Options
-h |
Print command line help |
- |
import structures from standard input |
--geometry WxH+X+Y |
set preferred window size (W x H) and location (X, Y) |
--real-time |
display input stream in real time |
--spreadsheet |
use spreadsheet-like viewer with one row per input record (default if the input file contains data fields) |
--gridbag |
use compact matrix-like viewer with more molecules in a row (default if the input file does not contain data fields) |
-c <number> |
maximum number of visible columns for GridBagView (default: 2) |
-r <number> |
maximum number of visible rows for GridBagView (default: 2) |
-n <number> |
maximum number of molecules to import (default: 1000) |
-s <number> |
index of the first molecule to import (default: 1) |
-S |
display unique SMILES code |
-f <f1>:<f2> |
show specified fields (<f1>, <f2>, ...) in the given order from an SDfile. Field names are separated by colons. |
Options for displaying additional atomic properties stored in SDfile:
-p <file> |
palette definition property file* |
-t <tagName> |
name of the tag in the SDfile that contains property symbols* |
* See the Property colors in MarvinView section
You can also pass options to Java VM when you run the application from command line.
Examples
-
Displaying the first 1000 structures from str.smi:
mview str.smi
-
Viewing 500 structures starting at the 9500-th one from str.smi:
mview -n 500 -s 9500 str.smi
-
Showing structures and 3 fields (ID, name, and stock) from stock.sdf:
mview -f "ID:name:stock" stock.sdf
-
Display in 2 columns, show SMILES code:
mview -Sc 2 stock.sdf
-
Search using JChem's command line search module and display the structure and the ID field from the results:
jcsearch -q 'Clc1ccccc1' -f sdf input.sdf | mview -f ID -
-
Displaying the progress of a command line molecular dynamics simulation in real time:
program_producing_molfiles_on_stdout | mview --real-time -
-
Atom coloring according to property symbols in SDFile:
mview -p colors.ini -t PPL stock.sdf