add conservation_hmm model and config

Author: rdk

build.gradle

@@ -20,7 +20,7 @@ apply plugin: 'idea'
 
 
 group = 'cz.siret'
-version = '2.4-dev.3'
+version = '2.3.1'
 
 
 description = 'Ligand binding site prediction based on machine learning.'
@@ -53,7 +53,6 @@ processResources {
     ]
 }
 
-
 task copyDependenciesToDist( type: Copy ) {
     into "$buildDir/../distro/bin/lib"
     from configurations.runtimeClasspath
@@ -179,4 +178,3 @@ dependencies {
     testImplementation 'junit:junit:4.13.2'
 
 }
-

distro/config/conservation_hmm.groovy

@@ -0,0 +1,14 @@
+import cz.siret.prank.program.params.Params
+
+/**
+ * P2Rank configuration for use with the new, HMMER-based conservation pipeline.
+ */
+(params as Params).with {
+
+    model = "conservation_hmm.model"
+
+    features = ["chem","volsite","protrusion","bfactor","conservation"]
+
+    load_conservation = true
+
+}

distro/models/conservation_hmm.model

@@ -12,6 +12,8 @@ import cz.siret.prank.utils.MathUtils
 import groovy.util.logging.Slf4j
 import org.apache.commons.lang3.StringUtils
 
+import javax.annotation.concurrent.ThreadSafe
+
 import static cz.siret.prank.geom.Atoms.intersection
 import static cz.siret.prank.geom.Atoms.union
 import static cz.siret.prank.utils.Cutils.head
@@ -23,9 +25,8 @@ import static java.util.Collections.emptyList
  * Represents evaluation of pocket prediction on a dataset of proteins
  *
  * Allows to collect results for a set of different pocket identification success criteria simultaneously.
- *
- * Threadsafe.
  */
+@ThreadSafe
 @Slf4j
 class Evaluation implements Parametrized {