biob_structure_checking作为命令行实用程序执行mdweb结构检查集。
biobb-structure-checking的Python项目详细描述
从mdweb进行结构检查
check_structure作为命令行执行mdweb结构检查集 公用事业。
它包括一些结构操作选项，如选择模型或链， 移除系统的组件，完成缺失的原子和一些质量 检查是否存在残留要求、酰胺取向或VDW冲突。
usage: checkStruc.py [-h] [-i INPUT_STRUCTURE_PATH] [-o OUTPUT_STRUCTURE_PATH]
[--version] [--data_dir DATA_DIR]
[--res_lib RES_LIB_PATH] [--data_lib DATA_LIBRARY_PATH]
[--json JSON_OUTPUT_PATH] [--quiet] [--check_only]
[--non_interactive] [--force_save]
[--pdb_server PDB_SERVER]
command ...
positional arguments:
command Command to execute (help: checkStruc commands)
options Specific command options
optional arguments:
-h, --help show this help message and exit
-i INPUT_STRUCTURE_PATH, --input INPUT_STRUCTURE_PATH
Input structure. Formats PDB|mmCIF. Remote pdb:{pdbid}
-o OUTPUT_STRUCTURE_PATH, --output OUTPUT_STRUCTURE_PATH
Output structure. Format PDB
--version show program's version number and exit
--data_dir DATA_DIR Override settings default data dir
--res_lib RES_LIB_PATH
Override settings default residue library (AMBER prep
format)
--data_lib DATA_LIBRARY_PATH
Override settings default data library
--json JSON_OUTPUT_PATH
Cummulated checking results on a json file
--quiet Reduces output, removing labels and progress info
--check_only Perform checks, structure is not modified
--non_interactive Do not prompt for missing parameters
--force_save Force saving an output file even if no modification
--pdb_server PDB_SERVER
Server for retrieving structures (default: RCSB|mmb)
--load Loads structure from PDB server into the local cache
--stats Loads structure and get basic statistics and headers
Available commands:
可用命令：
commands: This help
command_list: Run all tests from conf file
checkall: Perform all checks without fixes
load: Stores structure on local cache and provide basic statistics
1. System Configuration
=======================
models [--select_model model_num]
Detect/Select Models
chains [--select_chains chain_ids]
Detect/Select Chains
inscodes
Detects residues with insertion codes (no fix)
altloc [--select_altloc occupancy| alt_id | list of res_id:alt_id]
Detect/Select Alternative Locations
metals [--remove All | None | Met_ids_list | Residue_list]
Detect/Remove Metals
ligands [--remove All | None | Res_type_list | Residue_list]
Detect/Remove Ligands
remwat [--remove Yes|No]
Remove Water molecules
remh [remh --remove Yes|No]
Remove Hydrogen atoms from structure
mutateside [--mut mutation_list]
Mutate side chain with minimal atom replacement. Allows multiple mutations
addH [--mode auto | pH | interactive | interactive_his]
Add Hydrogen Atoms
2. Fix Structure Errors
amide [--fix All|None|Residue List]
Detect/Fix Amide atoms Assignment
chiral [--fix All|None|Residue List]
Detect/Fix Improper quirality
fixside [--fix All |None|Residue List]
Complete side chains
backbone [--fix All|None|Residue List]
Analyze main chain missing atoms and fragments. O, OXT atoms can be fixed
3. Structure Warnings
cistransbck Analyzes cis-trans dihedrals on backbone atoms
getss Detect SS Bonds
clashes Steric clashes (Severe, Apolar, Polar Donors, Polar Acceptors,
Ionic Positive, Ionic Negative)
依赖性
- python 3.x
- 生物圈
- 努比
- Biobb_模型（结构管理器）
欢迎加入QQ群-->： 979659372
