annotate mayachemtools/docs/scripts/man1/ModifySDFilesDataFields.1 @ 2:dfff2614510e draft

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author deepakjadmin
date Wed, 20 Jan 2016 12:15:15 -0500
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29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
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30 . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
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55 . nr % 0
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67 . ds #H 0
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80 . \" simple accents for nroff and troff
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89 .if t \{\
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90 . ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
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91 . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
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92 . ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
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93 . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
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94 . ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
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95 . ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
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96 .\}
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97 . \" troff and (daisy-wheel) nroff accents
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98 .ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
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99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
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100 .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
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101 .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
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102 .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
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103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
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104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
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105 .ds ae a\h'-(\w'a'u*4/10)'e
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106 .ds Ae A\h'-(\w'A'u*4/10)'E
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107 . \" corrections for vroff
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108 .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
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109 .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
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110 . \" for low resolution devices (crt and lpr)
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111 .if \n(.H>23 .if \n(.V>19 \
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112 \{\
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113 . ds : e
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114 . ds 8 ss
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115 . ds o a
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116 . ds d- d\h'-1'\(ga
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122 .\}
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123 .rm #[ #] #H #V #F C
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124 .\" ========================================================================
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125 .\"
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126 .IX Title "MODIFYSDFILESDATAFIELDS 1"
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127 .TH MODIFYSDFILESDATAFIELDS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 ModifySDFilesDataFields.pl \- Modify data fields in SDFile(s)
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 ModifySDFilesDataFields.pl SDFile(s)...
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137 .PP
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138 ModifySDFilesDataFields.pl [\fB\-d, \-\-detail\fR infolevel]
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139 [\fB\-\-datafieldscommon\fR newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]]
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140 [\fB\-\-datafieldsmap\fR newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]]
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141 [\fB\-\-datafieldsmapfile\fR filename] [\fB\-\-datafieldURL\fR URLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel]
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142 [\fB\-h, \-\-help\fR] [\fB\-k, \-\-keepolddatafields\fR all | unmappedonly | none] [\fB\-m, \-\-mode\fR molname | datafields | both]
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143 [\fB\-\-molnamemode\fR datafield | labelprefix] [\fB\-\-molname\fR datafieldname or prefixstring]
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144 [\fB\-\-molnamereplace\fR always | empty] [\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname]
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145 [\fB\-w, \-\-workingdir\fR dirname] SDFile(s)...
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146 .SH "DESCRIPTION"
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147 .IX Header "DESCRIPTION"
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148 Modify molname line and data fields in \fISDFile(s)\fR. Molname line can be replaced by a
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149 data field value or assigned a sequential \s-1ID\s0 prefixed with a specific string. For data
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150 fields and modification of their values, these types of options are supported: replace
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151 data field labels by another set of labels; combine values of multiple data fields and
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152 assign a new label; add specific set of data field labels and values to all compound
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153 records; and others.
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154 .PP
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155 The file names are separated by space.The valid file extensions are \fI.sdf\fR and \fI.sd\fR.
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156 All other file names are ignored. All the \s-1SD\s0 files in a current directory can be specified
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157 either by \fI*.sdf\fR or the current directory name.
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158 .SH "OPTIONS"
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159 .IX Header "OPTIONS"
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160 .IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
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161 .IX Item "-d, --detail infolevel"
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162 Level of information to print about compound records being ignored. Default: \fI1\fR. Possible
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163 values: \fI1, 2 or 3\fR.
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164 .IP "\fB\-\-datafieldscommon\fR \fInewfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]\fR" 4
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165 .IX Item "--datafieldscommon newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]"
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166 Specify data field labels and values for addition to each compound record. It's a comma delimited
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167 list of data field label and values pair. Default: \fInone\fR.
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168 .Sp
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169 Examples:
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170 .Sp
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171 .Vb 2
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172 \& DepositionDate,YYYY\-MM\-DD
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173 \& Source,www.domainname.org,ReleaseData,YYYY\-MM\-DD
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174 .Ve
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175 .IP "\fB\-\-datafieldsmap\fR \fInewfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]\fR" 4
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176 .IX Item "--datafieldsmap newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]"
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177 Specify how various data field labels and values are combined to generate a new data field
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178 labels and their values. All the comma delimited data fields, with in a semicolon delimited set,
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179 are mapped to the first new data field label along with the data field values joined via new
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180 line character. Default: \fInone\fR.
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181 .Sp
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182 Examples:
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183 .Sp
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184 .Vb 2
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185 \& Synonym,Name,SystematicName,Synonym;CmpdID,Extreg
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186 \& HBondDonors,SumNHOH
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187 .Ve
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188 .IP "\fB\-\-datafieldsmapfile\fR \fIfilename\fR" 4
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189 .IX Item "--datafieldsmapfile filename"
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190 Filename containing mapping of data fields. Format of data fields line in this file corresponds
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191 to \fB\-\-datafieldsmap\fR option. Example:
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192 .Sp
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193 .Vb 2
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194 \& Line 1: Synonym,Name,SystematicName,Synonym;CmpdID,Extreg
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195 \& Line 2: HBondDonors,SumNHOH
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196 .Ve
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197 .IP "\fB\-\-datafieldURL\fR \fIURLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel\fR" 4
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198 .IX Item "--datafieldURL URLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel"
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199 Specify how to generate a \s-1URL\s0 for retrieving compound data from a web server and add it
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200 to each compound record. \fIURLDataFieldLabel\fR is used as the data field label for \s-1URL\s0 value
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201 which is created by combining \fICGIScriptPath,CGIParamName,CmpdIDFieldLabel\fR values:
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202 CGIScriptPath?CGIParamName=CmpdIDFieldLabelValue. Default: \fInone\fR.
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203 .Sp
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204 Example:
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205 .Sp
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206 .Vb 1
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207 \& Source,http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID
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208 .Ve
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209 .IP "\fB\-h, \-\-help\fR" 4
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210 .IX Item "-h, --help"
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211 Print this help message.
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212 .IP "\fB\-k, \-\-keepolddatafields\fR \fIall | unmappedonly | none\fR" 4
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213 .IX Item "-k, --keepolddatafields all | unmappedonly | none"
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214 Specify how to transfer old data fields from input SDFile(s) to new SDFile(s) during
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215 \&\fIdatafields | both\fR value of \fB\-m, \-\-mode\fR option: keep all old data fields; write out the ones
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216 not mapped to new fields as specified by \fB\-\-datafieldsmap\fR or <\-\-datafieldsmapfile> options;
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217 or ignore all old data field labels. For \fImolname\fR \fB\-m \-\-mode\fR, old datafields are always kept.
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218 Possible values: \fIall | unmappedonly | none\fR. Default: \fInone\fR.
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219 .IP "\fB\-m, \-\-mode\fR \fImolname | datafields | both\fR" 4
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220 .IX Item "-m, --mode molname | datafields | both"
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221 Specify how to modify SDFile(s): \fImolname\fR \- change molname line by another datafield or value;
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222 \&\fIdatafield\fR \- modify data field labels and values by replacing one label by another, combining
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223 multiple data field labels and values, adding specific set of data field labels and values to all compound, or
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224 inserting an \s-1URL\s0 for compound retrieval to each record; \fIboth\fR \- change molname line and datafields
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225 simultaneously. Possible values: \fImolname | datafields | both\fR. Default: \fImolname\fR
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226 .IP "\fB\-\-molnamemode\fR \fIdatafield | labelprefix\fR" 4
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227 .IX Item "--molnamemode datafield | labelprefix"
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228 Specify how to change molname line for \fB\-m \-\-mode\fR option values of \fImolname | both\fR: use
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229 a datafield label value or assign a sequential \s-1ID\s0 prefixed with \fIlabelprefix\fR. Possible values:
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230 \&\fIdatafield | labelprefix\fR. Default: \fIlabelprefix\fR.
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231 .IP "\fB\-\-molname\fR \fIdatafieldname or prefixstring\fR" 4
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232 .IX Item "--molname datafieldname or prefixstring"
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233 Molname generation method. For \fIdatafield\fR value of \fB\-\-molnamemode\fR option, it corresponds
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234 to datafield label name whose value is used for molname; otherwise, it's a prefix string used for
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235 generating compound IDs like labelprefixstring<Number>. Default value, \fICmpd\fR, generates
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236 compound IDs like Cmpd<Number> for molname.
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237 .IP "\fB\-\-molnamereplace\fR \fIalways | empty\fR" 4
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238 .IX Item "--molnamereplace always | empty"
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239 Specify when to replace molname line for \fB\-m \-\-mode\fR option values of \fImolname | both\fR:
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240 always replace the molname line using \fB\-\-molname\fR option or only when it's empty. Possible
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241 values: \fIalways | empty\fR. Default: \fIempty\fR.
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242 .IP "\fB\-o, \-\-overwrite\fR" 4
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243 .IX Item "-o, --overwrite"
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244 Overwrite existing files.
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245 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
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246 .IX Item "-r, --root rootname"
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247 New \s-1SD\s0 file name is generated using the root: <Root>.<Ext>. Default new file
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248 name: <InitialSDFileName>ModifiedDataFields.<Ext>. This option is ignored for multiple
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249 input files.
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250 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
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251 .IX Item "-w, --workingdir dirname"
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252 Location of working directory. Default: current directory.
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253 .SH "EXAMPLES"
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254 .IX Header "EXAMPLES"
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255 To replace empty molname lines by Cmpd<CmpdNumber> and generate a new \s-1SD\s0 file
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256 NewSample1.sdf, type:
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257 .PP
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258 .Vb 1
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259 \& % ModifySDFilesDataFields.pl \-o \-r NewSample1 Sample1.sdf
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260 .Ve
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261 .PP
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262 To replace all molname lines by Mol_ID data field generate a new \s-1SD\s0 file
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263 NewSample1.sdf, type:
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264 .PP
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265 .Vb 2
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266 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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267 \& \-\-molnamereplace always \-r NewSample1 \-o Sample1.sdf
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268 .Ve
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269 .PP
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270 To replace all molname lines by Mol_ID data field, map Name and CompoundName to
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271 a new datafield Synonym, and generate a new \s-1SD\s0 file NewSample1.sdf, type:
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272 .PP
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273 .Vb 4
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274 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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275 \& \-\-molnamereplace always \-\-molname Mol_ID \-\-mode both
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276 \& \-\-datafieldsmap "Synonym,Name,CompoundName" \-r
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277 \& NewSample1 \-o Sample1.sdf
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278 .Ve
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279 .PP
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280 To replace all molname lines by Mol_ID data field, map Name and CompoundName to
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281 a new datafield Synonym, add common fields ReleaseDate and Source, and
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282 generate a new \s-1SD\s0 file NewSample1.sdf without keeping any old \s-1SD\s0 data fields, type:
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283 .PP
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284 .Vb 6
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285 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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286 \& \-\-molnamereplace always \-\-molname Mol_ID \-\-mode both
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287 \& \-\-datafieldsmap "Synonym,Name,CompoundName"
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288 \& \-\-datafieldscommon "ReleaseDate,yyyy\-mm\-dd,Source,
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289 \& www.mayachemtools.org" \-\-keepolddatafields none \-r
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290 \& NewSample1 \-o Sample1.sdf
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291 .Ve
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292 .PP
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293 \&\fBPreparing \s-1SD\s0 files PubChem deposition:\fR
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294 .PP
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295 Consider a \s-1SD\s0 file with these fields: Mol_ID, Name, Synonyms and Systematic_Name.
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296 And Mol_ID data field uniquely identifies your compound.
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297 .PP
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298 To prepare a new \s-1SD\s0 file CmpdDataForPubChem.sdf containing only required
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299 \&\s-1PUBCHEM_EXT_DATASOURCE_REGID\s0 field, type:
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300 .PP
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301 .Vb 4
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302 \& % ModifySDFilesDataFields.pl \-\-m datafields
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303 \& \-\-datafieldsmap
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304 \& "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID"
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305 \& \-r CmpdDataForPubChem \-o Sample1.sdf
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306 .Ve
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307 .PP
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308 To prepare a new \s-1SD\s0 file CmpdDataForPubChem.sdf containing only required
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309 \&\s-1PUBCHEM_EXT_DATASOURCE_REGID\s0 field and replace molname line with Mol_ID, type:
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310 .PP
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311 .Vb 5
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312 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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313 \& \-\-molnamereplace always \-\-molname Mol_ID \-\-mode both
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314 \& \-\-datafieldsmap
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315 \& "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID"
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316 \& \-r CmpdDataForPubChem \-o Sample1.sdf
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317 .Ve
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318 .PP
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319 In addition to required PubChem data field, you can also add optional PubChem data
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320 fields.
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321 .PP
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322 To map your Name, Synonyms and Systematic_Name data fields to optional
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323 \&\s-1PUBCHEM_SUBSTANCE_SYNONYM\s0 data field along with required \s-1ID\s0 field, type:
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324 .PP
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325 .Vb 6
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326 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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327 \& \-\-molnamereplace always \-\-molname Mol_ID \-\-mode both
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328 \& \-\-datafieldsmap
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329 \& "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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330 \& PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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331 \& \-r CmpdDataForPubChem \-o Sample1.sdf
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332 .Ve
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333 .PP
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334 To add your <domain.org> as \s-1PUBCHEM_EXT_SUBSTANCE_URL\s0 and link substance
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335 retrieval to your \s-1CGI\s0 script <http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID>
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336 via \s-1PUBCHEM_EXT_DATASOURCE_REGID\s0 field along with optional and required
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337 data fields, type:
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338 .PP
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339 .Vb 10
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340 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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341 \& \-\-molnamereplace always \-\-molname Mol_ID \-\-mode both
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342 \& \-\-datafieldsmap
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343 \& "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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344 \& PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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345 \& \-\-datafieldscommon
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346 \& "PUBCHEM_EXT_SUBSTANCE_URL,domain.org"
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347 \& \-\-datafieldURL "PUBCHEM_EXT_DATASOURCE_URL,
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348 \& http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID"
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349 \& \-r CmpdDataForPubChem \-o Sample1.sdf
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350 .Ve
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351 .PP
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352 And to add a publication date and request a release data using
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353 \&\s-1PUBCHEM_PUBLICATION_DATE\s0 and \s-1PUBCHEM_DEPOSITOR_RECORD_DATE\s0 data fields
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354 along with all the data fields in earlier examples, type:
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355 optional fields, type:
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356 .PP
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357 .Vb 12
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358 \& % ModifySDFilesDataFields.pl \-\-molnamemode datafield
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359 \& \-\-molnamereplace always \-\-molname Mol_ID \-\-mode both
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360 \& \-\-datafieldsmap
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361 \& "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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362 \& PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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363 \& \-\-datafieldURL "PUBCHEM_EXT_DATASOURCE_URL,
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364 \& http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID"
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365 \& \-\-datafieldscommon
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366 \& "PUBCHEM_EXT_SUBSTANCE_URL,domain.org,
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367 \& PUBCHEM_PUBLICATION_DATE,YYY\-MM\-DD,
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368 \& PUBCHEM_DEPOSITOR_RECORD_DATE,YYYY\-MM\-DD"
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369 \& \-r CmpdDataForPubChem \-o Sample1.sdf
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370 .Ve
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371 .SH "AUTHOR"
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372 .IX Header "AUTHOR"
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373 Manish Sud <msud@san.rr.com>
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374 .SH "SEE ALSO"
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375 .IX Header "SEE ALSO"
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376 InfoSDFiles.pl, JoinSDFiles.pl, MergeTextFilesWithSD.pl, SplitSDFiles.pl, SDFilesToHTML.pl
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377 .SH "COPYRIGHT"
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378 .IX Header "COPYRIGHT"
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379 Copyright (C) 2015 Manish Sud. All rights reserved.
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380 .PP
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381 This file is part of MayaChemTools.
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382 .PP
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383 MayaChemTools is free software; you can redistribute it and/or modify it under
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384 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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385 Software Foundation; either version 3 of the License, or (at your option)
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386 any later version.