def run_FoldX_AnalyseComplex_And_Agadir(self):
GUM.wait_for_grid_engine_job_to_complete(self.solubis_job_prefix,
'all Solubis jobs to finish')
self.all_mutants_in_Solubis_path = sorted(glob.glob('./*'))
foldx_instance = FoldX()
for mutant_in_Solubis_path in self.all_mutants_in_Solubis_path:
if os.path.isdir(mutant_in_Solubis_path):
mutant_folder_name = mutant_in_Solubis_path.split('/')[-1]
os.chdir(mutant_folder_name)
self._make_backup_of_runscript()
foldx_instance.prepare_for_FoldX_AnalyseComplex(
self.RepairPDB_pdb_name)
print os.getcwd()
# Note: _1_0 is random choice, other two are same.
# cwd is Results/pdbname/Runs/Solubis/mutant_name
relative_path_of_pdb_to_read = './'
relative_path_for_new_fasta_folder_to_write = './'
pdb_name_chain_fasta_dict = GUM.extract_pdb_name_fasta_and_chains_from_pdb(
self.RepairPDB_pdb_name + '_1_0.pdb',
relative_path_of_pdb_to_read)
GUM.write_fasta_to_folder(
pdb_name_chain_fasta_dict,
relative_path_for_new_fasta_folder_to_write)
grid_engine_job_name = self.analyze_complex_job_prefix + mutant_folder_name
agadir_results_path = os.getcwd()
python_script_with_path = self.results_pdb_path + '/../../SourceFiles/Scripts/run_agadir.py ' + \
agadir_results_path
self._run_runscript_on_grid_engine(grid_engine_job_name,
python_script_with_path)
os.chdir('./..') # is this Runs/Solubis folder ?
cwd = os.getcwd() # for debugging
else:
print mutant_in_Solubis_path
def _run_runscript_on_grid_engine(self, grid_engine_job_name,
python_script_with_path):
no_queue = ''
no_max_memory = ''
no_cluster = ''
using_runscript = True
GUM.build_job_q_bash(grid_engine_job_name, no_queue, no_max_memory,
no_cluster, using_runscript, self.foldx_path,
python_script_with_path)
subprocess.call('qsub job.q', shell=True)
def prepare_for_FoldX_BuildModel(self, mutant_name,
pdb_name_of_repaired_pdb):
path_to_runscript = './'
repaired_pdbs = 'RepairPDB_' + pdb_name_of_repaired_pdb + '.pdb'
show_sequence_detail = False
action = '<BuildModel>#,individual_list.txt'
print_networks = False
calculate_stability = False
GUM.build_runscript_for_pdbs(path_to_runscript, repaired_pdbs,
show_sequence_detail, action,
print_networks, calculate_stability)
individual_list_for_this_mutant_only = open('individual_list.txt', 'w')
individual_list_for_this_mutant_only.write(mutant_name + ';\n')
individual_list_for_this_mutant_only.close()
def _run_repair_on_grid_engine(self, pdb_name):
repair_python_script = 'repair.py'
self._print_OptProt_calling_script(repair_python_script)
grid_engine_job_name = self.repair_job_prefix + pdb_name
no_queue = ''
no_max_memory = ''
no_cluster = ''
using_runscript = False
python_script_with_path_and_qsub = self.scripts_path + '/' + repair_python_script + \
self.space + self.qsub_path
GUM.build_job_q_bash(grid_engine_job_name, no_queue, no_max_memory,
no_cluster, using_runscript, self.foldx_path,
python_script_with_path_and_qsub)
subprocess.call(self.qsub_path + 'qsub job.q', shell=True)
os.chdir(self.start_path)
def _parse_optionfile_for_computations_charge_proteinChains(
self, option_file):
for line in option_file:
if '#' in line:
continue
if 'Command:' in line:
self.command = line.split(':')[-1].strip(';\n').strip()
if 'Charge:' in line:
self.charge = line.split(':')[-1].strip(';\n').strip()
if 'ProteinChains:' in line:
self.underscore_separated_proteinChains = []
protein_chains_option = line.split(':')[-1].strip(';\n')
if protein_chains_option == 'All':
for pdb in self.pdb_list:
protein_chains_list = GUM.extract_all_chains_from_pdb(
pdb, './PDBs/')
self.underscore_separated_proteinChains = '_'.join(
protein_chains_list)
self.pdb_protein_chains_dict = {
pdb: self.underscore_separated_proteinChains
}
elif ',' in protein_chains_option:
protein_chains_list = protein_chains_option.split(',')
protein_chains_list_stripped = []
for protein_chain in protein_chains_list:
protein_chains_list_stripped.append(
protein_chain.strip())
self.underscore_separated_proteinChains = '_'.join(
protein_chains_list_stripped)
else:
self.underscore_separated_proteinChains = protein_chains_option
print 'Command to be executed:\t\t' + self.command
print 'Protein chains to be considered:\t' + self.underscore_separated_proteinChains
def prepare_for_FoldX_AnalyseComplex(self, repair_pdb_name):
_0_1_2_pdbs = ['0.pdb,', '1.pdb,', '2.pdb,']
repair_pdb_name_1_ = repair_pdb_name + '_1_'
wt_repair_pdb_name_1_ = 'WT_' + repair_pdb_name_1_
path_to_runscript = './'
pdbs_to_analyse = repair_pdb_name_1_ + _0_1_2_pdbs[0] + \
repair_pdb_name_1_ + _0_1_2_pdbs[1] + \
repair_pdb_name_1_ + _0_1_2_pdbs[2] + \
wt_repair_pdb_name_1_ + _0_1_2_pdbs[0] + \
wt_repair_pdb_name_1_ + _0_1_2_pdbs[1] + \
wt_repair_pdb_name_1_ + _0_1_2_pdbs[2]
show_sequence_detail = False
action = '<AnalyseComplex>#'
print_networks = False
calculate_stability = False
GUM.build_runscript_for_pdbs(path_to_runscript, pdbs_to_analyse,
show_sequence_detail, action,
print_networks, calculate_stability)
def run_yasara_agadir_repair(self):
if not os.path.exists('Results'):
os.makedirs('Results')
for pdb in self.pdb_list:
pdb_name = pdb.split('.')[0]
self._build_results_directory_tree_for_each(pdb)
# current directory Results/pdb
# self._run_yasara_to_organise_pdb(pdb, pdb_name)
self._copy_pdb_foldx_agadir_files_to_new_subdirectories(pdb)
relative_path_of_pdb_to_read = './PDBs/'
relative_path_for_new_fasta_folder_to_write = './'
pdb_name_chain_fasta_dict = GUM.extract_pdb_name_fasta_and_chains_from_pdb(
pdb, relative_path_of_pdb_to_read)
GUM.write_fasta_to_folder(
pdb_name_chain_fasta_dict,
relative_path_for_new_fasta_folder_to_write)
agadir_results_path = self.start_path + '/Results/' + pdb_name
agadir_instance = Agadir(agadir_results_path)
agadir_instance.run_agadir_with_fasta_files('./')
self._run_repair_on_grid_engine(pdb_name)
message_to_print = 'PDBs to be repaired'
GUM.wait_for_grid_engine_job_to_complete(self.repair_job_prefix,
message_to_print)
def write_summary_solubis_file(self):
GUM.wait_for_grid_engine_job_to_complete(
self.analyze_complex_job_prefix,
'all AnalyseComplex jobs to finish')
os.chdir(self.results_pdb_path)
solubis_summary_file = open('SummarySolubis.txt', 'w')
solubis_summary_file.write(
'Mutation\tProteinChahin\tddG\tdTANGO\tComplexSum\t')
has_I_AC_fxout_file_for_repair_pdb = False
if os.path.isfile('./Repair/' + self.Int_AnalyComp +
self.RepairPDB_pdb_name +
'.fxout'): # use absolute path?
has_I_AC_fxout_file_for_repair_pdb = True
interact_ac_pdb_fxout_file = open('./Repair/' +
self.Int_AnalyComp +
self.RepairPDB_pdb_name +
'.fxout').readlines()
protein_chain_complexes = []
for line in interact_ac_pdb_fxout_file[9:]:
protein_chain_1 = line.split('\t')[1]
protein_chain_2 = line.split('\t')[2]
protein_chain_complex = 'Complex_' + protein_chain_1 + '_' + protein_chain_2
protein_chain_complexes.append(protein_chain_complex)
tab_separated_protein_chain_complexes = "\t".join(
protein_chain_complexes)
solubis_summary_file.write(tab_separated_protein_chain_complexes +
'\n')
else:
solubis_summary_file.write('\n')
all_agadir_outputs_wt_pdb_chains = glob.glob(
'./Agadir/*') # use the absolute path here
TangoWT = 0
for agadir_outputs_wt_pdb_chain in all_agadir_outputs_wt_pdb_chains: # agadir_outputs_pdb_chains
if os.path.isdir(agadir_outputs_wt_pdb_chain):
print agadir_outputs_wt_pdb_chain
f = open(agadir_outputs_wt_pdb_chain + '/PSX_globaltotal.out',
'r').readlines()
TangoWT += float(f[1].split()[2])
print 'Tango GlobalTotal score for WT protein = ' + str(TangoWT)
os.chdir(self.results_pdb_Runs_Solubis_path)
for solubis_mutant_folder_path in self.all_mutants_in_Solubis_path:
if os.path.isdir(solubis_mutant_folder_path):
f = open(
solubis_mutant_folder_path + '/Average_BuildModel_' +
self.RepairPDB_pdb_name + '.fxout', 'r').readlines()
# # THIS IS THE FOLDX STABILITY VALUE # #
ddG = f[9].split()[2]
agadir_output_files_for_this_mutant_chain_paths = glob.glob(
solubis_mutant_folder_path + '/Agadir/*')
TangoMut = 0
for agadir_output_files_for_this_mutant_chain_path in agadir_output_files_for_this_mutant_chain_paths:
if os.path.isdir(
agadir_output_files_for_this_mutant_chain_path):
# redundant ? path_agad_list is obtained line above by getting everything in Agadir folder
# def get_globalTango_from_PSX_globaltotalout_file(path):
f = open(
agadir_output_files_for_this_mutant_chain_path +
'/PSX_globaltotal.out',
'r').readlines() # globalTango_file
TangoMut += float(f[1].split()[2])
path_agad = agadir_output_files_for_this_mutant_chain_path
# ./Runs/Solubis/AH92R/Agadir/RepairPDB_Ab82b0sLigand_H
print 'Tango GlobalTotal score for mutant protein = ' + str(
TangoMut)
print path_agad
# don't understand. Goes through all chains but only stores last one to open the tango file below
f = open(
path_agad + '/PSX_globaltotal.out',
'r').readlines() # opening the globalTango file again ?
print f[
1] # which it then just prints and doesn't use ? - is this leftover from debugging
if has_I_AC_fxout_file_for_repair_pdb:
repair_pdb_name_1_ = self.RepairPDB_pdb_name + '_1_'
wt_repair_pdb_name_1_ = 'WT_' + repair_pdb_name_1_
path_I_AC_repair_pdb_name_1_ = solubis_mutant_folder_path + '/' + self.Int_AnalyComp + repair_pdb_name_1_
path_I_AC_wt_repair_pdb_name_1_ = solubis_mutant_folder_path + '/' + self.Int_AnalyComp + wt_repair_pdb_name_1_
_0_1_2_fxout = ['0.fxout', '1.fxout', '2.fxout']
# for fxout in _0_1_2_fxout:
# _get_interaction_energies_from_I_AC_file(path_IAC_repair_pdb_name_1_ + fxout)
# complex_Mut1 = _get_interaction_energies_from_I_AC_file(path_IAC_repair_pdb_name_1_ + _0_1_2_fxout[0])
f = open(path_I_AC_repair_pdb_name_1_ + _0_1_2_fxout[0],
'r').readlines()
complex_Mut1 = []
for line in f[9:]:
complex_Mut1.append(float(line.split()[5]))
f = open(path_I_AC_repair_pdb_name_1_ + _0_1_2_fxout[1],
'r').readlines()
complex_Mut2 = []
for line in f[9:]:
complex_Mut2.append(float(line.split()[5]))
f = open(path_I_AC_repair_pdb_name_1_ + _0_1_2_fxout[2],
'r').readlines()
complex_Mut3 = []
for line in f[9:]:
complex_Mut3.append(float(line.split()[5]))
f = open(path_I_AC_wt_repair_pdb_name_1_ + _0_1_2_fxout[0],
'r').readlines()
complex_WT1 = []
for line in f[9:]:
complex_WT1.append(float(line.split()[5]))
f = open(path_I_AC_wt_repair_pdb_name_1_ + _0_1_2_fxout[1],
'r').readlines()
complex_WT2 = []
for line in f[9:]:
complex_WT2.append(float(line.split()[5]))
f = open(path_I_AC_wt_repair_pdb_name_1_ + _0_1_2_fxout[2],
'r').readlines()
complex_WT3 = []
for line in f[9:]:
complex_WT3.append(float(line.split()[5]))
dInteractionEnergies_per_complex_list = []
dInteractionEnergies_all_complexes_summed = 0
for x, line in enumerate(f[9:]):
average_interaction_energy_per_complex_WT = float(
(complex_WT1[x] + complex_WT2[x] + complex_WT3[x])
/ 3)
average_interaction_energy_per_complex_Mut = float(
(complex_Mut1[x] + complex_Mut2[x] +
complex_Mut3[x]) / 3)
dInteractionEnergies_for_each_complex = average_interaction_energy_per_complex_Mut - average_interaction_energy_per_complex_WT
dInteractionEnergies_all_complexes_summed += dInteractionEnergies_for_each_complex
dInteractionEnergies_per_complex_list.append(
str(dInteractionEnergies_for_each_complex))
dInteractionEnergies_per_complex = "\t".join(
dInteractionEnergies_per_complex_list)
else:
dInteractionEnergies_per_complex = ""
dInteractionEnergies_all_complexes_summed = 0
dTango = float(TangoMut) - float(TangoWT)
mutation_name = solubis_mutant_folder_path.split('/')[-1]
protein_chain = mutation_name[
1] # Does this give same as above two lines?
row_of_values_per_mutation = mutation_name + '\t' + protein_chain + '\t' + ddG + '\t' + str(dTango) + '\t' + \
str(dInteractionEnergies_all_complexes_summed) + '\t' + \
dInteractionEnergies_per_complex + '\n'
solubis_summary_file.write(row_of_values_per_mutation)
solubis_summary_file.close()