rem stringlengths 1 322k | add stringlengths 0 2.05M | context stringlengths 4 228k | meta stringlengths 156 215 |
|---|---|---|---|
self.driver.glr_lighting_disable() | def draw_tls_surface(self, Lx_eigen_vec, Lx_eigen_val, Lx_rho, Lx_pitch): """Draws the TLS probability surface for a single non-intersecting screw axis. Lx_eigen_val is the vaiance (mean square deviation MSD) of the rotation about the Lx_eigen_vec axis. """ ## create a unique list of bonds which will be used to ## ren... | 0779a1d6628e6acba115b7ba9004fcb5efdcc8b7 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/0779a1d6628e6acba115b7ba9004fcb5efdcc8b7/TLS.py | |
arec2["serial"] = arec1["serial"] arec2["chainID"] = arec1["chainID"] arec2["resName"] = arec1["resName"] arec2["resSeq"] = arec1["resSeq"] arec2["iCode"] = arec1["iCode"] arec2["name"] = arec1["name"] arec2["altLoc"] = arec1["altLoc"] arec2["element"] = arec1["element"] arec2["charge"] = arec1["charge"] | if arec1.has_key("serial"): arec2["serial"] = arec1["serial"] if arec1.has_key("chainID"): arec2["chainID"] = arec1["chainID"] if arec1.has_key("resName"): arec2["resName"] = arec1["resName"] if arec1.has_key("resSeq"): arec2["resSeq"] = arec1["resSeq"] if arec1.has_key("iCode"): arec2["iCode"] = arec1["iCode"] if arec... | def atom_common(arec1, arec2): arec2["serial"] = arec1["serial"] arec2["chainID"] = arec1["chainID"] arec2["resName"] = arec1["resName"] arec2["resSeq"] = arec1["resSeq"] arec2["iCode"] = arec1["iCode"] arec2["name"] = arec1["name"] arec2["altLoc"] = arec1["altLoc"] arec2["element"] = arec1["element"] arec2["ch... | 4a2bf3d6cbf5fd3c4e404b8b49e62876f1cec5ff /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4a2bf3d6cbf5fd3c4e404b8b49e62876f1cec5ff/PDBBuilder.py |
("sgroup", 56, 66, "string", "rjust", None), ("z", 67, 70, "integer", "rjust", None)] | ("sgroup", 56, 66, "string", "ljust", None), ("z", 67, 70, "integer", "ljust", None)] | def process(self, recs): """Returns a dictionary with attributes chain_id, num_res, and sequence_list """ seqres = {} | 6c2d587c1af39ee7b76fbae9bc6e8722151de2ca /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/6c2d587c1af39ee7b76fbae9bc6e8722151de2ca/PDB.py |
assert atm.occupancy >= 0.0 and atm.occupancy < 1.0 | assert atm.occupancy >= 0.0 and atm.occupancy <= 1.0 | def calc_atom_weight(atm): """Weight the least-squares fit according to this function. """ | a415833e5ff5acbecb068884a2d8765591db9289 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/a415833e5ff5acbecb068884a2d8765591db9289/tlsmd_analysis.py |
def __init__(self, form, text=None): | def __init__(self, form, text): | def __init__(self, form, text=None): Page.__init__(self, form) self.text = text | 7513555019c5fc099aa4aa56f3137e326a5a06fd /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7513555019c5fc099aa4aa56f3137e326a5a06fd/refineprep.py |
page = ErrorPage("The Job ID seems to be expired.") | page = ErrorPage(form, "The Job ID seems to be expired.") | def main(): form = cgi.FieldStorage() page = None job_id = check_job_id(form) if job_id==None: page = ErrorPage("The Job ID seems to be expired.") else: page = RefinePrepPage(form) try: print page.html_page() except RefinePrepError, err: text = '<center><p>%s</p></center>' % (err.text) page = ErrorPage(form, text) ... | 7513555019c5fc099aa4aa56f3137e326a5a06fd /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7513555019c5fc099aa4aa56f3137e326a5a06fd/refineprep.py |
except KeyError: | except IndexError: | def next_chain_id(suggest_chain_id): if suggest_chain_id != "": try: self.struct[suggest_chain_id] except KeyError: return suggest_chain_id for chain_id in "ABCDEFGHIJKLMNOPQRSTUVWXYZ": try: self.struct[chain_id] except KeyError: return chain_id | 9d8a841c203e73e58c0201cbce892f595442be7e /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/9d8a841c203e73e58c0201cbce892f595442be7e/StructureBuilder.py |
u_iso = atm_desc["u_iso"] | def lsq_fit_segment(self, frag_id1, frag_id2): """Performs a LSQ fit of TLS parameters for the protein segment starting with fragment index ifrag_start to (and including) the fragment ifrag_end. """ ## all return values here fit_info = {} ## calculate the start/end indexes of the start fragment ## and end fragment so ... | e84d51aa8f483309e902b29a0f740a21562abad5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e84d51aa8f483309e902b29a0f740a21562abad5/tlsmd_analysis.py | |
set_TLSiso_b(B_ISOW, i, u_iso, w) | set_TLSiso_b(B_ISOW, i, atm_desc["u_iso"], w) | def lsq_fit_segment(self, frag_id1, frag_id2): """Performs a LSQ fit of TLS parameters for the protein segment starting with fragment index ifrag_start to (and including) the fragment ifrag_end. """ ## all return values here fit_info = {} ## calculate the start/end indexes of the start fragment ## and end fragment so ... | e84d51aa8f483309e902b29a0f740a21562abad5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e84d51aa8f483309e902b29a0f740a21562abad5/tlsmd_analysis.py |
U_ISOW = matrixmultiply(A_ANISOW, X_ANISO) | def lsq_fit_segment(self, frag_id1, frag_id2): """Performs a LSQ fit of TLS parameters for the protein segment starting with fragment index ifrag_start to (and including) the fragment ifrag_end. """ ## all return values here fit_info = {} ## calculate the start/end indexes of the start fragment ## and end fragment so ... | e84d51aa8f483309e902b29a0f740a21562abad5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e84d51aa8f483309e902b29a0f740a21562abad5/tlsmd_analysis.py | |
def lsq_fit_segment(self, frag_id1, frag_id2): """Performs a LSQ fit of TLS parameters for the protein segment starting with fragment index ifrag_start to (and including) the fragment ifrag_end. """ ## all return values here fit_info = {} ## calculate the start/end indexes of the start fragment ## and end fragment so ... | e84d51aa8f483309e902b29a0f740a21562abad5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e84d51aa8f483309e902b29a0f740a21562abad5/tlsmd_analysis.py | ||
def lsq_fit_segment(self, frag_id1, frag_id2): """Performs a LSQ fit of TLS parameters for the protein segment starting with fragment index ifrag_start to (and including) the fragment ifrag_end. """ ## all return values here fit_info = {} ## calculate the start/end indexes of the start fragment ## and end fragment so ... | e84d51aa8f483309e902b29a0f740a21562abad5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e84d51aa8f483309e902b29a0f740a21562abad5/tlsmd_analysis.py | ||
return TLSGraphChainFastHybrid() | if USE_TLSMDMODULE==True: return TLSGraphChainFastHybrid() else: return TLSGraphChainHybrid() | def NewTLSGraphChain0(tls_model): """Generate and return the proper TLSGraphChain subclass for the requested TLS model. """ if tls_model=="HYBRID": return TLSGraphChainFastHybrid() if tls_model=="ANISO": return TLSGraphChainAnisotropic() if tls_model=="PLUGIN": return TLSGraphChainPlugin() raise Exception() | e84d51aa8f483309e902b29a0f740a21562abad5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e84d51aa8f483309e902b29a0f740a21562abad5/tlsmd_analysis.py |
'<p style="font-size:xx-small; margin-top:%dpx; line-height:12.5px">' % (plot.border_width)] | '<p style="font-size:xx-small; margin-top:%dpx">' % (plot.border_width)] l.append('<ul style="list-style-type:none;margin:0px;padding:0px">') | def html_chain_alignment_plot(self, chain): """generate a plot comparing all segmentations """ plot = sequence_plot.TLSSegmentAlignmentPlot() for ntls, cpartition in chain.partition_collection.iter_ntls_chain_partitions(): plot.add_tls_segmentation(cpartition) | d2709532e583d640a6277dcc18d10e99b4d1295e /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/d2709532e583d640a6277dcc18d10e99b4d1295e/html.py |
l.append('<a href=" | l.append('<li style="line-height:20px"><a href=" l.append('</ul>') | def html_chain_alignment_plot(self, chain): """generate a plot comparing all segmentations """ plot = sequence_plot.TLSSegmentAlignmentPlot() for ntls, cpartition in chain.partition_collection.iter_ntls_chain_partitions(): plot.add_tls_segmentation(cpartition) | d2709532e583d640a6277dcc18d10e99b4d1295e /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/d2709532e583d640a6277dcc18d10e99b4d1295e/html.py |
def gldl_iter_multidraw_animate(self): """ """ ## optimization: if a rotation of 0.0 degrees was already ## drawn, then there is no need to draw it again zero_rot = False for Lx_axis, Lx_rho, Lx_pitch, Lx_rot, Lx_scale in ( ("L1_eigen_vec", "L1_rho", "L1_pitch", "L1_rot", "L1_scale"), ("L2_eigen_vec", "L2_rho", "L2_pi... | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py | ||
self.driver.glr_translate(-rho) | self.driver.glr_translate(rho) | def gldl_iter_multidraw_animate(self): """ """ ## optimization: if a rotation of 0.0 degrees was already ## drawn, then there is no need to draw it again zero_rot = False for Lx_axis, Lx_rho, Lx_pitch, Lx_rot, Lx_scale in ( ("L1_eigen_vec", "L1_rho", "L1_pitch", "L1_rot", "L1_scale"), ("L2_eigen_vec", "L2_rho", "L2_pi... | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
self.driver.glr_translate(rho + screw) | self.driver.glr_translate(-rho + screw) | def gldl_iter_multidraw_animate(self): """ """ ## optimization: if a rotation of 0.0 degrees was already ## drawn, then there is no need to draw it again zero_rot = False for Lx_axis, Lx_rho, Lx_pitch, Lx_rot, Lx_scale in ( ("L1_eigen_vec", "L1_rho", "L1_pitch", "L1_rot", "L1_scale"), ("L2_eigen_vec", "L2_rho", "L2_pi... | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
L1_c = 0.0 | L1_c = 0.0 | def update_time(self): """Changes the time of the TLS group simulating harmonic motion. """ if self.tls_group.is_null(): return | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
L2_c = 0.0 | L2_c = 0.0 | def update_time(self): """Changes the time of the TLS group simulating harmonic motion. """ if self.tls_group.is_null(): return | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
L3_c = 0.0 | L3_c = 0.0 | def update_time(self): """Changes the time of the TLS group simulating harmonic motion. """ if self.tls_group.is_null(): return | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
gam = 0.5 | gam = 0.50 | def draw_tls_surface(self, Lx_eigen_vec, Lx_eigen_val, Lx_rho, Lx_pitch): """Draws the TLS probability surface for a single non-intersecting screw axis. Lx_eigen_val is the vaiance (mean square deviation MSD) of the rotation about the Lx_eigen_vec axis. """ ## create a unique list of bonds which will be used to ## ren... | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
step1 = rot_step * float(step) step2 = step1 + rot_step | rot_start = rot_step * float(step) rot_end = rot_step * float(step + 1) | def draw_tls_surface(self, Lx_eigen_vec, Lx_eigen_val, Lx_rho, Lx_pitch): """Draws the TLS probability surface for a single non-intersecting screw axis. Lx_eigen_val is the vaiance (mean square deviation MSD) of the rotation about the Lx_eigen_vec axis. """ ## create a unique list of bonds which will be used to ## ren... | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
rot1 = step1 * sign rot2 = step2 * sign | rot1 = rot_start * sign rot2 = rot_end * sign | def draw_tls_surface(self, Lx_eigen_vec, Lx_eigen_val, Lx_rho, Lx_pitch): """Draws the TLS probability surface for a single non-intersecting screw axis. Lx_eigen_val is the vaiance (mean square deviation MSD) of the rotation about the Lx_eigen_vec axis. """ ## create a unique list of bonds which will be used to ## ren... | 4d5284e4c4b1286073a18f9657c98f6fd520870d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/4d5284e4c4b1286073a18f9657c98f6fd520870d/TLS.py |
self.write(self.form_string(mstring)) | self.write(self.form_mstring(mstring)) | def write_mstring(self, mstring): self.write(self.form_string(mstring)) | f32de331f1af88fb64e8cc4cec6b143ca5ef3b76 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/f32de331f1af88fb64e8cc4cec6b143ca5ef3b76/mmCIF.py |
sys.stderr.write("Mail Client %s Not Found" % (conf.MSMTP)) | sys.stderr.write("mail client not found: %s" % (conf.MSMTP)) | def SendEmail(address, subject, body): if not os.path.isfile(conf.MSMTP): sys.stderr.write("Mail Client %s Not Found" % (conf.MSMTP)) return mlist = ["To: %s" % (address), "Subject: %s" % (subject), "", body] ## send mail using msmtp pobj = subprocess.Popen([conf.MSMTP, address], stdin = subprocess.PIPE, stdout = sub... | 6d7350dd61b4a559839fe339299061a4df5f7f5b /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/6d7350dd61b4a559839fe339299061a4df5f7f5b/email.py |
pobj = subprocess.Popen([conf.MSMTP, address], stdin = subprocess.PIPE, stdout = subprocess.PIPE, stderr = subprocess.STDOUT, close_fds = True, bufsize = 8192) | try: pobj = subprocess.Popen([conf.MSMTP, address], stdin = subprocess.PIPE, stdout = subprocess.PIPE, stderr = subprocess.STDOUT, close_fds = True, bufsize = 8192) except OSError: sys.stderr.write("[ERROR] mail client failed to execute: %s" % (conf.MSMTP)) return | def SendEmail(address, subject, body): if not os.path.isfile(conf.MSMTP): sys.stderr.write("Mail Client %s Not Found" % (conf.MSMTP)) return mlist = ["To: %s" % (address), "Subject: %s" % (subject), "", body] ## send mail using msmtp pobj = subprocess.Popen([conf.MSMTP, address], stdin = subprocess.PIPE, stdout = sub... | 6d7350dd61b4a559839fe339299061a4df5f7f5b /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/6d7350dd61b4a559839fe339299061a4df5f7f5b/email.py |
if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) | stats = {} stats["time"] = sec | def read_pdb(path): sec = time.time() records = pdbmodule.read(path) sec = time.time() - sec if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) for rec in records: if rec["RECORD"] == "REMARK": try: text = rec["text"] except KeyError: ... | 7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92/test.py |
if rec["RECORD"] == "REMARK": | rec_type = rec["RECORD"] if rec_type == "REMARK": | def read_pdb(path): sec = time.time() records = pdbmodule.read(path) sec = time.time() - sec if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) for rec in records: if rec["RECORD"] == "REMARK": try: text = rec["text"] except KeyError: ... | 7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92/test.py |
pass else: if text.find("RESOLUTION RANGE HIGH") == 1: print text | continue if text.find("RESOLUTION RANGE HIGH") == 1: try: stats["res"] = float(text[33:]) except ValueError: pass elif rec_type == "ATOM " or rec_type == "HETATM": try: stats["atoms"] += 1 except KeyError: stats["atoms"] = 1 elif rec_type == "ANISOU": try: stats["anisou"] += 1 except KeyError: stats["anisou"] = 1 ... | def read_pdb(path): sec = time.time() records = pdbmodule.read(path) sec = time.time() - sec if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) for rec in records: if rec["RECORD"] == "REMARK": try: text = rec["text"] except KeyError: ... | 7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92/test.py |
def read_pdb(path): sec = time.time() records = pdbmodule.read(path) sec = time.time() - sec if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) for rec in records: if rec["RECORD"] == "REMARK": try: text = rec["text"] except KeyError: ... | 7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92/test.py | ||
def read_pdb(path): sec = time.time() records = pdbmodule.read(path) sec = time.time() - sec if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) for rec in records: if rec["RECORD"] == "REMARK": try: text = rec["text"] except KeyError: ... | 7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92/test.py | ||
print str(i)+": ", read_pdb(pathx) | stats = read_pdb(pathx) print "%d:%s:%s" % (i, pathx, stats) | def read_pdb(path): sec = time.time() records = pdbmodule.read(path) sec = time.time() - sec if records != None: print "%s: %d records in %.2f seconds" % ( path, len(records), sec) else: print "%s: NO RECORDS" % (path) for rec in records: if rec["RECORD"] == "REMARK": try: text = rec["text"] except KeyError: ... | 7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7ec4c6518170b22cfaef5e2cd7fdbf21624c8b92/test.py |
"[Status: %s] " % (jdict.get('status', 'None'))] | "[State: %s] " % (jdict.get('state', 'None'))] | def log_job_end(jdict): ln = "" ln += "[%s]: " % (time.asctime(time.localtime(time.time()))) ln += "Finished Job %s" % (jdict["job_id"]) log_write(ln) ## write to a special log file if jdict.get("private_job", True): private_text = "private" else: private_text = "public" submit_time = jdict.get('submit_time', 0.0) r... | b48d806b00beca8c5e289445a77097960da89cac /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/b48d806b00beca8c5e289445a77097960da89cac/webtlsmdrund.py |
if atmx.name=="CA": yield atmx | if atmx.name in ["N","CA","C","O","CB"]: yield atmx | def iter_protein_atoms(sobjx): for fragx in sobjx.iter_amino_acids(): for atmx in fragx.iter_atoms(): if atmx.name=="CA": yield atmx | e106395b62b6f7c590f709d60deb6ca318c31727 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e106395b62b6f7c590f709d60deb6ca318c31727/html.py |
"""Iterates over all Atom objects. The iteration is preformed in order according to the Chain and Fragment ordering rules the Atom object is a part of. | """Iterates over all Atom objects according to the Structure defaults. | def iter_atoms(self): """Iterates over all Atom objects. The iteration is preformed in order according to the Chain and Fragment ordering rules the Atom object is a part of. """ for chain in self.iter_chains(): for atm in chain.iter_atoms(): yield atm | 5c7060c01cdfb5cacb07902a367f879ff7543e10 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5c7060c01cdfb5cacb07902a367f879ff7543e10/Structure.py |
"""Counts all Atom objects in the Structure's default alt_loc. | """Counts all Atom objects in according to the Structure defaults. | def count_atoms(self): """Counts all Atom objects in the Structure's default alt_loc. """ n = 0 for atm in self.iter_atoms(): n += 1 return n | 5c7060c01cdfb5cacb07902a367f879ff7543e10 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5c7060c01cdfb5cacb07902a367f879ff7543e10/Structure.py |
""" | """Iterates over all Atom objects including all atoms in multiple conformations. | def iter_all_atoms(self): """ """ for chain in self.iter_chains(): for atm in chain.iter_all_atoms(): yield atm | 5c7060c01cdfb5cacb07902a367f879ff7543e10 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5c7060c01cdfb5cacb07902a367f879ff7543e10/Structure.py |
"""Counts all Atom objects. | """Counts all Atom objects including all atoms in multiple conformations. | def count_all_atoms(self): """Counts all Atom objects. """ n = 0 for atm in self.iter_all_atoms(): n += 1 return n | 5c7060c01cdfb5cacb07902a367f879ff7543e10 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5c7060c01cdfb5cacb07902a367f879ff7543e10/Structure.py |
"Ethan Merrit") | "Ethan Merritt") | def __init__(self): gtk.Dialog.__init__(self, "About mmCIF Editor", None, 0) self.add_button(gtk.STOCK_CLOSE, gtk.RESPONSE_CLOSE) self.connect("delete-event", self.delete_event_cb) self.connect("response", self.delete_event_cb) | 845416a118287e7faa2f9e69392cad2bdc4545cc /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/845416a118287e7faa2f9e69392cad2bdc4545cc/cif_editor.py |
def refmac5_prep(xyzin, tlsin, xyzout, tlsout): | def refmac5_prep(xyzin, tlsin_list, xyzout, tlsout): | def refmac5_prep(xyzin, tlsin, xyzout, tlsout): """Use TLS model + Uiso for each atom. Output xyzout with the residual Uiso only. """ os.umask(022) ## load structure struct = LoadStructure(fil = xyzin) ## load and construct TLS groups tls_group_list = [] tls_file = TLSFile() tls_file.set_file_format(TLSFileFormatTL... | 9fd3d90c1518243c4a524d66eb34d0f807950d86 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/9fd3d90c1518243c4a524d66eb34d0f807950d86/refineprep.py |
tls_file = TLSFile() tls_file.set_file_format(TLSFileFormatTLSOUT()) tls_file.load(open(tlsin, "r")) for tls_desc in tls_file.tls_desc_list: tls_group = tls_desc.construct_tls_group_with_atoms(struct) fit_tls_group(tls_group) tls_group.tls_desc = tls_desc tls_group_list.append(tls_group) | for tlsin in tlsin_list: tls_file = TLSFile() tls_file.set_file_format(TLSFileFormatTLSOUT()) tls_file.load(open(tlsin, "r")) for tls_desc in tls_file.tls_desc_list: tls_group = tls_desc.construct_tls_group_with_atoms(struct) tls_group.tls_desc = tls_desc tls_group_list.append(tls_group) | def refmac5_prep(xyzin, tlsin, xyzout, tlsout): """Use TLS model + Uiso for each atom. Output xyzout with the residual Uiso only. """ os.umask(022) ## load structure struct = LoadStructure(fil = xyzin) ## load and construct TLS groups tls_group_list = [] tls_file = TLSFile() tls_file.set_file_format(TLSFileFormatTL... | 9fd3d90c1518243c4a524d66eb34d0f807950d86 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/9fd3d90c1518243c4a524d66eb34d0f807950d86/refineprep.py |
def refmac5_prep(xyzin, tlsin, xyzout, tlsout): """Use TLS model + Uiso for each atom. Output xyzout with the residual Uiso only. """ os.umask(022) ## load structure struct = LoadStructure(fil = xyzin) ## load and construct TLS groups tls_group_list = [] tls_file = TLSFile() tls_file.set_file_format(TLSFileFormatTL... | 9fd3d90c1518243c4a524d66eb34d0f807950d86 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/9fd3d90c1518243c4a524d66eb34d0f807950d86/refineprep.py | ||
if atm.sig_position: | if atm.sig_position != None: | def atom_common(arec1, arec2): arec2["serial"] = arec1["serial"] arec2["chainID"] = arec1["chainID"] arec2["resName"] = arec1["resName"] arec2["resSeq"] = arec1["resSeq"] arec2["iCode"] = arec1["iCode"] arec2["name"] = arec1["name"] arec2["altLoc"] = arec1["altLoc"] arec2["element"] = arec1["element"] arec2["ch... | 7a81f52999a846a8139b020afa81586b47e97200 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7a81f52999a846a8139b020afa81586b47e97200/PDB.py |
if atm.U: | if atm.U != None: | def atom_common(arec1, arec2): arec2["serial"] = arec1["serial"] arec2["chainID"] = arec1["chainID"] arec2["resName"] = arec1["resName"] arec2["resSeq"] = arec1["resSeq"] arec2["iCode"] = arec1["iCode"] arec2["name"] = arec1["name"] arec2["altLoc"] = arec1["altLoc"] arec2["element"] = arec1["element"] arec2["ch... | 7a81f52999a846a8139b020afa81586b47e97200 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7a81f52999a846a8139b020afa81586b47e97200/PDB.py |
if atm.sig_U: siguij_rec = siguij() | if atm.sig_U != None: siguij_rec = SIGUIJ() | def atom_common(arec1, arec2): arec2["serial"] = arec1["serial"] arec2["chainID"] = arec1["chainID"] arec2["resName"] = arec1["resName"] arec2["resSeq"] = arec1["resSeq"] arec2["iCode"] = arec1["iCode"] arec2["name"] = arec1["name"] arec2["altLoc"] = arec1["altLoc"] arec2["element"] = arec1["element"] arec2["ch... | 7a81f52999a846a8139b020afa81586b47e97200 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/7a81f52999a846a8139b020afa81586b47e97200/PDB.py |
self.segmentations = [] | self.configurations = [] | def __init__(self): ## bars are 15 pixels heigh self.pheight = ALIGN_HEIGHT ## spacing pixels between stacked bars self.spacing = ALIGN_SPACING ## background color self.bg_color = rgb_f2i((1.0, 1.0, 1.0)) self.frag_list = [] self.segmentations = [] | 95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1/html.py |
self.segmentations.append(tls_seg_desc) | self.configurations.append(tls_seg_desc) | def add_tls_segmentation(self, chainopt, ntls): """Add a TLS optimization to the alignment plot. """ tlsopt = chainopt["tlsopt"][ntls] ## get the list of TLS segments for the specified number of ## segments (ntls) tls_seg_desc = {} self.segmentations.append(tls_seg_desc) tls_seg_desc["chainopt"] = chainopt tls_seg_des... | 95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1/html.py |
if len(self.frag_list)==0 or len(self.segmentations)==0: | if len(self.frag_list)==0 or len(self.configurations)==0: | def plot(self, path): """Plot and write the png plot image to the specified path. """ if len(self.frag_list)==0 or len(self.segmentations)==0: return False nfrag = len(self.frag_list) target_width = 500 fw = int(round(float(ALIGN_TARGET_WIDTH) / nfrag)) fwidth = max(1, fw) | 95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1/html.py |
num_plots = len(self.segmentations) | num_plots = len(self.configurations) | def plot(self, path): """Plot and write the png plot image to the specified path. """ if len(self.frag_list)==0 or len(self.segmentations)==0: return False nfrag = len(self.frag_list) target_width = 500 fw = int(round(float(ALIGN_TARGET_WIDTH) / nfrag)) fwidth = max(1, fw) | 95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1/html.py |
for i in range(len(self.segmentations)): tls_seg_desc = self.segmentations[i] | for i in range(len(self.configurations)): tls_seg_desc = self.configurations[i] | def plot(self, path): """Plot and write the png plot image to the specified path. """ if len(self.frag_list)==0 or len(self.segmentations)==0: return False nfrag = len(self.frag_list) target_width = 500 fw = int(round(float(ALIGN_TARGET_WIDTH) / nfrag)) fwidth = max(1, fw) | 95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/95e4e59ca6c2fcbff881aa5f49bc4f4fc89aeee1/html.py |
if const.MAINCHAIN_ATOM_DICT.has_key(atom.name) is False: | if const.MAINCHAIN_ATOM_DICT.has_key(atm.name) is False: | def calc_include_atom(atm, reject_messages = False): """Filter out atoms from the model which will cause problems or cont contribute to the TLS analysis. """ if atm.position == None: return False if atm.occupancy < 0.1: if reject_messages == True: console.stdoutln("calc_include_atom(%s): rejected because of low occupa... | 8a073b457d87aac2cb7a4880ce71c77f6f8f23c9 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/8a073b457d87aac2cb7a4880ce71c77f6f8f23c9/atom_selection.py |
self.term_alpha = 0.75 | self.term_alpha = 0.5 | def __init__(self): self.visible = True self.width = 0 self.height = 0 self.zplane = 5000.0 | 556ea8e399ecff3095bf69074967705963f51e8d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/556ea8e399ecff3095bf69074967705963f51e8d/glutviewer.py |
print "lsq_fit_segment centroid = ", centroid | def lsq_fit_segment(self, frag_id1, frag_id2): """Performs a LSQ fit of TLS parameters for the protein segment starting with fragment index ifrag_start to (and including) the fragment ifrag_end. """ ## all return values here fit_info = {} ## calculate the start/end indexes of the start fragment ## and end fragment so ... | e788235f3f04bc81092738494ac5eb845aacc6ef /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/e788235f3f04bc81092738494ac5eb845aacc6ef/tlsmd_analysis.py | |
name = atm_map["name"] fragment_id = atm_map["fragment_id"] chain_id = atm_map["chain_id"] | name = atm_map.get("name", "") fragment_id = atm_map.get("fragment_id", "") chain_id = atm_map.get("chain_id", "") | def load_atom(self, atm_map): """Called repeatedly by the implementation of read_atoms to load all the data for a single atom. The data is contained in the atm_map argument, and is not well documented at this point. Look at this function and you'll figure it out. """ ## XXX -- I presently do not support more than one... | 5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23/StructureBuilder.py |
def load_atom(self, atm_map): """Called repeatedly by the implementation of read_atoms to load all the data for a single atom. The data is contained in the atm_map argument, and is not well documented at this point. Look at this function and you'll figure it out. """ ## XXX -- I presently do not support more than one... | 5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23/StructureBuilder.py | ||
atm_id = (name, alt_loc, fragment_id, chain_id) | def load_atom(self, atm_map): """Called repeatedly by the implementation of read_atoms to load all the data for a single atom. The data is contained in the atm_map argument, and is not well documented at this point. Look at this function and you'll figure it out. """ ## XXX -- I presently do not support more than one... | 5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23/StructureBuilder.py | |
atm_id = (name, alt_loc, fragment_id, chain_id) | def load_atom(self, atm_map): """Called repeatedly by the implementation of read_atoms to load all the data for a single atom. The data is contained in the atm_map argument, and is not well documented at this point. Look at this function and you'll figure it out. """ ## XXX -- I presently do not support more than one... | 5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23/StructureBuilder.py | |
debug("duplicate atom "+str(atm_id)) return | old_name = name i = 2 while self.atom_cache.has_key(atm_id): name = "%s%d" % (old_name, i) atm_id = (name, alt_loc, fragment_id, chain_id) i += 1 | def load_atom(self, atm_map): """Called repeatedly by the implementation of read_atoms to load all the data for a single atom. The data is contained in the atm_map argument, and is not well documented at this point. Look at this function and you'll figure it out. """ ## XXX -- I presently do not support more than one... | 5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5a1d5bac5e97c5e026ff1ec048c5d79e784e7f23/StructureBuilder.py |
stdout, stdin, stderr = popen2.popen3( (self.render_program_path, "-png", self.render_png_path, "-gamma", "1.5"), 32768*4) | pobj = popen2.Popen4([self.render_program_path, "-png", self.render_png_path, "-gamma", "1.5"], 32768) stdin = pobj.tochild | def close(self): for fil in self.fils: fil.close() | 1d63e693bf684922f0cc1d31f96bdf5c3b9f5cef /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/1d63e693bf684922f0cc1d31f96bdf5c3b9f5cef/R3DDriver.py |
else: stdout.read() stdout.close() stderr.read() stderr.close() | elif pobj is not None: pobj.wait() | def close(self): for fil in self.fils: fil.close() | 1d63e693bf684922f0cc1d31f96bdf5c3b9f5cef /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/1d63e693bf684922f0cc1d31f96bdf5c3b9f5cef/R3DDriver.py |
atom.calc_anisotropy() atom.calc_anisotropy3() | try: atom.calc_anisotropy() except ZeroDivisionError: pass try: atom.calc_anisotropy3() except ZeroDivisionError: pass | def atom_test(atom, stats): """Tests the mmLib.Structure.Atom object. """ stats["atom_count"] += 1 stats["testing"] = atom len(atom) alt_loc = atom.get_structure().get_default_alt_loc() atom.get_fragment() atom.get_chain() atom.get_model() atom.get_structure() visited_atm_list = [] for atm in atom.iter_alt_loc(... | 83d1b6500188bfe4caa9eaee09d2dda9ad26f7e0 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/83d1b6500188bfe4caa9eaee09d2dda9ad26f7e0/mmlib_test.py |
try: frag1 = self.segment[0] frag2 = self.segment[-1] except IndexError: return "AlphaHelix(%s %d)" % (self.helix_id, self.helix_class) return "AlphaHelix(%s %s %s...%s)" % ( self.helix_id, self.helix_class, str(frag1), str(frag2)) | return "AlphaHelix(%s %s %s:%s...%s:%s)" % ( self.helix_id, self.helix_class, self.chain_id1, self.fragment_id1, self.chain_id2, self.fragment_id2) | def __str__(self): try: frag1 = self.segment[0] frag2 = self.segment[-1] except IndexError: return "AlphaHelix(%s %d)" % (self.helix_id, self.helix_class) | 63febea20a5e8e7dad1aa889a68f883e88edae8a /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/63febea20a5e8e7dad1aa889a68f883e88edae8a/Structure.py |
if ref_tf>tls_tf: aatm.temp_factor = ((add_Uiso) + ref_tf - tls_tf)*U2B | if ref_tf > tls_tf: aatm.temp_factor = ((add_Uiso) + ref_tf - tls_tf)*Constants.U2B | def refmac5_prep(xyzin, tlsin_list, xyzout, tlsout): """Use TLS model + Uiso for each atom. Output xyzout with the residual Uiso only. """ os.umask(022) ## load structure struct = FileLoader.LoadStructure(fil = xyzin) ## load and construct TLS groups tls_group_list = [] tls_file = TLS.TLSFile() tls_file.set_file_fo... | 5cf3e0a446f3ad356a457839d6c6a478c04ac208 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5cf3e0a446f3ad356a457839d6c6a478c04ac208/refineprep.py |
aatm.temp_factor = (add_Uiso) * U2B | aatm.temp_factor = (add_Uiso) * Constants.U2B | def refmac5_prep(xyzin, tlsin_list, xyzout, tlsout): """Use TLS model + Uiso for each atom. Output xyzout with the residual Uiso only. """ os.umask(022) ## load structure struct = FileLoader.LoadStructure(fil = xyzin) ## load and construct TLS groups tls_group_list = [] tls_file = TLS.TLSFile() tls_file.set_file_fo... | 5cf3e0a446f3ad356a457839d6c6a478c04ac208 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5cf3e0a446f3ad356a457839d6c6a478c04ac208/refineprep.py |
outbase = string.join(listx, "_") | outbase ="_".join(listx) | def html_page(self): job_id = check_job_id(self.form) title = 'Input Files for Refmac5 TLS Refinement' x = '' x += self.html_head(title) x += self.html_title(title) | 5cf3e0a446f3ad356a457839d6c6a478c04ac208 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10674/5cf3e0a446f3ad356a457839d6c6a478c04ac208/refineprep.py |
usage: idle.py [-c command] [-d] [-e] [-s] [-t title] [arg] ... -c command run this command -d enable debugger -e edit mode; arguments are files to be edited -s run $IDLESTARTUP or $PYTHONSTARTUP before anything else -t title set title of shell window When neither -c nor -e is used, and... | usage: idle.py [-c command] [-d] [-i] [-r script] [-s] [-t title] [arg] ... idle file(s) (without options) edit the file(s) -c cmd run the command in a shell -d enable the debugger -i open an interactive shell -i file(s) open a shell and also an editor window for each file -r script run a file... | def isatty(self): return 1 | ddb3416a69f1ba1edc2a9d381df82a5bc051af6f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/ddb3416a69f1ba1edc2a9d381df82a5bc051af6f/PyShell.py |
opts, args = getopt.getopt(argv, "c:deist:") | opts, args = getopt.getopt(argv, "c:dir:st:") | def main(self, argv, noshell): cmd = None edit = 0 debug = 0 startup = 0 try: opts, args = getopt.getopt(argv, "c:deist:") except getopt.error, msg: sys.stderr.write("Error: %s\n" % str(msg)) sys.stderr.write(usage_msg) sys.exit(2) for o, a in opts: noshell = 0 if o == '-c': cmd = a if o == '-d': debug = 1 if o == '-... | ddb3416a69f1ba1edc2a9d381df82a5bc051af6f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/ddb3416a69f1ba1edc2a9d381df82a5bc051af6f/PyShell.py |
noshell = 0 | noshell = 0 | def main(self, argv, noshell): cmd = None edit = 0 debug = 0 startup = 0 try: opts, args = getopt.getopt(argv, "c:deist:") except getopt.error, msg: sys.stderr.write("Error: %s\n" % str(msg)) sys.stderr.write(usage_msg) sys.exit(2) for o, a in opts: noshell = 0 if o == '-c': cmd = a if o == '-d': debug = 1 if o == '-... | ddb3416a69f1ba1edc2a9d381df82a5bc051af6f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/ddb3416a69f1ba1edc2a9d381df82a5bc051af6f/PyShell.py |
if o == '-e': edit = 1 | if o == '-i': interactive = 1 if o == '-r': script = a | def main(self, argv, noshell): cmd = None edit = 0 debug = 0 startup = 0 try: opts, args = getopt.getopt(argv, "c:deist:") except getopt.error, msg: sys.stderr.write("Error: %s\n" % str(msg)) sys.stderr.write(usage_msg) sys.exit(2) for o, a in opts: noshell = 0 if o == '-c': cmd = a if o == '-d': debug = 1 if o == '-... | ddb3416a69f1ba1edc2a9d381df82a5bc051af6f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/ddb3416a69f1ba1edc2a9d381df82a5bc051af6f/PyShell.py |
elif not edit and args and args[0] != "-": interp.execfile(args[0]) | elif script: if os.path.isfile(script): interp.execfile(script) else: print "No script file: ", script | def main(self, argv, noshell): cmd = None edit = 0 debug = 0 startup = 0 try: opts, args = getopt.getopt(argv, "c:deist:") except getopt.error, msg: sys.stderr.write("Error: %s\n" % str(msg)) sys.stderr.write(usage_msg) sys.exit(2) for o, a in opts: noshell = 0 if o == '-c': cmd = a if o == '-d': debug = 1 if o == '-... | ddb3416a69f1ba1edc2a9d381df82a5bc051af6f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/ddb3416a69f1ba1edc2a9d381df82a5bc051af6f/PyShell.py |
def testNtoH(self): for func in socket.htonl, socket.ntohl: for i in (0, 1, ~0xffff, 2L): self.assertEqual(i, func(func(i))) biglong = 2**32L - 1 swapped = func(biglong) self.assert_(swapped == biglong or swapped == -1) self.assertRaises(OverflowError, func, 2L**34) | def testNtoHL(self): sizes = {socket.htonl: 32, socket.ntohl: 32, socket.htons: 16, socket.ntohs: 16} for func, size in sizes.items(): mask = (1L<<size) - 1 for i in (0, 1, 0xffff, ~0xffff, 2, 0x01234567, 0x76543210): self.assertEqual(i & mask, func(func(i&mask)) & mask) swapped = func(mask) self.assertEqual(swapped... | def testNtoH(self): for func in socket.htonl, socket.ntohl: for i in (0, 1, ~0xffff, 2L): self.assertEqual(i, func(func(i))) | 6b23db401df4d30fd8706dc573ddad8a6358351e /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/6b23db401df4d30fd8706dc573ddad8a6358351e/test_socket.py |
line = line.lstrip() | def _ascii_split(self, s, charset, firstline): # Attempt to split the line at the highest-level syntactic break # possible. Note that we don't have a lot of smarts about field # syntax; we just try to break on semi-colons, then whitespace. rtn = [] lines = s.splitlines() while lines: line = lines.pop(0) if firstline: ... | a2155165b8ce7df387780260143148938c957947 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/a2155165b8ce7df387780260143148938c957947/Header.py | |
sentence_end = ".?!" | sentence_end_re = re.compile(r'[%s]' r'[\.\!\?]' r'[\"\']?' % string.lowercase) | def islower (c): return c in string.lowercase | bce52ce3b3a50ba95e694d6e6b4dee7a5d5a0f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/bce52ce3b3a50ba95e694d6e6b4dee7a5d5a0f23/textwrap.py |
punct = self.sentence_end | pat = self.sentence_end_re | def _fix_sentence_endings (self, chunks): """_fix_sentence_endings(chunks : [string]) | bce52ce3b3a50ba95e694d6e6b4dee7a5d5a0f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/bce52ce3b3a50ba95e694d6e6b4dee7a5d5a0f23/textwrap.py |
if (chunks[i][-1] in punct and chunks[i+1] == " " and islower(chunks[i][-2])): | if chunks[i+1] == " " and pat.search(chunks[i]): | def _fix_sentence_endings (self, chunks): """_fix_sentence_endings(chunks : [string]) | bce52ce3b3a50ba95e694d6e6b4dee7a5d5a0f23 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/bce52ce3b3a50ba95e694d6e6b4dee7a5d5a0f23/textwrap.py |
dump(vars(values), write) | dump({'faultCode': values.faultCode, 'faultString': values.faultString}, write) | def dumps(self, values): out = [] write = out.append dump = self.__dump if isinstance(values, Fault): # fault instance write("<fault>\n") dump(vars(values), write) write("</fault>\n") else: # parameter block # FIXME: the xml-rpc specification allows us to leave out # the entire <params> block if there are no parameters... | fe46f7a5e71ba14dd7cf2188753cf578529a07dd /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/fe46f7a5e71ba14dd7cf2188753cf578529a07dd/xmlrpclib.py |
print "self.bdist_dir = %s" % self.bdist_dir print "self.format = %s" % self.format | def run (self): | 68b0de56b32b51627aa364331aa7b37c6a93b3c5 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/68b0de56b32b51627aa364331aa7b37c6a93b3c5/bdist_dumb.py | |
do_char(c, event) | do_char(c, event) | def do_key(self, event): (what, message, when, where, modifiers) = event c = chr(message & charCodeMask) if modifiers & cmdKey: if c == '.': raise self else: result = MenuKey(ord(c)) id = (result>>16) & 0xffff # Hi word item = result & 0xffff # Lo word if id: self.do_rawmenu(id, item, None, event) | 53cf06757b8d3c57f571e4792fd0e0ccac9de69c /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/53cf06757b8d3c57f571e4792fd0e0ccac9de69c/FrameWork.py |
args = args + to | if to[0] == '-to': to = to[1:] args = args + ('-to',) + tuple(to) | def put(self, data, to=None): args = (self.name, 'put', data) if to: args = args + to apply(self.tk.call, args) | f59254c5479eb2cf959502b211c95ed8d21cd76b /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/f59254c5479eb2cf959502b211c95ed8d21cd76b/Tkinter.py |
p = subprocess.Popen([sys.executable, "-c", "import os; os.abort()"]) | old_limit = self._suppress_core_files() try: p = subprocess.Popen([sys.executable, "-c", "import os; os.abort()"]) finally: self._unsuppress_core_files(old_limit) | def test_run_abort(self): # returncode handles signal termination p = subprocess.Popen([sys.executable, "-c", "import os; os.abort()"]) p.wait() self.assertEqual(-p.returncode, signal.SIGABRT) | 4633b74048f94164f8ab26e90df035094f59dadd /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/4633b74048f94164f8ab26e90df035094f59dadd/test_subprocess.py |
self._tk.deletecommand(cbname) | self._master.deletecommand(cbname) | def trace_vdelete(self, mode, cbname): self._tk.call("trace", "vdelete", self._name, mode, cbname) self._tk.deletecommand(cbname) | 2c2861fe5ce4abc92f5446142fe71f31bd18eccf /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/2c2861fe5ce4abc92f5446142fe71f31bd18eccf/Tkinter.py |
self._preprocess(body, headers, lang) | self._preprocess(body, headers, include_dirs, lang) | def try_cpp (self, body=None, headers=None, include_dirs=None, lang="c"): """Construct a source file from 'body' (a string containing lines of C/C++ code) and 'headers' (a list of header files to include) and run it through the preprocessor. Return true if the preprocessor succeeded, false if there were any errors. ('... | 57e7661ae761a48e4f9827701bb2df3fb3dc94f4 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/57e7661ae761a48e4f9827701bb2df3fb3dc94f4/config.py |
(src, out) = self._preprocess(body, headers, lang) | (src, out) = self._preprocess(body, headers, include_dirs, lang) | def search_cpp (self, pattern, body=None, headers=None, include_dirs=None, lang="c"): """Construct a source file (just like 'try_cpp()'), run it through the preprocessor, and return true if any line of the output matches 'pattern'. 'pattern' should either be a compiled regex object or a string containing a regex. If ... | 57e7661ae761a48e4f9827701bb2df3fb3dc94f4 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/57e7661ae761a48e4f9827701bb2df3fb3dc94f4/config.py |
if pattern.search(pattern): | if pattern.search(line): | def search_cpp (self, pattern, body=None, headers=None, include_dirs=None, lang="c"): """Construct a source file (just like 'try_cpp()'), run it through the preprocessor, and return true if any line of the output matches 'pattern'. 'pattern' should either be a compiled regex object or a string containing a regex. If ... | 57e7661ae761a48e4f9827701bb2df3fb3dc94f4 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/57e7661ae761a48e4f9827701bb2df3fb3dc94f4/config.py |
self._compile(body, headers, lang) | self._compile(body, headers, include_dirs, lang) | def try_compile (self, body, headers=None, include_dirs=None, lang="c"): """Try to compile a source file built from 'body' and 'headers'. Return true on success, false otherwise. """ from distutils.ccompiler import CompileError self._check_compiler() try: self._compile(body, headers, lang) ok = 1 except CompileError: o... | 57e7661ae761a48e4f9827701bb2df3fb3dc94f4 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/57e7661ae761a48e4f9827701bb2df3fb3dc94f4/config.py |
exts.append( Extension('audioop', ['audioop.c']) ) | def detect_modules(self): # Ensure that /usr/local is always used add_dir_to_list(self.compiler.library_dirs, '/usr/local/lib') add_dir_to_list(self.compiler.include_dirs, '/usr/local/include') | 37b50db622ccbd8c27e6b6cd7d932dab367056d0 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/37b50db622ccbd8c27e6b6cd7d932dab367056d0/setup.py | |
__version__ = " | __version__ = " | def testMultiply(self): self.assertEquals((0 * 10), 0) self.assertEquals((5 * 8), 40) | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py |
Note that decimal places (from zero) is usually not the same | Note that decimal places (from zero) are usually not the same | def failUnlessAlmostEqual(self, first, second, places=7, msg=None): """Fail if the two objects are unequal as determined by their difference rounded to the given number of decimal places (default 7) and comparing to zero. | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py |
import unittest | def loadTestsFromName(self, name, module=None): """Return a suite of all tests cases given a string specifier. | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py | |
issubclass(obj, unittest.TestCase)): | issubclass(obj, TestCase)): | def loadTestsFromName(self, name, module=None): """Return a suite of all tests cases given a string specifier. | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py |
elif isinstance(obj, unittest.TestSuite): | elif isinstance(obj, TestSuite): | def loadTestsFromName(self, name, module=None): """Return a suite of all tests cases given a string specifier. | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py |
if not isinstance(test, (unittest.TestCase, unittest.TestSuite)): | if not isinstance(test, (TestCase, TestSuite)): | def loadTestsFromName(self, name, module=None): """Return a suite of all tests cases given a string specifier. | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py |
timeTaken = float(stopTime - startTime) | timeTaken = stopTime - startTime | def run(self, test): "Run the given test case or test suite." result = self._makeResult() startTime = time.time() test(result) stopTime = time.time() timeTaken = float(stopTime - startTime) result.printErrors() self.stream.writeln(result.separator2) run = result.testsRun self.stream.writeln("Ran %d test%s in %.3fs" % (... | 99c020b458dc7210f2c230a25c6760727a00cc4d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/99c020b458dc7210f2c230a25c6760727a00cc4d/unittest.py |
def cmp(f1, f2, shallow=1, use_statcache=0): | def cmp(f1, f2, shallow=1, use_statcache=None): | def cmp(f1, f2, shallow=1, use_statcache=0): """Compare two files. Arguments: f1 -- First file name f2 -- Second file name shallow -- Just check stat signature (do not read the files). defaults to 1. use_statcache -- obsolete argument. Return value: True if the files are the same, False otherwise. This function... | c3a56c3f904f4e8e334426abe8f0e9de1635b125 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/c3a56c3f904f4e8e334426abe8f0e9de1635b125/filecmp.py |
def cmpfiles(a, b, common, shallow=1, use_statcache=0): | def cmpfiles(a, b, common, shallow=1, use_statcache=None): | def cmpfiles(a, b, common, shallow=1, use_statcache=0): """Compare common files in two directories. a, b -- directory names common -- list of file names found in both directories shallow -- if true, do comparison based solely on stat() information use_statcache -- obsolete argument Returns a tuple of three lists: fil... | c3a56c3f904f4e8e334426abe8f0e9de1635b125 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/c3a56c3f904f4e8e334426abe8f0e9de1635b125/filecmp.py |
raise getopt.error, 'need exactly two args' | raise getopt.GetoptError('need exactly two args', None) | def demo(): import sys import getopt options, args = getopt.getopt(sys.argv[1:], 'r') if len(args) != 2: raise getopt.error, 'need exactly two args' dd = dircmp(args[0], args[1]) if ('-r', '') in options: dd.report_full_closure() else: dd.report() | c3a56c3f904f4e8e334426abe8f0e9de1635b125 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/c3a56c3f904f4e8e334426abe8f0e9de1635b125/filecmp.py |
if self.optmize > 0: | if self.optimize > 0: | def _bytecode_filenames (self, py_filenames): bytecode_files = [] for py_file in py_filenames: if self.compile: bytecode_files.append(py_file + "c") if self.optmize > 0: bytecode_files.append(py_file + "o") | b1b6be8dc2262bce706e70372f90bff62f0ab960 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/b1b6be8dc2262bce706e70372f90bff62f0ab960/install_lib.py |
tmp_file.close() | _sync_close(tmp_file) | def add(self, message): """Add message and return assigned key.""" tmp_file = self._create_tmp() try: self._dump_message(message, tmp_file) finally: tmp_file.close() if isinstance(message, MaildirMessage): subdir = message.get_subdir() suffix = self.colon + message.get_info() if suffix == self.colon: suffix = '' else: ... | f1a9be4f2b606215ccf96e00683a2a8c9771cf75 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/f1a9be4f2b606215ccf96e00683a2a8c9771cf75/mailbox.py |
new_file.close() | _sync_close(new_file) | def flush(self): """Write any pending changes to disk.""" if not self._pending: return self._lookup() new_file = _create_temporary(self._path) try: new_toc = {} self._pre_mailbox_hook(new_file) for key in sorted(self._toc.keys()): start, stop = self._toc[key] self._file.seek(start) self._pre_message_hook(new_file) new_... | f1a9be4f2b606215ccf96e00683a2a8c9771cf75 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/f1a9be4f2b606215ccf96e00683a2a8c9771cf75/mailbox.py |
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