c1/c2 values by sum_partial_profiles function. see FoXS paper for details.
| void IMP::saxs::Profile::calculate_profile_partial | ( | const Particles & | particles1, |
| const Particles & | particles2, | ||
| const Vector< double > & | surface1 = Vector< double >(), |
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| const Vector< double > & | surface2 = Vector< double >(), |
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| FormFactorType | ff_type = HEAVY_ATOMS |
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| ) |
compute profile for fitting with hydration layer and excluded volume
| void IMP::saxs::Profile::distribution_2_profile | ( | const RadialDistributionFunction & | r_dist | ) |
convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr)
| void IMP::saxs::Profile::downsample | ( | Profile * | downsampled_profile, |
| unsigned int | point_number | ||
| ) | const |
downsample the profile to a given number of points
| double IMP::saxs::Profile::get_delta_q | ( | ) | const |
| double IMP::saxs::Profile::get_max_q | ( | ) | const |
| double IMP::saxs::Profile::get_min_q | ( | ) | const |
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
| bool IMP::saxs::Profile::is_uniform_sampling | ( | ) | const |
checks the sampling of experimental profile
| double IMP::saxs::Profile::mean_intensity | ( | ) | const |
calculate mean intensity
| void IMP::saxs::Profile::offset | ( | double | c | ) |
offset profile by c, I(q) = I(q) - c
| void IMP::saxs::Profile::profile_2_distribution | ( | RadialDistributionFunction & | rd, |
| double | max_distance | ||
| ) | const |
convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)*qr*sin(qr))
| double IMP::saxs::Profile::radius_of_gyration | ( | double | end_q_rg = 1.3 | ) | const |
compute radius of gyration with Guinier approximation
ln[I(q)]=ln[I(0)] - (q^2*rg^2)/3
| [in] | end_q_rg | determines the range of profile used for approximation: i.e. q*rg < end_q_rg. Use 1.3 for globular proteins, 0.8 for elongated |
| void IMP::saxs::Profile::read_partial_profiles | ( | const std::string & | file_name | ) |
read a partial profile from file (7 columns)
| void IMP::saxs::Profile::read_SAXS_file | ( | const std::string & | file_name, |
| bool | fit_file = false, |
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| double | max_q = 0.0, |
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| int | units = 1 |
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| ) |
reads SAXS profile from file
| [in] | file_name | profile file name |
| [in] | fit_file | if true, intensities are read from column 3 |
| [in] | max_q | read till maximal q value = max_q, or all if max_q<=0 |
| [in] | units | gets 1, 2, or 3 for unknown q units, 1/A, or 1/nm |
| void IMP::saxs::Profile::resample | ( | const Profile * | exp_profile, |
| Profile * | resampled_profile | ||
| ) | const |
return a profile that is sampled on the q values of the exp_profile
| void IMP::saxs::Profile::scale | ( | double | c | ) |
scale
| void IMP::saxs::Profile::set_ff_table | ( | FormFactorTable * | ff_table | ) |
| unsigned int IMP::saxs::Profile::size | ( | ) | const |
| void IMP::saxs::Profile::sum_partial_profiles | ( | double | c1, |
| double | c2, | ||
| bool | check_cashed = true |
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| ) |
computes full profile for given fitting parameters
| void IMP::saxs::Profile::write_partial_profiles | ( | const std::string & | file_name | ) | const |
write a partial profile to file
| void IMP::saxs::Profile::write_SAXS_file | ( | const std::string & | file_name, |
| double | max_q = 0.0 |
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| ) | const |
print to file
| [in] | file_name | output file name |
| [in] | max_q | output till maximal q value = max_q, or all if max_q<=0 |