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.\" ========================================================================
.\"
.IX Title "RG::Utils::Copf 3pm"
.TH RG::Utils::Copf 3pm "2013-11-20" "perl v5.18.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
RG::Utils::Copf \- Rost Lab perl utilities
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use RG::Utils::Copf;
.SH "FUNCTIONS"
.IX Header "FUNCTIONS"
See module source for description.
.IP "amino_acid_convert_3_to_1" 4
.IX Item "amino_acid_convert_3_to_1"
.PD 0
.IP "amino_acid_convert_3_to_1_ini" 4
.IX Item "amino_acid_convert_3_to_1_ini"
.IP "brIniErr" 4
.IX Item "brIniErr"
.IP "brIniGetArg" 4
.IX Item "brIniGetArg"
.IP "brIniHelp" 4
.IX Item "brIniHelp"
.IP "brIniHelpLoop" 4
.IX Item "brIniHelpLoop"
.IP "brIniHelpRdItself" 4
.IX Item "brIniHelpRdItself"
.IP "brIniRdDef" 4
.IX Item "brIniRdDef"
.IP "brIniSet" 4
.IX Item "brIniSet"
.IP "brIniWrt" 4
.IX Item "brIniWrt"
.IP "bynumber" 4
.IX Item "bynumber"
.IP "bynumber_high2low" 4
.IX Item "bynumber_high2low"
.IP "cleanUp" 4
.IX Item "cleanUp"
.IP "complete_dir" 4
.IX Item "complete_dir"
.IP "completeDir" 4
.IX Item "completeDir"
.IP "convAliGen" 4
.IX Item "convAliGen"
.IP "convDsspGen" 4
.IX Item "convDsspGen"
.IP "convFastamul2many" 4
.IX Item "convFastamul2many"
.IP "convFssp2Daf" 4
.IX Item "convFssp2Daf"
.IP "convFsspGen" 4
.IX Item "convFsspGen"
.IP "convGcg2fasta" 4
.IX Item "convGcg2fasta"
.IP "convHssp2seq" 4
.IX Item "convHssp2seq"
.IP "convHsspGen" 4
.IX Item "convHsspGen"
.IP "convMsf2saf" 4
.IX Item "convMsf2saf"
.IP "convPdb2seq" 4
.IX Item "convPdb2seq"
.IP "convPdbGen" 4
.IX Item "convPdbGen"
.IP "convPhd2dssp" 4
.IX Item "convPhd2dssp"
.IP "convPhd2seq" 4
.IX Item "convPhd2seq"
.IP "convPhdGen" 4
.IX Item "convPhdGen"
.IP "convPir2fasta" 4
.IX Item "convPir2fasta"
.IP "convPirmulGen" 4
.IX Item "convPirmulGen"
.IP "convSaf2many" 4
.IX Item "convSaf2many"
.IP "convSeq2fastaPerl" 4
.IX Item "convSeq2fastaPerl"
.IP "convSeq2seq" 4
.IX Item "convSeq2seq"
.IP "convSeq2seqOld" 4
.IX Item "convSeq2seqOld"
.IP "convSeqGen" 4
.IX Item "convSeqGen"
.IP "convSwiss2fasta" 4
.IX Item "convSwiss2fasta"
.IP "copf" 4
.IX Item "copf"
.IP "dsspGetChain" 4
.IX Item "dsspGetChain"
.IP "dsspRdSeq" 4
.IX Item "dsspRdSeq"
.IP "dsspWrtFromPhd" 4
.IX Item "dsspWrtFromPhd"
.IP "errSbr" 4
.IX Item "errSbr"
.IP "errSbrMsg" 4
.IX Item "errSbrMsg"
.IP "fastaRdGuide" 4
.IX Item "fastaRdGuide"
.IP "fastaRdMul" 4
.IX Item "fastaRdMul"
.IP "fastaWrt" 4
.IX Item "fastaWrt"
.IP "fastaWrtMul" 4
.IX Item "fastaWrtMul"
.IP "fctRunTimeLeft" 4
.IX Item "fctRunTimeLeft"
.IP "fctSeconds2time" 4
.IX Item "fctSeconds2time"
.IP "gcgRd" 4
.IX Item "gcgRd"
.IP "gcgWrt" 4
.IX Item "gcgWrt"
.IP "getDistanceNewCurveIde" 4
.IX Item "getDistanceNewCurveIde"
.IP "getFileFormatQuick" 4
.IX Item "getFileFormatQuick"
.IP "get_in_keyboard" 4
.IX Item "get_in_keyboard"
.IP "get_range" 4
.IX Item "get_range"
.IP "get_rangeHyphen" 4
.IX Item "get_rangeHyphen"
.IP "getSysARCH" 4
.IX Item "getSysARCH"
.IP "hsspCorrectNali" 4
.IX Item "hsspCorrectNali"
.IP "hsspGetChain" 4
.IX Item "hsspGetChain"
.IP "hsspGetChainLength" 4
.IX Item "hsspGetChainLength"
.IP "hsspRdAli" 4
.IX Item "hsspRdAli"
.IP "hsspRdHeader" 4
.IX Item "hsspRdHeader"
.IP "hsspRdSeqSecAccOneLine" 4
.IX Item "hsspRdSeqSecAccOneLine"
.IP "ini" 4
.IX Item "ini"
.IP "iniDef" 4
.IX Item "iniDef"
.IP "iniHelpLoc" 4
.IX Item "iniHelpLoc"
.IP "is_chain" 4
.IX Item "is_chain"
.IP "isDaf" 4
.IX Item "isDaf"
.IP "is_dssp" 4
.IX Item "is_dssp"
.IP "isFasta" 4
.IX Item "isFasta"
.IP "isFastaMul" 4
.IX Item "isFastaMul"
.IP "is_fssp" 4
.IX Item "is_fssp"
.IP "isGcg" 4
.IX Item "isGcg"
.IP "is_hssp" 4
.IX Item "is_hssp"
.IP "isMsf" 4
.IX Item "isMsf"
.IP "isPdb" 4
.IX Item "isPdb"
.IP "is_pdbid" 4
.IX Item "is_pdbid"
.IP "isPhdAcc" 4
.IX Item "isPhdAcc"
.IP "isPhdBoth" 4
.IX Item "isPhdBoth"
.IP "isPhdHtm" 4
.IX Item "isPhdHtm"
.IP "isPhdSec" 4
.IX Item "isPhdSec"
.IP "isPir" 4
.IX Item "isPir"
.IP "isPirMul" 4
.IX Item "isPirMul"
.IP "is_ppcol" 4
.IX Item "is_ppcol"
.IP "isRdb" 4
.IX Item "isRdb"
.IP "is_rdb_htmref" 4
.IX Item "is_rdb_htmref"
.IP "is_rdb_htmtop" 4
.IX Item "is_rdb_htmtop"
.IP "is_rdb_nnDb" 4
.IX Item "is_rdb_nnDb"
.IP "isSaf" 4
.IX Item "isSaf"
.IP "is_strip" 4
.IX Item "is_strip"
.IP "isSwiss" 4
.IX Item "isSwiss"
.IP "msfBlowUp" 4
.IX Item "msfBlowUp"
.IP "msfCheckFormat" 4
.IX Item "msfCheckFormat"
.IP "msfCompress" 4
.IX Item "msfCompress"
.IP "msfCountNali" 4
.IX Item "msfCountNali"
.IP "msfRd" 4
.IX Item "msfRd"
.IP "msfShorten" 4
.IX Item "msfShorten"
.IP "msfWrt" 4
.IX Item "msfWrt"
.IP "open_file" 4
.IX Item "open_file"
.IP "pdbExtrSequence" 4
.IX Item "pdbExtrSequence"
.IP "pirRdMul" 4
.IX Item "pirRdMul"
.IP "pirWrtMul" 4
.IX Item "pirWrtMul"
.IP "pirWrtOne" 4
.IX Item "pirWrtOne"
.IP "rdRdbAssociative" 4
.IX Item "rdRdbAssociative"
.IP "rdRdbAssociativeNum" 4
.IX Item "rdRdbAssociativeNum"
.IP "safCompress" 4
.IX Item "safCompress"
.IP "safRd" 4
.IX Item "safRd"
.IP "safWrt" 4
.IX Item "safWrt"
.IP "seqGenWrt" 4
.IX Item "seqGenWrt"
.IP "swissRdSeq" 4
.IX Item "swissRdSeq"
.IP "sysDate" 4
.IX Item "sysDate"
.IP "sysGetUserLoc" 4
.IX Item "sysGetUserLoc"
.IP "sysRunProg" 4
.IX Item "sysRunProg"
.IP "wrtLoc" 4
.IX Item "wrtLoc"
.PD
.SH "VARIABLES"
.IX Header "VARIABLES"
.SH "AUTHOR"
.IX Header "AUTHOR"
B. Rost <rost@rostlab.org>
L. Kajan <lkajan@rostlab.org>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
.IP "Main website" 4
.IX Item "Main website"
<http://rostlab.org/>