From 50454f438e2914f68c757ce15b67a17d8cfd8983 Mon Sep 17 00:00:00 2001
From: samuel hanot <smlhnt@gmail.com>
Date: Fri, 23 Feb 2018 10:49:14 +0100
Subject: [PATCH] documentation
---
pyext/src/restraint.py | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/pyext/src/restraint.py b/pyext/src/restraint.py
index 8e46615..d44b46e 100755
--- a/pyext/src/restraint.py
+++ b/pyext/src/restraint.py
@@ -183,6 +183,9 @@ class GaussianEMRestraintWrapper(object):
self.set_weight(weight)
def center_target_density_on_model(self):
+ '''
+ aligns the center of mass of the target GMM on the center of mass of the model
+ '''
target_com = IMP.algebra.Vector3D(0, 0, 0)
target_mass = 0.0
for p in self.target_ps:
@@ -228,6 +231,9 @@ class GaussianEMRestraintWrapper(object):
return com
def center_target_density_on_origin(self):
+ '''
+ aligns the center of mass of the target GMM on the origin
+ '''
target_com = self.get_center_of_mass()
print('target com', target_com)
model_com = IMP.algebra.Vector3D(0, 0, 0)
@@ -240,6 +246,10 @@ class GaussianEMRestraintWrapper(object):
# IMP.pmi.tools.translate_hierarchies(self.densities,v)
def center_model_on_target_density(self, input_object):
+ '''
+ aligns the model on the target density
+ @param input_objects IMP.pmi.representation.Representation or IMP.pmi.topology.State
+ '''
if type(input_object) is IMP.pmi.representation.Representation:
hier = input_object.prot
elif type(input_object) is IMP.pmi.topology.State:
@@ -271,6 +281,9 @@ class GaussianEMRestraintWrapper(object):
IMP.core.transform(IMP.core.XYZ(p), transformation)
def center_on_target_density(self):
+ '''
+ align the model on target GMM
+ '''
target_com = self.get_center_of_mass()
print('target com', target_com)
model_com = self.get_center_of_mass(target=False)
@@ -297,6 +310,10 @@ class GaussianEMRestraintWrapper(object):
def set_weight(self,weight):
+ '''
+ set the weight of the restraint
+ @param weight
+ '''
self.weight = weight
self.rs.set_weight(weight)
@@ -324,6 +341,9 @@ class GaussianEMRestraintWrapper(object):
return self.rb
def get_density_as_hierarchy(self):
+ '''
+ returns a hierarchy whose leaves are the gaussian particles of the target GMM
+ '''
if self.em_root_hier is None:
self.em_root_hier = IMP.atom.Copy.setup_particle(IMP.Particle(self.m),0)
self.em_root_hier.set_name("GaussianEMRestraint_density_"+self.label)
--
GitLab