'\" t
.\"     Title: inchi_main
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 09/18/2022
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "INCHI_MAIN" "1" "09/18/2022" "\ \&" "\ \&"
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.\" * Define some portability stuff
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.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
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.\" * set default formatting
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.nh
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.\" * MAIN CONTENT STARTS HERE *
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.SH "NAME"
inchi_main \- InChI library call example
.SH "SYNOPSIS"
.sp
\fIinchi_main inputFile [outputFile [logFile [problemFile]]] [\-option[ \-option\&...]]\fR
.SH "OPTIONS"
.PP
\fBInput\fR
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
STDIO: Use standard input/output streams
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
InpAux: Input structures in InChI default aux\&. info format (for use with STDIO)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SDF:DataHeader: Read from the input SDfile the ID under this DataHeader
.RE
.PP
\fBOutput\fR
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
AuxNone: Omit auxiliary information (default: Include)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SaveOpt: Save custom InChI creation options (non\-standard InChI)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
NoLabels: Omit structure number, DataHeader and ID from InChI output
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Tabbed: Separate structure number, InChI, and AuxInfo with tabs
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
OutputSDF: Convert InChI created with default aux\&. info to SDfile
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SdfAtomsDT: Output Hydrogen Isotopes to SDfile as Atoms D and T
.RE
.PP
\fBStructure perception\fR
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SNon: Exclude stereo (default: include absolute stereo)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
NEWPSOFF: Both ends of wedge point to stereocenters (default: a narrow end)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
DoNotAddH: All H are explicit (default: add H according to usual valences)
.RE
.PP
\fBStereo perception modifiers (non\-standard InChI)\fR
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SRel: Relative stereo
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SRac: Racemic stereo
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SUCF: Use Chiral Flag: On means Absolute stereo, Off \- Relative
.RE
.PP
\fBCustomizing InChI creation (non\-standard InChI)\fR
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SUU: Always include omitted unknown/undefined stereo
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
SLUUD: Make labels for unknown and undefined stereo different
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
RecMet: Include reconnected metals results
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
FixedH: Include Fixed H layer
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
KET: Account for keto\-enol tautomerism (experimental)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
15T: Account for 1,5\-tautomerism (experimental)
.RE
.PP
\fBGeneration\fR
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Wnumber: Set time\-out per structure in seconds; W0 means unlimited
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
WarnOnEmptyStructure: Warn and produce empty InChI for empty structure
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Key: Generate InChIKey
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
XHash1: Generate hash extension (to 256 bits) for 1st block of InChIKey
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
XHash2: Generate hash extension (to 256 bits) for 2nd block of InChIKey
.RE