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CreateView

This manual gives a walkthrough on the CreateView application:

Introduction

CreateView composes an SDfile that contains both structures and calculation results using the input SDfile of GenerateMD and a table containing the ordinal number of compounds in the SDfile and other data to be viewed. Such table can be created for example by Compr or Jarp. The generated SDfiles can be displayed by the MarvinView application or other SDF viewer.

Usage

CreateView can be used as a command line application in the following way:

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crview [<options>]

Prepare the usage of the crview script or batch file as described in Preparing the Usage of JChem Batch Files and Shell Scripts.

You can also call the CreateView Java class directly:

  • Under Win32 / Java 2 (assuming that JChem is installed in c:\jchem):
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    java -cp "c:\jchem\lib\jchem.jar;%CLASSPATH%" chemaxon.clustering.CreateView [<options>]
  • Under Unix / Java 2 (assuming that JChem is installed in /usr/local/jchem):
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    java -cp "/usr/local/jchem/lib/jchem.jar:$CLASSPATH" \ chemaxon.clustering.CreateView [<options>]

Because the utility has many parameters, it may be reasonable to create a shell script or a batch file for calling the software.

Options and creating input

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 -h --help this help message

 -s --input-sdf <file> input SDfile

 -t --input-table <file> input table (id values and other data)

 -o --output-sdf <file> output SDfile

 -i --id-name <col>[:<count>] name of columns storing the id's (indexes).

 <count> is the occurrence of the column.

 default: the id is the line number.

 -d --data-names <col1>:<col2>... name of columns to include in the SDfile

 -c --condition "<col><OP><cond>" condition checked. OP may be: =,<,>,<=,>=

Two input files have to be specified:

  • SDfile containing structures ( --input-sdf option).
  • A table containing the ordinal number of compounds from the SDfile and other data to be viewed ( --input-table option).

The structure of the input table should be the following:

  • headers of columns in column set 1 (1 row)
  • column set 1 (multiple rows)
  • headers of columns in column set 2 (1 row)
  • column set 2 (multiple rows)
  • ....

The --id-name [:] parameter determines which column contains the ordinal number of compounds to include in the generated SDfile. is substituted by the name of the column. (This name appears in the header.) If there are more column sets in the file with the same name of name of column, then :<count> determines which occurrence of the column should be used.

Examples

*Example #1 *

--id-name centr:2

The --data-names :... option chooses the columns of the column set, which should be included in the SDfile as data fields. Column names must be separated by a colon.

Example #2

--data-names clid:size

Using the --condition parameter, it can be determined which rows of the table should be included. Only one condition may be specified.

For example if --condition clid=2 is set, then only those compounds will be included in the SDfile, for which the value of the clid column is 2.