def structures_clash_MDanalysis(structure1, MDatoms):
'''determines whether two structures have any clashing atoms
the smallest structure should be the first argument to allow
this function to run quickly as possible'''
if verbose:
print "using MDAnalysis to find clash between structures", structure1.struct_id, "and", structure2.struct_id
struct1_com = pdb.center_of_mass(
structure1) # find center of mass of structure1
struct1_rad = pdb.molecular_radius(structure1) # find molecular radius
clashing = False
for atom2 in MDatoms: # for every atom in structure2
atom2_radius = radii[pdb.find_element(atom2.name)]
if numpy.linalg.norm(
numpy.array(struct1_com) -
numpy.array(atom2.pos)) < struct1_rad + atom2_radius:
# then we have to check this atom against every struct1 atom
for atom1 in structure1.get_atoms(
): # for every atom in structure1
atom1_radius = radii[
atom1.element] # radii[atom2.resname][atom2.name]
atom_dist = atom2_radius + atom1_radius
if numpy.linalg.norm(
numpy.array(atom1.coords) -
numpy.array(atom2.pos)) < atom_dist:
return True
return clashing
def structures_clash(structure1, structure2, tolerance=0.0):
'''determines whether two structures have any clashing atoms
the smallest structure should be the first argument to allow
this function to run quickly as possible
Input:
- structure1: a Structure() object, probably representing the receptor
- structure2: a Structure() object, probably representing the ligand
- tolerance: float, The distance, in Angstroms, to subtract from the addition of
the radii before a clash is rejected.
Output:
- clashing: a boolean representing whether the structures are clashing or
not.
'''
if verbose:
print "searching for clashes between structures", structure1.struct_id, "and", structure2.struct_id
struct1_com = pdb.center_of_mass(
structure1) # find center of mass of structure1
struct1_rad = pdb.molecular_radius(structure1) # find molecular radius
clashing = False
for atom2 in structure2.atoms: # for every atom in structure2
if atom2.radius == '0.0':
atom2_radius = pdb.radii[
atom2.
element] # if not included, then retrieve a standard radius for this atom
if verbose:
print "using dictionary on atom2. atom2.radius:", atom2.radius
else:
atom2_radius = float(atom2.radius)
# the statement below saves some computation time by being a semi-divide and conquer method. Could be better but I'm sure it will work just fine
if np.linalg.norm(np.array(struct1_com) -
np.array(atom2.coords)) < struct1_rad + atom2_radius:
# then we have to check this atom against every struct1 atom
for atom1 in structure1.get_atoms(
): # for every atom in structure1
if atom1.radius == '0.0':
atom1_radius = pdb.radii[
atom1.
element] # if not included, then retrieve a standard radius for this atom
if verbose:
print "using dictionary on atom1. atom1.radius:", atom1.radius
else:
atom1_radius = float(atom1.radius)
atom_dist = atom2_radius + atom1_radius
if np.linalg.norm(
np.array(atom1.coords) -
np.array(atom2.coords)) < atom_dist - tolerance:
return True
return clashing
def structures_clash(structure1, structure2, tolerance=0.0):
'''determines whether two structures have any clashing atoms
the smallest structure should be the first argument to allow
this function to run quickly as possible'''
if verbose:
print "searching for clashes between structures", structure1.struct_id, "and", structure2.struct_id
struct1_com = pdb.center_of_mass(
structure1) # find center of mass of structure1
struct1_rad = pdb.molecular_radius(structure1) # find molecular radius
clashing = False
for atom2 in structure2.atoms: # for every atom in structure2
#try:
#atom2_radius = float(radii[atom2.resname][atom2.name])
#except KeyError:
# look in the pdb for the radius itself
if atom2.radius == '0.0':
atom2_radius = radii[
atom2.
element] # if not included, then retrieve a standard radius for this atom
print "using dictionary on atom2. atom2.radius:", atom2.radius
else:
atom2_radius = float(atom2.radius)
# the statement below saves some computation time by being a semi-divide and conquer method. Could be better but I'm sure it will work just fine
if numpy.linalg.norm(
numpy.array(struct1_com) -
numpy.array(atom2.coords)) < struct1_rad + atom2_radius:
# then we have to check this atom against every struct1 atom
for atom1 in structure1.get_atoms(
): # for every atom in structure1
if atom1.radius == '0.0':
atom1_radius = radii[
atom1.
element] # if not included, then retrieve a standard radius for this atom
print "using dictionary on atom1. atom1.radius:", atom1.radius
else:
atom1_radius = float(atom1.radius)
#print atom1_radius
atom_dist = atom2_radius + atom1_radius
if numpy.linalg.norm(
numpy.array(atom1.coords) -
numpy.array(atom2.coords)) < atom_dist - tolerance:
#print numpy.linalg.norm(numpy.array(atom1.coords) - numpy.array(atom2.coords))
# then we have a clash
return True
return clashing