AtomUnit

Full name SMRUCC.genomics.Data.RCSB.PDB.Keywords.AtomUnit Assembly SMRUCC.genomics.Data.RCSB.PDB Members 6

the amino acid residue/atom model

00 Remarks

This type is the keyword level view of the unified atom model: all of the field storages are moved into the base class Atom, and the legacy property names are kept here as the compatibility aliases, so that the existing consumers (AminoAcid.SequenceGenerator, PDB.MaxSpace/MinSpace, ...) do not need any change.

01 Syntax

SMRUCC.genomics.Data.RCSB.PDB.Keywords.AtomUnit

02 Methods

Name	Overloads	Summary
InternalParser	1	Parse one raw ATOM record line.

03 Properties

Name	Overloads	Summary
AA_ID	1	氨基酸的名称简写（残基名）
AA_IDX	1	当前的氨基酸分子在Fasta序列之中的残基位置
Index	1	原子序号（PDB 列 7-11）
Atom	1	原子名称（PDB 列 13-16）
ChianID	1	链标识符（PDB 列 22）

04 Members

method InternalParser #

InternalParser(String)

Parse one raw ATOM record line.

Remarks

The legacy implementation split the line by the whitespace characters and then took the fields by the token index; that is broken for the fixed-column PDB format: when the chain identifier column is empty, the tokens shift left by one and the coordinates are read as (Y, Z, occupancy).

Parameters

Name Type Description

Name	Type	Description
`s`	`String`	The raw record line with the record name prefix, e.g. `ATOM 1 N SER A 1 25.289 6.282 7.602 1.00121.47 N` the fixed-column offsets are resolved by PdbLineParser.

s

String

The raw record line with the record name prefix, e.g.

 ATOM      1  N   SER A   1      25.289   6.282   7.602  1.00121.47           N

the fixed-column offsets are resolved by PdbLineParser.

Returns

Returns Nothing when the coordinate columns can not be parsed, the caller should skip such a record line.

property AA_ID #

AA_ID

氨基酸的名称简写（残基名）

Remarks

兼容别名，实际存储于 Atom.ResName。

property AA_IDX #

AA_IDX

当前的氨基酸分子在Fasta序列之中的残基位置

Remarks

兼容别名，实际存储于 Atom.ResSeq。

property Index #

Index

原子序号（PDB 列 7-11）

Remarks

兼容别名，实际存储于 Atom.Serial。

property Atom #

Atom

原子名称（PDB 列 13-16）

Remarks

兼容别名，实际存储于 Atom.AtomName。

property ChianID #

ChianID

链标识符（PDB 列 22）

Remarks

兼容别名，实际存储于 Atom.ChainID。注：该名称存在拼写错误（ChianID），保留仅为向后兼容，新代码请使用 Atom.ChainID。