#!/usr/bin/python #=========================================================== #Copyright(c)2013, IBMC, CNRS #All rights reserved. #NAME: rnatemplate.py #ABSTRACT: input a RNA sequence (fasta format), output the standard PDB format #DATE: Tue Sep 17 15:08:40 2013 #Usage: #VERSION: 0.01 #AUTHOR: Miao Zhichao #CONTACT: chichaumiau AT gmail DOT com #NOTICE: This is free software and the source code is freely #available. You are free to redistribute or modify under the #conditions that (1) this notice is not removed or modified #in any way and (2) any modified versions of the program are #also available for free. # ** Absolutely no Warranty ** #=========================================================== import sys Usage="""rnatemplate.py usage: input a RNA sequence (fasta format), output the standard PDB format ./rnatemplate.py fasta.file number_of_model(optional) >output.pdb fasta.file example: >RNA1 A length1 UGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAG CUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCA >RNA2 B length2 GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUC CCGUCUUCCGCUCCA """ A_temp="""ATOM %5d P A %c%4d 0.000 0.000 0.000 1.00 0.00 P ATOM %5d OP1 A %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d OP2 A %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d O5' A %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C5' A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C4' A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O4' A %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C3' A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O3' A %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C2' A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O2' A %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C1' A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N9 A %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C8 A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N7 A %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C5 A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C6 A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N6 A %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d N1 A %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C2 A %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N3 A %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C4 A %c%4d 0.000 0.000 0.000 1.00 0.00 C """ G_temp="""ATOM %5d P G %c%4d 0.000 0.000 0.000 1.00 0.00 P ATOM %5d OP1 G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d OP2 G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d O5' G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C5' G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C4' G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O4' G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C3' G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O3' G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C2' G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O2' G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C1' G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N9 G %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C8 G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N7 G %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C5 G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C6 G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O6 G %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d N1 G %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C2 G %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N2 G %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d N3 G %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C4 G %c%4d 0.000 0.000 0.000 1.00 0.00 C """ U_temp="""ATOM %5d P U %c%4d 0.000 0.000 0.000 1.00 0.00 P ATOM %5d OP1 U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d OP2 U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d O5' U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C5' U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C4' U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O4' U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C3' U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O3' U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C2' U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O2' U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C1' U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N1 U %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C2 U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O2 U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d N3 U %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C4 U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O4 U %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C5 U %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C6 U %c%4d 0.000 0.000 0.000 1.00 0.00 C """ C_temp="""ATOM %5d P C %c%4d 0.000 0.000 0.000 1.00 0.00 P ATOM %5d OP1 C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d OP2 C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d O5' C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C5' C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C4' C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O4' C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C3' C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O3' C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C2' C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O2' C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d C1' C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N1 C %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C2 C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d O2 C %c%4d 0.000 0.000 0.000 1.00 0.00 O ATOM %5d N3 C %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C4 C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d N4 C %c%4d 0.000 0.000 0.000 1.00 0.00 N ATOM %5d C5 C %c%4d 0.000 0.000 0.000 1.00 0.00 C ATOM %5d C6 C %c%4d 0.000 0.000 0.000 1.00 0.00 C """ #======================================================================= #Read fasta file #Input: fasta file #format: #~ >name1 chain1 length1 #~ sequence1 #~ >name2 chain2 length2 #~ sequence2 #~ ........ def readfasta(fp): name='xxx' chains=[] seqs=[] seq='' f=file(fp) for line in f: if len(line)<2:continue if line[0] == '#':continue if line[0] == '>': a=line.strip().split() if( len(a) < 2 ): print Usage exit(0) name=a[0][1:] chains.append(a[1][0]) if len(seq)>0: seqs.append(seq) seq='' else: seq+=line.strip().upper() seqs.append(seq) return chains,seqs def prepare_model(chains,seqs): n=1#line number temp_map={'A':A_temp,'U':U_temp,'C':C_temp,'G':G_temp,} number_map={'A':22,'U':20,'C':20,'G':23,} out='' for chain,seq in zip(chains,seqs): rsn=0# residue seq no for k,i in enumerate(seq): rsn+=1 xx=[] for j in range(0,number_map.get(i,0)): xx.append(n) xx.append(chain) xx.append(rsn) n+=1 temp=temp_map.get(i,None) if temp != None: out+=temp%tuple(xx) out+='TER %5d %c %c%4d \n'%(n,i,chain,rsn) n+=1 return out def format_pdb(fp,num=1): # AK2024 Changed number of default models in template to 1 from 5 chains,seqs=readfasta(fp) out='' for i in xrange(num): out+='MODEL %2d \n'%(i+1) out+=prepare_model(chains,seqs) out+='ENDMDL \n' out+='END \n' print out, if __name__ == '__main__': if( len(sys.argv) < 2 ): print Usage exit(0) elif (len(sys.argv) > 2): format_pdb(sys.argv[1],int(sys.argv[2])) else: format_pdb(sys.argv[1])