def update_ligand_information_in_panddaTable(inital_model_directory,xtal):
if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')):
ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details()
for ligand in ligands_in_file:
residue_name= ligand[0]
residue_chain= ligand[1]
residue_number= ligand[2]
residue_altLoc= ligand[3]
residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number)
event = db.execute_statement("select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='%s'" % xtal)
for coord in event:
db_pandda_dict = {}
event_x = float(str(coord[0]))
event_y = float(str(coord[1]))
event_z = float(str(coord[2]))
site_index = str(coord[3])
distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2],
event_x, event_y,event_z)
# if coordinate of ligand and event are closer than 7A, then we assume they belong together
if distance < 7:
db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name
db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain
db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number
db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc
db_pandda_dict['PANDDA_site_ligand_placed'] = 'True'
if db_pandda_dict != {}:
print '==> XCE: updating pandda Table of data source'
db.update_panddaTable(xtal, site_index, db_pandda_dict)
def update_ligand_information_in_panddaTable(inital_model_directory, xtal):
if os.path.isfile(os.path.join(inital_model_directory, xtal,
'refine.pdb')):
# ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details()
ligands_in_file = pdbtools(
os.path.join(inital_model_directory, xtal,
'refine.pdb')).get_residues_with_resname('LIG')
for ligand in ligands_in_file:
# residue_name= ligand[0]
# residue_chain= ligand[1]
# residue_number= ligand[2]
# residue_altLoc= ligand[3]
residue_name = ligand[0]
residue_chain = ligand[2]
residue_number = ligand[1]
residue_altLoc = 'X'
residue_xyz = pdbtools(
os.path.join(
inital_model_directory, xtal,
'refine.pdb')).get_center_of_gravity_of_residue_ish(
residue_chain, residue_number)
event = db.execute_statement(
"select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'"
.format(xtal))
for coord in event:
db_pandda_dict = {}
event_x = float(str(coord[0]))
event_y = float(str(coord[1]))
event_z = float(str(coord[2]))
site_index = str(coord[3])
distance = misc().calculate_distance_between_coordinates(
residue_xyz[0], residue_xyz[1], residue_xyz[2], event_x,
event_y, event_z)
# if coordinate of ligand and event are closer than 7A, then we assume they belong together
if distance < 7:
db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name
db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain
db_pandda_dict[
'PANDDA_site_ligand_sequence_number'] = residue_number
db_pandda_dict[
'PANDDA_site_ligand_altLoc'] = residue_altLoc
db_pandda_dict['PANDDA_site_ligand_placed'] = 'True'
if db_pandda_dict != {}:
print '==> XCE: updating pandda Table of data source'
db.update_panddaTable(xtal, site_index, db_pandda_dict)
def copy_pdb(self, xtal):
os.chdir(os.path.join(self.htmlDir, 'files'))
self.pdb = None
if os.path.isfile(
os.path.join(self.projectDir, xtal,
'refine.split.bound-state.pdb')):
self.pdb = pdbtools(
os.path.join(self.projectDir, xtal,
'refine.split.bound-state.pdb'))
self.Logfile.insert(
'%s: copying refine.split.bound-state.pdb to html directory' %
xtal)
os.system('/bin/cp %s/refine.split.bound-state.pdb %s.pdb' %
(os.path.join(self.projectDir, xtal), xtal))
else:
self.Logfile.error('%s: cannot find refine.split.bound-state.pdb' %
xtal)
def parse_ligand_validation(inital_model_directory,refinement_directory,xtal):
if os.path.isfile(os.path.join(refinement_directory, 'residue_scores.csv')):
with open(os.path.join(refinement_directory, 'residue_scores.csv'), 'rb') as csv_import:
csv_dict = csv.DictReader(csv_import)
for i, line in enumerate(csv_dict):
db_pandda_dict = {}
residue = line['']
if len(residue.split('-')) == 3:
residue_name = residue.split('-')[0]
print residue_name
residue_chain = residue.split('-')[1]
residue_number = residue.split('-')[2]
residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number)
event = db.execute_statement("select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='%s'" % xtal)
for coord in event:
db_pandda_dict = {}
event_x = float(str(coord[0]))
event_y = float(str(coord[1]))
event_z = float(str(coord[2]))
site_index = str(coord[3])
distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2],
event_x, event_y,event_z)
print 'distance',distance
# if coordinate of ligand and event are closer than 7A, then we assume they belong together
if distance < 7:
db_pandda_dict['PANDDA_site_ligand_id'] = residue
db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy']
db_pandda_dict['PANDDA_site_B_average'] = line['Average B-factor (Residue)']
db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio']
db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD']
db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC']
db_pandda_dict['PANDDA_site_RSR'] = line['RSR']
db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD']
if os.path.isfile(os.path.join(refinement_directory, 'residue_plots', residue + '.png')):
db_pandda_dict['PANDDA_site_spider_plot'] = os.path.join(refinement_directory,
'residue_plots',
residue + '.png')
else:
db_pandda_dict['PANDDA_site_spider_plot'] = ''
if db_pandda_dict != {}:
print '==> XCE: updating pandda Table of data source'
db.update_panddaTable(xtal, site_index, db_pandda_dict)
def parse_ligand_validation(inital_model_directory, refinement_directory,
xtal):
if os.path.isfile(os.path.join(refinement_directory,
'residue_scores.csv')):
with open(os.path.join(refinement_directory, 'residue_scores.csv'),
'rb') as csv_import:
csv_dict = csv.DictReader(csv_import)
for i, line in enumerate(csv_dict):
db_pandda_dict = {}
residue = line[''].replace(' ', '')
residueFilename = line['']
if len(residue.split('-')) == 2:
# residue_name = residue.split('-')[0]
# print residue_name
residue_chain = residue.split('-')[0]
residue_number = residue.split('-')[1]
residue_xyz = pdbtools(
os.path.join(inital_model_directory, xtal, 'refine.pdb'
)).get_center_of_gravity_of_residue_ish(
residue_chain, residue_number)
event = db.execute_statement(
"select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'"
.format(xtal))
for coord in event:
db_pandda_dict = {}
event_x = float(str(coord[0]))
event_y = float(str(coord[1]))
event_z = float(str(coord[2]))
site_index = str(coord[3])
distance = misc(
).calculate_distance_between_coordinates(
residue_xyz[0], residue_xyz[1], residue_xyz[2],
event_x, event_y, event_z)
print 'distance', distance
# if coordinate of ligand and event are closer than 7A, then we assume they belong together
if distance < 7:
db_pandda_dict['PANDDA_site_ligand_id'] = residue
db_pandda_dict['PANDDA_site_occupancy'] = line[
'Occupancy']
db_pandda_dict['PANDDA_site_B_average'] = line[
'Average B-factor (Residue)']
db_pandda_dict[
'PANDDA_site_B_ratio_residue_surroundings'] = line[
'Surroundings B-factor Ratio']
db_pandda_dict['PANDDA_site_rmsd'] = line[
'Model RMSD']
db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC']
db_pandda_dict['PANDDA_site_RSR'] = line['RSR']
db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD']
if os.path.isfile(
os.path.join(refinement_directory,
'residue_plots',
residueFilename + '.png')):
db_pandda_dict[
'PANDDA_site_spider_plot'] = os.path.join(
refinement_directory, 'residue_plots',
residueFilename + '.png')
else:
db_pandda_dict['PANDDA_site_spider_plot'] = ''
if db_pandda_dict != {}:
print '==> XCE: updating pandda Table of data source'
db.update_panddaTable(xtal, site_index,
db_pandda_dict)