Unverified Commit 6c698970 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Add rDock prm datatype

parent 43a696e3

lib/galaxy/config/sample/datatypes_conf.xml.sample

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@@ -732,6 +732,7 @@ 
    <datatype extension="rdata.camera.quick" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>

    <datatype extension="rdata.se" type="galaxy.datatypes.hdf5:HDF5SummarizedExperiment"  mimetype="text/html" display_in_upload="true"/>

    <datatype extension="rdock_as" type="galaxy.datatypes.binary:Binary" description="rDock active site format" subclass="true" display_in_upload="true"/>

    <datatype extension="prm" type="galaxy.datatypes.text:Prm" mimetype="text/plain" description="rDock prm format for system definition files, scoring function definition files and search protocol definition files" description_url="https://rdock.github.io/documentation/html_docs/reference-guide/file-formats.html" display_in_upload="true" />

    <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>

lib/galaxy/datatypes/test/test.prm

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RBT_PARAMETER_FILE_V1.00

TITLE R_1YET

RECEPTOR_FILE R_1YET_protein.mol2

RECEPTOR_FLEX 3.0



##################################################################

### CAVITY DEFINITION: REFERENCE LIGAND METHOD

##################################################################

SECTION MAPPER

        SITE_MAPPER RbtLigandSiteMapper

        REF_MOL 1YET_c.sd

        RADIUS 6.0

        SMALL_SPHERE 1.0

        MIN_VOLUME 100

        MAX_CAVITIES 1

        VOL_INCR 0.0

        GRIDSTEP 0.5

END_SECTION



#################################

#CAVITY RESTRAINT PENALTY

#################################

SECTION CAVITY

        SCORING_FUNCTION        RbtCavityGridSF

        WEIGHT                  1.0

END_SECTION

lib/galaxy/datatypes/text.py

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@@ -1422,3 +1422,29 @@ class FormattedDensity(Text): 
            (lines[9].strip() == end_header and lines[10].strip() == grid_points)

            or (lines[9].strip() == end_header_spin and lines[10].strip() == grid_points_spin)

        )





@build_sniff_from_prefix

class Prm(Text):

    """rDock prm format



    For system definition files, scoring function definition files and search

    protocol definition files.

    """



    file_ext = "prm"



    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:

        """

        Determines whether the file is in prm format, according to

        https://rdock.github.io/documentation/html_docs/reference-guide/file-formats.html



        >>> from galaxy.datatypes.sniff import get_test_fname

        >>> fname = get_test_fname("test.prm")

        >>> Prm().sniff(fname)

        True

        >>> fname = get_test_fname("larch_potentials.inp")

        >>> Prm().sniff(fname)

        False

        """

        return file_prefix.startswith("RBT_PARAMETER_FILE_V1.00")