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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/ExtractFromPDBFiles.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,508 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ExtractFromPDBFiles.pl \- Extract specific data from PDBFile(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ExtractFromPDBFiles.pl PDBFile(s)... +.PP +ExtractFromPDBFiles.pl [\fB\-a, \-\-Atoms\fR \*(L"AtomNum, [AtomNum...]\*(R" | \*(L"StartAtomNum, EndAtomNum\*(R" | +\&\*(L"AtomName, [AtomName...]\*(R"] [\fB\-c, \-\-chains\fR First | All | \*(L"ChainID, [ChainID,...]\*(R"] +[<\-\-CombineChains> yes | no] [\fB\-d, \-\-distance\fR number] [\fB\-\-DistanceMode\fR Atom | Hetatm | Residue | \s-1XYZ\s0] +[\fB\-\-DistanceOrigin\fR \*(L"AtomNumber, AtomName\*(R" | \*(L"HetatmNumber, HetAtmName\*(R" | \*(L"ResidueNumber, ResidueName, [ChainID]\*(R" | \*(L"X,Y,Z\*(R">] +[<\-\-DistanceSelectionMode> ByAtom | ByResidue] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepOldRecords\fR yes | no] +[\fB\-m, \-\-mode \fR Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | +ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens] +[\fB\-\-ModifyHeader\fR yes | no] [\fB\-\-NonStandardKeep\fR yes | no] [\fB\-\-NonStandardCode\fR character] +[\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname] \fB\-\-RecordMode\fR \fIAtom | Hetatm | AtomAndHetatm\fR] +[\fB\-\-Residues\fR \*(L"ResidueNum,[ResidueNum...]\*(R" | StartResidueNum,EndResiduNum ] +[\fB\-\-SequenceLength\fR number] [\fB\-\-SequenceRecords\fR Atom | SeqRes] +[\fB\-\-SequenceIDPrefix\fR FileName | HeaderRecord | Automatic] +[\fB\-\-WaterResidueNames\fR Automatic | \*(L"ResidueName, [ResidueName,...]\*(R"] +[\fB\-w, \-\-WorkingDir\fR dirname] PDBFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Extract specific data from \fIPDBFile(s)\fR and generate appropriate \s-1PDB\s0 or sequence file(s). +Multiple PDBFile names are separated by spaces. The valid file extension is \fI.pdb\fR. +All other file name extensions are ignored during the wild card expansion. All the \s-1PDB\s0 files +in a current directory can be specified either by \fI*.pdb\fR or the current directory name. +.PP +During \fIChains\fR and \fISequences\fR values of \fB\-m, \-\-mode\fR option, all \s-1ATOM/HETAM\s0 records +for chains after the first model in \s-1PDB\s0 fils containing data for multiple models are ignored. +.SH "OPTIONS" +.IX Header "OPTIONS" +.ie n .IP "\fB\-a, \-\-Atoms\fR \fI""AtomNum,[AtomNum...]"" | ""StartAtomNum,EndAtomNum"" | ""AtomName,[AtomName...]""\fR" 4 +.el .IP "\fB\-a, \-\-Atoms\fR \fI``AtomNum,[AtomNum...]'' | ``StartAtomNum,EndAtomNum'' | ``AtomName,[AtomName...]''\fR" 4 +.IX Item "-a, --Atoms AtomNum,[AtomNum...] | StartAtomNum,EndAtomNum | AtomName,[AtomName...]" +Specify which atom records to extract from \fIPDBFiles(s)\fR during \fIAtomNums\fR, +\&\fIAtomsRange\fR, and \fIAtomNames\fR value of \fB\-m, \-\-mode\fR option: extract records +corresponding to atom numbers specified in a comma delimited list of atom numbers/names, +or with in the range of start and end atom numbers. Possible values: \fI\*(L"AtomNum[,AtomNum,..]\*(R"\fR, +\&\fIStartAtomNum,EndAtomNum\fR, or \fI\*(L"AtomName[,AtomName,..]\*(R"\fR. Default: \fINone\fR. Examples: +.Sp +.Vb 3 +\& 10 +\& 15,20 +\& N,CA,C,O +.Ve +.IP "\fB\-c, \-\-chains\fR \fIFirst | All | ChainID,[ChainID,...]\fR" 4 +.IX Item "-c, --chains First | All | ChainID,[ChainID,...]" +Specify which chains to extract from \fIPDBFile(s)\fR during \fIChains | Sequences\fR value of +\&\fB\-m, \-\-mode\fR option: first chain, all chains, or a specific list of comma delimited chain IDs. +Possible values: \fIFirst | All | ChainID,[ChainID,...]\fR. Default: \fIFirst\fR. Examples: +.Sp +.Vb 3 +\& A +\& A,B +\& All +.Ve +.IP "\fB\-\-CombineChains\fR \fIyes | no\fR" 4 +.IX Item "--CombineChains yes | no" +Specify whether to combine extracted chains data into a single file during \fIChains\fR or +\&\fISequences\fR value of \fB\-m, \-\-mode\fR option. Possible values: \fIyes | no\fR. Default: \fIno\fR. +.Sp +During \fIChains\fR value of <\-m, \-\-mode> option with \fIYes\fR value of <\-\-CombineChains>, +extracted data for specified chains is written into a single file instead of individual file for each +chain. +.Sp +During \fISequences\fR value of <\-m, \-\-mode> option with \fIYes\fR value of <\-\-CombineChains>, +residues sequences for specified chains are extracted and concatenated into a single sequence +file instead of individual file for each chain. +.IP "\fB\-d, \-\-distance\fR \fInumber\fR" 4 +.IX Item "-d, --distance number" +Specify distance used to extract \s-1ATOM/HETATM\s0 recods during \fIDistance\fR value of +\&\fB\-m, \-\-mode\fR option. Default: \fI10.0\fR angstroms. +.Sp +\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR: +\&\s-1ATOM\s0, \s-1HETATM\s0 or both. +.IP "\fB\-\-DistanceMode\fR \fIAtom | Hetatm | Residue | \s-1XYZ\s0\fR" 4 +.IX Item "--DistanceMode Atom | Hetatm | Residue | XYZ" +Specify how to extract \s-1ATOM/HETATM\s0 records from \fIPDBFile(s)\fR during \fIDistance\fR value of +\&\fB\-m, \-\-mode\fR option: extract all the records within a certain distance specifed by \fB\-d, \-\-distance\fR +from an atom or hetro atom record, a residue, or any artbitrary point. Possible values: \fIAtom | +Hetatm | Residue | \s-1XYZ\s0\fR. Default: \fI\s-1XYZ\s0\fR. +.Sp +During \fIResidue\fR value of \fB\-\-distancemode\fR, distance of \s-1ATOM/HETATM\s0 records is calculated from +all the atoms in the residue and the records are selected as long as any atom of the residue lies with +in the distace specified using \fB\-d, \-\-distance\fR option. +.Sp +\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR: +\&\s-1ATOM\s0, \s-1HETATM\s0 or both. +.IP "\fB\-\-DistanceSelectionMode\fR \fIByAtom | ByResidue\fR" 4 +.IX Item "--DistanceSelectionMode ByAtom | ByResidue" +Specify how how to extract \s-1ATOM/HETATM\s0 records from \fIPDBFile(s)\fR during \fIDistance\fR value of +\&\fB\-m, \-\-mode\fR option for all values of \fB\-\-DistanceMode\fR option: extract only those \s-1ATOM/HETATM\s0 +records that meet specified distance criterion; extract all records corresponding to a residue as +long as one of the \s-1ATOM/HETATM\s0 record in the residue satisfies specified distance criterion. Possible +values: \fIByAtom, ByResidue\fR. Default value: \fIByAtom\fR. +.ie n .IP "\fB\-\-DistanceOrigin\fR \fI""AtomNumber,AtomName"" | ""HetatmNumber,HetAtmName"" | ""ResidueNumber,ResidueName[,ChainID]"" | ""X,Y,Z""\fR" 4 +.el .IP "\fB\-\-DistanceOrigin\fR \fI``AtomNumber,AtomName'' | ``HetatmNumber,HetAtmName'' | ``ResidueNumber,ResidueName[,ChainID]'' | ``X,Y,Z''\fR" 4 +.IX Item "--DistanceOrigin AtomNumber,AtomName | HetatmNumber,HetAtmName | ResidueNumber,ResidueName[,ChainID] | X,Y,Z" +This value is \fB\-\-distancemode\fR specific. In general, it identifies a point used to select +other \s-1ATOM/HETATMS\s0 with in a specific distance from this point. +.Sp +For \fIAtom\fR value of \fB\-\-distancemode\fR, this option corresponds to an atom specification. +Format: \fIAtomNumber,AtomName\fR. Example: +.Sp +.Vb 1 +\& 455,CA +.Ve +.Sp +For \fIHetatm\fR value of \fB\-\-distancemode\fR, this option corresponds to a hetatm specification. +Format: \fIHetatmNumber,HetAtmName\fR. Example: +.Sp +.Vb 1 +\& 5295,C1 +.Ve +.Sp +For \fIResidue\fR value of \fB\-\-distancemode\fR, this option corresponds to a residue specification. +Format: \fIResidueNumber, ResidueName[,ChainID]\fR. Example: +.Sp +.Vb 3 +\& 78,MSE +\& 977,RET,A +\& 978,RET,B +.Ve +.Sp +For \fI\s-1XYZ\s0\fR value of \fB\-\-distancemode\fR, this option corresponds to a coordinate of an +arbitrary point. Format: \fIX,Y,X\fR. Example: +.Sp +.Vb 1 +\& 10.044,19.261,\-4.292 +.Ve +.Sp +\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR: +\&\s-1ATOM\s0, \s-1HETATM\s0 or both. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-k, \-\-KeepOldRecords\fR \fIyes | no\fR" 4 +.IX Item "-k, --KeepOldRecords yes | no" +Specify whether to transfer old non \s-1ATOM\s0 and \s-1HETATM\s0 records from input PDBFile(s) to new +PDBFile(s) during \fIChains | Atoms | HetAtms | CAlphas | Distance| NonWater | NonHydrogens\fR +value of \fB\-m \-\-mode\fR option. By default, except for the \s-1HEADER\s0 record, all +other unnecessary non \s-1ATOM/HETATM\s0 records are dropped during the +generation of new \s-1PDB\s0 files. Possible values: \fIyes | no\fR. Default: \fIno\fR. +.IP "\fB\-m, \-\-mode \fR \fIChains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens\fR" 4 +.IX Item "-m, --mode Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens" +Specify what to extract from \fIPDBFile(s)\fR: \fIChains\fR \- retrieve records for +specified chains; \fISequences\fR \- generate sequence files for specific chains; +\&\fIAtoms\fR \- extract atom records; \fICAlphas\fR \- extract atom records for alpha +carbon atoms; \fIAtomNums\fR \- extract atom records for specified atom numbers; +\&\fIAtomsRange\fR \- extract atom records between specified atom number range; +\&\fIAtomNames\fR \- extract atom records for specified atom names; \fIResidueNums\fR +\&\- extract records for specified residue numbers; \fIResiduesRange\fR \- extract records +for residues between specified residue number range; \fIResidueNames\fR \- extract +records for specified residue names; \fIDistance\fR \- extract records with in a +certain distance from a specific position; \fINonWater\fR \- extract records corresponding +to residues other than water; \fINonHydrogens\fR \- extract non-hydrogen records. +.Sp +Possible values: \fIChains, Sequences Atoms, CAlphas, AtomNums, AtomsRange, +AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater, +NonHydrogens\fR. Default value: \fINonWater\fR +.Sp +During the generation of new \s-1PDB\s0 files, unnecessay \s-1CONECT\s0 records are dropped. +.Sp +For \fIChains\fR mode, data for appropriate chains specified by \fB\-\-c \-\-chains\fR option +is extracted from \fIPDBFile(s)\fR and placed into new \s-1PDB\s0 file(s). +.Sp +For \fISequences\fR mode, residues names using various sequence related options are +extracted for chains specified by \fB\-\-c \-\-chains\fR option from \fIPDBFile(s)\fR and +\&\s-1FASTA\s0 sequence file(s) are generated. +.Sp +For \fIDistance\fR mode, all \s-1ATOM/HETATM\s0 records with in a distance specified +by \fB\-d \-\-distance\fR option from a specific atom, residue or a point indicated by +\&\fB\-\-distancemode\fR are extracted and placed into new \s-1PDB\s0 file(s). +.Sp +For \fINonWater\fR mode, non water \s-1ATOM/HETATM\s0 record lines, identified using value of +\&\fB\-\-WaterResidueNames\fR, are extracted and written to new \s-1PDB\s0 file(s). +.Sp +For \fINonHydrogens\fR mode, \s-1ATOM/HETATOM\s0 record lines containing element symbol +other than \fIH\fR are extracted and written to new \s-1PDB\s0 file(s). +.Sp +For all other options, appropriate \s-1ATOM/HETATM\s0 records are extracted to generate new +\&\s-1PDB\s0 file(s). +.Sp +\&\fB\-\-RecordMode\fR option controls type of record lines to extract and process from +\&\fIPDBFile(s)\fR: \s-1ATOM\s0, \s-1HETATM\s0 or both. +.IP "\fB\-\-ModifyHeader\fR \fIyes | no\fR" 4 +.IX Item "--ModifyHeader yes | no" +Specify whether to modify \s-1HEADER\s0 record during the generation of new \s-1PDB\s0 files +for \fB\-m, \-\-mode\fR values of \fIChains | Atoms | CAlphas | Distance\fR. Possible values: +\&\fIyes | no\fR. Default: \fIyes\fR. By default, Classification data is replaced by \fIData extracted +using MayaChemTools\fR before writing out \s-1HEADER\s0 record. +.IP "\fB\-\-NonStandardKeep\fR \fIyes | no\fR" 4 +.IX Item "--NonStandardKeep yes | no" +Specify whether to include and convert non-standard three letter residue codes into +a code specified using \fB\-\-nonstandardcode\fR option and include them into sequence file(s) +generated during \fISequences\fR value of \fB\-m, \-\-mode\fR option. Possible values: \fIyes | no\fR. +Default: \fIyes\fR. +.Sp +A warning is also printed about the presence of non-standard residues. Any residue other +than standard 20 amino acids and 5 nucleic acid is considered non-standard; additionally, +\&\s-1HETATM\s0 residues in chains also tagged as non-standard. +.IP "\fB\-\-NonStandardCode\fR \fIcharacter\fR" 4 +.IX Item "--NonStandardCode character" +A single character code to use for non-standard residues. Default: \fIX\fR. Possible values: +\&\fI?, \-, or X\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New \s-1PDB\s0 and sequence file name is generated using the root: <Root><Mode>.<Ext>. +Default new file name: <PDBFileName>Chain<ChainID>.pdb for \fIChains\fR \fBmode\fR; +<PDBFileName>SequenceChain<ChainID>.fasta for \fISequences\fR \fBmode\fR; +<PDBFileName>DistanceBy<DistanceMode>.pdb for \fIDistance\fR \fB\-m, \-\-mode\fR +<PDBFileName><Mode>.pdb for \fIAtoms | CAlphas | NonWater | NonHydrogens\fR \fB\-m, \-\-mode\fR +values. This option is ignored for multiple input files. +.IP "\fB\-\-RecordMode\fR \fIAtom | Hetatm | AtomAndHetatm\fR" 4 +.IX Item "--RecordMode Atom | Hetatm | AtomAndHetatm" +Specify type of record lines to extract and process from \fIPDBFile(s)\fR during various +values of \fB\-m, \-\-mode\fR option: extract only \s-1ATOM\s0 record lines; extract only \s-1HETATM\s0 +record lines; extract both \s-1ATOM\s0 and \s-1HETATM\s0 lines. Possible values: \fIAtom | Hetatm +| AtomAndHetatm | \s-1XYZ\s0\fR. Default during \fIAtoms, CAlphas, AtomNums, AtomsRange, +AtomNames\fR values of \fB\-m, \-\-mode\fR option: \fIAtom\fR; otherwise: \fIAtomAndHetatm\fR. +.Sp +This option is ignored during \fIChains, Sequences\fR values of \fB\-m, \-\-mode\fR option. +.ie n .IP "\fB\-\-Residues\fR \fI""ResidueNum,[ResidueNum...]"" | ""StartResidueNum,EndResiduNum"" | ""ResidueName,[ResidueName...]""\fR" 4 +.el .IP "\fB\-\-Residues\fR \fI``ResidueNum,[ResidueNum...]'' | ``StartResidueNum,EndResiduNum'' | ``ResidueName,[ResidueName...]''\fR" 4 +.IX Item "--Residues ResidueNum,[ResidueNum...] | StartResidueNum,EndResiduNum | ResidueName,[ResidueName...]" +Specify which resiude records to extract from \fIPDBFiles(s)\fR during \fIResidueNums\fR, +\&\fIResiduesRange\fR,and \fIResidueNames\fR value of \fB\-m, \-\-mode\fR option: extract records +corresponding to residue numbers specified in a comma delimited list of residue numbers/names, +or with in the range of start and end residue numbers. Possible values: \fI\*(L"ResidueNum[,ResidueNum,..]\*(R"\fR, +\&\fIStartResidueNum,EndResiduNum\fR, or \fI<\*(L"ResidueName[,ResidueName,..]\*(R"\fR. Default: \fINone\fR. Examples: +.Sp +.Vb 3 +\& 20 +\& 5,10 +\& TYR,SER,THR +.Ve +.Sp +\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR: +\&\s-1ATOM\s0, \s-1HETATM\s0 or both. +.IP "\fB\-\-SequenceLength\fR \fInumber\fR" 4 +.IX Item "--SequenceLength number" +Maximum sequence length per line in sequence file(s). Default: \fI80\fR. +.IP "\fB\-\-SequenceRecords\fR \fIAtom | SeqRes\fR" 4 +.IX Item "--SequenceRecords Atom | SeqRes" +Specify which records to use for extracting residue names from \fIPDBFiles(s)\fR during +\&\fISequences\fR value of \fB\-m, \-\-mode\fR option: use \s-1ATOM\s0 records to compile a list +of residues in a chain or parse \s-1SEQRES\s0 record to get a list of residues. Possible values: +\&\fIAtom | SeqRes\fR. Default: \fIAtom\fR. +.IP "\fB\-\-SequenceIDPrefix\fR \fIFileName | HeaderRecord | Automatic\fR" 4 +.IX Item "--SequenceIDPrefix FileName | HeaderRecord | Automatic" +Specify how to generate a prefix for sequence IDs during \fISequences\fR value +of \fB\-m, \-\-mode\fR option: use input file name prefix; retrieve \s-1PDB\s0 \s-1ID\s0 from \s-1HEADER\s0 record; +or automatically decide the method for generating the prefix. The chain IDs are also +appended to the prefix. Possible values: \fIFileName | HeaderRecord | Automatic\fR. +Default: \fIAutomatic\fR +.ie n .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ""ResidueName,[ResidueName,...]""\fR" 4 +.el .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ``ResidueName,[ResidueName,...]''\fR" 4 +.IX Item "--WaterResidueNames Automatic | ResidueName,[ResidueName,...]" +Identification of water residues during \fINonWater\fR value of \fB\-m, \-\-mode\fR option. Possible values: +\&\fIAutomatic | \*(L"ResidueName,[ResidueName,...]\*(R"\fR. Default: \fIAutomatic\fR \- corresponds +to \*(L"\s-1HOH\s0,WAT,H20\*(R". You can also specify a different comma delimited list of residue names +to use for water. +.IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4 +.IX Item "-w, --WorkingDir dirname" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To extract non-water records from Sample2.pdb file and generate Sample2NonWater.pdb +file, type: +.PP +.Vb 1 +\& % ExtractFromPDBFiles.pl Sample2.pdb +.Ve +.PP +To extract non-water records corresponding to only \s-1ATOM\s0 records from Sample2.pdb file +and generate Sample2NonWater.pdb file, type: +.PP +.Vb 1 +\& % ExtractFromPDBFiles.pl \-\-RecordMode Atom Sample2.pdb +.Ve +.PP +To extract non-water records from Sample2.pdb file using \s-1HOH\s0 or \s-1WAT\s0 residue name for water along +with all old non-coordinate records and generate Sample2NewNonWater.pdb file, type: +.PP +.Vb 2 +\& % ExtractFromPDBFiles.pl \-m NonWater \-\-WaterResidueNames "HOH,WAT" +\& \-KeepOldRecords Yes \-r Sample2New \-o Sample2.pdb +.Ve +.PP +To extract non-hydrogens records from Sample2.pdb file and generate Sample2NonHydrogen.pdb +file, type: +.PP +.Vb 1 +\& % ExtractFromPDBFiles.pl \-m NonHydrogens Sample2.pdb +.Ve +.PP +To extract data for first chain in Sample2.pdb and generate Sample2ChainA.pdb, type +file, type: +.PP +.Vb 1 +\& % ExtractFromPDBFiles.pl \-m chains \-o Sample2.pdb +.Ve +.PP +To extract data for both chains in Sample2.pdb and generate Sample2ChainA.pdb and +Sample2ChainB.pdb, type: +.PP +.Vb 1 +\& % ExtractFromPDBFiles.pl \-m chains \-c All \-o Sample2.pdb +.Ve +.PP +To extract data for alpha carbons in Sample2.pdb and generate Sample2CAlphas.pdb, type: +.PP +.Vb 1 +\& % ExtractFromPDBFiles.pl \-m CAlphas \-o Sample2.pdb +.Ve +.PP +To extract records for specific residue numbers in all chains from Sample2.pdb file and generate +Sample2ResidueNums.pdb file, type: +.PP +.Vb 2 +\& % ExtractFromPDBFiles.pl \-m ResidueNums \-\-Residues "3,6" +\& Sample2.pdb +.Ve +.PP +To extract records for a specific range of residue number in all chains from Sample2.pdb +file and generate Sample2ResiduesRange.pdb file, type: +.PP +.Vb 2 +\& % ExtractFromPDBFiles.pl \-m ResiduesRange \-\-Residues "10,30" +\& Sample2.pdb +.Ve +.PP +To extract data for all \s-1ATOM\s0 and \s-1HETATM\s0 records with in 10 angstrom of an atom specifed by +atom serial number and name \*(L"1,N\*(R" in Sample2.pdb file and generate Sample2DistanceByAtom.pdb, +type: +.PP +.Vb 2 +\& % ExtractFromPDBFiles.pl \-m Distance \-\-DistanceMode Atom +\& \-\-DistanceOrigin "1,N" \-k No \-\-distance 10 \-o Sample2.pdb +.Ve +.PP +To extract data for all \s-1ATOM\s0 and \s-1HETATM\s0 records for complete residues with any atom or hetatm +less than 10 angstrom of an atom specifed by atom serial number and name \*(L"1,N\*(R" in Sample2.pdb +file and generate Sample2DistanceByAtom.pdb, type: +.PP +.Vb 3 +\& % ExtractFromPDBFiles.pl \-m Distance \-\-DistanceMode Atom +\& \-\-DistanceOrigin "1,N" \-\-DistanceSelectionMode ByResidue +\& \-k No \-\-distance 10 \-o Sample2.pdb +.Ve +.PP +To extract data for all \s-1ATOM\s0 and \s-1HETATM\s0 records with in 25 angstrom of an arbitrary point \*(L"0,0,0\*(R" +in Sample2.pdb file and generate Sample2DistanceByXYZ.pdb, type: +.PP +.Vb 2 +\& % ExtractFromPDBFiles.pl \-m Distance \-\-DistanceMode XYZ +\& \-\-DistanceOrigin "0,0,0" \-k No \-\-distance 25 \-o Sample2.pdb +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoPDBFiles.pl, ModifyPDBFiles.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.