_display.py

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 <a href="classIMP_1_1restrainer_1_1representation_1_1Representation.html">
            Representation</a> 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 '<Display>\n%s\n</Display>' %\
            ('\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)