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rajarshi / FPAccuracy.java
Created November 27, 2010 17:32
Evaluate fingerprint accuracy ...
package net.sf.cdk.tools;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.ExtendedFingerprinter;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.fingerprint.FingerprinterTool;
@rajarshi
rajarshi / gist:718123
Created November 27, 2010 18:01
c1cccnc1 O=Cc1c(O)c(ncc1COP(=O)(O)O)C DB00114
c3ccc1c(ncn1C2OCCC2)c3 O=C(N)CCC8C1=NC(=C(C7=NC(C)(C6NC(=C(C2=NC(=C1)C(C)(C)C2CCC(=O)N)C)C(C)(CCC(=O)NCC(OP(=O)(O)OC3C(O)C(OC3(CO))n5cnc4cc(c(cc45)C)C)C)C6(CC(=O)N))C(C)(CC(=O)N)C7CCC(=O)N)C)C8(C)(CC(=O)N).[C-]#N DB00115
c8ccc1c(ncn1C7OCC(OPOCCNCCCC6CC5NC6(=CC2=NC(CC2)=CC3=NC(CC3)=CC4=NC5(CC4)))C7)c8 O=C(N)CCC8C1=NC(=C(C7=NC(C)(C6NC(=C(C2=NC(=C1)C(C)(C)C2CCC(=O)N)C)C(C)(CCC(=O)NCC(OP(=O)(O)OC3C(O)C(OC3(CO))n5cnc4cc(c(cc45)C)C)C)C6(CC(=O)N))C(C)(CC(=O)N)C7CCC(=O)N)C)C8(C)(CC(=O)N).[C-]#N DB00115
C1CC4=NC1=CC2=NC(CC2)C5CC(C(=CC3=NC(CC3)=C4)N5)CCCNCCOPOC6COCC6 O=C(N)CCC8C1=NC(=C(C7=NC(C)(C6NC(=C(C2=NC(=C1)C(C)(C)C2CCC(=O)N)C)C(C)(CCC(=O)NCC(OP(=O)(O)OC3C(O)C(OC3(CO))n5cnc4cc(c(cc45)C)C)C)C6(CC(=O)N))C(C)(CC(=O)N)C7CCC(=O)N)C)C8(C)(CC(=O)N).[C-]#N DB00115
C1CC4=NC1=CC2=NC(CC2)C5CCC(=CC3=NC(CC3)=C4)N5 O=C(N)CCC8C1=NC(=C(C7=NC(C)(C6NC(=C(C2=NC(=C1)C(C)(C)C2CCC(=O)N)C)C(C)(CCC(=O)NCC(OP(=O)(O)OC3C(O)C(OC3(CO))n5cnc4cc(c(cc45)C)C)C)C6(CC(=O)N))C(C)(CC(=O)N)C7CCC(=O)N)C)C8
@rajarshi
rajarshi / foo.java
Created February 19, 2011 15:37
Weird SDF output
package net.sf.cdk.tools;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.SDFWriter;
import org.openscience.cdk.io.listener.PropertiesListener;
@rajarshi
rajarshi / gist:961340
Created May 8, 2011 12:30
OB make output
[ 0%] [ 1%] [ 1%] [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
Building C object src/formats/inchi103/CMakeFiles/inchi.dir/ichi_io.o
Building CXX object src/CMakeFiles/openbabel.dir/atom.o
Building C object src/formats/inchi103/CMakeFiles/inchi.dir/ichi_bns.o
[ 2%] Building CXX object src/CMakeFiles/openbabel.dir/base.o
[ 2%] Building C object src/formats/inchi103/CMakeFiles/inchi.dir/ichican2.o
[ 2%] [ 2%] Building C object src/formats/inchi103/CMakeFiles/inchi.dir/ichicano.o
Building CXX object src/CMakeFiles/openbabel.dir/bitvec.o
[ 3%] Building C object src/formats/inchi103/CMakeFiles/inchi.dir/ichicans.o
[ 3%] Building C object src/formats/inchi103/CMakeFiles/inchi.dir/ichiisot.o
@rajarshi
rajarshi / gist:1032182
Created June 17, 2011 19:59
2011-06-17 15:45:31,186 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2011-06-17 15:45:34,322 INFO [ fsclient.DropBox] (MainThread) Monitor parameters = {'default': {'ignoreSysFiles': True, 'importArgs': '', 'watchDir': '', 'readers': '', 'blockSize': 0, 'whitelist': [], 'ignoreDirEvents': True, 'blacklist': [], 'dirImportWait': 60, 'timeout': 0.0, 'pathMode': Follow, 'eventTypes': [Creation, Modification], 'timeToLive': 0L, 'timeToIdle': 600000L}}
2011-06-17 15:45:34,358 INFO [ fsclient.DropBox] (MainThread) Creating default dropbox directory: /NCGCHCS/OMERO/DropBox
2011-06-17 15:45:34,371 ERROR [ fsclient.DropBox] (MainThread) Failed to access proxy :
Traceback (most recent call last):
File "lib/python/fsDropBox.py", line 135, in run
fsServer = monitors.MonitorServerPrx.checkedCast(fsServer.ice_twoway())
File "/home/ome/OMERO.server-Beta-4.3.0/lib/python/omero_FS_ice.py", line 5
@rajarshi
rajarshi / gist:1032186
Created June 17, 2011 20:00
2011-06-17 15:45:19,840 INFO [ ome.services.blitz.Entry] ( main) Creating ome.fulltext. Please wait...
2011-06-17 15:45:21,087 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager
2011-06-17 15:45:23,239 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer
2011-06-17 15:45:23,650 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
2011-06-17 15:45:23,651 ERROR [ ome.services.blitz.Entry] ( main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [ome.fulltext], from group with resource name [classpath*:beanRefContext.xml]; neste
d exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.fulltext' defined in URL [jar:file:/home/ome/OMERO.server-Beta-4.3.0/lib/server/server.jar!/beanRef
Context.xml]: Instantiatio
@rajarshi
rajarshi / gist:1032188
Created June 17, 2011 20:01
================================================================================
OMERO Diagnostics 4.3.0-77345008
================================================================================
Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.4.3 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.4.5 (/usr/bin/psql)
@rajarshi
rajarshi / gist:1036306
Created June 20, 2011 19:02
2011-06-17 15:45:19,840 INFO [ ome.services.blitz.Entry] ( main) Creating ome.fulltext. Please wait...
2011-06-17 15:45:21,087 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager
2011-06-17 15:45:23,239 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer
2011-06-17 15:45:23,650 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
2011-06-17 15:45:23,651 ERROR [ ome.services.blitz.Entry] ( main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [ome.fulltext], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.fulltext' defined in URL [jar:file:/home/ome/OMERO.server-Beta-4.3.0/lib/server/server.jar!/beanRefContext.xml]: Instantiation
@rajarshi
rajarshi / gist:1139433
Created August 11, 2011 11:31
plot.propdist = function(
molecules=NULL,
selections=NULL,
descriptor="org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor",
...
) {
if (is.null(molecules)) stop("Data was not provided");
dframe = eval.desc(molecules, descriptor)
data = dframe[,1]
@rajarshi
rajarshi / gist:1364945
Created November 14, 2011 19:52
mol file with R and atom alias
463
CML DOM 12291008202D
35 39 0 0 0 0 0 0 0 0999 V2000
-2.0770 -0.1749 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
1.7759 1.6069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.1299 0.2560 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.4029 -1.9249 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.6629 1.7159 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.4029 1.7159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0