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fix bug in create_molecule(), fix bux in generate_trial_perpendicular…
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…(), improve docs
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@pm-blanco
pm-blanco committed Mar 13, 2024
1 parent bb2d1d3 commit 9876d54
Showing 1 changed file with 37 additions and 40 deletions.
77 changes: 37 additions & 40 deletions pyMBE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -678,11 +678,11 @@ def create_molecule(self, name, number_of_molecules, espresso_system, first_resi
n_samples=1,
on_surface=True)[0]
residues_info = self.create_residue(name=residue,
number_of_residues=1,
espresso_system=espresso_system,
central_bead_position=first_residue_position,
use_default_bond= use_default_bond,
backbone_vector=backbone_vector)
number_of_residues=1,
espresso_system=espresso_system,
central_bead_position=first_residue_position,
use_default_bond= use_default_bond,
backbone_vector=backbone_vector)
residue_id = next(iter(residues_info))
for index in self.df[self.df['residue_id']==residue_id].index:
self.add_value_to_df(key=('molecule_id',''),
Expand All @@ -706,10 +706,11 @@ def create_molecule(self, name, number_of_molecules, espresso_system, first_resi
use_default_bond=use_default_bond)
residue_position = residue_position+backbone_vector*l0
residues_info = self.create_residue(name=residue,
number_of_residues=1,
espresso_system=espresso_system,
central_bead_position=[residue_position],
use_default_bond= use_default_bond)
number_of_residues=1,
espresso_system=espresso_system,
central_bead_position=[residue_position],
use_default_bond= use_default_bond,
backbone_vector=backbone_vector)
residue_id = next(iter(residues_info))
for index in self.df[self.df['residue_id']==residue_id].index:
if not self.check_if_df_cell_has_a_value(index=index,key=('molecule_id','')):
Expand Down Expand Up @@ -929,6 +930,7 @@ def create_residue(self, name, espresso_system, number_of_residues, central_bead
particle_name2=side_chain_element,
hard_check=True,
use_default_bond=use_default_bond)

if backbone_vector is None:
bead_position=self.generate_trialvectors(center=central_bead_position,
radius=l0,
Expand All @@ -938,7 +940,7 @@ def create_residue(self, name, espresso_system, number_of_residues, central_bead
bead_position=self.generate_trial_perpendicular_vector(vector=backbone_vector,
center=central_bead_position,
radius=l0)

side_bead_id = self.create_particle(name=side_chain_element,
espresso_system=espresso_system,
position=[bead_position],
Expand Down Expand Up @@ -1528,48 +1530,43 @@ def generate_coordinates_outside_sphere(self, center, radius, max_dist, n_sample
coord_list.append (coord)
counter += 1
return coord_list

def generate_trial_perpendicular_vector(self,vector,center,radius):
"""
Generates an orthogonal vector with the same size as the input vector.
Generates an orthogonal vector to the input `vector`.
Args:
vector(`lst`): arbitrary vector.
center(`lst`): origin of the orthogonal vector.
radius(`float`): magnitude of the orthogonal vector.
Returns:
perpendicular_vector: Orthogonal vector with the same magnitude as the input vector.
"""

# FIXME:
# We should consider renaming the input arguments for clarity
# center --> origin
# radius --> magnitude

Args:
vector: Input vector for which an orthogonal vector needs to be generated.
Returns:
perpendicular_vector: Orthogonal vector with the same magnitude as the input vector.
"""
np_vec = self.np.array(vector)

if self.np.all(np_vec == 0):
raise ValueError('Zero vector')

# Generate a random vector with the same size as the input vector
random_vector = self.generate_trialvectors(center=center, radius=radius, n_samples=1, on_surface=True)[0]
random_vector = self.generate_trialvectors(center=center,
radius=radius,
n_samples=1,
on_surface=True)[0]

# Project the random vector onto the input vector and subtract the projection
projection = self.np.dot(random_vector, np_vec) / self.np.dot(np_vec, np_vec) * np_vec
perpendicular_vector = random_vector - projection
# Normalize the perpendicular vector to have the same magnitude as the input vector
perpendicular_vector /= self.np.linalg.norm(perpendicular_vector) / self.np.linalg.norm(np_vec)
return perpendicular_vector
'''
def generate_trial_perpendicular_vector(self, vector, center, radius):
"""
Generates a random vector perpendicular to `vector`.
Args:
vector(`lst`): Coordinates of the vector.
magnitude(`float`): magnitude of the vector perpendicular to `vector`.
Returns:
perpendicular_vector(`np.array`): random vector perpendicular to `vector`.
"""
np_vec=self.np.array(vector)
if np_vec[1] == 0 and np_vec[2] == 0 and np_vec[0] == 1:
raise ValueError('zero vector')
perp_vec = self.np.cross(np_vec, self.generate_trialvectors(center=center, radius=radius, n_samples=1, on_surface=True)[0])
norm_perp_vec = perp_vec/self.np.linalg.norm(perp_vec)
return center+norm_perp_vec*radius
'''
perpendicular_vector /= self.np.linalg.norm(perpendicular_vector)
return center+perpendicular_vector*radius

def generate_trialvectors(self, center, radius, n_samples, seed=None, on_surface=False):
"""
Uniformly samples points from a hypersphere. If on_surface is set to True, the points are
Expand All @@ -1579,7 +1576,7 @@ def generate_trialvectors(self, center, radius, n_samples, seed=None, on_surface
center(`lst`): Array with the coordinates of the center of the spheres.
radius(`float`): Radius of the sphere.
n_samples(`int`): Number of sample points to generate inside the sphere.
seed (`int`, optional): Seed for the random number generator
seed (`int`, optional): Seed for the random number generator.
on_surface (`bool`, optional): If set to True, points will be uniformly sampled on the surface of the hypersphere.
Returns:
Expand Down

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