def Refmac5RefinementPrep(webtlsmdd, job_id, chain_ntls):
"""Called with a list of tuples (chain_id, ntls).
Generates PDB and TLSIN files for refinement with REFMAC5.
Returns a single string if there is an error, otherwise a
dictionary of results is returned.
"""
struct_id = webtlsmdd.job_get_structure_id(job_id)
analysis_dir = webtlsmdd.job_get_analysis_dir(job_id)
analysis_base_url = webtlsmdd.job_get_analysis_base_url(job_id)
if not os.path.isdir(analysis_dir):
return "Job analysis directory does not exist"
old_dir = os.getcwd()
os.chdir(analysis_dir)
## input structure
pdbin = "%s.pdb" % (struct_id)
if not os.path.isfile(pdbin):
pdbin = None
for pdbx in glob.glob("*.pdb"):
if len(pdbx) == 8:
struct_id = pdbx[:4]
pdbin = pdbx
break
if pdbin is None:
os.chdir(old_dir)
return "Input PDB File %s Not Found" % (pdbin)
## the per-chain TLSOUT files from TLSMD must be merged
tlsins = []
for chain_id, ntls in chain_ntls:
tlsin = "%s_CHAIN%s_NTLS%d.tlsout" % (struct_id, chain_id, ntls)
if not os.path.isfile(tlsin):
os.chdir(old_dir)
return "Input TLSIN File %s Not Found" % (tlsin)
tlsins.append(tlsin)
## form unique pdbout/tlsout filenames
listx = [struct_id]
for chain_id, ntls in chain_ntls:
listx.append("CHAIN%s" % (chain_id))
listx.append("NTLS%d" % (ntls))
outbase = "_".join(listx)
pdbout = "%s.pdb" % (outbase)
## the tlsout from this program is going to be the tlsin
## for refinement, so it's important for the filename to have
## the tlsin extension so the user is not confused
tlsout = "%s.tlsin" % (outbase)
## make urls for linking
pdbout_url = "%s/%s" % (analysis_base_url, pdbout)
tlsout_url = "%s/%s" % (analysis_base_url, tlsout)
## create the files
tls_calcs.refmac5_prep(pdbin, tlsins, pdbout, tlsout)
os.chdir(old_dir)
return dict(pdbout=pdbout,
pdbout_url=pdbout_url,
tlsout=tlsout,
tlsout_url=tlsout_url)
def Refmac5RefinementPrep(job_id, struct_id, chain_ntls, wilson):
"""Called with a list of tuples (job_id, struct_id, [chain_id, ntls], wilson).
Generates PDB and TLSIN files for refinement with REFMAC5 + PHENIX.
Returns a single string if there is an error, otherwise a
dictionary of results is returned.
"""
try:
struct_id = mysql.job_get_structure_id(job_id)
except:
return "Could not find the directory related to job_id: %s" % job_id
if mysql.job_get_via_pdb(job_id) == 1:
## If a job was submitted via pdb.org, the results/analyses files are
## in a different directory/path and so does the URL.
pdb_id = struct_id
job_dir = os.path.join(conf.WEBTLSMDD_PDB_DIR, pdb_id)
job_url = os.path.join(conf.TLSMD_PUBLIC_URL, "pdb", pdb_id)
analysis_dir = os.path.join(job_dir, "ANALYSIS")
analysis_base_url = "%s/ANALYSIS" % (job_url)
else:
## User-submitted (non-pdb.org) results/analyses files are in the
## standard place (aka directory/path/url) and are deleted every
## DELETE_DAYS (see webtlsmdcleanup.py) days.
job_dir = os.path.join(conf.TLSMD_WORK_DIR, job_id)
job_url = os.path.join(conf.TLSMD_PUBLIC_URL, "jobs", job_id)
analysis_dir = os.path.join(job_dir, "ANALYSIS")
analysis_base_url = "%s/ANALYSIS" % (job_url)
if not os.path.isdir(analysis_dir):
return "Job analysis directory does not exist: %s" % analysis_dir
old_dir = os.getcwd()
os.chdir(analysis_dir)
## input structure
pdbin = "%s.pdb" % (struct_id)
if not os.path.isfile(pdbin):
pdbin = None
for pdbx in glob.glob("*.pdb"):
if len(pdbx) == 8:
struct_id = pdbx[:4]
pdbin = pdbx
break
if pdbin is None:
os.chdir(old_dir)
return "Input PDB File %s Not Found" % (pdbin)
## the per-chain TLSOUT files from TLSMD must be merged
tlsins = []
for chain_id, ntls in chain_ntls:
tlsin = "%s_CHAIN%s_NTLS%d.tlsout" % (struct_id, chain_id, ntls)
if not os.path.isfile(tlsin):
os.chdir(old_dir)
return "Input TLSIN File %s Not Found" % (tlsin)
tlsins.append(tlsin)
job_num = job_id.split("_")[0]
secure_dir = job_id.split("_")[1]
if not os.path.exists(secure_dir):
os.mkdir(secure_dir)
## form unique pdbout/tlsout filenames from job_id
pdbout1 = "%s/%s_TLS+Biso.pdb" % (secure_dir, job_num)
pdbout2 = "%s/%s_pureTLS.pdb" % (secure_dir, job_num)
## the tlsout from this program is going to be the tlsin
## for refinement, so it's important for the filename to have
## the tlsin extension so the user is not confused
tlsout1 = "%s/%s_TLS+Biso.tlsin" % (secure_dir, job_num)
tlsout2 = "%s/%s_pureTLS.tlsin" % (secure_dir, job_num)
phenix = "%s/%s.phenix" % (secure_dir, job_num)
## make urls for linking
pdbout_url1 = "%s/%s" % (analysis_base_url, pdbout1)
pdbout_url2 = "%s/%s" % (analysis_base_url, pdbout2)
tlsout_url1 = "%s/%s" % (analysis_base_url, tlsout1)
tlsout_url2 = "%s/%s" % (analysis_base_url, tlsout2)
phenix_url = "%s/%s" % (analysis_base_url, phenix)
## create the REFMAC/PHENIX files
tls_calcs.refmac5_prep(pdbin, tlsins, pdbout1, tlsout1)
tls_calcs.phenix_prep(pdbin, tlsins, phenix)
tls_calcs.refmac_pure_tls_prep(pdbin, tlsins, wilson, pdbout2, tlsout2)
os.chdir(old_dir)
return dict(pdbout1=pdbout1,
pdbout_url1=pdbout_url1,
pdbout2=pdbout2,
pdbout_url2=pdbout_url2,
tlsout1=tlsout1,
tlsout_url1=tlsout_url1,
tlsout2=tlsout2,
tlsout_url2=tlsout_url2,
phenix=phenix,
phenix_url=phenix_url)
def Refmac5RefinementPrep(webtlsmdd, job_id, chain_ntls):
"""Called with a list of tuples (chain_id, ntls).
Generates PDB and TLSIN files for refinement with REFMAC5.
Returns a single string if there is an error, otherwise a
dictionary of results is returned.
"""
struct_id = webtlsmdd.job_get_structure_id(job_id)
analysis_dir = webtlsmdd.job_get_analysis_dir(job_id)
analysis_base_url = webtlsmdd.job_get_analysis_base_url(job_id)
if not os.path.isdir(analysis_dir):
return "Job analysis directory does not exist"
old_dir = os.getcwd()
os.chdir(analysis_dir)
## input structure
pdbin = "%s.pdb" % (struct_id)
if not os.path.isfile(pdbin):
pdbin = None
for pdbx in glob.glob("*.pdb"):
if len(pdbx) == 8:
struct_id = pdbx[:4]
pdbin = pdbx
break
if pdbin is None:
os.chdir(old_dir)
return "Input PDB File %s Not Found" % (pdbin)
## the per-chain TLSOUT files from TLSMD must be merged
tlsins = []
for chain_id, ntls in chain_ntls:
tlsin = "%s_CHAIN%s_NTLS%d.tlsout" % (struct_id, chain_id, ntls)
if not os.path.isfile(tlsin):
os.chdir(old_dir)
return "Input TLSIN File %s Not Found" % (tlsin)
tlsins.append(tlsin)
## form unique pdbout/tlsout filenames
listx = [struct_id]
for chain_id, ntls in chain_ntls:
listx.append("CHAIN%s" % (chain_id))
listx.append("NTLS%d" % (ntls))
outbase ="_".join(listx)
pdbout = "%s.pdb" % (outbase)
## the tlsout from this program is going to be the tlsin
## for refinement, so it's important for the filename to have
## the tlsin extension so the user is not confused
tlsout = "%s.tlsin" % (outbase)
## make urls for linking
pdbout_url = "%s/%s" % (analysis_base_url, pdbout)
tlsout_url = "%s/%s" % (analysis_base_url, tlsout)
## create the files
tls_calcs.refmac5_prep(pdbin, tlsins, pdbout, tlsout)
os.chdir(old_dir)
return dict(pdbout = pdbout,
pdbout_url = pdbout_url,
tlsout = tlsout,
tlsout_url = tlsout_url)
def Refmac5RefinementPrep(job_id, struct_id, chain_ntls, wilson):
"""Called with a list of tuples (job_id, struct_id, [chain_id, ntls], wilson).
Generates PDB and TLSIN files for refinement with REFMAC5 + PHENIX.
Returns a single string if there is an error, otherwise a
dictionary of results is returned.
"""
try:
struct_id = mysql.job_get_structure_id(job_id)
except:
return "Could not find the directory related to job_id: %s" % job_id
if mysql.job_get_via_pdb(job_id) == 1:
## If a job was submitted via pdb.org, the results/analyses files are
## in a different directory/path and so does the URL.
pdb_id = struct_id
job_dir = os.path.join(conf.WEBTLSMDD_PDB_DIR, pdb_id)
job_url = os.path.join(conf.TLSMD_PUBLIC_URL, "pdb", pdb_id)
analysis_dir = os.path.join(job_dir, "ANALYSIS")
analysis_base_url = "%s/ANALYSIS" % (job_url)
else:
## User-submitted (non-pdb.org) results/analyses files are in the
## standard place (aka directory/path/url) and are deleted every
## DELETE_DAYS (see webtlsmdcleanup.py) days.
job_dir = os.path.join(conf.TLSMD_WORK_DIR, job_id)
job_url = os.path.join(conf.TLSMD_PUBLIC_URL, "jobs", job_id)
analysis_dir = os.path.join(job_dir, "ANALYSIS")
analysis_base_url = "%s/ANALYSIS" % (job_url)
if not os.path.isdir(analysis_dir):
return "Job analysis directory does not exist: %s" % analysis_dir
old_dir = os.getcwd()
os.chdir(analysis_dir)
## input structure
pdbin = "%s.pdb" % (struct_id)
if not os.path.isfile(pdbin):
pdbin = None
for pdbx in glob.glob("*.pdb"):
if len(pdbx) == 8:
struct_id = pdbx[:4]
pdbin = pdbx
break
if pdbin is None:
os.chdir(old_dir)
return "Input PDB File %s Not Found" % (pdbin)
## the per-chain TLSOUT files from TLSMD must be merged
tlsins = []
for chain_id, ntls in chain_ntls:
tlsin = "%s_CHAIN%s_NTLS%d.tlsout" % (struct_id, chain_id, ntls)
if not os.path.isfile(tlsin):
os.chdir(old_dir)
return "Input TLSIN File %s Not Found" % (tlsin)
tlsins.append(tlsin)
job_num = job_id.split("_")[0]
secure_dir = job_id.split("_")[1]
if not os.path.exists(secure_dir):
os.mkdir(secure_dir)
## form unique pdbout/tlsout filenames from job_id
pdbout1 = "%s/%s_TLS+Biso.pdb" % (secure_dir, job_num)
pdbout2 = "%s/%s_pureTLS.pdb" % (secure_dir, job_num)
## the tlsout from this program is going to be the tlsin
## for refinement, so it's important for the filename to have
## the tlsin extension so the user is not confused
tlsout1 = "%s/%s_TLS+Biso.tlsin" % (secure_dir, job_num)
tlsout2 = "%s/%s_pureTLS.tlsin" % (secure_dir, job_num)
phenix = "%s/%s.phenix" % (secure_dir, job_num)
## make urls for linking
pdbout_url1 = "%s/%s" % (analysis_base_url, pdbout1)
pdbout_url2 = "%s/%s" % (analysis_base_url, pdbout2)
tlsout_url1 = "%s/%s" % (analysis_base_url, tlsout1)
tlsout_url2 = "%s/%s" % (analysis_base_url, tlsout2)
phenix_url = "%s/%s" % (analysis_base_url, phenix)
## create the REFMAC/PHENIX files
tls_calcs.refmac5_prep(pdbin, tlsins, pdbout1, tlsout1)
tls_calcs.phenix_prep(pdbin, tlsins, phenix)
tls_calcs.refmac_pure_tls_prep(pdbin, tlsins, wilson, pdbout2, tlsout2)
os.chdir(old_dir)
return dict(pdbout1 = pdbout1,
pdbout_url1 = pdbout_url1,
pdbout2 = pdbout2,
pdbout_url2 = pdbout_url2,
tlsout1 = tlsout1,
tlsout_url1 = tlsout_url1,
tlsout2 = tlsout2,
tlsout_url2 = tlsout_url2,
phenix = phenix,
phenix_url = phenix_url)
