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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.


$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.


-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 - 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>


$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.


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:


  • -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


  • 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.



◆ 本文地址: http://platinhom.github.io/2015/11/25/sc_ligand_operate/, 转载请注明 ◆

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