本文整理汇总了Python中Bio.PDB.StructureBuilder.StructureBuilder.set_symmetry方法的典型用法代码示例。如果您正苦于以下问题：Python StructureBuilder.set_symmetry方法的具体用法？Python StructureBuilder.set_symmetry怎么用？Python StructureBuilder.set_symmetry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Bio.PDB.StructureBuilder.StructureBuilder的用法示例。
在下文中一共展示了StructureBuilder.set_symmetry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: StructureDecoder
# 需要导入模块: from Bio.PDB.StructureBuilder import StructureBuilder [as 别名]
# 或者: from Bio.PDB.StructureBuilder.StructureBuilder import set_symmetry [as 别名]
#.........这里部分代码省略.........
"""
for chain_ind in chain_indices:
self.chain_index_to_type_map[chain_ind] = entity_type
self.chain_index_to_seq_map[chain_ind] = sequence
self.chain_index_to_description_map[chain_ind] = description
def set_group_info(self, group_name, group_number, insertion_code,
group_type, atom_count, bond_count, single_letter_code,
sequence_index, secondary_structure_type):
"""Set the information for a group
:param group_name: the name of this group, e.g. LYS
:param group_number: the residue number of this group
:param insertion_code: the insertion code for this group
:param group_type: a string indicating the type of group (as found in the chemcomp dictionary.
Empty string if none available.
:param atom_count: the number of atoms in the group
:param bond_count: the number of unique bonds in the group
:param single_letter_code: the single letter code of the group
:param sequence_index: the index of this group in the sequence defined by the entity
:param secondary_structure_type: the type of secondary structure used
(types are according to DSSP and number to type mappings are defined in the specification)
"""
# MMTF uses a NUL character to indicate a blank insertion code, but
# StructureBuilder expects a space instead.
if insertion_code == "\x00":
insertion_code = " "
self.structure_bulder.init_seg(' ')
self.structure_bulder.init_residue(group_name, self.this_type,
group_number, insertion_code)
def set_model_info(self, model_id, chain_count):
"""Set the information for a model.
:param model_id: the index for the model
:param chain_count: the number of chains in the model
"""
self.structure_bulder.init_model(model_id)
def set_xtal_info(self, space_group, unit_cell):
"""Set the crystallographic information for the structure.
:param space_group: the space group name, e.g. "P 21 21 21"
:param unit_cell: an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma
"""
self.structure_bulder.set_symmetry(space_group, unit_cell)
def set_header_info(self, r_free, r_work, resolution, title,
deposition_date, release_date, experimnetal_methods):
"""Sets the header information.
:param r_free: the measured R-Free for the structure
:param r_work: the measure R-Work for the structure
:param resolution: the resolution of the structure
:param title: the title of the structure
:param deposition_date: the deposition date of the structure
:param release_date: the release date of the structure
:param experimnetal_methods: the list of experimental methods in the structure
"""
pass
def set_bio_assembly_trans(self, bio_assembly_index, input_chain_indices,
input_transform):
"""Set the Bioassembly transformation information. A single bioassembly can have multiple transforms.
:param bio_assembly_index: the integer index of the bioassembly
:param input_chain_indices: the list of integer indices for the chains of this bioassembly
:param input_transform: the list of doubles for the transform of this bioassmbly transform.
"""
pass
def finalize_structure(self):
"""Any functions needed to cleanup the structure."""
pass
def set_group_bond(self, atom_index_one, atom_index_two, bond_order):
"""Add bonds within a group.
:param atom_index_one: the integer atom index (in the group) of the first partner in the bond
:param atom_index_two: the integer atom index (in the group) of the second partner in the bond
:param bond_order: the integer bond order
"""
pass
def set_inter_group_bond(self, atom_index_one, atom_index_two, bond_order):
"""Add bonds between groups.
:param atom_index_one: the integer atom index (in the structure) of the first partner in the bond
:param atom_index_two: the integer atom index (in the structure) of the second partner in the bond
:param bond_order: the bond order
"""
pass