add analyse

.idea/CPI.iml

@@ -2,7 +2,10 @@
 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
     <content url="file://$MODULE_DIR$" />
-    <orderEntry type="jdk" jdkName="Python 3.6 (code)" jdkType="Python SDK" />
+    <orderEntry type="jdk" jdkName="Python 3.6 (py3.6)" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
+  <component name="PyDocumentationSettings">
+    <option name="renderExternalDocumentation" value="true" />
+  </component>
 </module>
\ No newline at end of file

.idea/misc.xml

 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6 (code)" project-jdk-type="Python SDK" />
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6 (py3.6)" project-jdk-type="Python SDK" />
 </project>
\ No newline at end of file

.idea/other.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="PySciProjectComponent">
+    <option name="PY_SCI_VIEW" value="true" />
+    <option name="PY_SCI_VIEW_SUGGESTED" value="true" />
+  </component>
+</project>
\ No newline at end of file

.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_16,_11_22_上午_[Default_Changelist]/shelved.patch

-Index: .idea/workspace.xml
-Index: .idea/workspace.xml
-IDEA additional info:
-Subsystem: com.intellij.openapi.diff.impl.patch.BaseRevisionTextPatchEP
-<+><?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<project version=\"4\">\n  <component name=\"ChangeListManager\">\n    <list default=\"true\" id=\"f877ac68-9cea-46d8-9125-207eebe5b5d6\" name=\"Default Changelist\" comment=\"\">\n      <change beforePath=\"$PROJECT_DIR$/.idea/workspace.xml\" beforeDir=\"false\" afterPath=\"$PROJECT_DIR$/.idea/workspace.xml\" afterDir=\"false\" />\n      <change beforePath=\"$PROJECT_DIR$/eval.py\" beforeDir=\"false\" afterPath=\"$PROJECT_DIR$/eval.py\" afterDir=\"false\" />\n      <change beforePath=\"$PROJECT_DIR$/experment_result/loss.png\" beforeDir=\"false\" afterPath=\"$PROJECT_DIR$/experment_result/learning_rate/loss.png\" afterDir=\"false\" />\n      <change beforePath=\"$PROJECT_DIR$/experment_result/loss.svg\" beforeDir=\"false\" />\n    </list>\n    <option name=\"SHOW_DIALOG\" value=\"false\" />\n    <option name=\"HIGHLIGHT_CONFLICTS\" value=\"true\" />\n    <option name=\"HIGHLIGHT_NON_ACTIVE_CHANGELIST\" value=\"false\" />\n    <option name=\"LAST_RESOLUTION\" value=\"IGNORE\" />\n  </component>\n  <component name=\"Git.Settings\">\n    <option name=\"RECENT_GIT_ROOT_PATH\" value=\"$PROJECT_DIR$\" />\n    <option name=\"UPDATE_TYPE\" value=\"REBASE\" />\n  </component>\n  <component name=\"ProjectId\" id=\"1qpu2Wq6VU5TQVQOm73pQEwAahA\" />\n  <component name=\"ProjectLevelVcsManager\">\n    <ConfirmationsSetting value=\"1\" id=\"Add\" />\n  </component>\n  <component name=\"ProjectViewState\">\n    <option name=\"hideEmptyMiddlePackages\" value=\"true\" />\n    <option name=\"showLibraryContents\" value=\"true\" />\n  </component>\n  <component name=\"PropertiesComponent\">\n    <property name=\"ASKED_ADD_EXTERNAL_FILES\" value=\"true\" />\n    <property name=\"RunOnceActivity.OpenProjectViewOnStart\" value=\"true\" />\n    <property name=\"RunOnceActivity.ShowReadmeOnStart\" value=\"true\" />\n    <property name=\"WebServerToolWindowFactoryState\" value=\"false\" />\n    <property name=\"restartRequiresConfirmation\" value=\"false\" />\n  </component>\n  <component name=\"RecentsManager\">\n    <key name=\"MoveFile.RECENT_KEYS\">\n      <recent name=\"$PROJECT_DIR$/experment_result/learning_rate\" />\n    </key>\n  </component>\n  <component name=\"RunManager\" selected=\"Python.eval\">\n    <configuration name=\"eval\" type=\"PythonConfigurationType\" factoryName=\"Python\" temporary=\"true\" nameIsGenerated=\"true\">\n      <module name=\"CPI\" />\n      <option name=\"INTERPRETER_OPTIONS\" value=\"\" />\n      <option name=\"PARENT_ENVS\" value=\"true\" />\n      <envs>\n        <env name=\"PYTHONUNBUFFERED\" value=\"1\" />\n      </envs>\n      <option name=\"SDK_HOME\" value=\"\" />\n      <option name=\"WORKING_DIRECTORY\" value=\"$PROJECT_DIR$\" />\n      <option name=\"IS_MODULE_SDK\" value=\"true\" />\n      <option name=\"ADD_CONTENT_ROOTS\" value=\"true\" />\n      <option name=\"ADD_SOURCE_ROOTS\" value=\"true\" />\n      <EXTENSION ID=\"PythonCoverageRunConfigurationExtension\" runner=\"coverage.py\" />\n      <option name=\"SCRIPT_NAME\" value=\"$PROJECT_DIR$/eval.py\" />\n      <option name=\"PARAMETERS\" value=\"\" />\n      <option name=\"SHOW_COMMAND_LINE\" value=\"false\" />\n      <option name=\"EMULATE_TERMINAL\" value=\"false\" />\n      <option name=\"MODULE_MODE\" value=\"false\" />\n      <option name=\"REDIRECT_INPUT\" value=\"false\" />\n      <option name=\"INPUT_FILE\" value=\"\" />\n      <method v=\"2\" />\n    </configuration>\n    <configuration name=\"run_interaction\" type=\"PythonConfigurationType\" factoryName=\"Python\" temporary=\"true\" nameIsGenerated=\"true\">\n      <module name=\"CPI\" />\n      <option name=\"INTERPRETER_OPTIONS\" value=\"\" />\n      <option name=\"PARENT_ENVS\" value=\"true\" />\n      <envs>\n        <env name=\"PYTHONUNBUFFERED\" value=\"1\" />\n      </envs>\n      <option name=\"SDK_HOME\" value=\"\" />\n      <option name=\"WORKING_DIRECTORY\" value=\"$PROJECT_DIR$\" />\n      <option name=\"IS_MODULE_SDK\" value=\"true\" />\n      <option name=\"ADD_CONTENT_ROOTS\" value=\"true\" />\n      <option name=\"ADD_SOURCE_ROOTS\" value=\"true\" />\n      <EXTENSION ID=\"PythonCoverageRunConfigurationExtension\" runner=\"coverage.py\" />\n      <option name=\"SCRIPT_NAME\" value=\"$PROJECT_DIR$/run_interaction.py\" />\n      <option name=\"PARAMETERS\" value=\"\" />\n      <option name=\"SHOW_COMMAND_LINE\" value=\"false\" />\n      <option name=\"EMULATE_TERMINAL\" value=\"false\" />\n      <option name=\"MODULE_MODE\" value=\"false\" />\n      <option name=\"REDIRECT_INPUT\" value=\"false\" />\n      <option name=\"INPUT_FILE\" value=\"\" />\n      <method v=\"2\" />\n    </configuration>\n    <recent_temporary>\n      <list>\n        <item itemvalue=\"Python.eval\" />\n        <item itemvalue=\"Python.run_interaction\" />\n      </list>\n    </recent_temporary>\n  </component>\n  <component name=\"SpellCheckerSettings\" RuntimeDictionaries=\"0\" Folders=\"0\" CustomDictionaries=\"0\" DefaultDictionary=\"application-level\" UseSingleDictionary=\"true\" transferred=\"true\" />\n  <component name=\"TaskManager\">\n    <task active=\"true\" id=\"Default\" summary=\"Default task\">\n      <changelist id=\"f877ac68-9cea-46d8-9125-207eebe5b5d6\" name=\"Default Changelist\" comment=\"\" />\n      <created>1617788646167</created>\n      <option name=\"number\" value=\"Default\" />\n      <option name=\"presentableId\" value=\"Default\" />\n      <updated>1617788646167</updated>\n      <workItem from=\"1617788647548\" duration=\"5550000\" />\n    </task>\n    <servers />\n  </component>\n  <component name=\"TypeScriptGeneratedFilesManager\">\n    <option name=\"version\" value=\"3\" />\n  </component>\n  <component name=\"Vcs.Log.Tabs.Properties\">\n    <option name=\"TAB_STATES\">\n      <map>\n        <entry key=\"MAIN\">\n          <value>\n            <State />\n          </value>\n        </entry>\n      </map>\n    </option>\n  </component>\n  <component name=\"XDebuggerManager\">\n    <breakpoint-manager>\n      <breakpoints>\n        <line-breakpoint enabled=\"true\" suspend=\"THREAD\" type=\"python-line\">\n          <url>file://$PROJECT_DIR$/eval.py</url>\n          <line>36</line>\n          <option name=\"timeStamp\" value=\"21\" />\n        </line-breakpoint>\n      </breakpoints>\n    </breakpoint-manager>\n  </component>\n  <component name=\"com.intellij.coverage.CoverageDataManagerImpl\">\n    <SUITE FILE_PATH=\"coverage/CPI$eval.coverage\" NAME=\"eval Coverage Results\" MODIFIED=\"1618396849549\" SOURCE_PROVIDER=\"com.intellij.coverage.DefaultCoverageFileProvider\" RUNNER=\"coverage.py\" COVERAGE_BY_TEST_ENABLED=\"true\" COVERAGE_TRACING_ENABLED=\"false\" WORKING_DIRECTORY=\"$PROJECT_DIR$\" />\n    <SUITE FILE_PATH=\"coverage/CPI$run_interaction.coverage\" NAME=\"run_interaction Coverage Results\" MODIFIED=\"1618133791228\" SOURCE_PROVIDER=\"com.intellij.coverage.DefaultCoverageFileProvider\" RUNNER=\"coverage.py\" COVERAGE_BY_TEST_ENABLED=\"true\" COVERAGE_TRACING_ENABLED=\"false\" WORKING_DIRECTORY=\"$PROJECT_DIR$\" />\n  </component>\n</project>
-Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
-<+>UTF-8
-===================================================================
-diff --git a/.idea/workspace.xml b/.idea/workspace.xml
---- a/.idea/workspace.xml	(revision 9ad087cc206a1aaa224fb400aceeebf955c664e1)
-+++ b/.idea/workspace.xml	(date 1618543228916)
-@@ -3,9 +3,6 @@
-   <component name="ChangeListManager">
-     <list default="true" id="f877ac68-9cea-46d8-9125-207eebe5b5d6" name="Default Changelist" comment="">
-       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
--      <change beforePath="$PROJECT_DIR$/eval.py" beforeDir="false" afterPath="$PROJECT_DIR$/eval.py" afterDir="false" />
--      <change beforePath="$PROJECT_DIR$/experment_result/loss.png" beforeDir="false" afterPath="$PROJECT_DIR$/experment_result/learning_rate/loss.png" afterDir="false" />
--      <change beforePath="$PROJECT_DIR$/experment_result/loss.svg" beforeDir="false" />
-     </list>
-     <option name="SHOW_DIALOG" value="false" />
-     <option name="HIGHLIGHT_CONFLICTS" value="true" />
+++ /dev/null

.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_16__11_22___Default_Changelist_.xml

-<changelist name="Uncommitted_changes_before_Update_at_2021_4_16,_11_22_上午_[Default_Changelist]" date="1618543353862" recycled="true" deleted="true">
-  <option name="PATH" value="$PROJECT_DIR$/.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_16,_11_22_上午_[Default_Changelist]/shelved.patch" />
-  <option name="DESCRIPTION" value="Uncommitted changes before Update at 2021/4/16, 11:22 上午 [Default Changelist]" />
-</changelist>
\ No newline at end of file

.idea/workspace.xml

@@ -2,9 +2,11 @@
 <project version="4">
   <component name="ChangeListManager">
     <list default="true" id="f877ac68-9cea-46d8-9125-207eebe5b5d6" name="Default Changelist" comment="">
-      <change beforePath="$PROJECT_DIR$/.gitignore" beforeDir="false" afterPath="$PROJECT_DIR$/.gitignore" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/CPI.iml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/CPI.iml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/misc.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/misc.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_16,_11_22_上午_[Default_Changelist]/shelved.patch" beforeDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_16__11_22___Default_Changelist_.xml" beforeDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/run_interaction.py" beforeDir="false" afterPath="$PROJECT_DIR$/run_interaction.py" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -51,7 +53,29 @@
       <recent name="$PROJECT_DIR$/experment_result/learning_rate" />
     </key>
   </component>
-  <component name="RunManager" selected="Python.run_interaction">
+  <component name="RunManager" selected="Python.normalize_data">
+    <configuration default="true" type="PythonConfigurationType" factoryName="Python">
+      <module name="CPI" />
+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="PARENT_ENVS" value="true" />
+      <envs>
+        <env name="PYTHONUNBUFFERED" value="1" />
+      </envs>
+      <option name="SDK_HOME" value="" />
+      <option name="WORKING_DIRECTORY" value="" />
+      <option name="IS_MODULE_SDK" value="false" />
+      <option name="ADD_CONTENT_ROOTS" value="true" />
+      <option name="ADD_SOURCE_ROOTS" value="true" />
+      <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+      <option name="SCRIPT_NAME" value="" />
+      <option name="PARAMETERS" value="" />
+      <option name="SHOW_COMMAND_LINE" value="true" />
+      <option name="EMULATE_TERMINAL" value="false" />
+      <option name="MODULE_MODE" value="false" />
+      <option name="REDIRECT_INPUT" value="false" />
+      <option name="INPUT_FILE" value="" />
+      <method v="2" />
+    </configuration>
     <configuration name="dataset" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
       <module name="CPI" />
       <option name="INTERPRETER_OPTIONS" value="" />
@@ -96,6 +120,25 @@
       <option name="INPUT_FILE" value="" />
       <method v="2" />
     </configuration>
+    <configuration name="normalize_data" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
+      <module name="CPI" />
+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="PARENT_ENVS" value="true" />
+      <option name="SDK_HOME" value="" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/utils" />
+      <option name="IS_MODULE_SDK" value="true" />
+      <option name="ADD_CONTENT_ROOTS" value="true" />
+      <option name="ADD_SOURCE_ROOTS" value="true" />
+      <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/utils/normalize_data.py" />
+      <option name="PARAMETERS" value="" />
+      <option name="SHOW_COMMAND_LINE" value="true" />
+      <option name="EMULATE_TERMINAL" value="false" />
+      <option name="MODULE_MODE" value="false" />
+      <option name="REDIRECT_INPUT" value="false" />
+      <option name="INPUT_FILE" value="" />
+      <method v="2" />
+    </configuration>
     <configuration name="run_interaction" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
       <module name="CPI" />
       <option name="INTERPRETER_OPTIONS" value="" />
@@ -142,6 +185,7 @@
     </configuration>
     <recent_temporary>
       <list>
+        <item itemvalue="Python.normalize_data" />
         <item itemvalue="Python.run_interaction" />
         <item itemvalue="Python.test" />
         <item itemvalue="Python.dataset" />
@@ -158,6 +202,7 @@
       <option name="presentableId" value="Default" />
       <updated>1617788646167</updated>
       <workItem from="1617788647548" duration="5550000" />
+      <workItem from="1619665316412" duration="2069000" />
     </task>
     <servers />
   </component>
@@ -174,6 +219,7 @@
         </entry>
       </map>
     </option>
+    <option name="oldMeFiltersMigrated" value="true" />
   </component>
   <component name="XDebuggerManager">
     <breakpoint-manager>
@@ -183,13 +229,19 @@
           <line>36</line>
           <option name="timeStamp" value="21" />
         </line-breakpoint>
+        <line-breakpoint enabled="true" suspend="THREAD" type="python-line">
+          <url>file://$PROJECT_DIR$/utils/normalize_data.py</url>
+          <line>10</line>
+          <option name="timeStamp" value="22" />
+        </line-breakpoint>
       </breakpoints>
     </breakpoint-manager>
   </component>
   <component name="com.intellij.coverage.CoverageDataManagerImpl">
-    <SUITE FILE_PATH="coverage/CPI$dataset.coverage" NAME="dataset Coverage Results" MODIFIED="1618641059668" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
     <SUITE FILE_PATH="coverage/CPI$test.coverage" NAME="test Coverage Results" MODIFIED="1618643206375" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
-    <SUITE FILE_PATH="coverage/CPI$eval.coverage" NAME="eval Coverage Results" MODIFIED="1618396849549" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+    <SUITE FILE_PATH="coverage/CPI$normalize_data.coverage" NAME="normalize_data Coverage Results" MODIFIED="1619667621484" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/utils" />
     <SUITE FILE_PATH="coverage/CPI$run_interaction.coverage" NAME="run_interaction Coverage Results" MODIFIED="1618917155441" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+    <SUITE FILE_PATH="coverage/CPI$eval.coverage" NAME="eval Coverage Results" MODIFIED="1618396849549" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+    <SUITE FILE_PATH="coverage/CPI$dataset.coverage" NAME="dataset Coverage Results" MODIFIED="1618641059668" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
   </component>
 </project>
\ No newline at end of file

utils/normalize_data.py

+import numpy as np
+
+def z_score(data, save):
+    with open(data, 'r') as f:
+        lines = f.readlines()
+    data = []
+    for line in lines:
+        aff = np.float64(line.strip())
+        data.append(aff)
+    data = np.array(lines)
+    ave = np.mean(data)
+    std = np.std(data)
+    new_affinity = (data - ave) / std
+    new_affinity = list(new_affinity)
+    with open(save, 'w') as f:
+        for aff in new_affinity:
+            f.write(str(aff) + '\n')
+
+
+
+
+
+if __name__ == '__main__':
+    data = '../data/test_ic50'
+    save = '../data/test_z_ic50'
+    z_score(data, save)
\ No newline at end of file