lib.structure.internal.displacements

33 """A special object for representing rotational and translational displacements between models.""" 34

35 - def __init__(self):

36 """Initialise the storage objects.""" 37 38 # The displacement structures. 39 self._translation_vector = {} 40 self._translation_distance = {} 41 self._rotation_matrix = {} 42 self._rotation_axis = {} 43 self._rotation_angle = {}

44 45

46 - def _calculate(self, id_from=None, id_to=None, coord_from=None, coord_to=None, centroid=None):

47 """Calculate the rotational and translational displacements using the given coordinate sets. 48 49 This uses the U{Kabsch algorithm<http://en.wikipedia.org/wiki/Kabsch_algorithm>}. 50 51 52 @keyword id_from: The ID string of the starting structure. 53 @type id_from: str 54 @keyword id_to: The ID string of the ending structure. 55 @type id_to: str 56 @keyword coord_from: The list of atomic coordinates for the starting structure. 57 @type coord_from: numpy rank-2, Nx3 array 58 @keyword coord_to: The list of atomic coordinates for the ending structure. 59 @type coord_to: numpy rank-2, Nx3 array 60 @keyword centroid: An alternative position of the centroid, used for studying pivoted systems. 61 @type centroid: list of float or numpy rank-1, 3D array 62 """ 63 64 # Initialise structures if necessary. 65 if not id_from in self._translation_vector: 66 self._translation_vector[id_from] = {} 67 if not id_from in self._translation_distance: 68 self._translation_distance[id_from] = {} 69 if not id_from in self._rotation_matrix: 70 self._rotation_matrix[id_from] = {} 71 if not id_from in self._rotation_axis: 72 self._rotation_axis[id_from] = {} 73 if not id_from in self._rotation_angle: 74 self._rotation_angle[id_from] = {} 75 76 # The Kabsch algorithm. 77 trans_vect, trans_dist, R, axis, angle, pivot = kabsch(name_from="'%s'"%id_from, name_to="'%s'"%id_to, coord_from=coord_from, coord_to=coord_to, centroid=centroid) 78 79 # Store the data. 80 self._translation_vector[id_from][id_to] = trans_vect 81 self._translation_distance[id_from][id_to] = trans_dist 82 self._rotation_matrix[id_from][id_to] = R 83 self._rotation_axis[id_from][id_to] = axis 84 self._rotation_angle[id_from][id_to] = angle

85 86

87 - def from_xml(self, str_node, dir=None, file_version=1):

88 """Recreate the structural object from the XML structural object node. 89 90 @param str_node: The structural object XML node. 91 @type str_node: xml.dom.minicompat.Element instance 92 @keyword dir: The name of the directory containing the results file. 93 @type dir: str 94 @keyword file_version: The relax XML version of the XML file. 95 @type file_version: int 96 """ 97 98 # Get the pairs of displacements. 99 pair_nodes = str_node.getElementsByTagName('pair') 100 101 # Loop over the pairs. 102 for pair_node in pair_nodes: 103 # Get the two models. 104 id_from = str(pair_node.getAttribute('id_from')) 105 id_to = str(pair_node.getAttribute('id_to')) 106 107 # Initialise structures if necessary. 108 if not id_from in self._translation_vector: 109 self._translation_vector[id_from] = {} 110 if not id_from in self._translation_distance: 111 self._translation_distance[id_from] = {} 112 if not id_from in self._rotation_matrix: 113 self._rotation_matrix[id_from] = {} 114 if not id_from in self._rotation_axis: 115 self._rotation_axis[id_from] = {} 116 if not id_from in self._rotation_angle: 117 self._rotation_angle[id_from] = {} 118 119 # A temporary container to place the Python objects into. 120 cont = ModelContainer() 121 122 # Recreate the Python objects. 123 xml_to_object(pair_node, cont, file_version=file_version) 124 125 # Repackage the data. 126 for name in ['translation_vector', 'translation_distance', 'rotation_matrix', 'rotation_axis', 'rotation_angle']: 127 # The objects. 128 obj = getattr(self, '_'+name) 129 obj_temp = getattr(cont, name) 130 131 # Store. 132 obj[id_from][id_to] = obj_temp

133 134

135 - def to_xml(self, doc, element):

136 """Create XML elements for each model. 137 138 @param doc: The XML document object. 139 @type doc: xml.dom.minidom.Document instance 140 @param element: The element to add the displacement XML elements to. 141 @type element: XML element object 142 """ 143 144 # Loop over the starting models. 145 start_models = sorted(self._translation_vector.keys()) 146 for id_from in start_models: 147 # Loop over the ending models. 148 end_models = sorted(self._translation_vector[id_from].keys()) 149 for id_to in end_models: 150 # Create an XML element for each pair. 151 pair_element = doc.createElement('pair') 152 element.appendChild(pair_element) 153 154 # Set the attributes. 155 pair_element.setAttribute('desc', 'The displacement from model %s to model %s' % (id_from, id_to)) 156 pair_element.setAttribute('id_from', id_from) 157 pair_element.setAttribute('id_to', id_to) 158 159 # The objects to store. 160 obj_names = [ 161 '_translation_vector', 162 '_translation_distance', 163 '_rotation_matrix', 164 '_rotation_axis', 165 '_rotation_angle' 166 ] 167 168 # Store the objects. 169 for i in range(len(obj_names)): 170 # Create a new element for this object, and add it to the main element. 171 sub_elem = doc.createElement(obj_names[i][1:]) 172 pair_element.appendChild(sub_elem) 173 174 # Get the sub-object. 175 subobj = getattr(self, obj_names[i])[id_from][id_to] 176 177 # Add the value to the sub element. 178 object_to_xml(doc, sub_elem, value=subobj)

Source Code for Module lib.structure.internal.displacements