def TLSMD_Main(struct_file_path = None,
sel_chain_ids = None,
html_report_dir = None):
console.cpu_time_stdoutln("->Starting TLSMD analysis: %s" % time.clock())
## create the analysis processor and load the structure, select chains
analysis = TLSMDAnalysis(
struct_file_path = struct_file_path,
sel_chain_ids = sel_chain_ids,
struct2_file_path = conf.globalconf.target_struct_path,
struct2_chain_id = conf.globalconf.target_struct_chain_id)
console.cpu_time_stdoutln("->LoadStructure: %s" % time.clock())
IndependentTLSSegmentOptimization(analysis)
console.cpu_time_stdoutln("->IndependentTLSSegmentOptimization: %s" % (
time.clock()))
RecombineIndependentTLSSegments(analysis)
console.cpu_time_stdoutln("->RecombineIndependentTLSSegments: %s" % (
time.clock()))
if analysis.struct2_file_path is not None and \
analysis.struct2_chain_id is not None:
console.stdoutln("SUPERIMPOSING HOMOLOGOUS STRUCTURE")
SuperimposeHomologousStructure(analysis)
if html_report_dir is not None and analysis.num_chains() > 0:
FitConstrainedTLSModel(analysis)
## generate summary page. Allows the user to see some information
## before the analysis is fully complete
console.stdoutln("GENERATING SUMMARY PAGE")
summary = html.HTMLSummaryReport(analysis)
summary.write_summary(html_report_dir)
console.cpu_time_stdoutln("->HTMLSummaryReport: %s" % time.clock())
if not conf.globalconf.skip_html:
## generate in-depth HTML report pages
console.stdoutln("GENERATING ANALYSIS/REPORT HTML PAGES")
report = html.HTMLReport(analysis)
report.write(html_report_dir)
## TODO: Figure out a way to gzip all TXT files once TLSMD is done
## with them. 2010-09-24
#import fnmatch
#import gzip
#abs_report_path = "%s/%s/%s" % (
# conf.TLSMD_WORK_DIR, conf.globalconf.job_id, html_report_dir)
#console.stdoutln("GZIP: Attempting to gzip all TXT files in: %s" % abs_report_path)
#for path, dirs, files in os.walk(abs_report_path):
# console.stdoutln("GZIP: report_dir = %s" % abs_report_path)
# for f in files:
# if fnmatch.fnmatch(f, '*.txt'):
# console.stdoutln("GZIP: found a TXT file: %s" % f)
# ## If we find a TXT file, gzip it
# f_in = open('%s/%s' % (abs_report_path, f), 'rb')
# f_out = gzip.open('%s/%s.gz' % (abs_report_path, f), 'wb')
# f_out.writelines(f_in)
# f_out.close()
# f_in.close()
# os.remove(f)
console.cpu_time_stdoutln("->TLSMD::Total_time: %s" % time.clock())
def run_minimization(self):
"""Run the HCSSSP minimization on the self.V, self.E graph, resulting
in the creation of the self.D, self.P, and self.T arrays which
contain
"""
chain = self.chain
chain_id = self.chain.chain_id
min_subsegment_len = self.min_subsegment_len
num_vertex = len(chain) + 1
## choose the TLS Model to fit for the chain
fit_method = self.get_fit_method(chain)
## build the vertex labels to reflect the protein structure
## the graph spans
vertices = []
for i in xrange(num_vertex):
## add the vertex label for i at Vi
if i == 0 :
vertex_label = "N-TERM"
elif i == num_vertex - 1:
vertex_label = "C-TERM"
else:
vertex_label = "%s{%s:%s}" % (
chain_id, chain[i-1].fragment_id, chain[i].fragment_id)
vertex_label = "V%d[%s]" % (i, vertex_label)
vertices.append(vertex_label)
## fit chain segments with TLS model and build residual graph to
## minimize
total_num_subsegments = calc_num_subsegments(chain.count_fragments(),
min_subsegment_len)
num_subsegments = 0
pcomplete = 0
pcomplete_old = 0
edges = []
console.stdoutln("=" * 80)
console.stdoutln("BUILDING RESIDUAL GRAPH TO MINIMIZE: chain_id=%s" % chain_id)
for frag_id1, frag_id2, i, j in iter_chain_subsegment_descs(chain, min_subsegment_len):
tlsdict = fit_method(frag_id1, frag_id2)
num_subsegments += 1
pcomplete = round(100.0 * num_subsegments / total_num_subsegments)
if pcomplete != pcomplete_old:
console.stdoutln("(%10d/%10d) %2d%% Complete" % (
num_subsegments, total_num_subsegments, pcomplete))
pcomplete_old = pcomplete
if tlsdict == None:
console.stderrln("no TLS group %s{%s..%s}" % (
chain_id, frag_id1, frag_id2))
raise SystemExit
if tlsdict.has_key("error") is True:
continue
if not tlsdict.has_key("residual"):
console.stderrln("no residual! %s{%s..%s}" % (
chain_id, frag_id1, frag_id2))
raise SystemExit
residual = tlsdict["residual"]
num_atoms = tlsdict["num_atoms"]
num_residues = tlsdict["num_residues"]
if residual < 0.0:
console.stdoutln("ERROR: Residual is negative!")
continue
msd = residual / num_residues
rmsd = math.sqrt(msd)
rmsd_b = rmsd * Constants.U2B
chi2 = msd * num_atoms
## XXX: Why is this set to 40? 2010-08-20
if num_atoms < 40:
continue
cost = residual
frag_range = (frag_id1, frag_id2)
edge = (i, j, cost, frag_range, tlsdict)
edges.append(edge)
console.cpu_time_stdoutln("->ResidualGraphMinimized chain_id=%s: %s" % (
chain_id, time.clock()))
## perform the minimization
if len(edges) > 0:
console.stdoutln("HCSSSP Minimizing: chain_id=%s" % (chain_id))
D, P, T = self.HCSSSP_minimize(vertices, edges, self.nparts)
self.minimized = True
self.V = vertices
self.D = D
self.P = P
self.T = T
else:
console.stdoutln("HCSSSP Minimizing: Unable to minimize chain_id=%s" % (
chain_id))
self.minimized = False
raise SystemExit
## free memory taken up from edges
edges = None
gc.collect()
except (RuntimeError, numpy.linalg.linalg.LinAlgError), e:
msg = " Runtime error for [%s]: %s, " % (
tls, e)
msg += "trying to continue..."
console.stdoutln(msg)
print console.formatExceptionInfo()
pass
## Track progress
progress += 0.4/analysis.num_chains()
progress_report = open("progress","w+")
print >> progress_report, progress
## progress_report.write(progress)
progress_report.close()
console.cpu_time_stdoutln("->FitConstrainedTLSModel: %s" % time.clock())
console.endln()
def SuperimposeHomologousStructure(analysis):
"""
"""
import structcmp
target_struct = FileIO.LoadStructure(fil = analysis.struct2_file_path)
target_chain = target_struct.get_chain(analysis.struct2_chain_id)
if target_chain is None:
console.stderrln(
"UNABLE TO LOAD TARGET STRUCTURE/CHAIN: %s:%s" % (
target_struct, target_chain))