From db4977a40953d0628f11cfc90d0f153edc5db048 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Wed, 11 Mar 2020 13:12:40 -0700
Subject: [PATCH] Add metadata to RMF output
---
include/GaussianEMRestraint.h | 18 ++++++++++++++++++
pyext/src/restraint.py | 2 ++
src/GaussianEMRestraint.cpp | 23 ++++++++++++++++++++++-
3 files changed, 42 insertions(+), 1 deletion(-)
diff --git a/include/GaussianEMRestraint.h b/include/GaussianEMRestraint.h
index 8f49094..58908d6 100755
--- a/include/GaussianEMRestraint.h
+++ b/include/GaussianEMRestraint.h
@@ -104,6 +104,15 @@ class IMPBAYESIANEMEXPORT GaussianEMRestraint : public Restraint
return exp(-unprotected_evaluate(NULL));
}
+ //! Set the filename corresponding to the density GMM particles
+ /** If the density GMM particles were read from a file, this method
+ can be used to tell the restraint so that it can track this
+ information back to the original EM density file, which is useful
+ for deposition. */
+ void set_density_filename(std::string density_fn) {
+ density_fn_ = get_absolute_path(density_fn);
+ }
+
//! Pre-calculate the density-density and model-model scores
/** This is automatically called by the constructor.
You only need to call it manually if you change Gaussian variances
@@ -129,9 +138,17 @@ class IMPBAYESIANEMEXPORT GaussianEMRestraint : public Restraint
const IMP_OVERRIDE;
virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
void show(std::ostream &out) const { out << "GEM restraint"; }
+
+ //! \return Information for writing to RMF files
+ RestraintInfo *get_static_info() const IMP_OVERRIDE;
+
+ //! \return Information for writing to RMF files
+ RestraintInfo *get_dynamic_info() const IMP_OVERRIDE;
+
IMP_OBJECT_METHODS(GaussianEMRestraint);
private:
+ double model_cutoff_dist_, density_cutoff_dist_;
ParticleIndexes model_ps_;
ParticleIndexes density_ps_;
ParticleIndex global_sigma_;
@@ -148,6 +165,7 @@ class IMPBAYESIANEMEXPORT GaussianEMRestraint : public Restraint
ParticleIndexes slope_ps_; //experiment
std::map<ParticleIndex,Float> map_score_dd_;
Float cached_score_term_;
+ std::string density_fn_;
//variables needed to tabulate the exponential
Floats exp_grid_;
diff --git a/pyext/src/restraint.py b/pyext/src/restraint.py
index 3de2f06..02e1a18 100755
--- a/pyext/src/restraint.py
+++ b/pyext/src/restraint.py
@@ -181,6 +181,8 @@ class GaussianEMRestraintWrapper(object):
cutoff_dist_model_data,
slope,
update_model, backbone_slope)
+ if target_fn != '':
+ self.gaussianEM_restraint.set_density_filename(target_fn)
print('done EM setup')
self.rs = IMP.RestraintSet(self.m, 'GaussianEMRestraint')
diff --git a/src/GaussianEMRestraint.cpp b/src/GaussianEMRestraint.cpp
index 732359e..ab49a55 100755
--- a/src/GaussianEMRestraint.cpp
+++ b/src/GaussianEMRestraint.cpp
@@ -26,7 +26,9 @@ GaussianEMRestraint::GaussianEMRestraint(Model *mdl, ParticleIndexes model_ps,
Float density_cutoff_dist, Float slope,
bool update_model, bool backbone_slope,
std::string name)
- : Restraint(mdl, name), model_ps_(model_ps), density_ps_(density_ps),
+ : Restraint(mdl, name), model_cutoff_dist_(model_cutoff_dist),
+ density_cutoff_dist_(density_cutoff_dist),
+ model_ps_(model_ps), density_ps_(density_ps),
global_sigma_(global_sigma), slope_(slope), update_model_(update_model) {
msize_ = model_ps.size();
@@ -281,4 +283,23 @@ ModelObjectsTemp GaussianEMRestraint::do_get_inputs() const {
return ret;
}
+RestraintInfo *GaussianEMRestraint::get_static_info() const {
+ IMP_NEW(RestraintInfo, ri, ());
+ ri->add_string("type", "IMP.bayesianem.GaussianEMRestraint");
+ if (!density_fn_.empty()) {
+ ri->add_filename("filename", density_fn_);
+ }
+ ri->add_float("model cutoff", model_cutoff_dist_);
+ ri->add_float("density cutoff", density_cutoff_dist_);
+ return ri.release();
+}
+
+RestraintInfo *GaussianEMRestraint::get_dynamic_info() const {
+ IMP_NEW(RestraintInfo, ri, ());
+ Float scale = IMP::isd::Scale(get_model(), global_sigma_).get_scale();
+ ri->add_float("global sigma", scale);
+ ri->add_float("score", get_last_score());
+ return ri.release();
+}
+
IMPBAYESIANEM_END_NAMESPACE
--
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