def get_clusters(self):
self.cluster_file_name = self.working_folder + "/cluster.xml"
self.qmmm_file_name = self.working_folder + "/qmmm.xml"
## write yoink input file to get interactions
write_yoink_infiles(self.cluster_file_name, self.qmmm_file_name,
self.pdb_hierarchy, self.yoink_dat_path)
self.pyoink.input_file = self.cluster_file_name
self.pyoink.update()
self.interaction_list, weight = self.pyoink.get_interactions_list()
self.interacting_pairs = len(self.interaction_list)
self.interaction_list += self.backbone_connections
## isolate altloc molecules
new_interaction_list = []
if (0):
for item in self.interaction_list:
contain_altlocs = set(
self.altloc_molecular_indices) & set(item)
if (len(contain_altlocs) == 0):
new_interaction_list.append(item)
self.interaction_list = new_interaction_list
import clustering
#t0 = time.time()
self.clustering = clustering.betweenness_centrality_clustering(
self.interaction_list,
size=len(self.pyoink.molecules),
maxnum_residues_in_cluster=self.maxnum_residues_in_cluster)
clusters = self.clustering.get_clusters()
self.clusters = sorted(
clusters, lambda x, y: 1 if len(x) < len(y) else -1
if len(x) > len(y) else 0)
def get_clusters(self):
#print(self.clustering)
n_residues = len(list(self.pdb_hierarchy.residue_groups()))
if (not self.clustering):
return (range(1, n_residues + 1, 1))
if (self.fast_interaction):
self.interaction_list = pair_interaction.run(
copy.deepcopy(self.pdb_hierarchy)) ##deepcopy
else: # to be deprecated.
self.cluster_file_name = self.working_folder + "/cluster.xml"
self.qmmm_file_name = self.working_folder + "/qmmm.xml"
## write yoink input file to get interactions
if (not self.fast_interaction):
from qrefine.utils.yoink_utils import write_yoink_infiles
write_yoink_infiles(self.cluster_file_name, self.qmmm_file_name,
self.pdb_hierarchy, self.yoink_dat_path)
self.pyoink.input_file = self.cluster_file_name
self.pyoink.update()
self.interaction_list, weight = self.pyoink.get_interactions_list()
self.interacting_pairs = len(self.interaction_list)
self.interaction_list += self.backbone_connections
## isolate altloc molecules
new_interaction_list = []
if (0):
for item in self.interaction_list:
contain_altlocs = set(
self.altloc_molecular_indices) & set(item)
if (len(contain_altlocs) == 0):
new_interaction_list.append(item)
self.interaction_list = new_interaction_list
import clustering
# t0 = time.time()
self.clustering = clustering.betweenness_centrality_clustering(
self.interaction_list,
size=n_residues,
maxnum_residues_in_cluster=self.maxnum_residues_in_cluster)
clusters = self.clustering.get_clusters()
self.clusters = sorted(
clusters, lambda x, y: 1 if len(x) < len(y) else -1
if len(x) > len(y) else 0)