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1 NAME
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2 ModifySDFilesDataFields.pl - Modify data fields in SDFile(s)
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3
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4 SYNOPSIS
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5 ModifySDFilesDataFields.pl SDFile(s)...
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6
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7 ModifySDFilesDataFields.pl [-d, --detail infolevel] [--datafieldscommon
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8 newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]]
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9 [--datafieldsmap newfieldlabel, oldfieldlabel, [oldfieldlabel,...];
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10 [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]]
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11 [--datafieldsmapfile filename] [--datafieldURL URLDataFieldLabel,
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12 CGIScriptPath, CGIParamName, CmpdIDFieldLabel] [-h, --help] [-k,
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13 --keepolddatafields all | unmappedonly | none] [-m, --mode molname |
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14 datafields | both] [--molnamemode datafield | labelprefix] [--molname
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15 datafieldname or prefixstring] [--molnamereplace always | empty] [-o,
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16 --overwrite] [-r, --root rootname] [-w, --workingdir dirname]
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17 SDFile(s)...
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18
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19 DESCRIPTION
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20 Modify molname line and data fields in *SDFile(s)*. Molname line can be
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21 replaced by a data field value or assigned a sequential ID prefixed with
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22 a specific string. For data fields and modification of their values,
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23 these types of options are supported: replace data field labels by
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24 another set of labels; combine values of multiple data fields and assign
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25 a new label; add specific set of data field labels and values to all
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26 compound records; and others.
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27
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28 The file names are separated by space.The valid file extensions are
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29 *.sdf* and *.sd*. All other file names are ignored. All the SD files in
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30 a current directory can be specified either by **.sdf* or the current
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31 directory name.
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32
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33 OPTIONS
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34 -d, --detail *infolevel*
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35 Level of information to print about compound records being ignored.
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36 Default: *1*. Possible values: *1, 2 or 3*.
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37
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38 --datafieldscommon *newfieldlabel, newfieldvalue, [newfieldlabel,
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39 newfieldvalue,...]*
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40 Specify data field labels and values for addition to each compound
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41 record. It's a comma delimited list of data field label and values
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42 pair. Default: *none*.
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43
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44 Examples:
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45
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46 DepositionDate,YYYY-MM-DD
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47 Source,www.domainname.org,ReleaseData,YYYY-MM-DD
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48
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49 --datafieldsmap *newfieldlabel, oldfieldlabel, [oldfieldlabel,...];
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50 [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]*
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51 Specify how various data field labels and values are combined to
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52 generate a new data field labels and their values. All the comma
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53 delimited data fields, with in a semicolon delimited set, are mapped
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54 to the first new data field label along with the data field values
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55 joined via new line character. Default: *none*.
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56
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57 Examples:
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58
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59 Synonym,Name,SystematicName,Synonym;CmpdID,Extreg
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60 HBondDonors,SumNHOH
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61
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62 --datafieldsmapfile *filename*
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63 Filename containing mapping of data fields. Format of data fields
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64 line in this file corresponds to --datafieldsmap option. Example:
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65
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66 Line 1: Synonym,Name,SystematicName,Synonym;CmpdID,Extreg
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67 Line 2: HBondDonors,SumNHOH
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68
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69 --datafieldURL *URLDataFieldLabel, CGIScriptPath, CGIParamName,
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70 CmpdIDFieldLabel*
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71 Specify how to generate a URL for retrieving compound data from a
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72 web server and add it to each compound record. *URLDataFieldLabel*
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73 is used as the data field label for URL value which is created by
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74 combining *CGIScriptPath,CGIParamName,CmpdIDFieldLabel* values:
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75 CGIScriptPath?CGIParamName=CmpdIDFieldLabelValue. Default: *none*.
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76
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77 Example:
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78
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79 Source,http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID
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80
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81 -h, --help
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82 Print this help message.
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83
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84 -k, --keepolddatafields *all | unmappedonly | none*
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85 Specify how to transfer old data fields from input SDFile(s) to new
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86 SDFile(s) during *datafields | both* value of -m, --mode option:
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87 keep all old data fields; write out the ones not mapped to new
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88 fields as specified by --datafieldsmap or <--datafieldsmapfile>
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89 options; or ignore all old data field labels. For *molname* -m
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90 --mode, old datafields are always kept. Possible values: *all |
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91 unmappedonly | none*. Default: *none*.
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92
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93 -m, --mode *molname | datafields | both*
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94 Specify how to modify SDFile(s): *molname* - change molname line by
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95 another datafield or value; *datafield* - modify data field labels
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96 and values by replacing one label by another, combining multiple
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97 data field labels and values, adding specific set of data field
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98 labels and values to all compound, or inserting an URL for compound
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99 retrieval to each record; *both* - change molname line and
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100 datafields simultaneously. Possible values: *molname | datafields |
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101 both*. Default: *molname*
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102
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103 --molnamemode *datafield | labelprefix*
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104 Specify how to change molname line for -m --mode option values of
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105 *molname | both*: use a datafield label value or assign a sequential
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106 ID prefixed with *labelprefix*. Possible values: *datafield |
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107 labelprefix*. Default: *labelprefix*.
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108
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109 --molname *datafieldname or prefixstring*
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110 Molname generation method. For *datafield* value of --molnamemode
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111 option, it corresponds to datafield label name whose value is used
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112 for molname; otherwise, it's a prefix string used for generating
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113 compound IDs like labelprefixstring<Number>. Default value, *Cmpd*,
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114 generates compound IDs like Cmpd<Number> for molname.
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115
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116 --molnamereplace *always | empty*
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117 Specify when to replace molname line for -m --mode option values of
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118 *molname | both*: always replace the molname line using --molname
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119 option or only when it's empty. Possible values: *always | empty*.
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120 Default: *empty*.
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121
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122 -o, --overwrite
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123 Overwrite existing files.
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124
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125 -r, --root *rootname*
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126 New SD file name is generated using the root: <Root>.<Ext>. Default
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127 new file name: <InitialSDFileName>ModifiedDataFields.<Ext>. This
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128 option is ignored for multiple input files.
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129
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130 -w, --workingdir *dirname*
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131 Location of working directory. Default: current directory.
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132
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133 EXAMPLES
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134 To replace empty molname lines by Cmpd<CmpdNumber> and generate a new SD
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135 file NewSample1.sdf, type:
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136
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137 % ModifySDFilesDataFields.pl -o -r NewSample1 Sample1.sdf
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138
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139 To replace all molname lines by Mol_ID data field generate a new SD file
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140 NewSample1.sdf, type:
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141
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142 % ModifySDFilesDataFields.pl --molnamemode datafield
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143 --molnamereplace always -r NewSample1 -o Sample1.sdf
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144
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145 To replace all molname lines by Mol_ID data field, map Name and
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146 CompoundName to a new datafield Synonym, and generate a new SD file
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147 NewSample1.sdf, type:
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148
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149 % ModifySDFilesDataFields.pl --molnamemode datafield
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150 --molnamereplace always --molname Mol_ID --mode both
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151 --datafieldsmap "Synonym,Name,CompoundName" -r
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152 NewSample1 -o Sample1.sdf
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153
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154 To replace all molname lines by Mol_ID data field, map Name and
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155 CompoundName to a new datafield Synonym, add common fields ReleaseDate
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156 and Source, and generate a new SD file NewSample1.sdf without keeping
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157 any old SD data fields, type:
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158
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159 % ModifySDFilesDataFields.pl --molnamemode datafield
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160 --molnamereplace always --molname Mol_ID --mode both
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161 --datafieldsmap "Synonym,Name,CompoundName"
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162 --datafieldscommon "ReleaseDate,yyyy-mm-dd,Source,
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163 www.mayachemtools.org" --keepolddatafields none -r
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164 NewSample1 -o Sample1.sdf
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165
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166 Preparing SD files PubChem deposition:
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167
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168 Consider a SD file with these fields: Mol_ID, Name, Synonyms and
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169 Systematic_Name. And Mol_ID data field uniquely identifies your
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170 compound.
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171
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172 To prepare a new SD file CmpdDataForPubChem.sdf containing only required
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173 PUBCHEM_EXT_DATASOURCE_REGID field, type:
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174
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175 % ModifySDFilesDataFields.pl --m datafields
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176 --datafieldsmap
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177 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID"
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178 -r CmpdDataForPubChem -o Sample1.sdf
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179
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180 To prepare a new SD file CmpdDataForPubChem.sdf containing only required
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181 PUBCHEM_EXT_DATASOURCE_REGID field and replace molname line with Mol_ID,
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182 type:
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183
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184 % ModifySDFilesDataFields.pl --molnamemode datafield
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185 --molnamereplace always --molname Mol_ID --mode both
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186 --datafieldsmap
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187 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID"
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188 -r CmpdDataForPubChem -o Sample1.sdf
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189
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190 In addition to required PubChem data field, you can also add optional
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191 PubChem data fields.
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192
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193 To map your Name, Synonyms and Systematic_Name data fields to optional
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194 PUBCHEM_SUBSTANCE_SYNONYM data field along with required ID field, type:
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195
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196 % ModifySDFilesDataFields.pl --molnamemode datafield
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197 --molnamereplace always --molname Mol_ID --mode both
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198 --datafieldsmap
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199 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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200 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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201 -r CmpdDataForPubChem -o Sample1.sdf
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202
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203 To add your <domain.org> as PUBCHEM_EXT_SUBSTANCE_URL and link substance
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204 retrieval to your CGI script
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205 <http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID> via
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206 PUBCHEM_EXT_DATASOURCE_REGID field along with optional and required data
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207 fields, type:
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208
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209 % ModifySDFilesDataFields.pl --molnamemode datafield
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210 --molnamereplace always --molname Mol_ID --mode both
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211 --datafieldsmap
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212 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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213 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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214 --datafieldscommon
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215 "PUBCHEM_EXT_SUBSTANCE_URL,domain.org"
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216 --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL,
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217 http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID"
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218 -r CmpdDataForPubChem -o Sample1.sdf
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219
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220 And to add a publication date and request a release data using
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221 PUBCHEM_PUBLICATION_DATE and PUBCHEM_DEPOSITOR_RECORD_DATE data fields
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222 along with all the data fields in earlier examples, type: optional
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223 fields, type:
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224
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225 % ModifySDFilesDataFields.pl --molnamemode datafield
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226 --molnamereplace always --molname Mol_ID --mode both
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227 --datafieldsmap
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228 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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229 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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230 --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL,
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231 http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID"
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232 --datafieldscommon
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233 "PUBCHEM_EXT_SUBSTANCE_URL,domain.org,
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234 PUBCHEM_PUBLICATION_DATE,YYY-MM-DD,
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235 PUBCHEM_DEPOSITOR_RECORD_DATE,YYYY-MM-DD"
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236 -r CmpdDataForPubChem -o Sample1.sdf
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237
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238 AUTHOR
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239 Manish Sud <msud@san.rr.com>
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240
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241 SEE ALSO
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242 InfoSDFiles.pl, JoinSDFiles.pl, MergeTextFilesWithSD.pl,
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243 SplitSDFiles.pl, SDFilesToHTML.pl
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244
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245 COPYRIGHT
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246 Copyright (C) 2015 Manish Sud. All rights reserved.
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247
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248 This file is part of MayaChemTools.
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249
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250 MayaChemTools is free software; you can redistribute it and/or modify it
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251 under the terms of the GNU Lesser General Public License as published by
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252 the Free Software Foundation; either version 3 of the License, or (at
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253 your option) any later version.
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254
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