import sys, os, time, string
common_files = "./common_files"
sys.path.append(common_files)
from fopen import *
pdb_dir = fopen("absolute_path_of_pdb_files")[0].strip()
#pdb_dir = "../pdb_files"
date_ = time.strftime("%d_%b_%Y")
difference = []
myfilesdict = {}
allfilesdict = {}
dead_files = []
try:
list = fopen("index.html")
except IOError:
# var = raw_input("The file index.html file was not found. Should we download the pdb index file from rscb servers? Type yes and press enter to continue with the download, type anything else and press enter to abort.\n")
# if var == "yes":
# os.system("wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/")
os.system(
"wget -e use_proxy=yes -e ftp_proxy=infpapxvip.it.unsw.edu.au:8080 ftp://ftp.pdbj.org/pub/pdb/data/structures/all/pdb/"
)
list = fopen("index.html")
# else:
# print "You will need to download the index.html file yourself from ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/ and place the file in this directory. Alternative you can re-run the script.\n"
# sys.exit()
#allfiles = [(line,line.split("\"")[1].split("/")[-1][:-2]) for line in list if line.find("a href") != -1 and line.find(".ent") != -1]
#allfiles = []
from fopen import *
pdb_dir = fopen("absolute_path_of_pdb_files")[0].strip()
flist = fopen("pdbaanr")
file = open("new_files_downloaded_on_pdbaanr","w")
import os
for ff in flist:
if os.path.exists(pdb_dir+ff.strip()):
file.write(ff)
def main(analysis_type, command_variables, threshold):
#pdb_dir = fopen("absolute_path_of_pdb_files")[0].strip()
pdb_dir = "../pdb_files"
x = Workbook()
x.add_sheet("NMR averaged model")
x.add_sheet("NMR multiple models")
x.add_sheet("X-RAY")
x.add_sheet("Other")
date_ = time.strftime("%d_%b_%Y")
x.save("../Analyses/" + analysis_type + "_" + date_ + ".xls")
# file pdb1a5n is missing, possibly because 1a5n does not contain ssbonds (correct)
#"pdb1tdy.ent","pdb1a5n.ent","pdb1cb6.ent","pdb2ac5.ent"
#for file in [pdb_dir+name for name in ["pdb1kdg.ent", "pdb1kdk.ent", "pdb1kdm.ent", "pdb1kdq.ent", "pdb1kdu.ent", "pdb1kdv.ent", "pdb1kdy.ent", "pdb1kdz.ent", "pdb1ke1.ent", "pdb1ke2.ent", "pdb1keb.ent", "pdb1keg.ent", "pdb1kek.ent", "pdb1kel.ent", "pdb1kem.ent", "pdb1ken.ent", "pdb1keo.ent", "pdb1kex.ent", "pdb1kf2.ent", "pdb1kf3.ent", "pdb1kf4.ent", "pdb1kf5.ent", "pdb1kf7.ent"]]:
# run(file,x)
#try:
# open("..\\Analyses\\basic_analysis_"+time.strftime("%a_%d_%b_%Y")+".xls","r")
#except IOError:
#for file in os.listdir(pdb_dir):
#for file in ["pdb1axi.ent"]:
# run(pdb_dir+file,x)
#n = len(os.listdir(pdb_dir))
erfile = open("error_" + analysis_type + "_" + date_ + ".log", "w")
#check command parameters
if len(command_variables) <= 1:
run_list = os.listdir(pdb_dir)
run_list.remove("dsspout")
print "1"
elif command_variables[1].find(".ent") != -1:
try:
run_list = [command_variables[1]]
print "2"
#pdb_dir = "./"
except IOError:
print "The file " + command_variables[1] + " was not found."
sys.exit(1)
else:
print "3"
try:
run_list = [
z.strip() for z in fopen("new_files_downloaded_on_" +
command_variables[1])
]
except IOError:
tag = "new_files_downloaded_on_"
print "The file \"" + tag + command_variables[
1] + "\" does not exist. Possible options are:"
for line in [z for z in os.listdir(".") if z[:24] == tag]:
print line
sys.exit(1)
###
###temp
# import string
# run_list = [z.replace(".dssp",".ent") for z in open("dssplist","r").read().split("\n") if z != ""]
# aer = run_list.index("pdb2gi7.ent")
# run_list = run_list[aer:]
# print run_list
# run_list = ["pdb2gi7.ent"]
###
#run_list = ["pdb2fz3.ent"]
#histogram - for analysing relationships between secondary structures and bond types
hist_ = {}
#run with specified command parameters in run list
# run_list = ["pdb1gpq.ent","pdb1gps.ent","pdb1gpt.ent","pdb1gpz.ent","pdb1gqb.ent","pdb1gqr.ent","pdb1gqs.ent","pdb1gqv.ent","pdb1gqz.ent","pdb1gr2.ent","pdb1gra.ent","pdb1grn.ent","pdb1grt.ent","pdb1gsk.ent","pdb1gsm.ent","pdb1gsn.ent","pdb1gsp.ent","pdb1gt6.ent","pdb1gtp.ent","pdb1gts.ent","pdb1gtt.ent","pdb1gu2.ent","pdb1gu3.ent","pdb1guj.ent","pdb1gur.ent","pdb1guv.ent","pdb1gv7.ent","pdb1gv8.ent","pdb1gv9.ent","pdb1gvc.ent","pdb1gvk.ent","pdb1gvl.ent","pdb1gvt.ent","pdb1gvu.ent","pdb1gvv.ent","pdb1gvw.ent","pdb1gvx.ent","pdb1gvz.ent","pdb1gw0.ent","pdb1gw2.ent","pdb1gwa.ent","pdb1gwb.ent","pdb1gwd.ent","pdb1gwn.ent","pdb1gwo.ent","pdb1gwt.ent","pdb1gwu.ent","pdb1gx2.ent","pdb1gx8.ent","pdb1gx9.ent","pdb1gxa.ent","pdb1gxd.ent","pdb1gxs.ent","pdb1gxv.ent","pdb1gxx.ent","pdb1gxy.ent","pdb1gxz.ent","pdb1gy0.ent","pdb1gyc.ent","pdb1gyd.ent","pdb1gye.ent","pdb1gyh.ent","pdb1gyo.ent","pdb1gz1.ent","pdb1gz2.ent","pdb1gz7.ent","pdb1gza.ent","pdb1gzb.ent","pdb1gzj.ent","pdb1gzm.ent","pdb1gzp.ent","pdb1gzq.ent","pdb1gzr.ent","pdb1gzy.ent","pdb1gzz.ent","pdb1h02.ent","pdb1h03.ent","pdb1h04.ent","pdb1h0b.ent","pdb1h0d.ent","pdb1h0g.ent","pdb1h0h.ent","pdb1h0i.ent","pdb1h0j.ent","pdb1h0l.ent","pdb1h0z.ent","pdb1h12.ent","pdb1h13.ent","pdb1h14.ent","pdb1h15.ent","pdb1h1b.ent","pdb1h1h.ent","pdb1h1n.ent","pdb1h20.ent","pdb1h22.ent","pdb1h23.ent","pdb1h2b.ent","pdb1h2p.ent","pdb1h2q.ent","pdb1h30.ent","pdb1h34.ent","pdb1h3j.ent","pdb1h3p.ent","pdb1h3t.ent","pdb1h3u.ent","pdb1h3v.ent","pdb1h3w.ent","pdb1h3x.ent","pdb1h3y.ent","pdb1h43.ent","pdb1h44.ent","pdb1h45.ent","pdb1h46.ent","pdb1h49.ent","pdb1h4i.ent","pdb1h4j.ent","pdb1h4p.ent","pdb1h4u.ent","pdb1h4w.ent","pdb1h52.ent","pdb1h53.ent","pdb1h55.ent","pdb1h57.ent","pdb1h58.ent","pdb1h59.ent","pdb1h5a.ent","pdb1h5b.ent","pdb1h5c.ent","pdb1h5d.ent","pdb1h5e.ent","pdb1h5f.ent","pdb1h5g.ent","pdb1h5h.ent","pdb1h5i.ent","pdb1h5j.ent","pdb1h5k.ent","pdb1h5l.ent","pdb1h5m.ent","pdb1h5o.ent","pdb1h5x.ent","pdb1h6m.ent","pdb1h6r.ent","pdb1h6v.ent","pdb1h75.ent","pdb1h76.ent","pdb1h7l.ent","pdb1h7q.ent","pdb1h80.ent","pdb1h81.ent","pdb1h82.ent","pdb1h83.ent","pdb1h84.ent","pdb1h86.ent","pdb1h87.ent","pdb1h8d.ent","pdb1h8i.ent","pdb1h8l.ent","pdb1h8n.ent","pdb1h8o.ent","pdb1h8p.ent","pdb1h8s.ent","pdb1h8u.ent","pdb1h8v.ent","pdb1h8x.ent","pdb1h8y.ent","pdb1h8z.ent","pdb1h91.ent","pdb1h9h.ent","pdb1h9i.ent","pdb1h9l.ent","pdb1h9v.ent","pdb1h9z.ent","pdb1ha0.ent","pdb1ha2.ent","pdb1ha6.ent","pdb1ha8.ent","pdb1ha9.ent","pdb1haa.ent","pdb1hae.ent","pdb1haf.ent","pdb1hag.ent","pdb1hah.ent","pdb1hai.ent","pdb1haj.ent"]
n = len(run_list)
typedict = {}
for type_ in ["lys_arg", "his", "asp_glu", "trp", "phe", "tyr"]:
typedict[type_] = (analysis_type == type_)
timestart = time.ctime()
for i, file in enumerate(run_list):
#for i,file in enumerate(["pdb1w4y.ent"]):
# print type(hist_)
hist_ = analysis.run(pdb_dir + file,
x,
erfile,
dist=threshold,
histogram=hist_,
lys_arg=typedict["lys_arg"],
his=typedict["his"],
asp_glu=typedict["asp_glu"],
trp=typedict["trp"],
phe=typedict["phe"],
tyr=typedict["tyr"])
m = int((i + 1) / float(n) * 10000) / 100.0
print str(m) + "% complete"
timefinish1 = time.ctime()
print "\nResults file is being saved. Please do not close the program window.\n"
##################################################################
##The histogram bit
def histcmp(a, b):
return (hist_[a] < hist_[b]) * 2 - 1
fffff = open("histogram_", "w")
hkeys = hist_.keys()[:]
hkeys.sort(histcmp)
x.add_sheet("Histogram")
histosheet = x.get_sheet(4)
histosheet.write(0, 0, "Secondary structure 1", style0)
histosheet.write(0, 1, "Secondary structure 2", style0)
histosheet.write(0, 2, "Disulfide Bond type", style0)
histosheet.write(0, 3, "Count", style0)
for row, h in enumerate(hkeys):
fffff.write(str(h) + " " * (21 - len(h)) + str(hist_[h]) + "\n")
histosheet.write(row + 1, 0, h[0])
histosheet.write(row + 1, 1, h[1])
histosheet.write(row + 1, 2, h[2:])
histosheet.write(row + 1, 3, hist_[h])
fffff.close()
##################################################################
x.save("..\\Analyses\\" + analysis_type + "_" + date_ + ".xls")
print "\nAnalysis complete and results saved.\n"
timefinish2 = time.ctime()
erfile.close()
print "start =", timestart
print "prcessed =", timefinish1
print "saved =", timefinish2
def main(analysis_type, command_variables, threshold):
pdb_dir = fopen(
"D:\\xampp\\htdocs\\python\\SSP\\absolute_path_of_pdb_files")[0].strip(
) ## EDIT
dssp_dir = None
#dssp_dir = "..\\pdb_files\\dsspout\\"
#pdb_dir = "..\\pdb_files\\"
x = Workbook()
x.add_sheet("X-RAY")
x.add_sheet("X-RAY 2")
x.add_sheet("X-RAY 3")
x.add_sheet("NMR averaged model")
x.add_sheet("NMR multiple models 1")
x.add_sheet("NMR multiple models 2")
x.add_sheet("Other")
date_ = time.strftime("%d%b%Y_%H%M%S")
write_path = "D:\\xampp\\htdocs\\python\\Analyses\\" + str(
int(random.random() * 100000000)) + "_" + date_ + ".xls"
inA = 0
if len(command_variables) == 2:
if command_variables[1] == '-A':
date_ = time.strftime("%d_%b_%Y")
write_path = "D:\\xampp\\htdocs\\python\\Analyses\\disulfide_analysis_" + date_ + ".xls"
command_variables.pop(1)
inA = 1
## EDIT
#x.save(write_path)
#x.save("..\\Analyses\\test.xls")
# file pdb1a5n is missing, possibly because 1a5n does not contain ssbonds (correct)
#"pdb1tdy.ent","pdb1a5n.ent","pdb1cb6.ent","pdb2ac5.ent"
#for file in [pdb_dir+name for name in ["pdb1kdg.ent", "pdb1kdk.ent", "pdb1kdm.ent", "pdb1kdq.ent", "pdb1kdu.ent", "pdb1kdv.ent", "pdb1kdy.ent", "pdb1kdz.ent", "pdb1ke1.ent", "pdb1ke2.ent", "pdb1keb.ent", "pdb1keg.ent", "pdb1kek.ent", "pdb1kel.ent", "pdb1kem.ent", "pdb1ken.ent", "pdb1keo.ent", "pdb1kex.ent", "pdb1kf2.ent", "pdb1kf3.ent", "pdb1kf4.ent", "pdb1kf5.ent", "pdb1kf7.ent"]]:
# run(file,x)
#try:
# open("..\\Analyses\\basic_analysis_"+time.strftime("%a_%d_%b_%Y")+".xls","r")
#except IOError:
#for file in os.listdir(pdb_dir):
#for file in ["pdb1axi.ent"]:
# run(pdb_dir+file,x)
#n = len(os.listdir(pdb_dir))
erfile = open("D:\\xampp\\htdocs\\python\\Errors\\error_" + analysis_type +
"_" + date_ + ".log", "w") ## EDIT
runlist = None
#check command parameters
if len(command_variables) < 2:
#command_variables.pop(0)
#run_list = []
run_list = os.listdir(pdb_dir)
run_list.remove("dsspout")
elif len(command_variables) >= 2:
command_variables.pop(0)
run_list = []
for i in command_variables:
if i.find("\\") == -1:
i = ".\\" + i
if i.lower().find('.ent') != -1 or i.lower().find('.pdb') != -1:
if not os.path.isfile(i):
erfile.write("The file " + i + " was not found.")
sys.exit(1)
run_list.append(i)
pdb_dir = ""
dssp_dir = pdb_dir + os.path.dirname(i) + "\\dsspout"
else:
run_list = []
run_list = command_variables[:]
print "Checking DSSP files... "
if dssp_dir == None:
dssp_dir = pdb_dir + os.path.dirname(run_list[0]) + "\\dsspout"
if not os.path.isdir(dssp_dir):
dssplist = []
else:
dssplist = os.listdir(dssp_dir)
newlist = {}
for j in dssplist:
newlist[j.split(".")[0].split("_")[0]] = 1
print len(newlist)
print len(run_list)
for i in run_list:
found = 0
print i[:-3].split("\\")[-1].rstrip(".")
if newlist.has_key(i[:-3].split("\\")[-1].rstrip(".")):
found = 1
if found == 0:
if not os.path.isdir(pdb_dir + os.path.dirname(i) + "\\dsspout"):
os.mkdir(pdb_dir + os.path.dirname(i) + "\\dsspout")
outpath = pdb_dir + os.path.dirname(i) + "\\dsspout" + "\\"
erfile.write("python create_dssp.py " + pdb_dir +
os.path.dirname(i) + "\\" + os.path.basename(i) +
" " + outpath)
os.system("python D:\\xampp\htdocs\python\SSP\create_dssp.py " +
pdb_dir + os.path.dirname(i) + "\\" +
os.path.basename(i) + " " + outpath)
print "CREATE "
print "Done"
# print "Checking DSSP files... "
# for i in run_list:
# dssp_dir = pdb_dir+os.path.dirname(i)+"\\dsspout"
# if not os.path.isdir(dssp_dir):
# dssplist = []
# else:
# dssplist = os.listdir(dssp_dir)
# found = 0
# for j in dssplist:
# if j.find(i[:-3].split("\\")[-1]) != -1:
# found = 1
# break;
# if found == 0:
# if not os.path.isdir(pdb_dir+os.path.dirname(i)+"\\dsspout"):
# os.mkdir(pdb_dir+os.path.dirname(i)+"\\dsspout")
# os.system("D:\\xampp\\htdocs\\python\\SSP\\dsspcmbi.exe "+pdb_dir+os.path.dirname(i)+"\\"+os.path.basename(i)+" > "+pdb_dir+os.path.dirname(i)+"\\dsspout\\"+i[:-3].split("\\")[-1]+"dssp") ## EDIT
# print "DSSP -> "+pdb_dir+os.path.basename(i)
# print "Done"
#else:
# try:
# run_list = [z.strip() for z in fopen("new_files_downloaded_on_"+command_variables[1])]
# except IOError:
# tag = "new_files_downloaded_on_"
# print "The file \""+tag+command_variables[1]+"\" does not exist. Possible options are:"
# for line in [z for z in os.listdir(".") if z[:24] == tag]:
# print line
# sys.exit(1)
###
###temp
# import string
# run_list = [z.replace(".dssp",".ent") for z in open("dssplist","r").read().split("\n") if z != ""]
# aer = run_list.index("pdb2gi7.ent")
# run_list = run_list[aer:]
# print run_list
# run_list = ["pdb2gi7.ent"]
###
#histogram - for analysing relationships between secondary structures and bond types
hist_ = {}
#run with specified command parameters in run list
# run_list = ["pdb1gpq.ent","pdb1gps.ent","pdb1gpt.ent","pdb1gpz.ent","pdb1gqb.ent","pdb1gqr.ent","pdb1gqs.ent","pdb1gqv.ent","pdb1gqz.ent","pdb1gr2.ent","pdb1gra.ent","pdb1grn.ent","pdb1grt.ent","pdb1gsk.ent","pdb1gsm.ent","pdb1gsn.ent","pdb1gsp.ent","pdb1gt6.ent","pdb1gtp.ent","pdb1gts.ent","pdb1gtt.ent","pdb1gu2.ent","pdb1gu3.ent","pdb1guj.ent","pdb1gur.ent","pdb1guv.ent","pdb1gv7.ent","pdb1gv8.ent","pdb1gv9.ent","pdb1gvc.ent","pdb1gvk.ent","pdb1gvl.ent","pdb1gvt.ent","pdb1gvu.ent","pdb1gvv.ent","pdb1gvw.ent","pdb1gvx.ent","pdb1gvz.ent","pdb1gw0.ent","pdb1gw2.ent","pdb1gwa.ent","pdb1gwb.ent","pdb1gwd.ent","pdb1gwn.ent","pdb1gwo.ent","pdb1gwt.ent","pdb1gwu.ent","pdb1gx2.ent","pdb1gx8.ent","pdb1gx9.ent","pdb1gxa.ent","pdb1gxd.ent","pdb1gxs.ent","pdb1gxv.ent","pdb1gxx.ent","pdb1gxy.ent","pdb1gxz.ent","pdb1gy0.ent","pdb1gyc.ent","pdb1gyd.ent","pdb1gye.ent","pdb1gyh.ent","pdb1gyo.ent","pdb1gz1.ent","pdb1gz2.ent","pdb1gz7.ent","pdb1gza.ent","pdb1gzb.ent","pdb1gzj.ent","pdb1gzm.ent","pdb1gzp.ent","pdb1gzq.ent","pdb1gzr.ent","pdb1gzy.ent","pdb1gzz.ent","pdb1h02.ent","pdb1h03.ent","pdb1h04.ent","pdb1h0b.ent","pdb1h0d.ent","pdb1h0g.ent","pdb1h0h.ent","pdb1h0i.ent","pdb1h0j.ent","pdb1h0l.ent","pdb1h0z.ent","pdb1h12.ent","pdb1h13.ent","pdb1h14.ent","pdb1h15.ent","pdb1h1b.ent","pdb1h1h.ent","pdb1h1n.ent","pdb1h20.ent","pdb1h22.ent","pdb1h23.ent","pdb1h2b.ent","pdb1h2p.ent","pdb1h2q.ent","pdb1h30.ent","pdb1h34.ent","pdb1h3j.ent","pdb1h3p.ent","pdb1h3t.ent","pdb1h3u.ent","pdb1h3v.ent","pdb1h3w.ent","pdb1h3x.ent","pdb1h3y.ent","pdb1h43.ent","pdb1h44.ent","pdb1h45.ent","pdb1h46.ent","pdb1h49.ent","pdb1h4i.ent","pdb1h4j.ent","pdb1h4p.ent","pdb1h4u.ent","pdb1h4w.ent","pdb1h52.ent","pdb1h53.ent","pdb1h55.ent","pdb1h57.ent","pdb1h58.ent","pdb1h59.ent","pdb1h5a.ent","pdb1h5b.ent","pdb1h5c.ent","pdb1h5d.ent","pdb1h5e.ent","pdb1h5f.ent","pdb1h5g.ent","pdb1h5h.ent","pdb1h5i.ent","pdb1h5j.ent","pdb1h5k.ent","pdb1h5l.ent","pdb1h5m.ent","pdb1h5o.ent","pdb1h5x.ent","pdb1h6m.ent","pdb1h6r.ent","pdb1h6v.ent","pdb1h75.ent","pdb1h76.ent","pdb1h7l.ent","pdb1h7q.ent","pdb1h80.ent","pdb1h81.ent","pdb1h82.ent","pdb1h83.ent","pdb1h84.ent","pdb1h86.ent","pdb1h87.ent","pdb1h8d.ent","pdb1h8i.ent","pdb1h8l.ent","pdb1h8n.ent","pdb1h8o.ent","pdb1h8p.ent","pdb1h8s.ent","pdb1h8u.ent","pdb1h8v.ent","pdb1h8x.ent","pdb1h8y.ent","pdb1h8z.ent","pdb1h91.ent","pdb1h9h.ent","pdb1h9i.ent","pdb1h9l.ent","pdb1h9v.ent","pdb1h9z.ent","pdb1ha0.ent","pdb1ha2.ent","pdb1ha6.ent","pdb1ha8.ent","pdb1ha9.ent","pdb1haa.ent","pdb1hae.ent","pdb1haf.ent","pdb1hag.ent","pdb1hah.ent","pdb1hai.ent","pdb1haj.ent"]
n = len(run_list)
typedict = {}
for type_ in ["lys_arg", "his", "asp_glu", "trp", "phe", "tyr"]:
typedict[type_] = (analysis_type == type_)
timestart = time.ctime()
for i, file in enumerate(run_list):
#for i,file in enumerate(["pdb1w4y.ent"]):
# print type(hist_)
print pdb_dir + file
hist_ = analysis.run(pdb_dir + file,
x,
erfile,
dist=threshold,
histogram=hist_,
lys_arg=typedict["lys_arg"],
his=typedict["his"],
asp_glu=typedict["asp_glu"],
trp=typedict["trp"],
phe=typedict["phe"],
tyr=typedict["tyr"])
m = int((i + 1) / float(n) * 10000) / 100.0
print str(m) + "% complete"
timefinish1 = time.ctime()
print "\nResults file is being saved. Please do not close the program window.\n"
##################################################################
##The histogram bit
def histcmp(a, b):
return (hist_[a] < hist_[b]) * 2 - 1
#fffff = open("histogram_","w")
#hkeys = hist_.keys()[:]
#hkeys.sort(histcmp)
#x.add_sheet("Histogram")
#histosheet = x.get_sheet(4)
#histosheet.write(0,0,"Secondary structure 1",style0)
#histosheet.write(0,1,"Secondary structure 2",style0)
#histosheet.write(0,2,"Disulfide Bond type",style0)
#histosheet.write(0,3,"Count",style0)
#for row,h in enumerate(hkeys):
# fffff.write(str(h)+" "*(21-len(h))+str(hist_[h])+"\n")
# histosheet.write(row+1,0,h[0])
# histosheet.write(row+1,1,h[1])
# histosheet.write(row+1,2,h[2:])
# histosheet.write(row+1,3,hist_[h])
#fffff.close()
##################################################################
realactive = x.get_active_sheet()
firstactive = 6
sheet = x.get_sheet(0)
if sheet.row(0).get_str_count() > 0:
firstactive = 0
sheet.set_first_visible_row(0)
sheet = x.get_sheet(1)
if sheet.row(0).get_str_count() > 0 and firstactive > 1:
firstactive = 1
sheet.set_first_visible_row(0)
sheet = x.get_sheet(2)
if sheet.row(0).get_str_count() > 0 and firstactive > 2:
firstactive = 2
sheet.set_first_visible_row(0)
sheet = x.get_sheet(3)
if sheet.row(0).get_str_count() > 0 and firstactive > 3:
firstactive = 3
sheet.set_first_visible_row(0)
sheet = x.get_sheet(4)
if sheet.row(0).get_str_count() > 0 and firstactive > 4:
firstactive = 3
sheet.set_first_visible_row(0)
sheet = x.get_sheet(5)
sheet.set_first_visible_row(0)
if sheet.row(0).get_str_count() > 0 and firstactive > 5:
firstactive = 5
sheet.set_first_visible_row(0)
sheet = x.get_sheet(6)
sheet.set_first_visible_row(0)
x.set_active_sheet(firstactive)
x.save(write_path)
if inA:
os.system(
"7z a -tzip -mx=9 D:\\xampp\\htdocs\\python\\Analyses\\disulfide_analysis_"
+ date_ + ".zip " + write_path)
print "\nAnalysis complete and results saved.\n"
timefinish2 = time.ctime()
erfile.close()
print "start =", timestart
print "prcessed =", timefinish1
print "saved =", timefinish2
#sorting and printing of histogram
#gives descending sort
#write histogram to spreadsheet
#cys["SSBOND 7 CYS A 1348 CYS A 1380"]
return write_path
from fopen import *
import os
pdb_dir = fopen("absolute_path_of_pdb_files")[0].strip()
file = open("new_files_downloaded_on_pdbaa.nr", "w")
l = fopen("pdbaa.nr")
for lien in l:
if lien[0] == ">":
name = "pdb" + lien[1:5].lower() + ".ent"
if os.path.exists(pdb_dir + name):
file.write(name + "\n")