本文整理汇总了Python中Library.library_is_amino_acid方法的典型用法代码示例。如果您正苦于以下问题：Python Library.library_is_amino_acid方法的具体用法？Python Library.library_is_amino_acid怎么用？Python Library.library_is_amino_acid使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Library的用法示例。
在下文中一共展示了Library.library_is_amino_acid方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: name_service
# 需要导入模块: import Library [as 别名]
# 或者: from Library import library_is_amino_acid [as 别名]
def name_service(self):
"""Runs the name service on all atoms needing to be named. This is a
complicated function which corrects most commonly found errors and
omissions from PDB files.
"""
if len(self.name_service_list) == 0:
return
## returns the next available chain_id in self.struct
## XXX: it's possible to run out of chain IDs!
def next_chain_id(suggest_chain_id):
if suggest_chain_id != "":
chain = self.struct.get_chain(suggest_chain_id)
if not chain:
return suggest_chain_id
## TODO: Add the following alphanumeric string to Constants.py, 2010-09-21
for chain_id in "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789":
chain = self.struct.get_chain(chain_id)
if not chain:
return chain_id
raise StructureBuilderError("name_service exhausted new chain_ids")
## NAME SERVICE FOR POLYMER ATOMS
## What if we are given a list of atoms with res_name, frag_id, and
## model_id where the frag_id are sequential? They can be sequential
## several ways using insertion codes, but large breaks often denote
## chain breaks.
## We need to handle the special case of a list of polymer residues
## which do not have chain_ids. This requires a first pass over the
## atom list using different rules than what we use for sorting out
## non-polymers.
current_polymer_type = None
current_polymer_model_id = None
current_polymer_chain_id = None
current_polymer_frag_id = None
current_polymer_res_name = None
current_polymer_name_dict = None
polymer_model_dict = {}
current_frag = None
current_frag_list = None
for atm in self.name_service_list[:]:
## determine the polymer type of the atom
if Library.library_is_amino_acid(atm.res_name):
polymer_type = "protein"
elif Library.library_is_nucleic_acid(atm.res_name):
polymer_type = "dna"
else:
## if the atom is not a polymer, we definitely have a break
## in this chain
current_polymer_type = None
current_polymer_model_id = None
current_polymer_chain_id = None
current_polymer_frag_id = None
current_polymer_res_name = None
current_polymer_name_dict = None
current_frag = None
current_frag_list = None
continue
fragment_id = Structure.FragmentID(atm.fragment_id)
## now we deal with conditions which can terminate the current
## polymer chain
if polymer_type!=current_polymer_type or \
atm.model_id!=current_polymer_model_id or \
atm.chain_id!=current_polymer_chain_id or \
fragment_id<current_polymer_frag_id:
current_polymer_type = polymer_type
current_polymer_model_id = atm.model_id
current_polymer_chain_id = atm.chain_id
current_polymer_frag_id = Structure.FragmentID(atm.fragment_id)
current_polymer_res_name = atm.res_name
current_polymer_name_dict = {atm.name: True}
## create new fragment
current_frag = [atm]
current_frag_list = [current_frag]
## create new fragment list (chain)
try:
model = polymer_model_dict[atm.model_id]
except KeyError:
model = [current_frag_list]
polymer_model_dict[atm.model_id] = model
else:
model.append(current_frag_list)
## we have now dealt with the atom, so it can be removed from
## the name service list
self.name_service_list.remove(atm)
continue
#.........这里部分代码省略.........