pv_convert.py
用于复合物的mae文件的处理, 例如合并entries, 分离出配体和蛋白等 1. 常用-m, -l, -r选项. -asl (atom specification language表达式)可以用于指定配体原子的识别准则, 从而区分配体or蛋白. 例如ASL表达式-asl "res.ptype \'LIG \'"
可以将配体名LIG的识别出来, 注意LIG后面还有空格,两个转义也是必须的. 更多ASL表达式可以参考 菜单Edit-Select->Atoms.
Usage:
$SCHRODINGER/run pv_convert.py -m <pose_viewer_file> [-M <radius>]...
$SCHRODINGER/run pv_convert.py -p|-l|-r <structure_file> ...
Converts pose viewer files into a series of complexes, and convert complexes into ligand-only, receptor-only, or pose viewer files. The -merge_pv mode takes an input pose viewer file and creates a file with a series of receptor-ligand complexes. The other modes take a file with one or more receptor-ligand complexes and extract the receptor and ligand into a pose viewer format maestro file, or extract the ligands into a file, or extract the the receptors into a file. The last molecule in the complex is assumed to be the ligand by default.
Copyright Schrodinger, LLC. All rights reserved.
Options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-m, -merge_pv Combine pose viewer receptor and poses into a series
of complexes.
-M MERGE_PV_RADIUS, -merge_pv_radius MERGE_PV_RADIUS
When combining pose viewer receptor and poses into a
series of complexes, only include receptor residues
within this distance, in angstroms, from the ligand.
-p, -split_pv Extract receptor and ligand from complexes, write as
pose viewer format file(s).
-l, -split_ligand Extract ligand from complexes, write ligand(s) to
output file(s).
-r, -split_receptor Extract receptor from complexes, write receptor(s) to
output file(s).
-a ASL, -asl ASL Optional ASL expression to identify the ligand
molecule from a receptor-ligand complex. The entire
string must be quoted, and internal quotes must be
escaped. e.g. -asl "res.ptype \'UNK \'".
-q, -quiet Run tasks without intermediate reporting.
-asl_file ASL_FILE Optional file containing the ASL expression. The
expression in the file supersedes -asl expression.
-s, -separate_files When splitting ligands/receptors from complexes put
each ligand/receptor into a unique file name (old
default mode).
structcat
structcat - concatenate structure files of various formats into one file
structcat可以将多个结构合在一起, 最常用就是pdb/mol2 合成mae文件. 支持压缩文件maegz. 另外一些简单的也可以利用cat, zcat, type等实现. 2.
$SCHRODINGER/utilities/structcat -i[<format>] <inputfile> [-i[<format>] <inputfile>...] [-o[<format>]] <outputfile>
(or)
$SCHRODINGER/utilities/structcat <inputfiles> -o[<format>] <outputfile>
<format> must be one of:
- mae : Maestro format
- sd : V2000 SDfile format
- pdb : PDB format
- mol2 : sybyl (.mol2) format
- smi : SMILES format
If <format> is omitted, the file extension is used to determine the format.
structconvert
这是个强大的功能, 用于转换各种格式和进行操作. 本体是几种转换工具的集合, 例如pdbconvert.
usage: structconvert.py [-h]
[-imm | -imol2 | -imae | -ismi | -icsv | -ipdb | -isd]
[-omm | -omol2 | -omae | -osmi | -ocsv | -opdb | -osd]
[-a] [-stereo {none,annotation,3d}] [-smi SMILESCol]
[-name nameCol]
[-split-nstructures STRUCTURES_PER_OUTPUTFILE | -split-nfiles OUTPUTFILE_COUNT]
[-n selectStr] [-no_color] [-no_dup_conect]
[-multbonds] [-warn_h] [-no_geometry] [-no_renum]
[-no_reorder] [-reorder_by_resnum]
[-reorder_by_sequence] [-no_fixelem] [-first_occ]
[-all_occ] [-remediated] [-hybrid36] [-psp]
[-ignore_obsolete] [-warn_obsolete]
[-use_component_dict] [-no_component_dict]
[-data DATA] [-model MODEL] [-num_models NUM_MODELS]
[-histidine HISTIDINE] [-occ OCC] [-nostereo]
[-noarom] [-nolewis] [-notypes] [-2D] [-u]
inputfile outputfile
positional arguments:
- inputfile
- outputfile
optional arguments:
-h, --help show this help message and exit
-a Append to output file instead of overwriting (not supported for all conversions)
-stereo {none,annotation,3d}
Stereochemsitry source when writing to SMILES (default 3d)
-smi SMILESCol User specified field of SMILES strings, either by name or by column index starting at 1. By default, SMILES column is the first column (CSV format only).
-name nameCol User specified field to use as molecule name, either by name or by column index. By default, it is the second column (CSV format only).
-split-nstructures STRUCTURES_PER_OUTPUTFILE
Split the output files in N structures per file (Only mae -> mae conversions)
-split-nfiles OUTPUTFILE_COUNT
Split the output into N files. (Only mae -> mae conversions)
-n selectStr The set of input structures to process:
1,4 - structures 1 and 4
1:10,14 - structures 1 through 10 and 14
2: - structures 2 through the end of file
:5,13:18 - structures 1 through 5 and 13 through 18
All structures are processed by default.
(This option is not supported by all conversions)
Input formats:
- -imm MacroModel (.dat) format
- -imol2 sybyl (.mol2) format
- -imae Maestro format
- -ismi SMILES format
- -icsv CSV file, SMILES with properties
- -ipdb PDB format
- -isd V2000 SDfile format
- -omm MacroModel (.dat) format
- -omol2 sybyl (.mol2) format
- -omae Maestro format
- -osmi SMILES format
- -ocsv CSV file, SMILES with properties
- -opdb PDB format
- -osd V2000 SDfile format
For conversion to/from PDB format, the following options are also supported:
参考pdbconvert的选项.
- -no_color
- -no_dup_conect
- -multbonds
- -warn_h
- -no_geometry
- -no_renum
- -no_reorder
- -reorder_by_resnum
- -reorder_by_sequence
- -no_fixelem
- -first_occ
- -all_occ
- -remediated
- -hybrid36
- -psp (非标准ASH,ARN,GLH,LYN,HIE,HIP等非标准名字残基的残基名保留下来) 3
- -ignore_obsolete
- -warn_obsolete
- -use_component_dict
- -no_component_dict
- -data DATA
- -model MODEL
- -num_models NUM_MODELS
- -histidine HISTIDINE
- -occ OCC
For conversion to/from SD format, the following options are also supported:
- -nostereo
- -noarom
- -nolewis
- -notypes
- -2D
- -u
Limitations:
- PDB and SMILES format can not be interconverted.
- Only first structure is written when writing to PDB format.
- Structures can not be written to the obsolete MM format.
- When SMILES are converted to Maestro format, the output structures are 2D (not valid for many programs). Use LigPrep to generate 3D Maestro structures from SMILES.
- Conversion to older/newer Maestro format is only supported for input Maestro format file.
Reference
-
How do I combine a receptor and a ligand from separate files into a file with a single entry for the complex? ↩
-
Can I combine Maestro files or other structure files from the command line? ↩
-
Why are structures that have residues ARN, ASH, GLH, LYN, HIE, HIP incorrectly changed to ARG, ASP, GLU, LYS, HIS when converted to PDB? ↩