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Added smiles output #47

Merged
merged 14 commits into from
Aug 16, 2021
Merged

Added smiles output #47

merged 14 commits into from
Aug 16, 2021

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javadev
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@javadev javadev commented Aug 6, 2021

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@javadev javadev mentioned this pull request Aug 6, 2021
IAtomContainer atomContainer = buildAtomContainer(mat);
try {
String smilesString = smilesGenerator.create(atomContainer);
outFile.write(smilesString + " " + String.valueOf(count) + "\n");
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@me It is better to use not count but new index variable

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Fixed.

@javadev
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javadev commented Aug 12, 2021

I changed key to the -smi/--smiles

usage: java -jar MAYGEN.jar -f <arg> [-v] [-t] [-d <arg>] [-m] [-smi]

Generates molecular structures for a given molecular formula.
The input is a molecular formula string.

For example 'C2OH4'.

If user wants an output file, the directory is needed to be specified.
It is also possible to generate SMILES instead of an SDF file, but it will
slow down the generation time. For this, use the '--smiles' option.

 -f,--formula <arg>   formula (required)
 -v,--verbose         print message
 -t,--tsvoutput       Output formula, number of structures and execution
                      time in CSV format.In multithread, the 4th column in
                      the output is the number of threads.
 -d,--filedir <arg>   Store output in given file
 -m,--multithread     Use multi thread
 -smi,--smiles        Store output in SMILES format in given file

Please report issues at https://github.com/MehmetAzizYirik/MAYGEN

@MehmetAzizYirik MehmetAzizYirik merged commit cd529b2 into MehmetAzizYirik:main Aug 16, 2021
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2 participants