Using custom float descriptors

Custom binary fingerprints and float vector descriptors can also be handled. Note that the custom descriptors expose only the serialization mechanisms of the underlying representations. No descriptor generation (from Molecules) is available in this case, so for queries also the custom descriptors must be used. Parts of the steps described below are implemented in self contained example script custom-floatv-workflow.sh found in the examples directory.

The basic workflow described below contains the following steps:

Using input file data/floatdesc.txt containing 16 2D vector descriptors in format <ID> <x1> <x2>
Import custom descriptors
Search custom descriptors

The second part of this document describes an example of handling large float vector collections and exposing them through the REST API.

Import custom descriptors

Note that the underlying context must be composed using a JavaScript hook (specified by -contextjs <SCRIPT>). This must be a valid JavaScript code which returns the OverlapAnalysisContext instance to be used (as the value of the last expression). Many initialized references and helper functions are available, use option -h to print command line help for details. Since the input is an arbitrary line oriented text file which might contains additional data the methods used for accessing descriptor and optionally ID parts are needed to be specified explicitly. Such specification is done by using splitters.

bin/importStorage.sh \
    -in data/floatdesc.txt \
    -splitter com.chemaxon.overlap.splits.AllButFirstToken \
    -idsplitter com.chemaxon.overlap.splits.FirstToken \
    -out custom-float-desc.bin \
    -id  custom-float-id.bin \
    -contextjs "ctx_from_descpb(bld_fv.length(2))"

Note that writing IDs (using options -id and -idsplitter) is optional.

Breakdown of the contents of the passed JavaScript fragment creating the OverlapAnalysisContext used:

Script part	Description
`ctx_from_descpb(..)`	Helper function which creates a default `OverlapAnalysisContext` from the associated `DescriptorParameters` builder.
`bld_fv`	A builder instance for `FvParameters` in default state.
`.length(..)`	Update builder with length parameter (see apidoc).

Import custom descriptors with filtering

File data/floats-1d.txt contains scalar (one dimensional) float value descriptors. This file also contains comment lines (starting with # characters) and empty lines. These lines should be skipped during import. Option -infilter can be used to specify such a filter.

bin/importStorage.sh \
    -in data/floats-1d.txt \
    -splitter com.chemaxon.overlap.splits.AllButFirstToken \
    -idsplitter com.chemaxon.overlap.splits.FirstToken \
    -out custom-float-desc.bin \
    -id  custom-float-id.bin \
    -contextjs "ctx_from_descpb(bld_fv.length(1))" \
    -infilter "(l.trim().length == 0 || l.trim().charAt(0) == '#') ? null : l"

Breakdown of the filter script hook

Script part	Description
`<CONDITION> ? <T> : <F>`	Conditional statement. Its value is the value of statement `<T>` then `<CONDITION>` is true, otherwise the value of `<F>`
`l`	The line processed by the scripting hook.
`l.trim()`	The line processed with leading and trailing white space characters removed. See JS reference.
`l.trim().length`	The length (in characters) of the processed line. See JS reference
`\|\|`	Logical or operator. Note that if the first expression is `true` the second is not evaluated. See description.
`l.trim().charAt(0)`	First non whitespace character of input line. If the input line is empty or contains only whitespace characters this is not evaluated by `\|\|`. See JS reference.
`null`	`null` value returned for lines to be skipped from further processing. These are empty, contains only whitespace characters or when the first non-whitespace character is `#`. See description.

Diagnostic dump storages

Peek into the contents of created storages.

bin/dumpStorage.sh \
    -in custom-float-desc.bin \
    -in custom-float-id.bin

Query descriptor storage

Inline query descriptors are set using parameter -qd. Query descriptors stored in a file can be read using -qdf. Note that query molecules (-qm or -qmf) can not be used, since we dont know how to generate the descriptors for them.

bin/searchStorage.sh \
    -frombytes custom-float-desc.bin \
    -qd "5.0 5.0" \
    -qd "5.0 0.0" \
    -qd "1.0 1.0" \
    -qd "1.0 0.0"

searchStorage can use IDs instead of plain structure indices. Parameter -idstorage can specify the associated ID storage.

bin/searchStorage.sh \
    -frombytes custom-float-desc.bin \
    -idstorage custom-float-id.bin \
    -qd "5.0 5.0" \
    -qd "5.0 0.0" \
    -qd "1.0 1.0" \
    -qd "1.0 0.0"

Large scale descriptor handling

We will generate and import 1M test descriptors each containing 5000 float values and a textual ID in the form of <ID> <DIM1> <DIM2> ... <DIM5000>.

Generate test data

Launch

bin/jseval.sh \
    -jsfile examples/randomFloatVector.js \
    -d dim=5000 \
    -d fillfactor=0.1 \
    -d count=1000000 \
    -d id=1 \
    -out large-float.txt

Execution time of the test data generation on an i7-4790 desktop machine was around 24 minutes.

Import storages

Expected memory requirements can be calculated from - the stored vector coordinate counts (in this example 5e3 * 1e6 = 5e9) - the size of the numeric representations (4 bytes per floats, 2 bytes per scaled shorts and 1 byte per scaled bytes) - and from an approximately 20% overhead for storage and garbage collection (using GC tuning below)

Import as float values:

bin/importStorage.sh \
    -Xmx24g \
    -XX:NewRatio=15 \
    -in large-float.txt \
    -splitter com.chemaxon.overlap.splits.AllButFirstToken \
    -idsplitter com.chemaxon.overlap.splits.FirstToken \
    -out large-float-desc-as-floats.bin \
    -id  large-float-desc-as-floats-id.bin \
    -contextjs "ctx_from_descpb(bld_fv.length(5000))"

Execution time: 2 min for importing, 2 min for writing binary blobs

Import as scaled short values:

bin/importStorage.sh \
    -Xmx12g \
    -XX:NewRatio=15 \
    -in large-float.txt \
    -splitter com.chemaxon.overlap.splits.AllButFirstToken \
    -idsplitter com.chemaxon.overlap.splits.FirstToken \
    -out large-float-desc-as-scaled-shorts.bin \
    -id  large-float-desc-as-scaled-shorts-id.bin \
    -contextjs "ctx_from_descpb(bld_fv.length(5000).numericRepresentation(nr_SCALED_SHORT).scaledMin(0.0).scaledMax(1.0))"

Due to a problem it does not work currently.

Launch embedded server

bin/gui.sh \
    -Xmx24g \
    -XX:NewRatio=15 \
    -idonly -name:large-float:-mid:large-float-desc-as-floats-id.bin \
    -desc -desc:large-float-desc-as-floats.bin:-mols:large-float:-name:large-float

Startup time: 2 min 10 sec

The -idonly <SPEC> option specifies a molecule storage which contains only IDs, all the molecules are considered missing.

Query embedded server

curl \
    -X POST \
    -H "Content-Type: application/x-www-form-urlencoded" \
    -d 'max-count=10&query-descriptor=0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.1584 0 0 0 0 0 0 0 0 0.4895 0 0.6142 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.4711 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.8992 0 0 0 0 0 0 0 0 0 0 0.3861 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5879 0 0 0 0.8991 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5626 0 0 0 0 0 0.5953 0.4104 0 0 0 0 0.2756 0 0 0 0 0 0 0 0 0.8512 0 0 0 0 0 0 0 0 0 0 0 0 0.1831 0 0 0 0.5303 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.8352 0 0 0 0.1517 0 0 0 0 0.7478 0 0 0 0 0.1364 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.3165 0.321 0 0 0 0 0 0.4582 0 0 0 0 0 0 0 0 0.9393 0 0 0 0 0 0 0 0 0 0 0 0 0.2264 0 0 0 0 0.9818 0 0.3367 0 0 0 0 0 0 0.5641 0 0 0 0 0 0 0 0.5736 0 0 0 0.793 0.7897 0 0 0.2936 0 0 0 0 0 0 0 0 0 0 0 0 0 0.4572 0 0 0.3877 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.6612 0.0463 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.6989 0 0 0 0 0 0 0 0 0 0 0 0 0.3111 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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    -g "http://localhost:8089/rest/descriptors/large-float/find-most-similars-by-descriptor" | python -m json.tool