def _x3d(filename):
import chimera
title = ""
try:
chimera.viewer.x3dWrite(filename, title)
except IOError, v:
raise chimera.NonChimeraError("Error writing x3d file: " + str(v))
def _exportSTL(filename):
# Determine endian-ness
import struct
if struct.pack("h", 1) == "\000\001":
big_endian = 1
else:
big_endian = 0
if big_endian:
raise chimera.NonChimeraError(
"Only support STL output on little-endian computers")
return _x3dConvert("x3d2stl", filename)
def _invoke(service, opts, pdb):
import multipart
try:
return multipart.post_multipart(
"helixweb.nih.gov",
"/cgi-bin/structbio/basic",
opts + [
( "pdb_file", "chimera", pdb ),
( "what", None, service ),
( "outputtype", None, "Raw" ),
]
)
except:
raise chimera.NonChimeraError("Error contacting "
"StrucTools web server")
def _x3dConvert(prog, filename):
import chimera, os
title = ""
prog = os.path.join(os.environ["CHIMERA"], "bin", prog)
try:
from SubprocessMonitor import Popen, PIPE
cmd = [prog, '-o', filename]
proc = Popen(cmd, stdin=PIPE)
chimera.viewer.x3dWrite(proc.stdin, 0, title)
proc.stdin.close()
returncode = proc.wait()
if returncode == 1:
raise chimera.NonChimeraError("Error writing %s" % (filename))
elif returncode != 0:
raise RuntimeError("'%s' exited with error code %d" %
(prog, returncode))
except chimera.error, v:
raise chimera.UserError(v)
# Colors and saves movies of a Chimera model from various angles
# Imports
import getopt, sys # Allows for command line arguments
import os
import chimera
from chimera import runCommand as rc
try:
opts, args = getopt.getopt(sys.argv[1:], '', [
'rep=', 'test=', 'qID=', 'rID=', 'lengthID=', 'cutoff=', 'colorType=',
'testType=', 'attr=', 'minVal=', 'maxVal=', 'frameCount='
])
except getopt.error as message:
raise chimera.NonChimeraError(
"%s: %s" % (__name__, message)) # Prints error if present
rep = ''
test = '' # doesn't actually exist in GUI3 script
qID = ''
rID = ''
lengthID = '' # amino acid count
cutoff = ''
colorType = '' # rg, yb, or om
testType = '' # flux or corr
attr = '' # delta, pval, or stat
max_value = ''
min_value = ''
frame_count = ''
# Assigns option values to variables
def make_mutants():
try:
opts, args = getopt.getopt(sys.argv[1:], '', [
'rID=', 'outdir=', 'chain=', 'start=', 'end=', 'chainR=', 'startR='
])
except getopt.error as message:
raise chimera.NonChimeraError(
"%s: %s" % (__name__, message)) # Prints error if present
# initialize
rID = ''
outdir = ''
chain = ''
start = ''
end = ''
chainR = ''
startR = ''
# Assigns option values to variables
for o, a in opts:
if o == '--rID':
rID = a
if o == '--outdir':
outdir = a
if o == '--chain':
chain = a
if o == '--start':
start = a
if o == '--end':
end = a
if o == '--chainR':
chainR = a
if o == '--startR':
startR = a
# Ensures that all variables have been assigned and ends script if any are missing
assert (len(rID) != 0)
assert (len(outdir) != 0)
assert (len(chain) != 0)
assert (len(start) != 0)
assert (len(end) != 0)
assert (len(chainR) != 0)
assert (len(startR) != 0)
# open PDB file
file_out = open('%s/mutants_chain%s.txt' % (outdir, chain), 'a')
model = "1"
pdb_file = "%s.pdb" % (rID)
#out_dir = "%s" % (outdir)
#pdb_file = "1zbb_bound.pdb"
print(outdir)
print(pdb_file)
# redefine as integer
start = int(start)
end = int(end) + 1
startR = int(startR)
CapChain = chain.upper()
for x in range(start, end):
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
myres = mol.findResidue(x - 1) # reads residue
myres = str(myres)
print("myres=%s" % myres)
if (myres != "DA %s.%s" %
(x, CapChain)): # swap only if nucleotides differ
rc("swapna A :%s.%s" % (x, chain))
y = startR - x + 1
rc("swapna T :%s.%s" % (y, chainR))
rc("write 0 %s/%s_mutA%s_chain%s.pdb" % (outdir, rID, x, chain))
file_out.write('%s_mutA%s_chain%s\n' % (rID, x, chain))
rc("close 0")
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
myres = mol.findResidue(x - 1) # reads residue
myres = str(myres)
if (myres != "DT %s.%s" %
(x, CapChain)): # swap only if nucleotides differ
rc("swapna T :%s.%s" % (x, chain))
y = startR - x + 1
rc("swapna A :%s.%s" % (y, chainR))
rc("write 0 %s/%s_mutT%s_chain%s.pdb" % (outdir, rID, x, chain))
file_out.write('%s_mutT%s_chain%s\n' % (rID, x, chain))
rc("close 0")
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
myres = mol.findResidue(x - 1) # reads residue
myres = str(myres)
if (myres != "DC %s.%s" %
(x, CapChain)): # swap only if nucleotides differ
rc("swapna C :%s.%s" % (x, chain))
y = startR - x + 1
rc("swapna G :%s.%s" % (y, chainR))
rc("write 0 %s/%s_mutC%s_chain%s.pdb" % (outdir, rID, x, chain))
file_out.write('%s_mutC%s_chain%s\n' % (rID, x, chain))
rc("close 0")
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
myres = mol.findResidue(x - 1) # reads residue
myres = str(myres)
if (myres != "DG %s.%s" %
(x, CapChain)): # swap only if nucleotides differ
rc("swapna G :%s.%s" % (x, chain))
y = startR - x + 1
rc("swapna C :%s.%s" % (y, chainR))
rc("write 0 %s/%s_mutG%s_chain%s.pdb" % (outdir, rID, x, chain))
file_out.write('%s_mutG%s_chain%s\n' % (rID, x, chain))
rc("close 0")
file_out.close()
return rID, outdir, startR, chainR, chain, start, end
def make_mutants():
try:
opts, args = getopt.getopt(
sys.argv[1:], '',
['rID=', 'outdir=', 'chain=', 'start=', 'end=', 'alnID=', 'Vnum='])
except getopt.error as message:
raise chimera.NonChimeraError(
"%s: %s" % (__name__, message)) # Prints error if present
# initialize
rID = ''
outdir = ''
chain = ''
start = ''
end = ''
alnID = ''
Vnum = ''
# Assigns option values to variables
for o, a in opts:
if o == '--rID':
rID = a
if o == '--outdir':
outdir = a
if o == '--chain':
chain = a
if o == '--start':
start = a
if o == '--end':
end = a
if o == '--alnID':
alnID = a
if o == '--Vnum':
Vnum = a
# Ensures that all variables have been assigned and ends script if any are missing
assert (len(rID) != 0)
assert (len(outdir) != 0)
assert (len(chain) != 0)
assert (len(start) != 0)
assert (len(end) != 0)
assert (len(alnID) != 0)
assert (len(Vnum) != 0)
# ctl directory
indir = "%s_ctl" % (outdir)
# open PDB
file_out = open('%s/mutants_chain%s.txt' % (outdir, chain), 'a')
model = "1"
pdb_file = "%s.pdb" % (rID)
#out_dir = "%s" % (outdir)
#pdb_file = "1zbb_bound.pdb"
aln_file = "%s.aln" % (alnID)
print(outdir)
print(pdb_file)
print(aln_file)
# redefine as integer
start = int(start)
end = int(end) + 1
Vnum = int(Vnum)
for x in range(1, Vnum + 1):
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc('read ~/Desktop/%s/variant%s.com' % (indir, x))
file_out.write('%s_variant%s_chain%s\n' % (rID, x, chain))
# Close the file
file_out.close()
return rID, outdir, chain, start, end
def make_mutants():
try:
opts, args = getopt.getopt(sys.argv[1:], '', ['rID=', 'outdir=', 'chain=', 'start=', 'end='])
except getopt.error as message:
raise chimera.NonChimeraError("%s: %s" % (__name__, message)) # Prints error if present
# initialize
rID = ''
outdir = ''
chain = ''
start = ''
end = ''
# Assigns option values to variables
for o,a in opts:
if o == '--rID':
rID = a
if o == '--outdir':
outdir = a
if o == '--chain':
chain = a
if o == '--start':
start = a
if o == '--end':
end = a
# Ensures that all variables have been assigned and ends script if any are missing
assert(len(rID) != 0)
assert(len(outdir) != 0)
assert(len(chain) != 0)
assert(len(start) != 0)
assert(len(end) != 0)
# open PDB
file_out = open('%s/mutants_chain%s.txt' % (outdir, chain), 'a' )
model = "1"
pdb_file = "%s.pdb" % (rID)
#out_dir = "%s" % (outdir)
#pdb_file = "1zbb_bound.pdb"
print(outdir)
print(pdb_file)
# redefine as integer
start = int(start)
end = int(end)+1
for x in range(start,end):
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa ALA :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutALA%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutALA%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa ARG :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutARG%s_chain%s.pdb\n" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutARG%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa ASN :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutASN%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutASN%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa ASP :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutASP%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutASP%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa CYS :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutCYS%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutCYS%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa GLU :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutGLU%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutGLU%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa GLN :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutGLN%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutGLN%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa GLY :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutGLY%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutGLY%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa HIS :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutHIS%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutHIS%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa ILE :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutILE%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutILE%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa LEU :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutLEU%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutLEU%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa LYS :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutLYS%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutLYS%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa MET :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutMET%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutMET%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa PHE :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutPHE%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutPHE%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa PRO :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutPRO%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutPRO%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa SER :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutSER%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutSER%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa THR :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutTHR%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutTHR%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa TRP :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutTRP%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutTRP%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa TYR :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutTYR%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutTYR%s_chain%s\n' % (rID, x, chain))
mol = chimera.openModels.open(pdb_file)[0] # Opens molecule
rc("swapaa VAL :%s.%s" % (x, chain))
rc("write 0 %s/%s_mutVAL%s_chain%s.pdb" % (outdir, rID, x, chain))
rc("close 0")
file_out.write('%s_mutVAL%s_chain%s\n' % (rID, x, chain))
# Close the file
file_out.close()
return rID, outdir, chain, start, end
