Source code for RigidBodyParser

#===============================================================================
#     This file is part of TEMPy.
#     
#     TEMPy is a software designed to help the user in the manipulation 
#     and analyses of macromolecular assemblies using 3D electron microscopy maps. 
#     
#	  Copyright  2015 Birkbeck College University of London. 
#
#				Authors: Maya Topf, Daven Vasishtan, Arun Prasad Pandurangan,
#						Irene Farabella, Agnel-Praveen Joseph, Harpal Sahota
# 
#     This software is made available under GPL V3 license
#     http://www.gnu.org/licenses/gpl-3.0.html
#     
#     
#     Please cite your use of TEMPy in published work:
#     
#     Farabella, I., Vasishtan, D., Joseph, A.P., Pandurangan, A.P., Sahota, H. & Topf, M. (2015). J. Appl. Cryst. 48.
#
#===============================================================================

from TEMPy.ProtRep_Biopy import BioPy_Structure,BioPyAtom

[docs]class RBParser: """A class to read Rigid Body files""" def __init__(self): pass
[docs] @staticmethod def read_FlexEM_RIBFIND_files(file_in,structure_instance,list_out=True): """ Read a rigid body files in Flex-EM format (text file) using residue numbers in a structure instance. Each line describes one rigid body by specifying the initial and final residue of each of the segments in that rigid body (eg, '2 6 28 30' means that residues 2-6 and 28-30 will be included in the same rigid body). We recommend to use the RIBFIND server for accurately identifying Rigid Bodies in a protein structures. Arguments: *file_in* Rigid Body File in Flex EM format *structure_instance* Structure Instance to manipulate *list_out* True return a list of the Rigid Bodies structure instances (each line in the file). False will print them separately. """ ssefile = open(file_in, 'rU') nsse = 0 RB_structureinstance_tot=[] for line in ssefile: if line.startswith("#"): pass else: sselist = [] nsse += 1 if len(line) < 3: continue tokens = line.split() if len(tokens) < 2: continue chainID = '' for i in range(len(tokens)/2): start = int(tokens[i*2].split(':')[0]) end = int(tokens[i*2+1].split(':')[0]) sselist.append([start,end]) if ':' in tokens[i*2]: chainID = tokens[i*2].split(':')[1] if not tokens[i*2+1].split(':')[1] == chainID: print 'Check chain IDs in rigid body file', tokens[i*2] #Combine SSEs into one structure sse_struct_list = structure_instance.break_into_segments(sselist,chainID) sse_struct = structure_instance.combine_SSE_structures(sse_struct_list) RB_structureinstance_tot.append(sse_struct.copy()) ssefile.close() if list_out: try: return RB_structureinstance_tot except UnboundLocalError: print "wrong residues number" else: for structure in RB_structureinstance_tot: try: return structure except UnboundLocalError: print "wrong residues number"
[docs] @staticmethod def RBfileToRBlist(file_in): """ Read a rigid body files in Flex-EM format (text file) using residue numbers in a list of segments. Each line describes one rigid body by specifying the initial and final residue of each of the segments in that rigid body (eg, '2 6 28 30' means that residues 2-6 and 28-30 will be included in the same rigid body). We recommend to use the RIBFIND server for accurately identifying Rigid Bodies in a protein structures. Arguments: *file_in* Rigid Body File in Flex EM format *list_out* Return a list of segments (each line in the file). The list of rigid body is defined as: [[riA,rfA],..,[riB,rfB]] where : riA is the starting residues number of segment A. rfA is the final residues number of segment A. """ ssefile = open(file_in, 'rU') nsse = 0 RB_structureinstance_tot=[] for line in ssefile: if line.startswith("#"): pass else: sselist = [] nsse += 1 if len(line) < 3: continue tokens = line.split() if len(tokens) < 2: continue for i in range(len(tokens)/2): start = tokens[i*2] end = tokens[i*2+1] sselist.append([start,end]) RB_structureinstance_tot.append(sselist) ssefile.close() return RB_structureinstance_tot