Batch Molecular Weight Calculation

Calculate weights from text file (Automation)

Molecular weights of compounds (formulas) listed in a text file can be computed and written to an output file. The Formula Finder can be also be run in batch analysis mode using appropriate Batch Analysis Commands (see below). In addition, amino acid sequences can be converted from 1 to 3 letter notation (or from 3 to 1 letter notation).

Initiate batch analysis mode by either choosing "Calculate weights" from under the File menu and selecting the file, or by using the /F:filename switch at the command line. The input file must be a text file with each line containing a single molecular formula, an amino acid sequence, a numeric mass to use for the formula finder, a batch analysis command (see below), or a comment (beginning with a ; or ').

Batch Molecular Weight Computation

The default mode for batch analysis is molecular weight computation. To use this mode, the text file need only contain a single, valid molecular formula on each line. Each formula's molecular weight will be computed, and the results written to the output file (see below for filename). The output file will contain the original formula, plus its molecular weight, separated by a Tab (configurable using DELIMETER=). By default, the standard deviation is included, formatted depending on the current setting for the standard deviation mode. Whether or not to include the standard deviation, in addition to its format, can be customized using STDDEVMODE=. If there is an error in the formula, the error will be listed in the output file. If a FF= Batch Command was issued earlier in the file, a MW= command can be used to switch back to Molecular Weight Computation mode (see the example input file below).

The Batch Analysis Command WEIGHTMODE={AVERAGE|ISOTOPIC|INTEGER} can be used to set the weight mode for computations. For example, to switch to isotopic mode use WEIGHTMODE=ISOTOPIC and to switch back to average mode use WEIGHTMODE=AVERAGE. You can suppress the display of the source formula using MWSHOWSOURCEFORMULA=OFF. You can suppress the display of the formula's mass using SHOWMASS=OFF. This is useful if you simply wish to convert formulas to their empirical formula (using EMPIRICAL=ON).

If you need to compute the mass of peptides listed in 1-letter notation, you can use ONELETTERPEPTIDEWEIGHTMODE=ON. The default prefix and suffix groups for the peptides are H and OH, though this can be changed with PEPTIDEWEIGHTMODEPEPTIDEPREFIX and PEPTIDEWEIGHTMODEPEPTIDESUFFIX. To compute the mass of peptides listed in 3-letter notation, simply use the default MW= molecular weight computation mode. However, note that 3-letter abbreviation peptide formulas must explicitly include the H and OH in the formula to obtain the correct mass. For example, GlyLeuTyr will return a mass of 333.38234, while HGLyLeuTyrOH (or H-GlyLeuTyr-OH) will return the correct mass of 351.39762 (in average mass mode).

Batch Formula Finder Mode

In order to enter formula finder mode you must place the command FF= on a line in the input text file. You may also optionally specify which elements to use for the formula finder searching by listing them on the same line as the FF= command, separated by commas (if not specified, the previously enabled elements will be used). The Batch Analysis commands MAXHITS=num and TOLERANCE=num can be used to specify the maximum number of hits or the search tolerance. If either of these commands is omitted, the values currently set in the Molecular Weight Calculator Formula Finder window will be used.

Once formula finder mode has been enabled (using FF=), a list of numeric values to match elemental combinations to can be given, with each value listed on its own line. For each value, a list of matching empirical formulas will be determined, and the results written to the output file. The MAXHITS= or TOLERANCE= command can be given at any time in the list in order to change one of the values. Additionally, the FF= command can be re-issued with a new list of search elements to use. Finally, the MW= command can be used to switch back to Molecular Weight Computation Mode.

Batch Amino Acid Notation Conversion Mode

The third mode for batch analysis is amino acid sequence notation conversion. Use AACONVERT3TO1=ON for 3 letter to 1 letter conversion, or AACONVERT1TO3=ON for the reverse. After this, each line will be treated as a sequence and converted as desired. By default the source sequence is outputted, followed by the converted sequence. To prevent output of the source sequence, use the command AASHOWSEQUENCEBEINGCONVERTED=OFF

Output File and Automation

The output filename will be the input filename, plus the extension ".out". For example, if the input file is "formulas.txt", the output file will be "formulas.txt.out". If the /F:filename switch is used on the command line, the Molecular Calculator program will exit upon completion of processing the input file. Additionally, you can specify an alternate output filename using the /O:outfile switch. Use the /Y switch to suppress the "Are you sure you want to replace?" dialog box from appearing when an existing output file is found.

To process a number of files at once, simply create a batch file (.BAT) containing lines to call the Molecular Weight calculator program and process each file. For example, you could create GO.BAT containing the lines:

Then, run GO.BAT and the files will be processed.

Batch Analysis Command Summary

Values in brackets [] are optional (do not use the brackets). Words in curly brackes {} are a list of potential words; choose just one of the words and do not use the curly brackes or comma. num is a valid number

Command and options Explanation Default

MW=
Enable Normal Molecular Weight Computation mode

WEIGHTMODE={AVERAGE|ISOTOPIC|INTEGER}
Weight mode to use. The weight mode in effect the last time the program was run (or the current weight mode if the program is running).

STDDEVMODE={SHORT|SCIENTIFIC|DECIMAL|OFF}
The standard deviation mode, defining how to format the standard deviation of each element's weight The standard deviation mode in effect the last time the program was run (or the current standard deviation mode if the program is running).

MWSHOWSOURCEFORMULA={ON|OFF}
When ON, will output the source formula, followed by either the molecular weight, the empirical formula, or the formula with expanded abbreviations, separating the two with the currently defined delimeter.
ON

CAPITALIZED={ON|OFF}
If ON, will output the source formula properly capitalized. For example, c6h6 would be outputted as C6H6. Default is OFF.
OFF

EMPIRICAL={ON|OFF}
If ON, will convert the source formula to its empirical formula and output the result. If MWSHOWSOURCEFORMULA=ON, will show the source formula before the empirical formula, separating with the currently defined delimeter. Unless SHOWMASS=OFF, the molecular weight will also be outputted.
OFF

EXPANDABBREVIATIONS={ON|OFF}
If ON, will expand the abbreviations in the source formula to their elemental equivalent, and output the result. If MWSHOWSOURCEFORMULA=ON, will show the source formula before the resultant formula, separating with the currently defined delimeter. Unless SHOWMASS=OFF, the molecular weight will also be outputted.
OFF

SHOWMASS={ON|OFF}
When ON, will output the mass of each formula encountered in normal weight computation mode.
ON

ONELETTERPEPTIDEWEIGHTMODE={ON|OFF}
When ON, will treat the input formulas as peptides in 1-letter notation. The default peptide prefix is H and default peptide suffix is OH. Use PEPTIDEWEIGHTMODEPEPTIDEPREFIX and PEPTIDEWEIGHTMODEPEPTIDESUFFIX to change the default prefix and suffix. Note that this mode is not appropriate for computing masses of peptides in 3-letter notation. Those peptide masses can be computed using the Normal Molecular Weight Computation (MW=) mode.
OFF

PEPTIDEWEIGHTMODEPEPTIDEPREFIX={custom formula}
Use this to set a custom prefix formula for peptide masses computed when ONELETTERPEPTIDEWEIGHTMODE=ON.
H

PEPTIDEWEIGHTMODEPEPTIDESUFFIX={custom formula}
Use this to set a custom suffix formula for peptide masses.
OH

DELIMETER={<TAB>|<SPACE>| <ENTER>|<CRLF>|custom symbol}
The delimeter to use to separate the source formula and the computed mass, or the source sequence and the converted sequence. Use one of the standard <> commands (for example DELIMETER=<TAB>) or provide a custom symbol (for example DELIMETER=, to set the delimeter to a comma)
<TAB>

AACONVERT3TO1={ON|OFF}
When ON, will treat each line as a set of 3 letter amino acid abbreviations, and will output the equivalent 1 letter sequence.
OFF

AACONVERT1TO3={ON|OFF}
When ON, will treat each line as a set of 1 letter amino acid abbreviations, and will output the equivalent 3 letter sequence.
OFF

AASPACEEVERY10={ON|OFF}
When ON, will add a space every 10 residues in the output sequence.
OFF

AA1TO3USEDASH={ON|OFF}
When ON, will separate each residue with a dash (only applicable for 1 to 3 letter conversion).
OFF

AASHOWSEQUENCEBEINGCONVERTED={ON|OFF}
When ON, will output the source sequence, followed by the converted sequence, separated the currently defined delimeter. It is useful to set this option to OFF if you are converting long sequences.
ON

FF=[Element1[,Element2][,...]]
Enable Formula Finder mode. Optionally provide a comma-separated list of elements or abbreviations to search for. If no list of elements is supplied after the equals sign, then the options last used for the formula finder will be used.

MAXHITS=num
Define the maximum number of formula finder hits

TOLERANCE=num
Set the formula finder search tolerance

; Comment
Insert a comment by starting a line with a semicolon or an apostrophe. You cannot add a comment on the same line as a Batch Analysis Command or any other text to be used for computation.

ECHOCOMMENTS={ON|OFF}
When ON, will write any blank lines and comment lines found in the source file to the output file.
OFF

VERBOSEMODE={ON|OFF}
When ON, will write a comment to the output file each time a command is found in the source file. Error messages will be written to the output file regardless of the VERBOSEMODE setting.
ON

Command and options	Explanation	Default
MW=	Enable Normal Molecular Weight Computation mode
WEIGHTMODE={AVERAGE\|ISOTOPIC\|INTEGER}	Weight mode to use.	The weight mode in effect the last time the program was run (or the current weight mode if the program is running).
STDDEVMODE={SHORT\|SCIENTIFIC\|DECIMAL\|OFF}	The standard deviation mode, defining how to format the standard deviation of each element's weight	The standard deviation mode in effect the last time the program was run (or the current standard deviation mode if the program is running).
MWSHOWSOURCEFORMULA={ON\|OFF}	When ON, will output the source formula, followed by either the molecular weight, the empirical formula, or the formula with expanded abbreviations, separating the two with the currently defined delimeter.	ON
CAPITALIZED={ON\|OFF}	If ON, will output the source formula properly capitalized. For example, c6h6 would be outputted as C6H6. Default is OFF.	OFF
EMPIRICAL={ON\|OFF}	If ON, will convert the source formula to its empirical formula and output the result. If MWSHOWSOURCEFORMULA=ON, will show the source formula before the empirical formula, separating with the currently defined delimeter. Unless SHOWMASS=OFF, the molecular weight will also be outputted.	OFF
EXPANDABBREVIATIONS={ON\|OFF}	If ON, will expand the abbreviations in the source formula to their elemental equivalent, and output the result. If MWSHOWSOURCEFORMULA=ON, will show the source formula before the resultant formula, separating with the currently defined delimeter. Unless SHOWMASS=OFF, the molecular weight will also be outputted.	OFF
SHOWMASS={ON\|OFF}	When ON, will output the mass of each formula encountered in normal weight computation mode.	ON
ONELETTERPEPTIDEWEIGHTMODE={ON\|OFF}	When ON, will treat the input formulas as peptides in 1-letter notation. The default peptide prefix is H and default peptide suffix is OH. Use PEPTIDEWEIGHTMODEPEPTIDEPREFIX and PEPTIDEWEIGHTMODEPEPTIDESUFFIX to change the default prefix and suffix. Note that this mode is not appropriate for computing masses of peptides in 3-letter notation. Those peptide masses can be computed using the Normal Molecular Weight Computation (MW=) mode.	OFF
PEPTIDEWEIGHTMODEPEPTIDEPREFIX={custom formula}	Use this to set a custom prefix formula for peptide masses computed when ONELETTERPEPTIDEWEIGHTMODE=ON.	H
PEPTIDEWEIGHTMODEPEPTIDESUFFIX={custom formula}	Use this to set a custom suffix formula for peptide masses.	OH
DELIMETER={<TAB>\|<SPACE>\| <ENTER>\|<CRLF>\|custom symbol}	The delimeter to use to separate the source formula and the computed mass, or the source sequence and the converted sequence. Use one of the standard <> commands (for example DELIMETER=<TAB>) or provide a custom symbol (for example DELIMETER=, to set the delimeter to a comma)	<TAB>
AACONVERT3TO1={ON\|OFF}	When ON, will treat each line as a set of 3 letter amino acid abbreviations, and will output the equivalent 1 letter sequence.	OFF
AACONVERT1TO3={ON\|OFF}	When ON, will treat each line as a set of 1 letter amino acid abbreviations, and will output the equivalent 3 letter sequence.	OFF
AASPACEEVERY10={ON\|OFF}	When ON, will add a space every 10 residues in the output sequence.	OFF
AA1TO3USEDASH={ON\|OFF}	When ON, will separate each residue with a dash (only applicable for 1 to 3 letter conversion).	OFF
AASHOWSEQUENCEBEINGCONVERTED={ON\|OFF}	When ON, will output the source sequence, followed by the converted sequence, separated the currently defined delimeter. It is useful to set this option to OFF if you are converting long sequences.	ON
FF=[Element1[,Element2][,...]]	Enable Formula Finder mode. Optionally provide a comma-separated list of elements or abbreviations to search for.	If no list of elements is supplied after the equals sign, then the options last used for the formula finder will be used.
MAXHITS=num	Define the maximum number of formula finder hits
TOLERANCE=num	Set the formula finder search tolerance
; Comment	Insert a comment by starting a line with a semicolon or an apostrophe. You cannot add a comment on the same line as a Batch Analysis Command or any other text to be used for computation.
ECHOCOMMENTS={ON\|OFF}	When ON, will write any blank lines and comment lines found in the source file to the output file.	OFF
VERBOSEMODE={ON\|OFF}	When ON, will write a comment to the output file each time a command is found in the source file. Error messages will be written to the output file regardless of the VERBOSEMODE setting.	ON

Example Input File

; Set weight mode
WEIGHTMODE=AVERAGE

; Set Standard Deviation mode
STDDEVMODE=OFF

; Return capitalized (formatted) formulas
CAPITALIZED=ON

fecl3-6h2o

; Expand abbreviations
EXPANDABBREVIATIONS=ON

etoac

; Don't display the source formula
MWSHOWSOURCEFORMULA=OFF
etoac

; Don't display the weight
SHOWWEIGHT=OFF
etoac

; Convert to empirical formula
; Note: no need to use EXPANDABBREVIATIONS=OFF
EMPIRICAL=ON

fecl3-6h2o
etoac

; Re-enable display of the source formula
MWSHOWSOURCEFORMULA=ON
UreaC4(NH2)4Ca

; Convert amino acid sequence from 1 letter to 3 letter sequence
AACONVERT3TO1=ON

GluGlaPheLeu
Val-Ile-Arg

AASPACEEVERY10=ON
; For really long sequences, can disable display of the source sequence
AASHOWSEQUENCEBEINGCONVERTED=OFF
GluGlaPheLeuVAlIleArgPheTyrMetCysValGluGlaGluGlaPheLeuVAlIleArgPheTyrMetCysValGluGla

AACONVERT1TO3=ON
FLEELYR
MLTSCDEEF

AASHOWSEQUENCEBEINGCONVERTED=ON
AA1TO3USEDASH=ON
FLEELYR

; To re-enable plain molecular weight computation, use MW=
; Note: this will also disable EMPIRICAL= and EXPANDABBREVIATIONS=
;       Further, it will automatically re-enable SHOWWEIGHT
MW=

C4N8OH2

; Compute the mass of peptides given in 1-letter notation
ONELETTERPEPTIDEWEIGHTMODE=ON

FLEELYR
MLTSCDEEF

; Don't show the source formula when computing the peptide's mass
MWSHOWSOURCEFORMULA=OFF

MLTSCDEEF

; Enable formula finder mode using FF=, specifying the elements to use in searching
; Can also specify weight mode, maximum number of hits, and tolerance
FF=C,H,N,O,Cl,Bpy
WEIGHTMODE=ISOTOPIC
MAXHITS=5
TOLERANCE=0.05
403.84
300.58

; The tolerance can be changed
TOLERANCE=0.02
403.885

; The maximum number of hits can be changed
MAXHITS=10
632.43

; The search elements can be changed
FF=N,Br,H,Li
MAXHITS=2
389.32

; Can disable verbose output
VERBOSEMODE=OFF
; Additionally, could enable echo of comments
ECHOCOMMENTS=ON
; Switching back (this comment is in the source file)

MW=
MWSHOWSOURCEFORMULA=ON
NH2
C6H5Cl
^13C6H5Cl

WEIGHTMODE=AVERAGE
FeCl3-6H2O



; So is this one, along with the 3 blank lines above
MWSHOWSOURCEFORMULA=OFF
NH2
C6H5Cl
^13C6H5Cl
FeCl3-6H2O

VERBOSEMODE=ON
DELIMETER=<SPACE>
CAPITALIZED=on
c6h5cl

DELIMETER= >
c6h5cl

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