Skip to content

DLA-Ranker
DLA-Ranker
Commit 736d637d by DLA-Ranker
Options

Updates

parent 901a69e1
Showing with 68 additions and 659 deletions
Representation/deepScoring/.idea/codeStyles/codeStyleConfig.xml deleted 100644 → 0
<component name="ProjectCodeStyleConfiguration">
<state>
<option name="PREFERRED_PROJECT_CODE_STYLE" value="Default" />
</state>
</component>
\ No newline at end of file
Representation/deepScoring/.idea/deepScoring.iml deleted 100644 → 0
<?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$">
<excludeFolder url="file://$MODULE_DIR$/venv" />
</content>
<orderEntry type="jdk" jdkName="Python 3.5" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
<component name="TestRunnerService">
<option name="projectConfiguration" value="Twisted Trial" />
<option name="PROJECT_TEST_RUNNER" value="Twisted Trial" />
</component>
</module>
\ No newline at end of file
Representation/deepScoring/.idea/inspectionProfiles/Project_Default.xml deleted 100644 → 0
<component name="InspectionProjectProfileManager">
<profile version="1.0">
<option name="myName" value="Project Default" />
<inspection_tool class="PyPep8Inspection" enabled="false" level="WEAK WARNING" enabled_by_default="false">
<option name="ignoredErrors">
<list>
<option value="E111" />
<option value="E114" />
</list>
</option>
</inspection_tool>
</profile>
</component>
\ No newline at end of file
Representation/deepScoring/.idea/misc.xml deleted 100644 → 0
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.5" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
Representation/deepScoring/.idea/modules.xml deleted 100644 → 0
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/.idea/deepScoring.iml" filepath="$PROJECT_DIR$/.idea/deepScoring.iml" />
</modules>
</component>
</project>
\ No newline at end of file
Representation/deepScoring/.idea/vcs.xml deleted 100644 → 0
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="VcsDirectoryMappings">
<mapping directory="$PROJECT_DIR$/.." vcs="Git" />
</component>
</project>
\ No newline at end of file
Representation/deepScoring/.idea/workspace.xml deleted 100644 → 0
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="BookmarkManager">
<bookmark url="file://$PROJECT_DIR$/model_v2_routed.py" line="333" mnemonic="0" />
</component>
<component name="ChangeListManager">
<list default="true" id="00efe61e-f958-47bc-ac47-8f00ac974674" name="Default" comment="">
<change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
<change beforePath="$PROJECT_DIR$/.ipynb_checkpoints/Untitled-checkpoint.ipynb" beforeDir="false" />
<change beforePath="$PROJECT_DIR$/.ipynb_checkpoints/routing_analysis-checkpoint.ipynb" beforeDir="false" afterPath="$PROJECT_DIR$/.ipynb_checkpoints/routing_analysis-checkpoint.ipynb" afterDir="false" />
<change beforePath="$PROJECT_DIR$/Untitled.ipynb" beforeDir="false" />
<change beforePath="$PROJECT_DIR$/commands.sh" beforeDir="false" afterPath="$PROJECT_DIR$/commands.sh" afterDir="false" />
<change beforePath="$PROJECT_DIR$/dump_params.py" beforeDir="false" afterPath="$PROJECT_DIR$/dump_params.py" afterDir="false" />
<change beforePath="$PROJECT_DIR$/evaluation.py" beforeDir="false" afterPath="$PROJECT_DIR$/evaluation.py" afterDir="false" />
<change beforePath="$PROJECT_DIR$/feeding_order_20k" beforeDir="false" />
<change beforePath="$PROJECT_DIR$/model_v2_routed.py" beforeDir="false" afterPath="$PROJECT_DIR$/model_v2_routed.py" afterDir="false" />
<change beforePath="$PROJECT_DIR$/routing_analysis.ipynb" beforeDir="false" afterPath="$PROJECT_DIR$/routing_analysis.ipynb" afterDir="false" />
<change beforePath="$PROJECT_DIR$/stat_casp.py" beforeDir="false" afterPath="$PROJECT_DIR$/stat_casp.py" afterDir="false" />
</list>
<option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
<option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" />
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
<option name="LAST_RESOLUTION" value="IGNORE" />
</component>
<component name="DockManager">
<window id="1">
<content type="file-editors">
<state>
<leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
<file pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/model_v2_routed.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="180">
<caret line="280" column="64" selection-start-line="280" selection-start-column="53" selection-end-line="280" selection-end-column="64" />
<folding>
<element signature="e#0#38#0" expanded="true" />
<element signature="e#6685#8651#0" />
<element signature="e#8742#9713#0" />
<element signature="e#9840#10622#0" />
<element signature="e#10695#11739#0" />
<element signature="e#16697#16992#0" />
</folding>
</state>
</provider>
</entry>
</file>
<file pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/train_model_v2.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="270">
<caret line="18" selection-start-line="18" selection-end-line="18" />
<folding>
<element signature="e#0#38#0" expanded="true" />
<element signature="e#311#338#1" />
<element signature="e#451#5209#0" />
<element signature="e#3209#3442#0" />
<element signature="e#3604#3646#1" />
<element signature="e#3812#4551#0" />
<element signature="e#4833#5182#0" />
<element signature="e#5441#6556#0" />
<element signature="e#6928#6974#0" />
<element signature="e#1977#2118#0" />
<element signature="e#7253#7376#0" />
<element signature="e#7412#7572#0" />
<element signature="e#7701#8030#0" />
<element signature="e#8254#8963#0" />
<element signature="e#9179#9970#0" />
<element signature="e#9400#9779#0" />
<element signature="e#7620#7860#0" />
<element signature="e#9952#10240#0" />
<element signature="e#9526#16057#0" />
<element signature="e#11307#12245#0" />
<element signature="e#11199#11293#0" />
<element signature="e#18634#19447#0" />
<element signature="e#17680#19769#0" />
<marker date="1534836904481" expanded="true" signature="7653:7658" ph="..." />
<marker date="1534836904481" expanded="true" signature="8206:8211" ph="..." />
<marker date="1534836904481" expanded="true" signature="8541:8802" ph="..." />
</folding>
</state>
</provider>
</entry>
</file>
<file pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/stat_casp.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="30">
<caret line="2" selection-start-line="2" selection-end-line="2" />
<folding>
<element signature="e#0#18#0" expanded="true" />
<marker date="1534856642790" expanded="true" signature="29:32" ph="..." />
</folding>
</state>
</provider>
</entry>
</file>
<file pinned="false" current-in-tab="true">
<entry file="file://$PROJECT_DIR$/evaluation.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="773">
<caret line="498" column="19" selection-start-line="498" selection-start-column="19" selection-end-line="498" selection-end-column="19" />
<folding>
<element signature="e#311#327#1" />
<element signature="e#510#686#0" />
<element signature="e#736#1406#0" />
<element signature="e#1555#2841#0" />
<element signature="e#3107#3671#0" />
<element signature="e#3942#4518#0" />
<element signature="e#4013#4040#0" />
<element signature="e#4732#6688#0" />
<element signature="e#13867#20434#0" />
<marker date="1534929766177" expanded="true" signature="3420:3429" ph="..." />
<marker date="1534929766177" expanded="true" signature="13867:15247" ph="..." />
</folding>
</state>
</provider>
</entry>
</file>
</leaf>
</state>
</content>
</window>
</component>
<component name="FUSProjectUsageTrigger">
<session id="1836573880">
<usages-collector id="statistics.lifecycle.project">
<counts>
<entry key="project.closed" value="2" />
<entry key="project.open.time.4" value="1" />
<entry key="project.open.time.7" value="1" />
<entry key="project.open.time.9" value="4" />
<entry key="project.opened" value="6" />
</counts>
</usages-collector>
<usages-collector id="statistics.file.extensions.open">
<counts>
<entry key="ipynb" value="2" />
<entry key="py" value="11" />
</counts>
</usages-collector>
<usages-collector id="statistics.file.types.open">
<counts>
<entry key="IPNB" value="2" />
<entry key="Python" value="11" />
</counts>
</usages-collector>
<usages-collector id="statistics.file.types.edit">
<counts>
<entry key="Python" value="23310" />
</counts>
</usages-collector>
<usages-collector id="statistics.file.extensions.edit">
<counts>
<entry key="py" value="23310" />
</counts>
</usages-collector>
</session>
</component>
<component name="FileEditorManager">
<leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
<file pinned="false" current-in-tab="true">
<entry file="file://$PROJECT_DIR$/compare_losses.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="654">
<caret line="116" column="12" lean-forward="true" selection-start-line="116" selection-start-column="12" selection-end-line="116" selection-end-column="12" />
<folding>
<element signature="e#0#18#0" expanded="true" />
<marker date="1534836899136" expanded="true" signature="305:543" ph="..." />
</folding>
</state>
</provider>
</entry>
</file>
</leaf>
</component>
<component name="FileTemplateManagerImpl">
<option name="RECENT_TEMPLATES">
<list>
<option value="Python Script" />
</list>
</option>
</component>
<component name="FindInProjectRecents">
<findStrings>
<find>compute_pred_dir</find>
<find>num_retype</find>
<find>is_res</find>
<find>FLAGS</find>
<find>sys</find>
<find>dln</find>
<find>update_range</find>
<find>feeding_strategy.update_range()</find>
<find>router_type</find>
<find>print</find>
<find>id</find>
<find>NB_TYPE</find>
<find>validation</find>
<find>batch_norm</find>
<find>fc_layer</find>
<find>choose_casp</find>
<find>res_to_onehot</find>
<find>dropout</find>
<find>prop</find>
<find>tot</find>
<find>measure</find>
<find>.sco fi</find>
</findStrings>
</component>
<component name="Git.Settings">
<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$/.." />
</component>
<component name="IdeDocumentHistory">
<option name="CHANGED_PATHS">
<list>
<option value="$PROJECT_DIR$/compute_gdt.py" />
<option value="$PROJECT_DIR$/models/model_v2.py" />
<option value="$PROJECT_DIR$/models/train_model_v2.py" />
<option value="$PROJECT_DIR$/three_dl.py" />
<option value="$PROJECT_DIR$/model_v2.py" />
<option value="$PROJECT_DIR$/model_v2_resnet.py" />
<option value="$PROJECT_DIR$/train_model_v2 _routed_res.py" />
<option value="$PROJECT_DIR$/load_data.py" />
<option value="$PROJECT_DIR$/train_model_v2_rout_res.py" />
<option value="$PROJECT_DIR$/model_v2_routed_res.py" />
<option value="$PROJECT_DIR$/train_model_v2_t1.py" />
<option value="$PROJECT_DIR$/train_model_v2_t2.py" />
<option value="$PROJECT_DIR$/train_model_v2_t3.py" />
<option value="$PROJECT_DIR$/train_model_v2_t4.py" />
<option value="$PROJECT_DIR$/train_model_v2_t5.py" />
<option value="$PROJECT_DIR$/train_model_v2_t6.py" />
<option value="$PROJECT_DIR$/train_model_v2_t7.py" />
<option value="$PROJECT_DIR$/train_model_v2_t8.py" />
<option value="$PROJECT_DIR$/train_model_v2_t9.py" />
<option value="$PROJECT_DIR$/train_model_v2_t10.py" />
<option value="$PROJECT_DIR$/verifs.ipynb" />
<option value="$USER_HOME$/save/tests_cluster/compare_losses.py" />
<option value="$PROJECT_DIR$/compare_losses.py" />
<option value="$PROJECT_DIR$/train_model_v2.py" />
<option value="$PROJECT_DIR$/model_v2_routed.py" />
<option value="$PROJECT_DIR$/stat_casp.py" />
<option value="$PROJECT_DIR$/evaluation.py" />
</list>
</option>
</component>
<component name="ProjectFrameBounds" extendedState="6">
<option name="x" value="1920" />
<option name="y" value="-4" />
<option name="width" value="1680" />
<option name="height" value="1054" />
</component>
<component name="ProjectInspectionProfilesVisibleTreeState">
<entry key="Project Default">
<profile-state>
<expanded-state>
<State />
<State>
<id>Python</id>
</State>
</expanded-state>
<selected-state>
<State>
<id>PyUnreachableCodeInspection</id>
</State>
</selected-state>
</profile-state>
</entry>
</component>
<component name="ProjectLevelVcsManager" settingsEditedManually="true" />
<component name="ProjectView">
<navigator proportions="" version="1">
<foldersAlwaysOnTop value="true" />
</navigator>
<panes>
<pane id="Scope" />
<pane id="ProjectPane">
<subPane>
<expand>
<path>
<item name="deepScoring" type="b2602c69:ProjectViewProjectNode" />
<item name="deepScoring" type="462c0819:PsiDirectoryNode" />
</path>
</expand>
<select />
</subPane>
</pane>
</panes>
</component>
<component name="PropertiesComponent">
<property name="last_opened_file_path" value="$PROJECT_DIR$" />
<property name="run.code.analysis.last.selected.profile" value="pProject Default" />
<property name="settings.editor.selected.configurable" value="preferences.sourceCode" />
</component>
<component name="RecentsManager">
<key name="MoveFile.RECENT_KEYS">
<recent name="$PROJECT_DIR$/models/deprecated" />
</key>
<key name="CopyFile.RECENT_KEYS">
<recent name="$PROJECT_DIR$" />
</key>
</component>
<component name="RunDashboard">
<option name="ruleStates">
<list>
<RuleState>
<option name="name" value="ConfigurationTypeDashboardGroupingRule" />
</RuleState>
<RuleState>
<option name="name" value="StatusDashboardGroupingRule" />
</RuleState>
</list>
</option>
</component>
<component name="RunManager">
<configuration name="train_model_v2" type="PythonConfigurationType" factoryName="Python" temporary="true">
<module name="deepScoring" />
<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="$PROJECT_DIR$" />
<option name="IS_MODULE_SDK" value="true" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/train_model_v2.py" />
<option name="PARAMETERS" value="" />
<option name="SHOW_COMMAND_LINE" value="false" />
<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>
<recent_temporary>
<list>
<item itemvalue="Python.train_model_v2" />
</list>
</recent_temporary>
</component>
<component name="SvnConfiguration">
<configuration />
</component>
<component name="TaskManager">
<task active="true" id="Default" summary="Default task">
<changelist id="00efe61e-f958-47bc-ac47-8f00ac974674" name="Default" comment="" />
<created>1530263149469</created>
<option name="number" value="Default" />
<option name="presentableId" value="Default" />
<updated>1530263149469</updated>
</task>
<servers />
</component>
<component name="TodoView">
<todo-panel id="selected-file">
<is-autoscroll-to-source value="true" />
</todo-panel>
<todo-panel id="all">
<are-packages-shown value="true" />
<is-autoscroll-to-source value="true" />
</todo-panel>
</component>
<component name="ToolWindowManager">
<frame x="1920" y="-4" width="1680" height="1054" extended-state="6" />
<editor active="true" />
<layout>
<window_info active="true" content_ui="combo" id="Project" order="0" visible="true" weight="0.14583333" />
<window_info id="Structure" order="1" side_tool="true" weight="0.25" />
<window_info id="Favorites" order="2" side_tool="true" />
<window_info anchor="bottom" id="Message" order="0" />
<window_info anchor="bottom" id="Find" order="1" weight="0.32911393" />
<window_info anchor="bottom" id="Run" order="2" weight="0.32969034" />
<window_info anchor="bottom" id="Debug" order="3" weight="0.4" />
<window_info anchor="bottom" id="Cvs" order="4" weight="0.25" />
<window_info anchor="bottom" id="Inspection" order="5" weight="0.4" />
<window_info anchor="bottom" id="TODO" order="6" sideWeight="0.49945414" weight="0.32992566" />
<window_info anchor="bottom" id="Python Console" order="7" sideWeight="0.49945414" weight="0.32992566" />
<window_info anchor="bottom" id="Terminal" order="8" sideWeight="0.49945414" weight="0.32992566" />
<window_info anchor="bottom" id="Version Control" order="9" sideWeight="0.49945414" weight="0.32992566" />
<window_info anchor="bottom" id="Event Log" order="10" sideWeight="0.50054586" side_tool="true" visible="true" weight="0.05057956" />
<window_info anchor="right" id="Commander" internal_type="SLIDING" order="0" type="SLIDING" weight="0.4" />
<window_info anchor="right" id="Ant Build" order="1" weight="0.25" />
<window_info anchor="right" content_ui="combo" id="Hierarchy" order="2" weight="0.25" />
</layout>
<layout-to-restore>
<window_info content_ui="combo" id="Project" order="0" visible="true" weight="0.14880952" />
<window_info id="Structure" order="1" side_tool="true" weight="0.25" />
<window_info id="Favorites" order="2" side_tool="true" />
<window_info anchor="bottom" id="Message" order="0" />
<window_info anchor="bottom" id="Find" order="1" weight="0.32911393" />
<window_info anchor="bottom" id="Run" order="2" weight="0.32969034" />
<window_info anchor="bottom" id="Debug" order="3" weight="0.4" />
<window_info anchor="bottom" id="Cvs" order="4" weight="0.25" />
<window_info anchor="bottom" id="Inspection" order="5" weight="0.4" />
<window_info anchor="bottom" id="TODO" order="6" />
<window_info anchor="bottom" id="Python Console" order="7" />
<window_info anchor="bottom" id="Terminal" order="8" />
<window_info anchor="bottom" id="Version Control" order="9" show_stripe_button="false" />
<window_info anchor="bottom" id="Event Log" order="10" side_tool="true" />
<window_info anchor="right" id="Commander" internal_type="SLIDING" order="0" type="SLIDING" weight="0.4" />
<window_info anchor="right" id="Ant Build" order="1" weight="0.25" />
<window_info anchor="right" content_ui="combo" id="Hierarchy" order="2" weight="0.25" />
</layout-to-restore>
</component>
<component name="VcsContentAnnotationSettings">
<option name="myLimit" value="2678400000" />
</component>
<component name="editorHistoryManager">
<entry file="file://$PROJECT_DIR$/models/deprecated/plot.py">
<provider selected="true" editor-type-id="text-editor" />
</entry>
<entry file="file://$PROJECT_DIR$/models/deprecated/plot_eval.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="150">
<caret line="10" column="3" selection-start-line="10" selection-start-column="3" selection-end-line="10" selection-end-column="4" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/models/model_v2.py" />
<entry file="file://$PROJECT_DIR$/models/train_model_v2.py" />
<entry file="file://$PROJECT_DIR$/three_dl.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="15">
<caret line="150" column="70" lean-forward="true" selection-start-line="150" selection-start-column="14" selection-end-line="150" selection-end-column="70" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/models/deprecated/eval_model.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="-1789" />
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/model_v2_resnet.py" />
<entry file="file://$PROJECT_DIR$/model_v2_routed_twice.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="362">
<caret line="60" column="4" selection-start-line="60" selection-start-column="4" selection-end-line="64" selection-end-column="72" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/train_model_v2 _routed_res.py" />
<entry file="file://$PROJECT_DIR$/model_v2_capsnet.py" />
<entry file="file://$PROJECT_DIR$/load_data.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="2370">
<caret line="168" selection-start-line="168" selection-end-line="168" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/train_model_v2_rout_res.py" />
<entry file="file://$PROJECT_DIR$/model_v2_routed_res.py" />
<entry file="file://$PROJECT_DIR$/model_v2_routed_res_t1.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t1.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t2.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t3.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t4.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t5.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t6.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t7.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t8.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t9.py" />
<entry file="file://$PROJECT_DIR$/train_model_v2_t10.py" />
<entry file="file://$PROJECT_DIR$/verifs.ipynb">
<provider selected="true" editor-type-id="ipnb-editor">
<state>
<selected id="0" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/model.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="2520">
<caret line="176" selection-start-line="176" selection-end-line="176" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/routing_analysis_bis.ipynb">
<provider selected="true" editor-type-id="ipnb-editor">
<state>
<selected id="0" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/model_v2.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="210">
<caret line="18" column="97" selection-start-line="18" selection-start-column="97" selection-end-line="18" selection-end-column="97" />
</state>
</provider>
</entry>
<entry file="file://$USER_HOME$/save/tests_cluster/compare_losses.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="450">
<caret line="45" column="26" lean-forward="true" selection-start-line="45" selection-start-column="26" selection-end-line="45" selection-end-column="26" />
<folding>
<element signature="e#0#18#0" expanded="true" />
</folding>
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/train_model_v2.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="270">
<caret line="18" selection-start-line="18" selection-end-line="18" />
<folding>
<element signature="e#0#38#0" expanded="true" />
<element signature="e#311#338#1" />
<element signature="e#451#5209#0" />
<element signature="e#3209#3442#0" />
<element signature="e#3604#3646#1" />
<element signature="e#3812#4551#0" />
<element signature="e#4833#5182#0" />
<element signature="e#5441#6556#0" />
<element signature="e#6928#6974#0" />
<element signature="e#1977#2118#0" />
<element signature="e#7253#7376#0" />
<element signature="e#7412#7572#0" />
<element signature="e#7701#8030#0" />
<element signature="e#8254#8963#0" />
<element signature="e#9179#9970#0" />
<element signature="e#9400#9779#0" />
<element signature="e#7620#7860#0" />
<element signature="e#9952#10240#0" />
<element signature="e#9526#16057#0" />
<element signature="e#11307#12245#0" />
<element signature="e#11199#11293#0" />
<element signature="e#18634#19447#0" />
<element signature="e#17680#19769#0" />
<marker date="1534836904481" expanded="true" signature="7653:7658" ph="..." />
<marker date="1534836904481" expanded="true" signature="8206:8211" ph="..." />
<marker date="1534836904481" expanded="true" signature="8541:8802" ph="..." />
</folding>
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/stat_casp.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="30">
<caret line="2" selection-start-line="2" selection-end-line="2" />
<folding>
<element signature="e#0#18#0" expanded="true" />
<marker date="1534856642790" expanded="true" signature="29:32" ph="..." />
</folding>
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/model_v2_routed.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="180">
<caret line="280" column="64" selection-start-line="280" selection-start-column="53" selection-end-line="280" selection-end-column="64" />
<folding>
<element signature="e#0#38#0" expanded="true" />
<element signature="e#6685#8651#0" />
<element signature="e#8742#9713#0" />
<element signature="e#9840#10622#0" />
<element signature="e#10695#11739#0" />
<element signature="e#16697#16992#0" />
</folding>
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/compare_losses.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="654">
<caret line="116" column="12" lean-forward="true" selection-start-line="116" selection-start-column="12" selection-end-line="116" selection-end-column="12" />
<folding>
<element signature="e#0#18#0" expanded="true" />
<marker date="1534836899136" expanded="true" signature="305:543" ph="..." />
</folding>
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/evaluation.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="773">
<caret line="498" column="19" selection-start-line="498" selection-start-column="19" selection-end-line="498" selection-end-column="19" />
<folding>
<element signature="e#311#327#1" />
<element signature="e#510#686#0" />
<element signature="e#736#1406#0" />
<element signature="e#1555#2841#0" />
<element signature="e#3107#3671#0" />
<element signature="e#3942#4518#0" />
<element signature="e#4013#4040#0" />
<element signature="e#4732#6688#0" />
<element signature="e#13867#20434#0" />
<marker date="1534929766177" expanded="true" signature="3420:3429" ph="..." />
<marker date="1534929766177" expanded="true" signature="13867:15247" ph="..." />
</folding>
</state>
</provider>
</entry>
</component>
</project>
\ No newline at end of file
Representation/deepScoring/.ipynb_checkpoints/routing_analysis-checkpoint.ipynb deleted 100644 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
Representation/generate_cubes.py
...@@ -30,7 +30,7 @@ import scr ...@@ -30,7 +30,7 @@ import scr
from numpy import asarray from numpy import asarray
from sklearn.preprocessing import OneHotEncoder from sklearn.preprocessing import OneHotEncoder
import subprocess import subprocess
import deepScoring.load_data as load import load_data as load
from sklearn.preprocessing import MinMaxScaler from sklearn.preprocessing import MinMaxScaler
logging.basicConfig(filename='manager.log', filemode='w', format='%(levelname)s: %(message)s', level=logging.DEBUG) logging.basicConfig(filename='manager.log', filemode='w', format='%(levelname)s: %(message)s', level=logging.DEBUG)
......
Representation/scr.py
...@@ -11,9 +11,8 @@ import os ...@@ -11,9 +11,8 @@ import os
import sys import sys
from os import path, remove from os import path, remove
#sys.path.insert(1, '../lib/') sys.path.insert(1, '../lib/')
#import tools as tl import tools as tl
NACCESS_PATH = 'naccess'
def rimcoresup(rsa_rec,rsa_lig,rsa_complex): def rimcoresup(rsa_rec,rsa_lig,rsa_complex):
'''INPUT: file rsa da NACCESS. '''INPUT: file rsa da NACCESS.
...@@ -180,11 +179,11 @@ def rimcoresup(rsa_rec,rsa_lig,rsa_complex): ...@@ -180,11 +179,11 @@ def rimcoresup(rsa_rec,rsa_lig,rsa_complex):
def get_scr(rec, lig, com, name): def get_scr(rec, lig, com, name):
#print('rec', path.basename(rec.replace('pdb', 'rsa'))) #print('rec', path.basename(rec.replace('pdb', 'rsa')))
cmdcompl=NACCESS_PATH + ' ' + com cmdcompl=tl.NACCESS_PATH + ' ' + com
os.system(cmdcompl) os.system(cmdcompl)
cmdrec=NACCESS_PATH + ' ' + rec cmdrec=tl.NACCESS_PATH + ' ' + rec
os.system(cmdrec) os.system(cmdrec)
cmdlig=NACCESS_PATH + ' ' + lig cmdlig=tl.NACCESS_PATH + ' ' + lig
os.system(cmdlig) os.system(cmdlig)
# ('GLN', 'B', '44', '55.7', 'receptor') # ('GLN', 'B', '44', '55.7', 'receptor')
......
lib/tools.py 0 → 100644
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 7 16:33:47 2020
@author: mohseni
"""
import logging
import numpy as np
import pickle
import shutil
import pypdb
import pandas as pd
import protein as pr
from prody import *
from os import path, mkdir, remove, getenv, listdir, system
from io import StringIO
import urllib
import re
import glob
from subprocess import CalledProcessError, check_call
import traceback
import sys
import gzip
#========================================================
#NACCESS
NACCESS_PATH='naccess'
#========================================================
def save_obj(obj, name):
with open(name + '.pkl', 'wb') as f:
pickle.dump(obj, f, pickle.HIGHEST_PROTOCOL)
def load_obj(name):
with open(name + '.pkl', 'rb') as f:
return pickle.load(f)
def do_processing(cases, function, use_multiprocessing):
if use_multiprocessing:
import multiprocessing
max_cpus = 30
manager = multiprocessing.Manager()
report_dict = manager.dict()
pool = multiprocessing.Pool(processes = min(max_cpus, multiprocessing.cpu_count()))
else:
report_dict = dict()
for args in cases:
args += (report_dict,)
if use_multiprocessing:
pool.apply_async(function, args = args)
else:
function(*args)
if use_multiprocessing:
pool.close()
pool.join()
return dict(report_dict)
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment