#!/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()
#if first: # delta1 = mp1 - 1 # delta2 = mp2 - 1 # first = False if side == 1: #aln[mp1 - delta1] = mp2 - delta2 aln[mp1] = mp2 elif side == 2: #aln[mp2 - delta2] = mp1 - delta1 aln[mp2] = mp1 else: print('"side" is not acceptable. See usage') sys.exit(2) ns = NinfoSet() file_ninfo = NinfoFile(sys.argv[1]) file_ninfo.open_to_read() file_ninfo.read_all(ns) file_ninfo.close() ns_new = NinfoSet() # 両方のユニットともターゲットのときは、 # 両方のIDがalnに含まれていないとaddしない # BondLengths add1 = False add2 = False for ni in ns.bondlengths: if ni.iunit1 == target: if ni.imp1un in aln:
#!/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 1] [input ninfo 2]") sys.exit(2) nf = NinfoFile(sys.argv[1]) nf.open_to_read() ns1 = NinfoSet() nf.read_all(ns1) nf.close() nf = NinfoFile(sys.argv[2]) nf.open_to_read() ns2 = NinfoSet() nf.read_all(ns2) nf.close() nhb1 = len(ns1.hbondDTs) nhb2 = len(ns2.hbondDTs) # Do not use index 0 flag1 = [False] * (nhb1 + 1) flag2 = [False] * (nhb2 + 1)
@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) != 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
dih2_iunit1=seq_1, 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:
#!/usr/bin/env python ''' @author: Naoto Hori ''' import sys from cafysis.file_io.ninfo import NinfoFile from cafysis.elements.ninfo import NinfoSet if len(sys.argv) != 6: print( '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')
import sys from cafysis.file_io.ninfo import NinfoFile, NinfoSet def show_usage(): print('') print(' usage: ninfo_split.py [ninfo file] [prefix (can be dir)]') print('') if len(sys.argv) != 3: show_usage() sys.exit(2) f_ninfo = NinfoFile(sys.argv[1]) f_ninfo.open_to_read() ninfo = NinfoSet() f_ninfo.read_all(ninfo) f_ninfo.close() out_prefix = sys.argv[2] ninfo.update_info() nUnit = ninfo.max_unit print(nUnit) ninfo_out = {} for i in range(1, nUnit + 1): for j in range(i, nUnit + 1): ninfo_out[(i, j)] = NinfoSet() for bd in ninfo.bondlengths:
dih1_imp4=pre_mp_1 + imp_5, dih1_iunit1=ic_2 + 1, dih1_iunit2=ic_1 + 1, dih1_imp1un=imp_2, dih1_imp2un=imp_1, dih1_imp3un=imp_3, dih1_imp4un=imp_5, dih1_native=dih1_native, dih1_coef=DT13.HB_DIH_CHAIN, dih2_imp1=pre_mp_1 + imp_1, dih2_imp2=pre_mp_2 + imp_2, dih2_imp3=pre_mp_2 + imp_4, dih2_imp4=pre_mp_2 + imp_6, dih2_iunit1=ic_1 + 1, dih2_iunit2=ic_2 + 1, dih2_imp1un=imp_1, dih2_imp2un=imp_2, dih2_imp3un=imp_4, dih2_imp4un=imp_6, dih2_native=dih2_native, dih2_coef=DT13.HB_DIH_CHAIN, ) ns.hbondDTs.append(hb) #nf = NinfoFile('ninfo_RNA13_pdb.ninfo') nf = NinfoFile(sys.argv[-1]) nf.open_to_write() nf.write_all(ns) nf.close()
''' if __name__ == '__main__': pass import sys from cafysis.elements.ninfo import NinfoSet from cafysis.file_io.ninfo import NinfoFile from cafysis.file_io.pdb import PdbFile if len(sys.argv) != 4: print ("Usage: SCRIPT [ninfo file] [pdb file] [output file]") 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() file_pdb = PdbFile(sys.argv[2]) file_pdb.open_to_read() chains = file_pdb.read_all() xyz = [] for c in chains: for i in range(c.num_atom()): xyz.append(c.get_atom(i).xyz)
# -*- coding: utf-8 -*- ''' Created on 2012/01/19 @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)])
dih1_imp4=imp_S2, dih1_iunit1=1, dih1_iunit2=1, dih1_imp1un=imp_P1, dih1_imp2un=imp_S1, dih1_imp3un=imp_P2, dih1_imp4un=imp_S2, dih1_native=ARNA.DIH_PSPS, dih1_coef=DT15.ST_DIH, dih1_type_str='PSPS', dih2_imp1=imp_S1, dih2_imp2=imp_P2, dih2_imp3=imp_S2, dih2_imp4=imp_P3, dih2_iunit1=1, dih2_iunit2=1, dih2_imp1un=imp_S1, dih2_imp2un=imp_P2, dih2_imp3un=imp_S2, dih2_imp4un=imp_P3, dih2_native=ARNA.DIH_SPSP, dih2_coef=DT15.ST_DIH, dih2_type_str='SPSP') ns.basestackDTs.append(bs) from cafysis.file_io.ninfo import NinfoFile nf = NinfoFile('ninfo_ssRNA15.ninfo') nf.open_to_write() nf.write_all(ns) nf.close()
elif linesp[0] == 'locaxis': re1 = re.match('^\d+$', linesp[1]) re2 = re.match('^\d+$', linesp[2]) re3 = re.match('^\d+$', linesp[3]) if re1: linesp[1] = int(linesp[1]) if re2: linesp[2] = int(linesp[2]) if re3: linesp[3] = int(linesp[3]) cmds.append(tuple(linesp)) elif linesp[0] == 'def_ninfo': name = linesp[1] filename = linesp[2] nf = NinfoFile(filename) nf.open_to_read() ns = NinfoSet() nf.read_all(ns) nf.close() defs[name] = ('ninfo', filename, ns) elif linesp[0] == 'q': cmds.append(tuple(linesp)) elif linesp[0] == 'dock': cmds.append(tuple(linesp)) elif linesp[0] == 'enc': cmds.append(tuple(linesp))