def overlap(self, overlap_idx, rest):
'''
# select position with overlap value in restriction: rest
# e.g. rest=[0.1,0.5] overlap ratio : 0.1 <= value <= 0.5
Args:
overlap_idx: int index for overlap table
rest: typle: (a,b) , restriction a < value < b
list: [a,b] , restriction a <= value <= b
None: no restriction
Returns: self
'''
_, _, df = db.get_success_data(overlap_idx, dataframe=True)
primary_key = db.primary_key_for(overlap_idx)
df = df[primary_key+['overlap_ratio']]
df = table(df).apply_rest('overlap_ratio',rest)
if self.position is None:
self.position = df
else:
self.position = self.docked & df
return self
def ligand_size(self, ligand_idx, rest):
'''
select the ligand for the size in restriciton : rest
e.g. rest=(None,20) for the ligand could be fit into the box with size 20 A
Args:
ligand_idx: int
rest: typle: (a,b) , restriction a < value < b
list: [a,b] , restriction a <= value <= b
None: no restriction
'''
_, _, df = db.get_success_data(ligand_idx, dataframe=True)
primary_key = db.primary_key_for(ligand_idx)
df = df[primary_key + ['max_size_on_axis']]
df = table(df).apply_rest('max_size_on_axis', rest)
if self.ligand is None:
self.ligand = df
else:
self.ligand = self.ligand & df
try:
folder_name = db.get_folder(ligand_idx)
self.ligand_folder = '{}_{}'.format(ligand_idx, folder_name)
except:
pass
return self
def docked(self, docked_idx):
'''
load available docked ligand from table with idx: docked_idx
set docked_folder
Args:
docked_idx: int
Returns: self
'''
_, _, df = db.get_success_data(docked_idx, dataframe=True)
primary_key = db.primary_key_for(docked_idx)
df = df[primary_key]
df = table(df)
if self.ligand is None:
self.ligand = df
else:
self.ligand = self.ligand & df
folder_name = db.get_folder(docked_idx)
self.docked_folder = '{}_{}'.format(docked_idx, folder_name )
return self
def crystal(self, crystal_idx):
'''
load available ligand from table with idx: crystal_idx
set ligand_folder
Args:
crystal_idx: int
Returns: self
'''
table_name, _, df = db.get_success_data(crystal_idx, dataframe=True)
primary_key = db.primary_key_for(crystal_idx)
df = df[primary_key]
df = table(df)
print df
#print df
if self.ligand is None:
self.ligand = df
else:
self.ligand = self.ligand & df
try:
folder_name = db.get_folder(crystal_idx)
self.ligand_folder = '{}_{}'.format(crystal_idx, folder_name)
except:
pass
return self
def receptor(self, receptor_idx, rest):
'''
load available receptor from table with idx: receptor_idx
set receptor_folder
Args:
receptor_idx: int
rest: typle: (a,b) , restriction a < value < b
list: [a,b] , restriction a <= value <= b
None: no restriction
Returns:
'''
_, _, df = db.get_success_data(receptor_idx, dataframe=True)
primary_key = db.primary_key_for(receptor_idx)
df = df[primary_key+['resolution']]
df = table(df).apply_rest('resolution',rest)
if self.ligand is None:
self.ligand = df
else:
self.ligand = self.ligand & df
folder_name = db.get_folder(receptor_idx)
self.receptor_folder = '{}_{}'.format(receptor_idx, folder_name)
return self
def druglike_molecules(self, idx):
"""
Restrictions are in order of [hbond_donors, hbonds_acceptors, has_disorder, has_3d_structure, is_organometallic, is_polymeric, is_organic, r_factor, molecular_weight]
"""
restrictions = {"hbond_donors":[None, 5], "hbond_acceptors":[None, 10], "has_disorder":[0, 0], "has_3d_structure":[1, 1], "is_organometallic":[0, 0], "is_polymeric":[0, 0], "is_organic":[1, 1], "r_factor":[0, 15], "molecular_weight":[150.0, 600.0]} #"temperature":[150, 310]}
_, _, df = db.get_success_data(idx, dataframe=True)
primary_key = db.primary_key_for(idx)
for rest in restrictions:
df = table(df).apply_rest(rest, restrictions[rest])
if self.ligand is None:
self.ligand = df
else:
self.ligand = self.ligand & df
folder_name = db.get_folder(idx)
self.ligand_folder = '{}_{}'.format(idx, folder_name)
self.data_type = 'csd'
return self
def exclusion(self, ex_idx):
'''
load the ligand that should be exclude from table with idx: ex_idx
Args:
ex_idx: int
Returns: self
'''
_, _, df = db.get_success_data(ex_idx, dataframe=True)
primary_key = db.primary_key_for(ex_idx)
df = df[primary_key]
df = table(df)
if self.exclude is None:
self.exclude = df
else:
self.exclude = self.exclude | df
return self
def nondruglike_molecules(self, idx):
"""
Restrictions are in order of [hbond_donors, hbonds_acceptors, has_disorder, has_3d_structure, is_organometallic, is_polymeric, is_organic, r_factor, molecular_weight]
"""
restrictions = {"hbond_donors":[None, 5], "hbond_acceptors":[None, 10], "has_disorder":[0, 0], "has_3d_structure":[1, 1], "is_organometallic":[0, 0], "is_polymeric":[0, 0], "is_organic":[1, 1], "r_factor":[0, 15], "molecular_weight":[150.0, 600.0]} #"temperature":[150, 310]}
_, _, df_all = db.get_success_data(idx, dataframe=True)
primary_key = db.primary_key_for(idx)
df_drugs = df_all.copy()
for rest in restrictions:
df_drugs = table(df_drugs).apply_rest(rest, restrictions[rest])
df_merge = df_all.merge(df_drugs, indicator=True, how='outer')
df_nondrug = df_merge[df_merge['_merge'] == 'left_only']
if self.ligand is None:
self.ligand = df_nondrug
else:
self.ligand = self.ligand & df_nondrug
folder_name = db.get_folder(idx)
self.ligand_folder = '{}_{}'.format(idx, folder_name)
self.data_type = 'csd'
return self