pass else: ns_new.basepairs.append(ni) add1 = False add2 = False # BaseStacks add1 = False add2 = False for ni in ns.basestacks: if ni.iunit1 == target: if ni.imp1un in aln: ni.imp1un = aln[ni.imp1un] add1 = True if ni.iunit2 == target: if ni.imp2un in aln: ni.imp2un = aln[ni.imp2un] add2 = True if ((ni.iunit1 == target and not add1) or (ni.iunit2 == target and not add2)): pass else: ns_new.basestacks.append(ni) add1 = False add2 = False out_ninfo = NinfoFile(sys.argv[5]) out_ninfo.open_to_write() out_ninfo.write_all(ns_new) out_ninfo.close()
#!/usr/bin/env python import sys from cafysis.file_io.ninfo import NinfoFile from cafysis.elements.ninfo import NinfoSet if len(sys.argv) != 3: print ('Usage: SCRIPT [input ninfo] [output ninfo]') sys.exit(2) ninfo = NinfoFile(sys.argv[1]) ninfo.open_to_read() ns = NinfoSet() ninfo.read_all(ns) ninfo.close() ns.update_info() ns.sort_by_mp() ns.reassign_id() ninfo = NinfoFile(sys.argv[-1]) ninfo.open_to_write() ninfo.write_all(ns) ninfo.close()
dih2_iunit2=seq_2, dih2_imp1un=imp_1_un, dih2_imp2un=imp_2_un, dih2_imp3un=imp_4_un, dih2_imp4un=imp_6_un, dih2_native=dih2_native, dih2_coef=CHT18.HB_DIH_CHAIN, ) ns.hbondDTs.append(hb) ########################### ## Generate ninfo file ## ########################### nf = NinfoFile(args.outfile) nf.open_to_write() nf.write_all(ns) nf.close() ################################### ## Generate exv file (optional) ## ################################### if args.exvfile: n_sep_nlocal_P = 3 n_sep_nlocal_S = 3 n_sep_nlocal_B = 2 if args.end5 == 'P': nmp = 3 * n_nt else: nmp = 3 * n_nt - 1
if len(sys.argv) != 10: print( 'Usage: SCRIPT [ninfo (one-by-one)] [unit] [dist] [side] [unit] [dist] [side] [edc (post_edc.out)] [out]' ) print('') sys.exit(2) fninfo_in = NinfoFile(sys.argv[1]) fninfo_in.open_to_read() ns = NinfoSet() fninfo_in.read_all(ns) ns.update_info() fninfo_in.close() fninfo_out = NinfoFile(sys.argv[-1]) fninfo_out.open_to_write() unit_aln1 = int(sys.argv[2]) aln1 = {} side = int(sys.argv[4]) for line in open(sys.argv[3]): linesp = line.split() res1 = int(linesp[0]) # Dunkle res mp1 = int(linesp[1]) # Dunkle mp res2 = int(linesp[2]) # Jenner res mp2 = int(linesp[3]) # Jenner mp #linesp[4] # dist if side == 1: aln1[mp1] = mp2 elif side == 2: aln1[mp2] = mp1
'Usage: SCRIPT [ninfo file] [edc file] [dist(aln) file] [factor] [output ninfo file]' ) sys.exit(2) f_ninfo = NinfoFile(sys.argv[1]) f_edc = open(sys.argv[2], 'r') f_dist = open(sys.argv[3], 'r') factor = float(sys.argv[4]) f_out_ninfo = NinfoFile(sys.argv[-1]) f_ninfo.open_to_read() ninfo = NinfoSet() f_ninfo.read_all(ninfo) f_ninfo.close() f_out_ninfo.open_to_write() f_out_ninfo._file.write('#0: ' + sys.argv[0] + '\n') f_out_ninfo._file.write('#1: ' + sys.argv[1] + '\n') f_out_ninfo._file.write('#2: ' + sys.argv[2] + '\n') f_out_ninfo._file.write('#3: ' + sys.argv[3] + '\n') f_out_ninfo._file.write('#4: ' + sys.argv[4] + '\n') f_out_ninfo._file.write('#5: ' + sys.argv[5] + '\n') aln = {} # Read from dist file ''' # Jenner Dunkle # res mp res mp dist 1 1 4 11 1.55 1 2 4 12 8.02 2 3 5 13 0.93
imp2_offset += c2.num_res() imp1_offset += c1.num_res() return if __name__ == '__main__': import sys if len(sys.argv) != 3: print ('Usage: %SCRIPT [input PDB] [output ninfo]') sys.exit(2) from cafysis.file_io.pdb import PdbFile from cafysis.file_io.ninfo import NinfoFile from cafysis.elements.ninfo import NinfoSet f = PdbFile(sys.argv[1]) f.open_to_read() chains = f.read_all() f.close() ns = NinfoSet() generate_FENEs(chains, ns) generate_LJs(chains, ns) f_ninfo = NinfoFile(sys.argv[-1]) f_ninfo.open_to_write() f_ninfo.write_all(ns) f_ninfo.close()
@author: Naoto Hori ''' import sys from cafysis.file_io.ninfo import NinfoFile from cafysis.elements.ninfo import NinfoSet if __name__ == '__main__': if len(sys.argv) != 3: print('Usage: %SCRIPT [input ninfo file] [output prefix]') sys.exit(2) file_ninfo = NinfoFile(sys.argv[1]) file_ninfo.open_to_read() ns = NinfoSet() file_ninfo.read_all(ns) ns.update_info() file_ninfo.close() prefix = sys.argv[2] ndi = ns.dict_of_ninfoset_by_unit() for i in range(1, ns.max_unit + 1): for j in range(i, ns.max_unit + 1): if ndi[(i, j)].max_unit != 0: file_out = NinfoFile(prefix + '%03i_%03i.ninfo' % (i, j)) file_out.open_to_write() file_out.write_all(ndi[(i, j)]) #file_out.write_unit(ns, i, j) file_out.close()