def get_qm_file_name_and_pdb_hierarchy(fragment_extracts, index):
fragment_selection = fragment_extracts.fragment_super_selections[index]
fragment_hierarchy = fragment_extracts.pdb_hierarchy_super.select(
fragment_selection)
sub_working_folder = fragment_extracts.working_folder + "/" + str(
index) + "/"
if (not os.path.isdir(sub_working_folder)):
os.mkdir(sub_working_folder)
qm_pdb_file = sub_working_folder + str(index) + ".pdb"
complete_qm_pdb_file = qm_pdb_file[:-4] + "_capping.pdb"
if (fragment_extracts.debug): ## for degugging
fragment_hierarchy.write_pdb_file(
file_name=qm_pdb_file,
crystal_symmetry=fragment_extracts.expansion_cs)
ph = completion.run(pdb_hierarchy=fragment_hierarchy,
crystal_symmetry=fragment_extracts.expansion_cs,
model_completion=False,
original_pdb_filename=fragment_extracts.expansion_file)
##for debugging
if (fragment_extracts.debug):
fragment_hierarchy.write_pdb_file(
file_name=qm_pdb_file,
crystal_symmetry=fragment_extracts.expansion_cs)
ph.write_pdb_file(file_name=complete_qm_pdb_file)
return os.path.abspath(complete_qm_pdb_file), ph
def write_cluster_and_fragments_pdbs(fragments, directory):
# write current fragment and cluster PDBs into ./<directory>
# makes a fresh(!) <directory>
F = fragments
if not F.save_clusters:
return
from shutil import rmtree
cwd = os.getcwd()
frag_dir = os.path.join(cwd, directory)
expansion_file = os.path.join(cwd, fragments.expansion_file)
if os.path.exists(frag_dir):
rmtree(frag_dir)
os.mkdir(frag_dir)
os.chdir(frag_dir)
for index, selection_fragment in enumerate(F.fragment_selections):
cluster_selection = F.cluster_selections[index]
frag_selection = F.fragment_super_selections[index]
index_cluster = F.pdb_hierarchy.select(cluster_selection)
index_frag = F.pdb_hierarchy_super.select(frag_selection)
filename_cluster = "%s_cluster.pdb" % (index)
filename_frag = "%s_frag.pdb" % (index)
filename_capped = "%s_capped0.pdb" % (index)
index_cluster.write_pdb_file(file_name=filename_cluster,
crystal_symmetry=F.expansion_cs)
index_frag.write_pdb_file(file_name=filename_frag,
crystal_symmetry=F.expansion_cs)
capped_hierarchy = completion.run(pdb_hierarchy=index_frag,
crystal_symmetry=F.expansion_cs,
model_completion=False,
original_pdb_filename=expansion_file)
#capped_hierarchy = F.fragment_capped_initial[index]
capped_hierarchy.write_pdb_file(file_name=filename_capped,
crystal_symmetry=F.expansion_cs)
log = open('fragment_info.txt', 'w')
print >> log, '~ # clusters : ', len(F.cluster_atoms)
print >> log, '~ list of atoms per cluster:'
print >> log, '~ ', [len(x) for x in F.cluster_atoms]
print >> log, '~ list of atoms per fragment:'
print >> log, '~ ', [len(x) for x in F.fragment_super_atoms]
os.chdir(cwd)
def get_qm_file_name_and_pdb_hierarchy(fragment_extracts, index):
fragment_selection = fragment_extracts.fragment_super_selections[index]
fragment_hierarchy = fragment_extracts.pdb_hierarchy_super.select(
fragment_selection)
sub_working_folder = fragment_extracts.working_folder + "/" + str(
index) + "/"
if (not os.path.isdir(sub_working_folder)):
os.mkdir(sub_working_folder)
qm_pdb_file = sub_working_folder + str(index) + ".pdb"
complete_qm_pdb_file = qm_pdb_file[:-4] + "_capping.pdb"
# if(fragment_extracts.debug):
if (1): # at least for now
fragment_hierarchy.write_pdb_file(
file_name=qm_pdb_file,
crystal_symmetry=fragment_extracts.expansion_cs)
# re-capping because geometry of the fragment has changed.
ph = completion.run(pdb_hierarchy=fragment_hierarchy,
crystal_symmetry=fragment_extracts.expansion_cs,
model_completion=False,
original_pdb_filename=fragment_extracts.expansion_file)
# we now want this file by default
ph.write_pdb_file(file_name=complete_qm_pdb_file,
crystal_symmetry=fragment_extracts.expansion_cs)
return os.path.abspath(complete_qm_pdb_file), ph
def get_fragment_hierarchies_and_charges(self):
def pdb_hierarchy_select(atoms_size, selection):
selection_array = flex.bool(atoms_size, False)
for item in selection:
if (item <= atoms_size):
selection_array[item - 1] = True
return selection_array
self.fragment_selections = []
self.fragment_super_selections = []
self.fragment_charges = []
self.cluster_selections = []
self.buffer_selections = []
for i in range(len(self.fragment_super_atoms)):
fragment_selection = pdb_hierarchy_select(
self.pdb_hierarchy.atoms_size(), self.fragment_super_atoms[i])
## QM part is fragment_super
fragment_super_selection = pdb_hierarchy_select(
self.pdb_hierarchy_super.atoms_size(),
self.fragment_super_atoms[i])
fragment_super_hierarchy = self.pdb_hierarchy_super.select(
fragment_super_selection)
if (self.debug):
fragment_super_hierarchy.write_pdb_file(file_name=str(i) +
"-origin-cs.pdb")
fragment_super_hierarchy.write_pdb_file(
file_name=str(i) + ".pdb",
crystal_symmetry=self.expansion.cs_box)
charge_hierarchy = completion.run(
pdb_hierarchy=fragment_super_hierarchy,
crystal_symmetry=self.expansion.cs_box,
model_completion=False,
original_pdb_filename=self.expansion_file)
raw_records = charge_hierarchy.as_pdb_string(
crystal_symmetry=self.expansion.cs_box)
if (1):
charge_hierarchy.write_pdb_file(
file_name=str(i) + "_capping.pdb",
crystal_symmetry=self.expansion.cs_box)
self.charge_service.update_pdb_hierarchy(
charge_hierarchy,
self.expansion.cs_box,
)
#TODO: do not why self.charge_service could not right charge
#charge = self.charge_service.get_total_charge()
charge = charges_class(pdb_filename=str(i) +
"_capping.pdb").get_total_charge()
#the capping pdb file causes problem for tests, remove it
os.remove(str(i) + "_capping.pdb")
self.fragment_super_selections.append(fragment_super_selection)
#
self.fragment_selections.append(fragment_selection)
self.fragment_charges.append(charge)
cluster_selection = pdb_hierarchy_select(
self.pdb_hierarchy.atoms_size(), self.cluster_atoms[i])
self.cluster_selections.append(cluster_selection)
s = fragment_selection == cluster_selection
buffer_selection = fragment_selection.deep_copy().set_selected(
s, False)
self.buffer_selections.append(buffer_selection)
if (self.debug):
fragment_super_hierarchy.write_pdb_file(
file_name=str(i) + "_frag.pdb",
crystal_symmetry=self.expansion.cs_box)
cluster_pdb_hierarchy = self.pdb_hierarchy.select(
cluster_selection)
cluster_pdb_hierarchy.write_pdb_file(
file_name=str(i) + "_cluster.pdb",
crystal_symmetry=self.expansion.cs_box)