import IMP
import IMP.display
class Display(object):
"""Store Display"""
def __init__(self):
self._children = list()
def create_log(self, repr, log_name):
"""Create Chimera log.
@param repr
Representation object.
@param log_name Log name
@return IMP::display::WriteOptimizerState"""
# Try to create Chimera log (like in display_log.py example)
log = IMP.display.WriteOptimizerState(IMP.display.ChimeraWriter(log_name))
# Find IMP particle that corresponds to a representation id
for child in self._children:
child.find_model_decorator(repr)
# Detach parents and children, so the geometries are separate (so that
# we can set separate colors)
for child in self._children:
child.detach_parent()
# Add geometries of proper colors to the log
for child in self._children:
child.create_xyz(1.0, 1.0, 1.0, log)
# Reunite parents with children
for child in self._children:
child.attach_parent()
return log
def __str__(self):
return '\n%s\n' %\
('\n'.join([child._to_str(1) for child in self._children]))
class _DisplayNode(object):
counter = 0
def __init__(self, attributes):
id = attributes.get('id')
if id:
self.id = id
else:
self.id = 'object_%d' % _DisplayNode.counter
_DisplayNode.counter += 1
self._children = list()
def get_color(self):
for child in self._children:
if isinstance(child, _DisplayColor):
return child
return None
def find_model_decorator(self, repr):
particle = repr.find_by_id(self.id)
if particle and particle.model_decorator:
self.model_decorator = particle.model_decorator
else:
self.model_decorator = None
for child in self._children:
child.find_model_decorator(repr)
def detach_parent(self):
if self.model_decorator:
self.parent = self.model_decorator.get_parent()
self.parent.remove_child(self.model_decorator)
for child in self._children:
child.detach_parent()
def attach_parent(self):
if self.model_decorator:
self.parent.add_child(self.model_decorator)
for child in self._children:
child.attach_parent()
def create_xyz(self, r, g, b, log):
color = self.get_color()
if color:
r = color.r
g = color.g
b = color.b
atom_list = list()
if self.model_decorator:
atoms = IMP.atom.get_by_type(self.model_decorator,
IMP.atom.XYZR_TYPE)
for atomh in atoms:
for atom in IMP.atom.get_leaves(atomh):
atom_list.append(atom)
if len(atom_list) >0:
c = IMP.container.ListSingletonContainer(atom_list)
geometry = IMP.core.XYZRsGeometry(c)
geometry.set_name(self.id)
geometry.set_color(IMP.display.Color(r, g, b))
log.add_geometry(geometry)
for child in self._children:
child.create_xyz(r, g, b, log)
def _attr_to_str(self):
return ('DisplayNode', 'id="%s"' % self.id)
def _to_str(self, level):
indent = ' '*level
name, strattr = self._attr_to_str()
if not self._children:
return '%s<%s %s/>' % (indent, name, strattr)
else:
return '%s<%s %s>\n%s\n%s%s>' %\
(indent, name, strattr,
'\n'.join([child._to_str(level + 1)
for child in self._children]), indent, name)
def __str__(self):
return self._to_str(0)
class _DisplayColor(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
self.r = float(attributes.get('r', 0))
self.g = float(attributes.get('g', 0))
self.b = float(attributes.get('b', 0))
def _attr_to_str(self):
return ('Color', 'id="%s" r="%s" g="%s" b="%s"' %
(self.id, self.r, self.g, self.b))
class _DisplayResidue(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
self.start = int(attributes.get('start', -1))
self.end = int(attributes.get('end', -1))
def _attr_to_str(self):
return ('Residue', 'id="%s" start="%s" end="%s"' %
(self.id, self.start, self.end))
class _DisplayUniverse(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Universe', 'id="%s"' % self.id)
class _DisplayCollection(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Collection', 'id="%s"' % self.id)
class _DisplayAssembly(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Assembly', 'id="%s"' % self.id)
class _DisplaySegment(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Segment', 'id="%s"' % self.id)
class _DisplayMolecule(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Molecule', 'id="%s"' % self.id)
class _DisplayProtein(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Protein', 'id="%s"' % self.id)
class _DisplayNucleicAcid(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('NucleicAcid', 'id="%s"' % self.id)
class _DisplayChain(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Chain', 'id="%s"' % self.id)
class _DisplayFragment(_DisplayNode):
def __init__(self, attributes):
_DisplayNode.__init__(self, attributes)
def _attr_to_str(self):
return ('Fragment', 'id="%s"' % self.id)