def create_ensembles_section(self, ample_dict):
self.rm_pending_section()
ensembles_data = ample_dict['ensembles_data']
self.summary_tab_ensemble_sec_id = "ensembles"
pyrvapi.rvapi_add_section(self.summary_tab_ensemble_sec_id,
"Ensembles", self.summary_tab_id, 0, 0, 1, 1, True)
if ample_dict['import_ensembles']:
rstr = 'Imported {0} ensembles.'.format(len(ensembles_data))
pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0, 0, 1, 1)
else:
# Get the ensembling data
d = ensembler.collate_cluster_data(ensembles_data)
clusters = d['clusters']
rstr = ""
rstr += "Ensemble Results<br/>"
rstr += "----------------<br/><br/>"
rstr += "Cluster method: {0}<br/>".format(d['cluster_method'])
rstr += "Cluster score type: {0}<br/>".format(d['cluster_score_type'])
rstr += "Truncation method: {0}<br/>".format(d['truncation_method'])
rstr += "Percent truncation: {0}<br/>".format(d['percent_truncation'])
rstr += "Side-chain treatments: {0}<br/>".format(d['side_chain_treatments'])
rstr += "Number of clusters: {0}<br/><br/>".format(len(clusters.keys()))
rstr += "Generated {0} ensembles<br/><br/>".format(len(ensembles_data))
pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0, 0, 1, 1)
ensemble_table = "ensemble_table"
pyrvapi.rvapi_add_table1(self.summary_tab_ensemble_sec_id + "/" + ensemble_table, "Ensembling Results", 1, 0, 1, 1, True)
tdata = []
for i, cluster_num in enumerate(sorted(d['clusters'].keys())):
header = True if i == 0 else False
tdata += ensembler.cluster_table_data(clusters, cluster_num, d['side_chain_treatments'], header=header)
self.fill_table(ensemble_table, tdata, tooltips=self._ensemble_tooltips)
return
def create_summary_tab(self, ample_dict):
self._create_summary_tab()
if self.do_create_ensembles_section(ample_dict):
self.create_ensembles_section(ample_dict)
if not self._got_mrbump_results(ample_dict):
return self.summary_tab_id
if not self.summary_tab_results_sec_id:
self.rm_pending_section()
# Only create the table once
self.summary_tab_results_sec_id = "mrbump"
pyrvapi.rvapi_add_section(self.summary_tab_results_sec_id,
"MRBUMP", self.summary_tab_id, 0, 0, 1, 1, True)
self.summary_tab_results_sec_table_id = "mrbump_table"
pyrvapi.rvapi_add_table1(self.summary_tab_results_sec_id + "/" + self.summary_tab_results_sec_table_id,
"MRBUMP Results", 1, 0, 1, 1, True)
mrb_results = ample_dict.get('mrbump_results')
if not mrb_results == self.old_mrbump_results:
# We set old_mrbump_results when we create the results_tab
self.fill_table(self.summary_tab_results_sec_table_id,
mrbump_util.ResultsSummary().results_table(mrb_results),
tooltips=self._mrbump_tooltips)
if not self.summary_tab_survey_sec_id and not self.ccp4i2:
# Only create the table once
self.summary_tab_survey_sec_id = "survey"
pyrvapi.rvapi_add_section(self.summary_tab_survey_sec_id, "Feedback", self.summary_tab_id, 0, 0, 1, 1, True)
rstr = "<h2>How did we do?</h2><h3>Please follow this link and leave some feedback:</h3><a href='{0}' style='color: blue'>{0}</a>".format(reference_manager.survey_url)
pyrvapi.rvapi_add_text(rstr, self.summary_tab_survey_sec_id, 0, 0, 1, 1)
return self.summary_tab_id
def __init__(self, parent, title, column_sort_index=None, column_sort_order_reverse=False, opened=False):
self._identifier = parent.identifier + "/" + self.unique_id("table")
super(Table, self).__init__(parent)
self._content = []
self._opened = opened
self._column_sort_index = column_sort_index
self._column_sort_order_reverse = column_sort_order_reverse
self._title = title
pyrvapi.rvapi_add_table1(self._identifier, self._title, 1, 0, 1, 1, self._opened)
def create_summary_tab(self, ample_dict):
#
# Summary Tab
#
self._create_summary_tab()
if not (ample_dict['single_model_mode'] or ample_dict['homologs'] or ample_dict['ideal_helices']) and \
bool(ample_dict['ensembles_data']) and not self.summary_tab_ensemble_sec_id:
self.rm_pending_section()
ensembles_data = ample_dict['ensembles_data']
self.summary_tab_ensemble_sec_id = "ensembles"
pyrvapi.rvapi_add_section(self.summary_tab_ensemble_sec_id,
"Ensembles", self.summary_tab_id, 0, 0,
1, 1, True)
# Get the ensembling data
d = ensembler.collate_cluster_data(ensembles_data)
clusters = d['clusters']
rstr = ""
rstr += "Ensemble Results<br/>"
rstr += "----------------<br/><br/>"
rstr += "Cluster method: {0}<br/>".format(d['cluster_method'])
rstr += "Cluster score type: {0}<br/>".format(
d['cluster_score_type'])
rstr += "Truncation method: {0}<br/>".format(
d['truncation_method'])
rstr += "Percent truncation: {0}<br/>".format(
d['percent_truncation'])
rstr += "Side-chain treatments: {0}<br/>".format(
d['side_chain_treatments'])
rstr += "Number of clusters: {0}<br/><br/>".format(
len(clusters.keys()))
rstr += "Generated {0} ensembles<br/><br/>".format(
len(ensembles_data))
pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0,
0, 1, 1)
ensemble_table = "ensemble_table"
pyrvapi.rvapi_add_table1(
self.summary_tab_ensemble_sec_id + "/" + ensemble_table,
"Ensembling Results", 1, 0, 1, 1, True)
# for cluster_num in sorted(clusters.keys()):
# rstr += "\n"
# rstr += "Cluster {0}\n".format(cluster_num)
# rstr += "Number of models: {0}\n".format(clusters[cluster_num]['cluster_num_models'])
# rstr += "Cluster centroid: {0}\n".format(clusters[cluster_num]['cluster_centroid'])
# rstr += "\n"
# tdata = cluster_table_data(clusters, cluster_num)
# rstr += tableFormat.pprint_table(tdata)
#
cluster_num = 1
tdata = ensembler.cluster_table_data(clusters, cluster_num,
d['side_chain_treatments'])
self.fill_table(ensemble_table,
tdata,
tooltips=self._ensemble_tooltips)
#
# MRBUMP Results
#
if not self._got_mrbump_results(ample_dict): return self.summary_tab_id
if not self.summary_tab_results_sec_id:
self.rm_pending_section()
# Only create the table once
self.summary_tab_results_sec_id = "mrbump"
pyrvapi.rvapi_add_section(self.summary_tab_results_sec_id,
"MRBUMP", self.summary_tab_id, 0, 0, 1,
1, True)
self.summary_tab_results_sec_table_id = "mrbump_table"
pyrvapi.rvapi_add_table1(
self.summary_tab_results_sec_id + "/" +
self.summary_tab_results_sec_table_id, "MRBUMP Results", 1, 0,
1, 1, True)
mrb_results = ample_dict['mrbump_results']
if not mrb_results == self.old_mrbump_results:
# We set old_mrbump_results when we create the results_tab
self.fill_table(
self.summary_tab_results_sec_table_id,
mrbump_util.ResultsSummary().results_table(mrb_results),
tooltips=self._mrbump_tooltips)
#
# Survey section
#
if not self.summary_tab_survey_sec_id and not self.ccp4i2:
# Only create the table once
self.summary_tab_survey_sec_id = "survey"
pyrvapi.rvapi_add_section(self.summary_tab_survey_sec_id,
"Feedback", self.summary_tab_id, 0, 0, 1,
1, True)
rstr = "<h2>How did we do?</h2><h3>Please follow this link and leave some feedback:</h3><a href='{0}' style='color: blue'>{0}</a>".format(
ample_util.survey_url)
pyrvapi.rvapi_add_text(rstr, self.summary_tab_survey_sec_id, 0, 0,
1, 1)
return self.summary_tab_id
def create_morda_db_results_tab(self, morda_db_results, morda_db_mr_results, results_to_display):
"""Function to create the MoRDa Database results tab
Parameters
----------
morda_db_results : str
Path to the file containing the MoRDa db results
morda_db_mr_results : str
Path to the file containing the MoRDa db MR results
results_to_display : int
Number of results to display
Returns
-------
object
Page containing the results from the MoRDa db search
"""
self._create_morda_db_results_tab()
if os.path.isfile(morda_db_results):
section_title = 'MoRDa database AMORE Rotation Search Results'
uid = str(uuid.uuid4())
sec = section_title.replace(" ", "_") + uid
tab = self.morda_db_results_tab_id
table = "table" + uid
pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, False)
table_title = "MoRDa datbase AMORE Rotation Search Results"
pyrvapi.rvapi_add_table1(sec + "/" + table, table_title, 2, 0, 1, 1, 100)
df = pandas.read_csv(morda_db_results)
self.create_table(df, table)
section_title = "AMORE Rotation Search Graphs"
uid = str(uuid.uuid4())
graph_sec = section_title.replace(" ", "_") + uid
graph_widget = "graphWidget" + uid
pyrvapi.rvapi_add_section(graph_sec, section_title, tab, 0, 0, 1, 1, True)
self.create_graphs(df, graph_sec, graph_widget)
if os.path.isfile(morda_db_mr_results):
section_title = 'Molecular Replacement Search Results'
uid = str(uuid.uuid4())
sec = section_title.replace(" ", "_") + uid
tab = self.morda_db_results_tab_id
table = "table" + uid
pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, False)
table_title = "Molecular Replacement Search Results"
pyrvapi.rvapi_add_table1(sec + "/" + table, table_title, 2, 0, 1, 1, 100)
df = pandas.read_csv(morda_db_mr_results)
self.create_table(df, table)
self.morda_db_df = df
section_title = 'Top {0} MoRDa database Search Downloads'.format(results_to_display)
uid = str(uuid.uuid4())
download_sec = section_title.replace(" ", "_") + uid
pyrvapi.rvapi_add_section(download_sec, section_title, tab, 0, 0, 1, 1, True)
section_title = 'Top {0} MoRDa database Search Log Files'.format(results_to_display)
uid = str(uuid.uuid4())
logfile_sec = section_title.replace(" ", "_") + uid
pyrvapi.rvapi_add_section(logfile_sec, section_title, tab, 0, 0, 1, 1, False)
for i in range(0, results_to_display):
try:
pdb_code = df.loc[i][0]
mr_workdir = os.path.join(self.work_dir, 'output_files')
mr_log = os.path.join(mr_workdir, '{0}_mr.log'.format(pdb_code))
ref_pdb = os.path.join(mr_workdir, '{0}_refinement_output.pdb'.format(pdb_code))
ref_mtz = os.path.join(mr_workdir, '{0}_refinement_output.mtz'.format(pdb_code))
ref_log = os.path.join(mr_workdir, '{0}_ref.log'.format(pdb_code))
ref_map = os.path.join(mr_workdir, '{0}_refmac_2fofcwt.map'.format(pdb_code))
diff_map = os.path.join(mr_workdir, '{0}_refmac_fofcwt.map'.format(pdb_code))
pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files(
[ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]
))
self.store_entry_in_rvapi_meta(
i + 1, "full", pdb_code, pdb, mtz, map_, dmap, False)
self.output_result_files(
download_sec, dmap, map_, mtz, pdb)
self.output_log_files(logfile_sec, mr_log, ref_log)
except KeyError:
logger.debug("No result found at position %s", (i + 1))
def create_lattice_results_tab(self, lattice_results, lattice_mr_results, results_to_display):
"""Function to create the lattice results tab
Parameters
----------
lattice_results : str
Path to the file containing the lattice results
lattice_mr_results : str
Path to the file containing the lattice MR results
results_to_display : int
Number of results to display
Returns
-------
object
Page containing the results from the lattice parameter search
"""
self._create_lattice_results_tab()
if os.path.isfile(lattice_results):
section_title = 'Lattice Parameter Search Results'
uid = str(uuid.uuid4())
sec = section_title.replace(" ", "_") + uid
tab = self.lattice_results_tab_id
table = "table" + uid
pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, True)
table_title = "Lattice Parameter Search Results"
pyrvapi.rvapi_add_table1(sec + "/" + table, table_title, 2, 0, 1, 1, 100)
df = pandas.read_csv(lattice_results)
self.create_table(df, table)
if os.path.isfile(lattice_mr_results):
section_title = 'Molecular Replacement Search Results'
uid = str(uuid.uuid4())
sec = section_title.replace(" ", "_") + uid
tab = self.lattice_results_tab_id
table = "table" + uid
pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, True)
table_title = "Molecular Replacement Search Results"
pyrvapi.rvapi_add_table1(sec + "/" + table, table_title, 2, 0, 1, 1, 100)
df = pandas.read_csv(lattice_mr_results)
self.create_table(df, table)
section_title = 'Top {0} Lattice Parameter Search Downloads'.format(results_to_display)
uid = str(uuid.uuid4())
download_sec = section_title.replace(" ", "_") + uid
pyrvapi.rvapi_add_section(download_sec, section_title, tab, 0, 0, 1, 1, True)
section_title = 'Top {0} Lattice Parameter Search Log Files'.format(results_to_display)
uid = str(uuid.uuid4())
logfile_sec = section_title.replace(" ", "_") + uid
pyrvapi.rvapi_add_section(logfile_sec, section_title, tab, 0, 0, 1, 1, False)
self.lattice_df = df
for i in range(0, results_to_display):
try:
pdb_code = df.loc[i][0]
mr_workdir = os.path.join(self.work_dir, 'output_files', pdb_code)
mr_log = os.path.join(mr_workdir, '{0}_mr.log'.format(pdb_code))
ref_pdb = os.path.join(mr_workdir, '{0}_refinement_output.pdb'.format(pdb_code))
ref_mtz = os.path.join(mr_workdir, '{0}_refinement_output.mtz'.format(pdb_code))
ref_log = os.path.join(mr_workdir, '{0}_ref.log'.format(pdb_code))
ref_map = os.path.join(mr_workdir, '{0}_refmac_2fofcwt.map'.format(pdb_code))
diff_map = os.path.join(mr_workdir, '{0}_refmac_fofcwt.map'.format(pdb_code))
pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files(
[ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]
))
self.store_entry_in_rvapi_meta(
i + 1, "latt", pdb_code, pdb, mtz, map_, dmap, False)
self.output_result_files(
download_sec, dmap, map_, mtz, pdb)
self.output_log_files(logfile_sec, mr_log, ref_log)
except KeyError:
logger.debug("No result found at position %s", (i + 1))
else:
for i in range(0, results_to_display):
try:
df = pandas.read_csv(lattice_results)
pdb_code = df.loc[i][0]
mr_log = None
ref_pdb = os.path.join(self.work_dir, 'latt', 'mr_search', 'mr_models', '{}.pdb'.format(pdb_code))
ref_mtz = None
ref_log = None
ref_map = None
diff_map = None
pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files(
[ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]
))
if i == 0:
best = True
else:
best = False
self.store_entry_in_rvapi_meta(
i + 1, "latt", pdb_code, pdb, mtz, map_, dmap, best)
except KeyError:
logger.debug("No result found at position %s", (i + 1))
def create_morda_db_results_tab(self, morda_db_results, morda_db_mr_results, results_to_display):
"""Function to create the MoRDa Database results tab
Parameters
----------
morda_db_results : str
Path to the file containing the MoRDa db results
morda_db_mr_results : str
Path to the file containing the MoRDa db MR results
results_to_display : int
Number of results to display
Returns
-------
object
Page containing the results from the MoRDa db search
"""
self._create_morda_db_results_tab()
if os.path.isfile(morda_db_results):
section_title = 'MoRDa database AMORE Rotation Search Results'
uid = str(uuid.uuid4())
sec = section_title.replace(" ", "_") + uid
tab = self.morda_db_results_tab_id
table = "table" + uid
pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, False)
table_title = "MoRDa datbase AMORE Rotation Search Results"
pyrvapi.rvapi_add_table1(sec + "/" + table, table_title, 2, 0, 1, 1, 100)
df = pandas.read_csv(morda_db_results)
self.create_table(df, table)
section_title = "AMORE Rotation Search Graphs"
uid = str(uuid.uuid4())
graph_sec = section_title.replace(" ", "_") + uid
graph_widget = "graphWidget" + uid
pyrvapi.rvapi_add_section(graph_sec, section_title, tab, 0, 0, 1, 1, True)
self.create_graphs(df, graph_sec, graph_widget)
if os.path.isfile(morda_db_mr_results):
section_title = 'Molecular Replacement Search Results'
uid = str(uuid.uuid4())
sec = section_title.replace(" ", "_") + uid
tab = self.morda_db_results_tab_id
table = "table" + uid
pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, False)
table_title = "Molecular Replacement Search Results"
pyrvapi.rvapi_add_table1(sec + "/" + table, table_title, 2, 0, 1, 1, 100)
df = pandas.read_csv(morda_db_mr_results)
self.create_table(df, table)
self.morda_db_df = df
section_title = 'Top {0} MoRDa database Search Downloads'.format(results_to_display)
uid = str(uuid.uuid4())
download_sec = section_title.replace(" ", "_") + uid
pyrvapi.rvapi_add_section(download_sec, section_title, tab, 0, 0, 1, 1, True)
section_title = 'Top {0} MoRDa database Search Log Files'.format(results_to_display)
uid = str(uuid.uuid4())
logfile_sec = section_title.replace(" ", "_") + uid
pyrvapi.rvapi_add_section(logfile_sec, section_title, tab, 0, 0, 1, 1, False)
for i in range(0, results_to_display):
pdb_code = df.loc[i][0]
mr_workdir = os.path.join(self.work_dir, 'output_files')
mr_log = os.path.join(mr_workdir, '{0}_mr.log'.format(pdb_code))
ref_pdb = os.path.join(mr_workdir, '{0}_refinement_output.pdb'.format(pdb_code))
ref_mtz = os.path.join(mr_workdir, '{0}_refinement_output.mtz'.format(pdb_code))
ref_log = os.path.join(mr_workdir, '{0}_ref.log'.format(pdb_code))
ref_map = os.path.join(mr_workdir, '{0}_refmac_2fofcwt.map'.format(pdb_code))
diff_map = os.path.join(mr_workdir, '{0}_refmac_fofcwt.map'.format(pdb_code))
pdb, mtz, map_, dmap, mr_log, ref_log = list(
self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]))
try:
self.store_entry_in_rvapi_meta(i + 1, "full", pdb_code, pdb, mtz, map_, dmap, False)
self.output_result_files(download_sec, dmap, map_, mtz, pdb)
self.output_log_files(logfile_sec, mr_log, ref_log)
except KeyError:
logger.debug("No result found at position %s", (i + 1))