molclass/molclass.conf.xml at master · jwildenhain/molclass · GitHub

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<?xml version="1.0" encoding="UTF-8"?>

<config>

		<!-- PHP PEAR DB INFO -->
		<DB_DataObject>

			<dsn>mysqli://molclass_user:YCuRzNoe@localhost/molclass</dsn>

			<proxy>full</proxy>
			<schema_location>/var/www/html/tools/DataObjects</schema_location>
			<class_location>/var/www/html/tools/DataObjects</class_location>
			<require_prefix>DataObjects/</require_prefix>
			<class_prefix>DataObjects_</class_prefix>
		</DB_DataObject>

		<!-- General DB INFO -->

		<database>molclass</database>
		<hostname>localhost</hostname>
		<rw_user>molclass_user</rw_user>
		<rw_password>YCuRzNoe</rw_password>
		<ro_user>molclass_user</ro_user>
		<ro_password>YCuRzNoe</ro_password>


		<!-- PHP parameters -->

                <www_server>http://localhost/</www_server>
		<website>http://localhost/molclass</website>
		<url>localhost/molclass</url>
                <molclassemail>MolClassEmailReport@localhost</molclassemail>


                <php_upload>./uploads/</php_upload>
		<toolsdir>./tools/sdftools/</toolsdir>
		<site_header_image>./images/header.png</site_header_image>

                <!-- Tables on MolClass website - how many to list -->
                <ViewModelNumberPerPage>25</ViewModelNumberPerPage>
                <ViewHitMoleculesPerPage>20</ViewHitMoleculesPerPage>
                <ViewPredictionResultsPerPage>25</ViewPredictionResultsPerPage>
                <ViewModelsPerMolecule>25</ViewModelsPerMolecule>
                <ViewBatchTable>25</ViewBatchTable>
                <ViewBatchDetailTable>25</ViewBatchDetailTable>
                <ViewSingleMoleculePredictionTable>25</ViewSingleMoleculePredictionTable>


		<!-- TABLES -->
		<molstructable>moldb_molstruc</molstructable>
		<moldatatable>moldb_moldata</moldatatable>
		<molstattable>moldb_molstat</molstattable>
		<molfgtable>moldb_molfg</molfgtable>
		<molfgbtable>moldb_molfgb</molfgbtable>
		<molbfptable>moldb_molbfp</molbfptable>
		<fpdeftable>moldb_fpdef</fpdeftable>
		<molhfptable>moldb_molhfp</molhfptable>
		<strucinfotable>sdftags</strucinfotable>
		<plateinfotable>plate_info</plateinfotable>
		<cdkdesctable>cdk_descriptors</cdkdesctable>
		<batchlisttable>batchlist</batchlisttable>
		<batchmoltable>batchmols</batchmoltable>
		<fingerprinttable>fingerprints</fingerprinttable>
		<modeltable>class_models</modeltable>
		<predtable>prediction_list</predtable>
		<predmoltable>prediction_mols</predmoltable>
		<timeouttable>timeout_mols</timeouttable>
		<datatypetable>data_types</datatypetable>
		<classschemetable>class_schemes</classschemetable>
		<inchikeytable>inchi_key</inchikeytable>
		<smilestable>smiles</smilestable>
		<moltypetable>mol_type</moltypetable>
		<tempbatchmoltesttable>temp_batchmol_test</tempbatchmoltesttable>
		<tempbatchmollearntable>temp_batchmol_learn</tempbatchmollearntable>

		<!-- MolDB parameters -->
		<bitmapURLdir>bitmaps</bitmapURLdir>
		<digits>8</digits>
		<subdirdigits>4</subdirdigits>
		<sitename>MolClass</sitename>
		<CHECKMOL>/usr/local/bin/checkmol</CHECKMOL>
		<MATCHMOL>/usr/local/bin/matchmol</MATCHMOL>
		<StructureSearchMaxHits>500</StructureSearchMaxHits>
		<StructureSearchMaxCandidates>2000</StructureSearchMaxCandidates>

		<!-- Java only parameters for CDK and Weka -->
                <setCDKdescriptortimeout>600000</setCDKdescriptortimeout>
                <setThreadPoolTimeout>130000</setThreadPoolTimeout>
                <crossValidateModel>10</crossValidateModel>
                <setDistributionSpread>5.0</setDistributionSpread>

                <!-- depricated -->
		<model_pred_dir>./tools/model_pred/</model_pred_dir>

<Navigation_Board_Open>
	<Home>/index.php</Home>
	<Structure_Search>/structure_search.php</Structure_Search>
	<Prediction_List>/prediction_list.php</Prediction_List>
	<Download>/contact.php</Download>
	<Login>/user_login.php</Login>
	<SDF_Upload>/sdf_upload.php</SDF_Upload>
	<Model_Creation>/model_creation.php</Model_Creation>
</Navigation_Board_Open>

<Global_Design_Parameters>
	<author>Nicholas Fitzgerald, Ryusuke Kimura and Jan Wildenhain</author>
	<content_type>text/html; charset=iso-8859-1</content_type>
	<description>MolClass predicts bioactivity of small molecule by means of Machine Learning method with high throughput screening data.</description>
	<keywords>screening, virtual screening, machine learning, highthrouput screening</keywords>
	<page_width>671</page_width>
	<footer_table_note>Wellcome Trust Centre for Cell Biology, University of Edinburgh</footer_table_note>
	<filecache>cache/</filecache>
	<plate_image_folder>plateimg/</plate_image_folder>
	<tool_mol2png_application>/home/jw/tools/ChemAxon/MarvinBeans/bin/molconvert</tool_mol2png_application>
	<tool_mol2png_options>png:w160</tool_mol2png_options>
	<tool_upload_folder>./uploads/</tool_upload_folder>
</Global_Design_Parameters>


</config>