def prepare(self):
self.Logfile.insert('======== preparing HTML summary ========')
self.makeFolders()
self.copy_jscss()
html = XChemMain.html_header()
firstFile = True
for xtal in self.db.samples_for_html_summary():
self.db_dict = self.db.get_db_dict_for_sample(xtal)
if firstFile:
if self.db_dict['ProteinName'] == 'None':
self.Logfile.warning('could not determine protein name')
try:
self.protein_name = xtal.split('-')[0]
self.Logfile.warning(
'xtal name = %s => setting protein name to %s' %
(xtal, self.protein_name))
except IndexError:
self.Logfile.warning(
'could not determine protein name from cystal name; setting to None'
)
self.protein_name = ''
else:
self.protein_name = self.db_dict['ProteinName']
self.Logfile.insert('protein name is: ' +
self.protein_name)
self.copy_pdb(xtal)
self.copy_mtz(xtal)
# self.copy_electron_density(xtal)
self.copy_ligand_files(xtal)
for ligand in self.ligands_in_pdbFile(xtal):
ligName = ligand.split('-')[0]
ligChain = ligand.split('-')[1]
ligNumber = ligand.split('-')[2]
eventMap = self.find_matching_event_map_from_database(
xtal, ligand)
if eventMap:
self.cut_and_copy_map(xtal, ligand + '.pdb', eventMap,
xtal + '_' + ligand + '_event.ccp4',
'F', 'PHIF')
x, y, z = self.pdb.get_centre_of_gravity_of_residue(ligand)
self.copy_spider_plot(xtal, ligand)
pdbID = self.db_dict['Deposition_PDB_ID']
compoundImage = xtal + '_' + self.db_dict[
'CompoundCode'] + '.png'
compoundCIF = xtal + '_' + self.db_dict['CompoundCode'] + '.cif'
residuePlot = xtal + '_' + ligand + '.png'
pdb = xtal + '.pdb'
event = xtal + '_' + ligand + '_event.ccp4'
thumbNail = xtal + '_' + ligand + '_thumb.png'
resoHigh = self.db_dict['DataProcessingResolutionHigh']
spg = self.db_dict['RefinementSpaceGroup']
unitCell = self.db_dict['DataProcessingUnitCell']
os.chdir(os.path.join(self.projectDir, xtal))
FWT = xtal + '-' + ligand + '_2fofc.ccp4'
self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,
'FWT', 'PHWT')
DELFWT = xtal + '-' + ligand + '_fofc.ccp4'
self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map',
DELFWT, 'DELFWT', 'PHDELWT')
ligConfidence = self.db.get_ligand_confidence_for_ligand(
xtal, ligChain, ligNumber, ligName)
if ligConfidence.startswith('0'):
self.Logfile.warning(
'%s: ligand confidence of %s-%s-%s is %s; ignoring...'
% (xtal, ligChain, ligNumber, ligName, ligConfidence))
continue
modelStatus = self.db_dict['RefinementOutcome']
if firstFile:
html += XChemMain.html_ngl(
pdb, eventMap.replace(self.projectDir, ''), FWT,
DELFWT, ligand)
html += XChemMain.html_download(self.protein_name)
html += XChemMain.html_guide()
html += XChemMain.html_table_header()
firstFile = False
html += XChemMain.html_table_row(xtal, pdbID, ligand,
compoundImage, residuePlot,
pdb, event, thumbNail,
resoHigh, spg, unitCell, FWT,
DELFWT, ligConfidence,
modelStatus)
self.make_thumbnail(xtal, x, y, z, ligand, eventMap)
self.prepare_for_download(xtal, pdb, event, compoundCIF,
ligand)
self.prepare_zip_archives()
# html = XChemMain.html_download_all_section(html,self.protein_name)
self.write_html_file(html)
self.Logfile.insert(
'======== finished preparing HTML summary ========')
def prepare(self, whichSamples):
self.Logfile.insert('======== preparing HTML summary ========')
self.makeFolders()
self.copy_jscss()
html = XChemMain.html_header()
firstFile = True
for xtal in self.db.samples_for_html_summary(whichSamples):
self.db_dict = self.db.get_db_dict_for_sample(xtal)
if firstFile:
if self.db_dict['ProteinName'] == 'None':
self.Logfile.warning('could not determine protein name')
try:
self.protein_name = xtal.split('-')[0]
self.Logfile.warning(
'xtal name = %s => setting protein name to %s' %
(xtal, self.protein_name))
except IndexError:
self.Logfile.warning(
'could not determine protein name from cystal name; setting to None'
)
self.protein_name = ''
else:
self.protein_name = self.db_dict['ProteinName']
self.Logfile.insert('protein name is: ' +
self.protein_name)
self.copy_pdb(xtal)
self.copy_mtz(xtal)
# self.copy_electron_density(xtal)
self.copy_ligand_files(xtal)
os.chdir(os.path.join(self.projectDir, xtal))
ligandDict = XChemUtils.pdbtools_gemmi(
'refine.pdb').center_of_mass_ligand_dict('LIG')
self.Logfile.insert(
xtal +
': saving ligand(s) of type LIG in refine.pdb as PDB files...')
XChemUtils.pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG')
for ligand in ligandDict:
self.Logfile.insert(xtal + ': current ligand -> ' + ligand)
os.chdir(os.path.join(self.projectDir, xtal))
# for ligand in self.ligands_in_pdbFile(xtal):
ligName = ligand.split('-')[0]
ligChain = ligand.split('-')[1]
ligNumber = ligand.split('-')[2]
# eventMap = self.find_matching_event_map_from_database(xtal, ligand)
# if eventMap:
# self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap))
# self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF')
# eventMap = xtal + '_' + ligand + '_event.ccp4'
# else:
# self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap))
eventMap = ''
# self.Logfile.insert(xtal + ': looking for' + xtal + '_' + ligand + '_event.ccp4')
if os.path.isfile(xtal + '_' + ligand + '_event.ccp4'):
eventMap = xtal + '_' + ligand + '_event.ccp4'
# self.Logfile.insert(xtal + ': found ' + eventMap)
# else:
# self.Logfile.error(xtal + ': cannot find' + xtal + '_' + ligand + '_event.ccp4')
# x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand)
x = ligandDict[ligand][0]
y = ligandDict[ligand][1]
z = ligandDict[ligand][2]
self.copy_spider_plot(xtal, ligand)
pdbID = self.db_dict['Deposition_PDB_ID']
compoundImage = xtal + '_' + self.db_dict[
'CompoundCode'] + '.png'
compoundCIF = xtal + '_' + self.db_dict['CompoundCode'] + '.cif'
residuePlot = xtal + '_' + ligand + '.png'
pdb = xtal + '.pdb'
event = xtal + '_' + ligand + '_event.ccp4'
thumbNail = xtal + '_' + ligand + '_thumb.png'
resoHigh = self.db_dict['DataProcessingResolutionHigh']
spg = self.db_dict['RefinementSpaceGroup']
unitCell = self.db_dict['DataProcessingUnitCell']
t = ''
for ax in unitCell.split():
t += str(round(float(ax), 1)) + ' '
unitCell = t[:-1]
os.chdir(os.path.join(self.projectDir, xtal))
# FWT = xtal + '-' + ligand + '_2fofc.ccp4'
# self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT')
# DELFWT = xtal + '-' + ligand + '_fofc.ccp4'
# self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT')
if os.path.isfile('refine.mtz'):
self.Logfile.insert('%s: found refine.mtz' % xtal)
FWTmap, DELFWTmap = self.prepare_e_density_maps(
xtal, ligand)
self.copy_electron_density(xtal, ligand, eventMap)
ligConfidence = self.db.get_ligand_confidence_for_ligand(
xtal, ligChain, ligNumber, ligName)
if ligConfidence.startswith('0'):
self.Logfile.warning(
'%s: ligand confidence of %s-%s-%s is %s; ignoring...'
% (xtal, ligChain, ligNumber, ligName, ligConfidence))
self.Logfile.warning(
'%s: this seems unlikely because this structure is apparently ready for deposition'
% xtal)
self.Logfile.warning(
'%s: will set it to "not assigned" for now, but please update in soakDB'
% xtal)
ligConfidence = 'not assigned'
modelStatus = self.db_dict['RefinementOutcome']
if firstFile:
html += XChemMain.html_ngl(
pdb, eventMap.replace(self.projectDir, ''), FWTmap,
DELFWTmap, ligand)
html += XChemMain.html_download(self.protein_name)
html += XChemMain.html_guide()
html += XChemMain.html_table_header()
firstFile = False
html += XChemMain.html_table_row(xtal, pdbID, ligand,
compoundImage, residuePlot,
pdb, event, thumbNail,
resoHigh, spg, unitCell,
FWTmap, DELFWTmap,
ligConfidence, modelStatus)
self.make_thumbnail(xtal, x, y, z, ligand, eventMap)
self.prepare_for_download(xtal, pdb, event, compoundCIF,
ligand)
self.prepare_zip_archives()
# html = XChemMain.html_download_all_section(html,self.protein_name)
self.write_html_file(html)
self.Logfile.insert(
'======== finished preparing HTML summary ========')