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#
# PDB version 2 to version 3 converter. This routine also will correct DNA/RNA names
#
def usage():
print "%s -i input -o output -a altnames " %sys.argv[0]
print "%s --input input --output output --altnames altnames " %sys.argv[0]
print 'input - input pdb file: It must be defied'
print 'output - output pdb file: If it is not defined then it is created using input file name'
print 'altnames - file with alternative names: If it is not defined the it is taken from %s' % os.getenv("CLIBD_MON", "")
def substring_replace(s,t,i1,j1):
# Replace s[i:j] by t. Take care of lengths
i,j=i1,j1
k=j-i
if(k<0) :
i,j=j,i
k=-k
if len(t) < k :
tt = t
for i in range(len(t),k) :
tt = tt + " "
elif(len(t) > k):
tt = t[:k]
else:
tt=t
s=s[:i]+tt+s[j:]
return s
def known_pdb_corrs(allines):
n=0
for aa in allines:
resname = aa[17:20].strip()
if (aa[0:4]=="ATOM" or aa[0:4]=="HETA") :
if(resname=="Ad") :
resname = "DA"
elif (resname == "Cd") :
resname = "DC"
elif (resname == "Td") :
resname = "DT"
elif (resname == "Gd") :
resname = "DG"
elif (resname == "Ud") :
resname = "DU"
elif (resname == "Ar") :
resname == "A"
elif (resname == "Cr") :
resname == "C"
elif (resname == "Tr") :
resname = "T"
elif (resname == "Ur") :
resname = "U"
allines[n] = substring_replace(aa,resname,16,19)
n=n+1
return allines
#
# There might some more to fiddle around. They need to be put here are put in another function
def known_dnarna_corrs(alllines):
n = 0
for aa in allines:
resname = aa[17:20].strip()
if (aa[0:4]=="ATOM" or aa[0:4]=="HETA") :
if(resname in ) :
if( check_dnarna() == 0) :
substring_replace(aa)
def process_alts(residue,alts):
altsthis = []
resname = residue[1][17:20]
print "resname %s" %resname
n = 0
for bb in alts:
if(bb[0] == resname):
n = n +1
altsthis.append(bb)
if(n <1) : return residue
natall = 0
nalt = 0
nat = 0
atreal1 = []
atreal2 = []
for ats in residue:
natall = natall+1
atom = ats[12:16].strip()
print atom
for ats_alt in altsthis:
if atom==ats_alt[2] :
nalt=nalt+1
atreal1.append([ats_alt[1],ats_alt[3]])
elif atom==ats_alt[1] :
atreal2.append([ats_alt[1],ats_alt[3]])
nat = nat + 1
if (nalt == natall) :
#
# replace atoms
nat = 0
for ats in residue:
nat = nat + 1
atom = ats[12:4].strp()
for ats_alt in altsthis:
if(atom==ats_alt[2]) :
#
# Take care: atom names may need to be written
# in a fashion pdb wants
atom = atreal1[nat][0].strip()
element = atreal1[nat][1].strip()
if (len(element) == 1) :
if(len(atom) < 4): atom = " "+atom
element = " "+element
ats = substring_replace(ats,atom,12,16)
l=len(ats)
residue[nat-1] = substring_replace(ats,element,76,l)
break
elif(nat==natall):
print nat
elif(nat !=natall) :
print nat, natall
print "we have a problem"
print "At least some of the atoms in residues %s have neither alt no real atom correspondence" %resnum
sys.exit()
return residue
#
# Main body of the program
#
import getopt, sys, os
#
# Read and interpret command line options
try:
opts, args = getopt.getopt(sys.argv[1:],"i:a:o:h",["input=","altnames=","output=","help"])
except getopt.GetoptError, err:
# print help information and exit:
print str(err) # will print something like "option -a not recognized"
usage()
sys.exit(2)
#
pdbout = " "
altnames = " "
pdbin = " "
for o,a in opts:
if o in ("-i","--input"):
pdbin=a
elif o in ("-a", "--altnames"):
altnames = a
elif o in ("-o","--output"):
pdbout = a
elif o in ("-h","--help"):
usage()
sys.exit()
#
# Make sure that necessary files exist
if(pdbin == "" or not os.path.isfile(pdbin)):
print "Input pdb file must be defined and it must exist"
usage()
sys.exit()
if(pdbout == " " or len(pdbout) < 0):
l = pdbin.find(".pdb")
if( l > 0) :
pdbout=pdbin[0:l]+"_v3.pdb"
else:
pdbout = "v3.pdb"
if altnames==" " :
altnames = os.getenv("CLIBD_MON", "")+"pdb_alt_names.txt"
if( not os.path.isfile(altnames)) :
print "File with altnames - %s does not exist" %altnames
#
# Now ready to do the job
# Read the list of monomers with their alts
altatoms = []
i=0
j=0
with open(altnames,"r") as alts:
for aaa in alts:
aaa=aaa.strip()
bbb =aaa.split()
if(bbb[0] == "resname") :
#
# New residue
bsave = bbb[1]
elif(bbb[0] == "atom") :
#
# read the residue further
altatoms.append([bsave,bbb[1],bbb[3],bbb[5]])
#
# Now read pdb file and organise it. Remove hydrogens and aniso cards
dictPDB = ["REMARK","SCALE1","CRYST1","MTRX1","MTRX2","MTRX3","ATOM","HETATM","LINK","MODRES","ORIGX","HEADER"]
allines=[]
with open(pdbin,"r") as pdbin:
for line1 in pdbin:
line = line1.rstrip()
element = " "
if (line[0:4] == 'ATOM' or line[0:4] == 'HETA') and len(line) > 77 :
element = line[76:78].strip()
for aa in dictPDB:
if line[0:6].rstrip() == aa and element != 'H' :
#
# Remove charges from atom names. They should be on the element nam
atom = line[12:16]
ip=atom.find("+")
if(ip < 0) : ip=atom.find("-")
if(ip > 0) : atom = atom[0:ip]
l=len(atom)
if atom[l-1:l] == "," : atom = substring_replace(atom,"'",l-1,l)
line = substring_replace(line,atom,12,16)
allines.append(line)
allines = known_pdb_corrs(allines)
#
# Correct known potential problems
#
# Start processing this pdb
resnumOld ="Something Unreasonable"
residue = []
#out = open(pdbout,"w")
toout = []
nres = 0
for aa in allines:
if aa[0:4]=="ATOM" or aa[0:6]=="HETATM" :
resnum = aa[21:27]
resname = aa[17:20]
if (resnum == resnumOld) :
nres = nres + 1
residue.append(aa)
else:
if resnumOld != "Something Unreasonable" :
#
# Process this residue
residue1 = process_alts(residue,altatoms)
for line in residue1:
toout.append(line)
nres = 1
residue = [aa]
resnumOld = resnum
else:
if nres > 0:
residue1 = process_alts(residue,altatoms)
for line in reside1:
print line
toout.append(line)
nres = 0
toout.append(aa)
print nres
if nres > 0:
residue1 = process_alts(residue,altatoms)
for line in residue1:
print line
toout.append(line)
out = open(pdbout,"w")
for aa in toout:
out.write(aa+"\n")
out.close()
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