1 from __future__
import print_function
6 import pyRMSD.RMSDCalculator
10 def parse_custom_ranges(ranges_file):
13 with open(ranges_file)
as fh:
16 return d[
'density_custom_ranges']
19 def get_particles_from_superposed(
20 cluster_conform_i, cluster_conform_0, align, ps, trans,
22 def _to_vector3ds(numpy_array):
28 calculator_name =
"QCP_SERIAL_CALCULATOR"
30 calculator_name =
"NOSUP_SERIAL_CALCULATOR"
32 conforms = numpy.array([cluster_conform_0, cluster_conform_i])
34 if symm_groups
is None:
35 calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
39 if calculator_name ==
'NOSUP_SERIAL_CALCULATOR':
41 s1 = parse_symm_groups_for_pyrmsd(symm_groups)
42 calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
44 fittingCoordsets=conforms,
45 calculationCoordsets=conforms,
46 calcSymmetryGroups=s1,
49 calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
51 fittingCoordsets=conforms,
52 calcSymmetryGroups=[],
53 fitSymmetryGroups=symm_groups)
55 check1 = (calculator_name ==
'NOSUP_SERIAL_CALCULATOR')
56 check2 = symm_groups
is not None
60 rmsd, superposed_fit, _calc_fit = calculator.pairwise(
61 0, 1, get_superposed_coordinates=
True)
63 rmsd, superposed_fit = calculator.pairwise(
64 0, 1, get_superposed_coordinates=
True)
71 _to_vector3ds(superposed_fit[0]), _to_vector3ds(cluster_conform_0))
73 for particle_index
in range(len(superposed_fit[1])):
78 return rmsd, ps, trans
82 """Compute mean density maps from structures.
83 Keeps a dictionary of density maps,
84 keys are in the custom ranges. When you call add_subunits_density, it adds
85 particle coordinates to the existing density maps.
88 def __init__(self, custom_ranges=None, resolution=20.0, voxel=5.0,
91 @param list of particles decorated with mass, radius, and XYZ
92 @param resolution The MRC resolution of the output map
94 @param voxel The voxel size for the output map (lower is slower)
97 self.MRCresolution = resolution
99 self.count_models = 0.0
101 self.bead_names = bead_names
102 self.custom_ranges = custom_ranges
106 self.particle_indices_in_custom_ranges = {}
108 for density_name
in self.custom_ranges:
109 self.particle_indices_in_custom_ranges[density_name] = []
112 for index, beadname
in enumerate(self.bead_names):
113 for density_name
in self.custom_ranges:
115 for domain
in self.custom_ranges[density_name]:
116 if self._is_contained(beadname, domain):
117 self.particle_indices_in_custom_ranges[
118 density_name].append(index)
121 def normalize_density(self):
124 def _create_density_from_particles(self, ps, name,
125 kernel_type=
'GAUSSIAN'):
126 '''Internal function for adding to densities.
127 pass XYZR particles with mass and create a density from them.
128 kernel type options are GAUSSIAN, BINARIZED_SPHERE, and SPHERE.'''
131 dmap.set_was_used(
True)
133 if name
not in self.densities:
134 self.densities[name] = dmap
140 dmap3.set_was_used(
True)
142 dmap3.add(self.densities[name])
143 self.densities[name] = dmap3
145 def _is_contained(self, bead_name, domain):
146 """ domain can be the name of a single protein or a tuple
147 (start_residue,end_residue,protein_name)
148 bead is a string of type moleculeName_startResidue_endResidue
151 (bead_protein, bead_res_start,
152 bead_res_end, bead_copy) = bead_name.rsplit(
"_", 3)
155 if isinstance(domain, tuple):
156 domain_protein = domain[2]
158 domain_protein = domain
160 if "." in domain_protein:
161 spl = domain_protein.split(
".")
162 domain_protein = spl[0]
163 domain_copy = int(spl[1])
165 domain_copy = bead_copy = -1
167 if bead_protein != domain_protein
or int(bead_copy) != domain_copy:
171 if isinstance(domain, tuple):
172 bead_residues = set(range(int(bead_res_start),
173 int(bead_res_end)+1))
174 domain_residues = set(range(int(domain[0]),
176 return not domain_residues.isdisjoint(bead_residues)
181 """Add a frame to the densities.
182 @param ps List of particles decorated with XYZR and Mass.
184 self.count_models += 1.0
186 particles_custom_ranges = {}
187 for density_name
in self.custom_ranges:
188 particles_custom_ranges[density_name] = []
191 for density_name
in self.custom_ranges:
193 in self.particle_indices_in_custom_ranges[density_name]:
194 particles_custom_ranges[density_name].append(
198 for density_name
in self.custom_ranges:
199 self._create_density_from_particles(
200 particles_custom_ranges[density_name], density_name)
202 def get_density_keys(self):
203 return list(self.densities.keys())
206 """Get the current density for some component name"""
207 if name
not in self.densities:
210 return self.densities[name]
212 def write_mrc(self, path=".", file_prefix=""):
214 for density_name
in self.densities:
215 mrc = os.path.join(path, file_prefix +
"_" + density_name +
".mrc")
216 self.densities[density_name].
multiply(1. / self.count_models)
217 densmap[density_name] = mrc
219 self.densities[density_name], mrc,
def get_density
Get the current density for some component name.
Compute mean density maps from structures.
Class for sampling a density map from particles.
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
DensityMap * create_density_map(const IMP::algebra::GridD< 3, S, V, E > &arg)
Create a density map from an arbitrary IMP::algebra::GridD.
def add_subunits_density
Add a frame to the densities.
Basic utilities for handling cryo-electron microscopy 3D density maps.
A decorator for a particle with x,y,z coordinates.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m)
Transformation3D get_transformation_aligning_first_to_second(Vector3Ds a, Vector3Ds b)