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߶(ߴ8߲H߱P߰XgNg`XPH@80(<$!d 9-ߒT%߁ @%܄hd3 d%@%$h fe @%$h fe[@%$h g@%$h feV@%$h gߕ40hf $-@%feV%@%  %ߟDߙS ޿  %0hg@%!!޿ggߙ  %0hg@%޿g0h@%  %0h@%g  %@%$h fe@%$h fe/$f$ t$ b$ f$t$b0%@%$hfeF $M$N$T$ m$ T$ N$h$M$m0%@%fez  0h@%feV%$h  %߁D!ߙP ޿  %0hg@%!!޿ggߙ  %0hg@%޿g0h@%  %0h$h$ p$ p$ h$p$p0%fe@% % $o$o@%$h0% fe$l$l@%$h0% fe$h$h@%$h0% fe<$ v$ d$v$d@%$h0% fej0h@%feV#@%  %ߟDߙS޿  %0hg@%޿ggߙ  %0hg@%޿g0h@%  %0h@%fe  %@%$h fe@%$h fe @%$h fe !@%$h fe 0h߶0@%fe V$@%  %ߟDߙS ޿  %0hg@%!޿ggߙ  %0hg@%޿g0h@%  %0h@%fe   %@%$h fe @%$h fe ?߼ ߿(ߵ8ߴ@߳H߲P߱X߰`gpload_fingerprints.cOpening "%s" for reading load_fingerprints.cUnable to open "%s" for reading load_fingerprints.cOpening "%s" for reading load_fingerprints.cUnable to open "%s" for reading load_fingerprints.cASSUMING: 32 bit integer and 8 bit character load_fingerprints.cReading in fingerprints and names Neighbor Lists: [%2d:%9s,%.6lf]%d %s %.6lf eliminate.cEliminating node because of minimum tanimoto: %s, %s, %f eliminate.cEliminating node because of maximum neighbor: %s, %s, %d neighbor_of: Calculates and returns the desired neighbors of the specified compounds. neighbor_of.cGenerating the fingerprint sources neighbor_of.cGenerating the neighbors neighbor_of.cPrinting out the results neighbor_of.cCleaning up the matrix neighbor_of.cDeleting %s neighbor_of.cDeleting %s neighbor_of.cDeleting %s neighbor_of.cDeleting %s Memory allocation error in gen_onbits_array() generate_fp_sources.c%d Base compound filenames found generate_fp_sources.c%d Loose base compounds specified generate_fp_sources.c%d Target compound filenames found generate_fp_sources.c%d Loose target compounds specified baseXXXXXXgenerate_fp_sources.cCould not generate temp name generate_fp_sources.cCould not open %s for writing generate_fp_sources.cTemp file for loose base compounds: "%s" targetXXXXXXgenerate_fp_sources.cCould not generate temp name generate_fp_sources.cCould not open %s for writing generate_fp_sources.cTemp file for loose target compounds: "%s" generate_fp_sources.cTotal number of base fingerprint sources: %d generate_fp_sources.cTotal number of target fingerprint sources: %d Failure to insert (%s,%s,%f) because of maximum neighbor constraint (%d/%d) Inserting (%s,%s,%f) before (%s,%s,%f) unload_fingerprints.cFreeing fingerprints for "%s" unload_fingerprints.cClosing files for "%s" generate_neighbors.cLoading base fingerprint sources into memory generate_neighbors.cUnable to load fingerprints for "%s" generate_neighbors.c%d total base compounds generate_neighbors.c%d total target compounds generate_neighbors.cMemory allocation error generate_neighbors.cMemory allocation error generate_neighbors.cLargest base fingerprint source contains %d compounds generate_neighbors.cLargest target fingerprint source contains %d compounds generate_neighbors.cMemory allocation error generate_neighbors.cLoading fingerprints for target "%s" generate_neighbors.cGenerating %d tanimotos for base "%s" and target "%s" generate_neighbors.cUnloading fingerprints for target "%s" generate_neighbors.cUnloading base fingerprints Error: Unexpected parsing error on command line: "%s" Error: Incorrect number of arguments for target compounds Error: Incorrect number of arguments for target compounds Error: Incorrect number of arguments for base compounds Error: Incorrect number of arguments for base compounds Error: Unrecognized option on command line: "%s" Error: Unrecognized option on command line: "%s" Error: Incorrect number of arguments for logfile Error: Illegal file name for logfile "%s" Error: Incorrect number of arguments for outfile Error: Illegal file name for outfile "%s" Error: Unrecognized option parsing command line: "%s" Type "neighbor_of %c%c" for help Error: Unable to open logfile "%s" for writing parse_cmd_line.c Process: %d ----------------- Logging started: %s Error: Unable to open outfile "%s" for writing Process: %d ----------------- Started: %s Error: Unable to open debugging file "%s" for writing parse_cmd_line.c Process: %d ----------------- %s Debugging started: %s Standardparse_cmd_line.cDebugging..... parse_cmd_line.c%s Debugging info being printed to "%s" Standardparse_cmd_line.cMin tanimoto: %f; Max tanimoto: %f parse_cmd_line.cMin neighbor: %d; Max neighbor: %d parse_cmd_line.cError: No target compounds specified parse_cmd_line.cType "neighbor_of %c%c" for help parse_cmd_line.cError: No base compounds specified parse_cmd_line.cType "neighbor_of %c%c" for help prepare_fingerprints.cError: Could not open "%s" for reading prepare_fingerprints.cCounting the compounds in the smiles file wc -l %sprepare_fingerprints.cOpening a pipe to "%s" prepare_fingerprints.cUnable to execute "%s" prepare_fingerprints.c%d lines prepare_fingerprints.cClosing pipe to "%s" prepare_fingerprints.cError: Unrecognized smiles file: "%s". Not of format .%s prepare_fingerprints.cFingerprint file for "%s": "%s" prepare_fingerprints.cCreating fingerprint file for "%s" /dd/bin/cluster/a5create_finger -sf %s -dtprepare_fingerprints.cError: Unable to create fingerprints for "%s" prepare_fingerprints.cError: Unable to create fingerprints for "%s" neighbor_of ============================================================================ For the provided base compounds, it computes and returns the target compounds which are their neighbors. The neighbors returned will be subject to the minimum and maximum specified restrictions on the neighbor index and similarity (tanimoto) value. Compounds can be specified individually or by filename. If the fingerprint for a compound does not exist, it will be created. << More >>---------------------------------------------------------------------------- neighbor_of %c<%c|%c>[%c] ... %c Signifies that this is part of the base set of compounds %c Signifies that this is part of the target set of compounds %c Signifies that this is a list of file names rather than SMILES strings This is the number of smiles strings or files This is the th argument in the list of arguments. If the arguments are smiles files, each argument is a file name. If the arguments are actual smiles strings, each argument is a quoted expression of the form: " " %c<%c|%c><%c|%c> %c Signifies this is a minimum value %c Signifies this is a maximum value %c Signifies this is a neighbor index %c Signifies this is a tanimoto value The value to use for the minimum or maximum neighbor index or tanimoto value << More >> %c%c[%c|%c] %c Defaults to printing plain text output %c Overrides the default plain text output and prints the output in a "prettyprint" format %c Overrides the defalut plain text output and prints the output in a HTML format %c%c %c Specifies that the file to be used for logging output is %c%c %c Specifies that the file to be used for logging errors is %c%c %c Displays this help on neighbor_of %c%c[%c] [filename] %c Specifies that debugging is to be used and the optionally specified file is to be used for logging debugging statements. If no file is specified, prints the debugging statements to stdout %c Specifies that verbose debugging is to be used WARNING: Verbose debugging is, well, quite verbose. << More >>Examples: ---------------------------------------------------------------------------- neighbor_of -b1 "O=N(C1=CC=CC(N2N=NN=C2[NH2])=C1)=O MyCmpd" -tf1 test.smi -l tmp.err -o tmp.out -d tmp.debug Generates the neighbor list of MyCmpd fromthe compounds in test.smi, logging errors to tmp.log, output to tmp.out, and debugging info to tmp.debug neighbor_of -bf2 test1.smi test2.smi -tf3 test3.smi test4.smi test5.smi Generates the neighbor lists for test1.smi and test2.smi from the compounds in test3.smi, test4.smi, and test5.smi, printing errors and output to stdout. neighbor_of -d -bf1 test1.smi -tf1 test2.smi -pp Generates the neighbor list for test1.smi from the compounds in test2.smi, printing errors, output, and debugging info to stdout in a "prettyprint" format. << More >>Known Bugs: ---------------------------------------------------------------------------- Inexplicably crashes in insert() when either debugging or verbose debugging is on, printing to stdout, and both the errors and output are being logged to file. ?%s %d: r%s %d: %s %d: r%s %d: %s %d: %s %d: %-9s%s %-9s %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: rm %s%s %d: rm %s%s %d: rm %s%s %d: rm %s%s %d: %s %d: %s %d: %s %d: %s%s.smi%s %d: w%s %d: %s %d: %s%s.smi%s %d: w%s %d: %s %d: %s %s %s %d: %s %d: %s %d: order.c%s %d: order.c%s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: %s %d: a%s %d: aa%s %d: Verbose%s %d: %s %d: Verbose%s %d: %s %d: %s %d: %s %d: %s %d: %s %d: r%s %d: %s %d: %s %d: r%s %d: %d%s %d: %s %d: .smi%s%s.fp%s %d: .fp%s %d: r%s %d: r%s %d: %sr%s %d: Usage: 4X$WW9<20-@0PsQ `"() *,609P:CW0X^0c\@P  H    4    t k ԁ   d  D \ Ԃ   d 6  d  @ @@ P @! #P,0 ? @F67777777777777 77 7/jerry/redwood/work/irix/lib/libc/libc_64mips4/csu/crt1text.s/jerry/redwood/work/irix/lib/libc/libc_64mips4/csu__startpxdpx(_mcountxpxP)/jerry/redwood/work/irix/lib/libc/libc_64mips4/csu/crt1tinit.s/jerry/redwood/work/irix/lib/libc/libc_64mips4/csu*8/ch5/mjcibu/neighbor_of/load_fingerprints.c/ch5/mjcibu/neighbor_of-DMIPSEB -D_MIPSEB -D_PIC -D__DSO__ -D__EXTENSIONS__ -D__INLINE_INTRINSICS -DLANGUAGE_C -Dmips -Dunix -Dsgi -Dhost_mips -D_LONGLONG -D_SGI_SOURCE -D_LANGUAGE_C -D_MODERN_C -D__sgi -D__host_mips -D_SYSTYPE_SVR4 -D_SVR4_SOURCE -D__unix -D_COMPILER_VERSION=601 -O2 -D__mips=4 -D_MIPS_ISA=_MIPS_ISA_MIPS4 -D_MIPS_SIM=_MIPS_SIM_ABI64 -D_MIPS_FPSET=32 -D_MIPS_SZINT=32 -D_MIPS_SZLONG=64 -D_MIPS_SZPTR=64 -I/usr/include,load_fingerprints[/ch5/mjcibu/neighbor_of/print.c/ch5/mjcibu/neighbor_of-DMIPSEB -D_MIPSEB -D_PIC -D__DSO__ -D__EXTENSIONS__ -D__INLINE_INTRINSICS -DLANGUAGE_C -Dmips -Dunix -Dsgi -Dhost_mips -D_LONGLONG -D_SGI_SOURCE -D_LANGUAGE_C -D_MODERN_C -D__sgi -D__host_mips 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