def test_calcall3(self):
try:
qcalc = os.path.join(os.environ["QBIN_DIR"], "Qcalc6")
except KeyError:
raise Exception("QBIN_DIR environment variable not defined.")
dirs = [
"data/qgroupcontrib/testrep1", "data/qgroupcontrib/testrep2",
"data/qgroupcontrib/testrep3"
]
pdb = "data/qgroupcontrib/dfpase_dfp_start.pdb"
qgc = QGroupContrib(qcalc, dirs, pdb, "q_enfiles.list", [0.86, 0.14],
[0.46, 0.54], 15, 20, 1, 1,
[4841, 4842, 4843, 4844])
try:
qgc.calcall()
except KeyboardInterrupt:
qgc.kill_event.set()
raise
de1, de2, lras, reorgs = qgc.gcs_stats.get_columns([5, 9, 13, 17])
assert is_close(de1[4], -0.475)
assert is_close(de2[4], -0.84)
assert is_close(lras[4], -0.6575)
assert is_close(reorgs[4], 0.1825)
def test_calcall(self):
try:
qcalc = os.path.join(os.environ["QBIN_DIR"], "Qcalc6")
except KeyError:
raise Exception("QBIN_DIR environment variable not defined.")
dirs = [
"data/qgroupcontrib/testrep1", "data/qgroupcontrib/testrep2",
"data/qgroupcontrib/testrep3"
]
pdb = "data/qgroupcontrib/dfpase_dfp_start.pdb"
qgc = QGroupContrib(qcalc, dirs, pdb, "q_enfiles.list", [0.86, 0.14],
[0.46, 0.54], 15, 20, 1, 1, None)
try:
qgc.calcall()
except KeyboardInterrupt:
qgc.kill_event.set()
raise
de1, de2, lras, reorgs = qgc.gcs_stats.get_columns([5, 9, 13, 17])
# Glu19
# qcalc manual calculation + pen&paper
# REP1:
# E1_1 = 79.51, E2_1 = 68.34, E1_2 = 79.42, E2_2 = 65.88
# de1 = -11.17, de2 = -13.54, lra = -12.355, reorg = 1.185
# REP2:
# E1_1 = 76.02, E2_1 = 64.62, E1_2 = 79.88, E2_2 = 67.55
# de1 = -11.4, de2 = -12.33, lra = -11.865, reorg = 0.465
# means:
# de1 = -11.285, de2 = -12.935, lra = -12.11, reorg = 0.825
assert is_close(de1[4], -11.285)
assert is_close(de2[4], -12.935)
assert is_close(lras[4], -12.11)
assert is_close(reorgs[4], 0.825)
def test_calcall2(self):
try:
qcalc = os.path.join(os.environ["QBIN_DIR"], "Qcalc6")
except KeyError:
raise Exception("QBIN_DIR environment variable not defined.")
dirs = [
"data/qgroupcontrib/testrep1", "data/qgroupcontrib/testrep2",
"data/qgroupcontrib/testrep3"
]
pdb = "data/qgroupcontrib/dfpase_dfp_start.pdb"
# set the iscale to 4.0
qgc = QGroupContrib(qcalc, dirs, pdb, "q_enfiles.list", [0.86, 0.14],
[0.46, 0.54], 15, 20, 4.0, 1, None)
try:
qgc.calcall()
except KeyboardInterrupt:
qgc.kill_event.set()
raise
de1, de2, lras, reorgs = qgc.gcs_stats.get_columns([5, 9, 13, 17])
try:
qgc.calcall()
except KeyboardInterrupt:
qgc.kill_event.set()
raise
de1, de2, lras, reorgs = qgc.gcs_stats.get_columns([5, 9, 13, 17])
# Glu19 scaled down by 4 (see above)
assert is_close(de1[4], -2.82125)
assert is_close(de2[4], -3.23375)
assert is_close(lras[4], -3.0275)
assert is_close(reorgs[4], 0.20625)
def gc(args):
if not os.path.lexists(args.pdb):
print "This file went missing: {}".format(args.pdb)
sys.exit(1)
if args.qmaskfile:
try:
qmask = open(args.qmaskfile, "r").read().split()
if not qmask:
raise IOError
except IOError:
print "Can't read '{}' or file empty".format(args.qmaskfile)
sys.exit(1)
else:
qmask = None
lambdas = []
for lamb in args.lra_l:
try:
lamb = float(lamb)
if lamb < 0 or lamb > 1:
raise ValueError
except ValueError:
print "FATAL! Lambda values make no sense. 0 <= lambda <= 1 please."
sys.exit(1)
lambdas.append((lamb, 1 - lamb))
calcdirs = args.dirs
if not calcdirs:
lsdir = os.listdir(os.getcwd())
calcdirs = [f for f in lsdir if os.path.isdir(f)]
if not calcdirs:
calcdirs = [
os.getcwd(),
]
print "No subdirectories. Calculating in current directory only.\n"
else:
print "Will use these directories for calculating GCs (use --dirs to "\
"change this): {}\n".format(", ".join(calcdirs))
qgc = QGroupContrib(args.qcalc_exec, calcdirs, args.pdb,
QScfg.get("files", "en_list_fn"), lambdas[0],
lambdas[1], args.resid_first, args.resid_last,
args.scale_ionized, args.nthreads, qmask)
try:
qgc.calcall()
except QGroupContribError as error_msg:
print "\nMassive fail:\n{}\n".format(error_msg)
sys.exit(1)
except KeyboardInterrupt:
qgc.kill_event.set()
raise
# writeout QCalc inputs and outputs
if args.writeout:
for calcdir, (qcinps, qcouts) in qgc._qcalc_io.iteritems():
for i, qci in enumerate(qcinps):
fn = os.path.join(calcdir, "q_calc.gc.{}.inp".format(i + 1))
try:
open(fn, 'w').write(qci)
except OSError as err:
print "Error when writing to {}: {}".format(fn, err)
else:
print "Wrote {}".format(fn)
for i, qco in enumerate(qcouts):
fn = os.path.join(calcdir, "q_calc.gc.{}.out".format(i + 1))
try:
open(fn, 'w').write(qco)
except OSError as err:
print "Error when writing to {}: {}".format(fn, err)
else:
print "Wrote {}".format(fn)
# write out details and top 10 GCs to stdout and outfile
if not qgc.gcs:
top_gcs = "None, all directories failed..."
top_gcs_reorg = "None, all directories failed..."
else:
top_rows = sorted(qgc.gcs_stats.get_rows(),
key=lambda x: -abs(x[13]))[:10]
out_l = ["{:<10} {:>10} {:>10}".format("# Residue", "Mean", "Stdev")]
for row in top_rows:
rid, rn, el, elstd = row[0], row[1], row[13], row[14]
tmp = "{}_{}".format(rn.capitalize(), rid)
tmp2 = "{:<10} {:10.2f} {:10.2f}".format(tmp, el, elstd)
out_l.append(tmp2)
top_gcs = "\n".join(out_l)
top_rows = sorted(qgc.gcs_stats.get_rows(),
key=lambda x: -abs(x[17]))[:10]
out_l = ["{:<10} {:>10} {:>10}".format("# Residue", "Mean", "Stdev")]
for row in top_rows:
rid, rn, el, elstd = row[0], row[1], row[17], row[18]
tmp = "{}_{}".format(rn.capitalize(), rid)
tmp2 = "{:<10} {:10.2f} {:10.2f}".format(tmp, el, elstd)
out_l.append(tmp2)
top_gcs_reorg = "\n".join(out_l)
outstr = """
{gc_details}
Top LRA (el) contributions:
{top_gcs}
Top REORG (el) contributions:
{top_gcs_reorg}
""".format(gc_details=qgc.details,
top_gcs=top_gcs,
top_gcs_reorg=top_gcs_reorg)
print outstr
fn_out = args.output_fn
backup = backup_file(fn_out)
if backup:
print "# Backed up '{}' to '{}'".format(fn_out, backup)
open(fn_out, "w").write(outstr)
print "Wrote '{}'...".format(fn_out)
# convert plots to json and write them out
fn_out = args.plots_out
plots = qgc.plotdata
jsonenc = plotdata.PlotDataJSONEncoder(indent=2)
backup = backup_file(fn_out)
if backup:
print "# Backed up '{}' to '{}'".format(fn_out, backup)
open(fn_out, 'w').write(jsonenc.encode(plots))
print "Wrote '{}'... (q_plot.py is your "\
"friend)".format(fn_out)
# writeout the pdbgc if requested
if args.pdbgc_out:
backup = backup_file(args.pdbgc_out)
if backup:
print "# Backed up '{}' to '{}'".format(args.pdbgc_out, backup)
open(args.pdbgc_out, 'w').write(qgc.get_pdbgc())
print "Wrote '{}'... (use Pymol/Chimera/VMD and color by occupancy "\
"(LRA) or B-factor (reorg))".format(args.pdbgc_out)