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Chapter 5. MoKa command-line
The command-line version of MoKa is a very convenient tool to perform large batch computations and to integrate the MoKa prediction engine in any existing workflow.
Example usage:
moka_cli -o output.txt -s FILE_ID --load-model=mymodel.mkd --show-qp input.sdf |
The full set of available options is shown when you run moka_cli without parameters:
usage: ./moka_cli [options] filename
options are:
-h, --help display this help
--version show version info
-v, --verbose show all warning messages
--input-type=<sd|mol2> input file type ( autodetect )
-o, --output=FILE output file name
--output-type=<txt|sd> output file type ( txt )
-s, --sd-field=NAME use the specified SD field to retrieve
the structure ID
--load-model=<database> use a custom model database for predictions
--acid-values=NUM output at most NUM acid values ( all )
--basic-values=NUM output at most NUM basic values ( all )
--acid-lo-limit=VALUE low cutoff value for acid pKa ( -10.0 )
--acid-hi-limit=VALUE high cutoff value for acid pKa ( 20.0 )
--basic-lo-limit=VALUE low cutoff value for basic pKa ( -10.0 )
--basic-hi-limit=VALUE high cutoff value for basic pKa ( 20.0 )
--show-qp add qp values to output
--hide-sd remove SD values from output
--logp=<value> use <value> for logP instead of internal
prediction engine
--logd=<pH:logD> calculate logP from the given logD value.
implies:
--show-logp
conflicts with:
--logp
--logp-attribute
--show-logd
--logp-attribute=<name> read logP value from SD attribute <name>
--show-logp add logP prediction to output (sd only)
--show-logd=<pH list> add logD prediction to output (sd only)
--tautomer replace input structure with most suitable
tautomer
<ph list> is a comma separated list of the following:
* single value
* range ( min-max )
Examples:
* single value: --show-logd=6
* single range: --show-logd=6-10
* multiple values: --show-logd=6,7,8
* mixed: --show-logd=6,7-10 |
5.1. Output format
The output capabilities of MoKa depends on the chosen output format. The plain text (txt) format is useful when only pKa predictions are required, while the SD format can include all other data together with the molecular structure.
5.1.1. Plain text (txt) format
When using the the plain text (txt) format, the output file has one line for each input compound. Each line has the following format:
NAME CH UT IC ( a|b PK ATOM SD QP ) * IC |
And the fields are:
NAME - the molecule name
CH - covalent hydration flag: 0 (false) or 1 (true)
UT - unstable tautomer flag: 0 (false), 1 (true) or - (not computed)
IC - number of ionizable centers
Then, for each ionizable center:
a|b - type of ionizable center (acid or basic)
PK - predicted pKa value
ATOM - atom number
SD - standard deviation of prediction
QP - quality parameter
Note: By default, the SD value is printed while the QP value is not
This is what the output .txt file looks like:
5.1.2. SD file format
When using the SD format as output, the result line with pKa predictions is added to an SD attribute named "MoKa". The line is formatted in the same way as the txt output format.
Additionally, when LogP and LogD options are active, two attributes named "MoKa.LogP" and "MoKa.LogD" are associated to the structure; the former has a single value, while the latter is composed by one or more pairs [pH: LogD]
A sample output is reproduced herein:
$ moka_cli --show-logp --show-logd=4-8 --output-type=sd pyridine.sdf
Pyridine
6 6 0 0 0 1 V2000
0.0000 1.5000 0.0000 C 0 0 0 0 0 0
0.8500 2.0000 0.0000 C 0 0 0 0 0 0
1.7250 1.5000 0.0000 C 0 0 0 0 0 0
1.7250 0.5000 0.0000 C 0 0 0 0 0 0
0.8500 0.0000 0.0000 N 0 0 0 0 0 0
0.0000 0.5000 0.0000 C 0 0 0 0 0 0
4 5 2 0
5 6 1 0
2 3 2 0
1 2 1 0
3 4 1 0
1 6 2 0
M END
> <MoKa> v1.1.0-RC1
Pyridine 0 - 1 b 4.97 5 0.51
> <MoKa.LogD>
4: -0.27
4.5: 0.15
5: 0.46
5.5: 0.63
6: 0.7
6.5: 0.73
7: 0.74
7.5: 0.74
8: 0.74
> <MoKa.LogP>
0.74
$$$$ |
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