def __init__(self,
name: str,
coh_AASeq: AASeq,
doc_AASeq: AASeq,
purples: int,
j=False,
originals=None,
doc_wt=False):
self.name = name
self.coh_AASeq = coh_AASeq
self.doc_AASeq = doc_AASeq
self.purples = purples
if not j:
name_split = name.split('_')
a_ind = name_split.index('A')
self.coh_wt = name_split[a_ind - 1]
self.doc_wt = name_split[a_ind + 1]
elif doc_wt:
self.coh_wt = '1ohz'
self.doc_wt = doc_wt
else:
self.coh_wt = '1ohz'
self.doc_wt = originals[name[:-3] +
'.pdb.gz'].split('_A_')[1].split('_')[0]
pos_str = coh_AASeq.get_positions(positions_dict['1ohz'])
self.coh_switch = ''.join(
[type_dict[a] if a in type_dict.keys() else 'c' for a in pos_str])
doc_str = doc_AASeq.get_positions(list(doc21ohz[self.doc_wt].keys()))
self.doc_switch = ''.join(
[type_dict[a] if a in type_dict.keys() else 'c' for a in doc_str])
def __init__(self, name: str, coh_AASeq: AASeq, doc_AASeq: AASeq, purples: int, j=False, originals=None, doc_wt=False):
self.name = name
self.coh_AASeq = coh_AASeq
self.doc_AASeq = doc_AASeq
self.purples = purples
if not j:
name_split = name.split('_')
a_ind = name_split.index('A')
self.coh_wt = name_split[a_ind-1]
self.doc_wt = name_split[a_ind+1]
elif doc_wt:
self.coh_wt = '1ohz'
self.doc_wt = doc_wt
else:
self.coh_wt = '1ohz'
self.doc_wt = originals[name[:-3]+'.pdb.gz'].split('_A_')[1].split('_')[0]
pos_str = coh_AASeq.get_positions(positions_dict['1ohz'])
self.coh_switch = ''.join([type_dict[a] if a in type_dict.keys() else 'c' for a in pos_str])
doc_str = doc_AASeq.get_positions(list(doc21ohz[self.doc_wt].keys()))
self.doc_switch = ''.join([type_dict[a] if a in type_dict.keys() else 'c' for a in doc_str])
def extract_charge_configuration(seq: AASeq, positions: list):
res_in_poses = seq.get_positions(positions)
charge = [
res2charge[a] if a in res2charge.keys() else 'c' for a in res_in_poses
]
return charge
def extract_charge_configuration(seq: AASeq, positions: list):
res_in_poses = seq.get_positions(positions)
charge = [res2charge[a] if a in res2charge.keys() else "c" for a in res_in_poses]
return charge
