From 6c698970354fd0a3b9668e4ed1dbd08822f284b4 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 10 Mar 2025 17:29:58 +0000
Subject: [PATCH] Add rDock prm datatype

---
 .../config/sample/datatypes_conf.xml.sample   |  1 +
 lib/galaxy/datatypes/test/test.prm            | 26 +++++++++++++++++++
 lib/galaxy/datatypes/text.py                  | 26 +++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/test.prm

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 96447c66461..edd029bd986 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -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"/>
diff --git a/lib/galaxy/datatypes/test/test.prm b/lib/galaxy/datatypes/test/test.prm
new file mode 100644
index 00000000000..b7c2114e148
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.prm
@@ -0,0 +1,26 @@
+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
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 6c6b587aaa4..3c67057dbc2 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -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")