Source code for Assembly

##===============================================================================
#     This file is part of TEMPy.
#     It describes the implementation of Assembly class for the purpose of fitting multiple component into the assembly map
#     
#     TEMPy is a software designed to help the user in the manipulation 
#     and analyses of macromolecular assemblies using 3D electron microscopy maps. 
#     
#     Copyright 2010-2014 TEMPy Inventors and Birkbeck College University of London.
#                          The TEMPy Inventors are: Maya Topf, Daven Vasishtan, 
#                           Arun Prasad Pandurangan, Irene Farabella, Agnel-Praveen Joseph,
#                          Harpal Sahota
# 
# 
#     TEMPy is available under Public Licence.
#     
#     Please cite your use of TEMPy in published work:
#     
#     Vasishtan D, Topf M. (2011) J Struct Biol 174:333-343. Scoring functions for cryoEM density fitting.
#     Pandurangan AP, Vasishtan D, Topf M. (2015) Structure 23:2365-2376. GAMMA-TEMPy: Simultaneous fitting of components in 3D-EM Maps of their assembly using genetic algorithm.
#===============================================================================

from TEMPy.ProtRep_Biopy import *
from TEMPy.StructureBlurrer import StructureBlurrer
#from EMMap import *
#from MapParser import *
#from PDBParser import *
#from StructureBlurrer import *
#from Vector import *
#from VQ import *
#from Quaternion import *


[docs]class Assembly: """ A class to represent multi-subunit component and its corresponding density map. """ def __init__(self, structList): """ A constructor to initialise the assembly object. Arguments: *structList* A list of BioPy_Structure objects. """ self.structList = structList self.initMapList = [] self.mapList = []
[docs] def build_maps(self, resolution, template_map, sig_coeff=0.356): """ Build list of maps corresponding to the protein components in the structList. Arguments: *resolution* Desired resolution of the density map in Angstrom units. *template_map* A map object that will be uesd as the template to build maps of for the individual maps. Usually the input map used for the assembly fitting. *sigma_coeff* the sigma value (multiplied by the resolution) that controls the width of the Gaussian. Default values is 0.356. """ sb = StructureBlurrer() for x in self.structList: self.mapList.append(sb.gaussian_blur(x, resolution, template_map, sig_coeff)) self.initMapList.append(self.mapList[-1].copy())
[docs] def randomise_structs(self, max_trans, max_rot, v_grain=30, rad=False): """ Randomise the position and orientation of the protein components in the structList. Arguments: *max_trans* Maximum translation permitted *max_rot* Maximum rotation permitted (in degree if rad=False) *v_grain* Graning Level for the generation of random vetors (default=30) """ for x in self.structList: x.randomise_position(max_trans, max_rot, v_grain, rad)
[docs] def randomise_structs_and_maps(self, max_trans, max_rot, v_grain=30, rad=False): """ Randomise the position and orientation of the protein components and its corresponding map objects. Arguments: *max_trans* Maximum translation permitted *max_rot* Maximum rotation permitted (in degree if rad=False) *v_grain* Graning Level for the generation of random vetors (default=30) """ if len(self.mapList) != len(self.structList): print 'Maps not built yet' else: for x in range(len(self.structList)): com = self.structList[x].CoM.copy() rx,ry,rz,ra,tx,ty,tz = self.structList[x].randomise_position(max_trans, max_rot, v_grain, rad, verbose=True) self.mapList[x] = self.mapList[x].rotate_by_axis_angle(rx, ry, rz, ra, com) self.mapList[x] = self.mapList[x].translate(tx,ty,tz)
[docs] def reset_structs(self): """ Translate the list of structure objects back into initial position. """ for x in self.structList: x.reset_position()
[docs] def reset_maps(self): """ Undo all the transformations applied to the list of map objects and restore it to its original state. """ for x in range(len(self.mapList)): self.mapList[x] = self.initMapList[x].copy()
[docs] def reset_all(self): """ Reset the map and structure objects to is initial state. """ self.reset_maps() self.reset_structs()
[docs] def move_map_and_prot_by_aa(self, index, rx, ry, rz, ra, tx, ty, tz): """ Translate and rotate the structure and map objects in the assembly around its centre given an axis and angle. Arguments: *index* Index of the structure and map list. *rx,ry,rz* Axis to rotate about, ie. rx,ry,rz = 0,0,1 rotates the structure and map round the xy-plane. *ra* Angle (in degrees) to rotate map. *tx,ty,tz* Distance in Angstroms to move structure and map in respective x, y, and z directions. """ com = self.structList[index].CoM.copy() self.structList[index].rotate_by_axis_angle(rx, ry, rz, ra, tx, ty, tz) self.mapList[index] = self.mapList[index].rotate_by_axis_angle(rx, ry, rz, ra, com) self.mapList[index] = self.mapList[index].translate(tx,ty,tz)
[docs] def move_map_and_prot_by_euler(self, index, rx, ry, rz, tx, ty, tz): """ Translate and rotate the structure and map objects in the assembly around its centre using Euler angles. Arguments: *index* Index of the structure and map list. *rx,ry,rz* Axis to rotate about, ie. rx,ry,rz = 0,0,1 rotates the structure and map round the xy-plane. *ra* Angle (in degrees) to rotate map. *tx,ty,tz* Distance in Angstroms to move structure and map in respective x, y, and z directions. """ com = self.structList[index].CoM.copy() self.structList[index].rotate_by_euler(rx, ry, rz, 0, 0, 0) self.structList[index].translate(tx,ty,tz) self.mapList[index] = self.mapList[index].rotate_by_euler(rx, ry, rz, com) self.mapList[index] = self.mapList[index].translate(tx,ty,tz)
[docs] def move_map_and_prot_by_mat(self, index, mat, tx, ty, tz): """ Translate and rotate the structure and map objects around pivot given by CoM using a translation vector and a rotation matrix respectively. Arguments: *mat* 3x3 matrix used to rotate structure and map objects. *tx,ty,tz* Distance in Angstroms to move structure and map in respective x, y, and z directions. """ com = self.structList[index].CoM.copy() self.structList[index].rotate_by_mat(mat) self.structList[index].translate(tx,ty,tz) self.mapList[index] = self.mapList[index].rotate_by_matrix(mat, com) self.mapList[index] = self.mapList[index].translate(tx,ty,tz)
[docs] def move_map_and_prot_by_quat(self, index, tx, ty, tz, q_param, mat): """ Translate the structure objects using a translation vector and rotate it using a quaternion object Translate and rotate the map objects around pivot given by CoM using a translation vector and a rotation matrix respectively. Arguments: *index* Index of the structure and map list. *tx,ty,tz* Distance in Angstroms to move structure and map in respective x, y, and z directions. *q_param* Is a list of type [w, x, y, z] which represents a quaternion vector used for rotation *mat* 3x3 matrix used to rotate structure and map objects. """ com = self.structList[index].CoM.copy() self.structList[index].rotate_by_quaternion(q_param) self.structList[index].translate(tx,ty,tz) self.mapList[index] = self.mapList[index].rotate_by_matrix(mat, com) self.mapList[index] = self.mapList[index].translate(tx,ty,tz)
[docs] def combine_structs(self): """ Used to combine the list of structure objects into a single structure object """ if len(self.structList)>1: return self.structList[0].combine_structures(self.structList[1:]) elif len(self.structList)==1: return self.structList[0] else: print 'No structures found'
[docs] def combine_maps(self): """ Used to combine the list of map objects into a single map object """ if len(self.mapList)>1: newMap = self.mapList[0].copy() for x in self.mapList[1:]: newMap.fullMap += x.fullMap return newMap elif len(self.structList)==1: return self.mapList[0].copy() else: print 'No maps found'
[docs] def make_VQ_points(self, threshold, noOfPoints, lap_fil, epochs=300): """ Cluster the density maps in the assembly object into n points using vector quantisation algorithm. Arguments: *emmap* Map (to be clustered) instance. *threshold* voxels with density above this value are used in the VQ run. *noOfPoints* Number of Vector quantisation points to output. *lap_fil* True if you want to Laplacian filter the map first, False otherwise. Note that filtering the map change the density values of the map, which is relevant for the threshold parameter. *epochs* Number of iterations to run the Vector quantisation algorithm. Default is set to 300 Return: A list of vector objects containing the vector quatisation points """ vq = [] if len(self.mapList) > 0: for s in range(len(self.mapList)): vq.append(get_VQ_points(self.mapList[s], threshold, noOfPoints[s], epochs, None, lap_fil)) return vq
[docs] def write_all_to_files(self, templateName): """ Write the all the strucrure and map objects separately to a pdb and mrc formatted file respectively. Arguments: *templateName* A string representing the prefix of the file name """ for x in range(len(self.structList)): self.structList[x].write_to_PDB(templateName+str(x)+'.pdb') if len(self.mapList) > 0: self.mapList[x].write_to_MRC_file(templateName+str(x)+'.mrc')
# Methods not used #========================================================================================================= # def make_sub_VQ_points(self, i, threshold, noOfPoints, lap_fil, epochs=300): # vq = [] # if len(self.mapList) > 0: # vq.append(get_VQ_points(self.mapList[i], threshold, noOfPoints, epochs, None, lap_fil)) # return vq # def make_subVQ_points(self, threshold, noOfPoints, lap_fil, epochs=300): # vq = [] # vq.append(get_VQ_points(self.mapList[0], threshold, noOfPoints, epochs, None, lap_fil)) # return vq #=========================================================================================================