You can also call the
CreateView Java class directly:
Under Win32 / Java 2 (assuming that JChem is installed in c:\jchem):
Under Unix / Java 2 (assuming that JChem is installed in /usr/local/jchem):
Because the utility has many parameters, it may be reasonable to create a shell script or a batch file for calling the software.
-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:
The --id-name <col>[:<count>] parameter determines which column contains the ordinal number of compounds to include in the generated SDfile. <col> 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.
The --data-names <col1>:<col2>... 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.
Using the --condition <col><OP><cond> 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.