From 1deca607f16dc5a17ca5c4db9c9bd726725a5dd3 Mon Sep 17 00:00:00 2001 From: Daniel Leidert Date: Mon, 2 Mar 2009 19:02:56 +0000 Subject: [PATCH] * doc/babel.1, doc/obchiral.1, doc/obconformer.1, doc/obenergy.1, doc/obfit.1, doc/obgen.1, doc/obgrep.1, doc/obminimize.1, doc/obprobe.1, doc/obprop.1, doc/obrotamer.1, doc/obrotate.1, doc/roundtrip.1: Prevent hyphenation of URLs. Fixed an mdoc issue. --- ChangeLog | 7 +++++++ doc/babel.1 | 6 +++--- doc/obchiral.1 | 4 ++-- doc/obconformer.1 | 4 ++-- doc/obenergy.1 | 6 +++--- doc/obfit.1 | 6 +++--- doc/obgen.1 | 6 +++--- doc/obgrep.1 | 6 +++--- doc/obminimize.1 | 6 +++--- doc/obprobe.1 | 5 +++-- doc/obprop.1 | 4 ++-- doc/obrotamer.1 | 4 ++-- doc/obrotate.1 | 6 +++--- doc/roundtrip.1 | 4 ++-- 14 files changed, 41 insertions(+), 33 deletions(-) diff --git a/ChangeLog b/ChangeLog index 050b24cf4..4d00880cd 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,10 @@ +2009-03-02 Daniel Leidert + + * doc/babel.1, doc/obchiral.1, doc/obconformer.1, doc/obenergy.1, + doc/obfit.1, doc/obgen.1, doc/obgrep.1, doc/obminimize.1, + doc/obprobe.1, doc/obprop.1, doc/obrotamer.1, doc/obrotate.1, + doc/roundtrip.1: Prevent hyphenation of URLs. Fixed an mdoc issue. + 2009-03-02 Daniel Leidert * src/formats/smilesformat.cpp: Correct use of sprintf(). diff --git a/doc/babel.1 b/doc/babel.1 index d7021bc88..88d0e39d4 100644 --- a/doc/babel.1 +++ b/doc/babel.1 @@ -21,7 +21,7 @@ chemistry and related areas. .Pp Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages -<\fBhttp://openbabel.org/\fR>. +\%<\fBhttp://openbabel.org/\fR>. .Sh OPTIONS .Re If only input and ouput files are given, Open Babel will guess the @@ -342,7 +342,7 @@ Split a multi-molecule file into new1.smi, new2.smi, etc.: .Xr obrotate 1 , .Xr obrotamer 1 . The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS .An -nosplit A cast of many, including the currrent maintainers @@ -351,7 +351,7 @@ A cast of many, including the currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br diff --git a/doc/obchiral.1 b/doc/obchiral.1 index 51d7a56ba..4f4591d4a 100644 --- a/doc/obchiral.1 +++ b/doc/obchiral.1 @@ -22,7 +22,7 @@ Open Babel library (libopenbabel). .Xr obrotate 1 . .br The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS The obchiral program was written by .An Nick England @@ -34,7 +34,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 2005 Nick England. .br diff --git a/doc/obconformer.1 b/doc/obconformer.1 index 99b4de241..e8e454832 100644 --- a/doc/obconformer.1 +++ b/doc/obconformer.1 @@ -29,7 +29,7 @@ it to rotamer1.sdf after 100 geometry optimization steps .Xr obrotate 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS .An -nosplit Open Babel is developed by a cast of many, including currrent maintainers @@ -38,7 +38,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br diff --git a/doc/obenergy.1 b/doc/obenergy.1 index 279803e8a..73e05fc71 100644 --- a/doc/obenergy.1 +++ b/doc/obenergy.1 @@ -41,10 +41,10 @@ out all individual energy interactions: .Xr obrotamer 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Pp The web pages for Open Babel Molecular Mechanics can be found at: -<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR> +\%<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR> .Sh AUTHORS The obenergy program was contributed by .An Tim Vandermeersch. @@ -56,7 +56,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 2007 by Tim Vandermeersch. .Pp diff --git a/doc/obfit.1 b/doc/obfit.1 index 5cc293eea..a94cf33ec 100644 --- a/doc/obfit.1 +++ b/doc/obfit.1 @@ -32,10 +32,10 @@ Align all the molecules in 'testmv.sdf' on a single molecule of 'testref.sdf' by .Xr obrotate 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Pp A guide for constructing SMARTS patterns can be found at: -<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR> +\%<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR> .Sh AUTHORS The obfit program was contributed by .An Fabien Fontaine @@ -47,7 +47,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br diff --git a/doc/obgen.1 b/doc/obgen.1 index 4042f9e8e..ba510e508 100644 --- a/doc/obgen.1 +++ b/doc/obgen.1 @@ -38,10 +38,10 @@ UFF forcefield: .Xr obconformer 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Pp The web pages for Open Babel Molecular Mechanics can be found at: -<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR> +\%<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR> .Sh AUTHORS The obgen program was contributed by .An Tim Vandermeersch. @@ -53,7 +53,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 2007-2008 by Tim Vandermeersch. .Pp diff --git a/doc/obgrep.1 b/doc/obgrep.1 index 000df9a79..11573b63c 100644 --- a/doc/obgrep.1 +++ b/doc/obgrep.1 @@ -60,10 +60,10 @@ directory (i.e., *.smi) .Xr obrotate 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Pp A guide for constructing SMARTS patterns can be found at: -<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR> +\%<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR> .Sh AUTHORS The obgrep program was contributed by .An Fabien Fontaine @@ -75,7 +75,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br diff --git a/doc/obminimize.1 b/doc/obminimize.1 index 79d8a8f30..b3f87dc80 100644 --- a/doc/obminimize.1 +++ b/doc/obminimize.1 @@ -51,10 +51,10 @@ steepest descent algorithm and convergence criteria 1e-5: .Xr obrotamer 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Pp The web pages for Open Babel Molecular Mechanics can be found at: -<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR> +\%<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR> .Sh AUTHORS The minimize program was contributed by .An Tim Vandermeersch. @@ -66,7 +66,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 2007 by Tim Vandermeersch. .Pp diff --git a/doc/obprobe.1 b/doc/obprobe.1 index 0e7fd8b3a..497d15131 100644 --- a/doc/obprobe.1 +++ b/doc/obprobe.1 @@ -29,6 +29,7 @@ the molecule. MMFF94 atom type .It Ar pchg MMFF94 partial charge +.El .Sh EXAMPLES .Pp Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen @@ -42,7 +43,7 @@ hydrophobic atom with no partial charge: .Xr babel 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS The obprobe program was contributed by .An Tim Vandermeersch. @@ -54,7 +55,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 2006-2008 by Tim Vandermeersch .br diff --git a/doc/obprop.1 b/doc/obprop.1 index 1041292fb..697610b5a 100644 --- a/doc/obprop.1 +++ b/doc/obprop.1 @@ -66,7 +66,7 @@ The "$$$" is the separator between multiple molecular entries in a file .Xr obrotate 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS The obprop program was contributed by .An Fabien Fontaine @@ -78,7 +78,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 2003 by Fabien Fontaine .br diff --git a/doc/obrotamer.1 b/doc/obrotamer.1 index 0af0cdbde..e624bbee5 100644 --- a/doc/obrotamer.1 +++ b/doc/obrotamer.1 @@ -27,7 +27,7 @@ it to rotamer1.sdf .Xr obrotate 1 . .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS .An -nosplit Open Babel is developed by a cast of many, including currrent maintainers @@ -36,7 +36,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br diff --git a/doc/obrotate.1 b/doc/obrotate.1 index 9218bbf1e..e883420a3 100644 --- a/doc/obrotate.1 +++ b/doc/obrotate.1 @@ -60,10 +60,10 @@ Keep the aliphatic chain fixed and move the pyridyl ring: .Pp .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Pp A guide for constructing SMARTS patterns can be found at: -<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR> +\%<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR> .Sh AUTHORS The obgrep program was contributed by .An Fabien Fontaine @@ -75,7 +75,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br diff --git a/doc/roundtrip.1 b/doc/roundtrip.1 index 501926ecc..0749ab551 100644 --- a/doc/roundtrip.1 +++ b/doc/roundtrip.1 @@ -24,7 +24,7 @@ Compare two files created via a roundtrip test .Xr babel 1 .Pp The web pages for Open Babel can be found at: -<\fBhttp://openbabel.org/\fR> +\%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS .An -nosplit Open Babel is developed by a cast of many, including currrent maintainers @@ -33,7 +33,7 @@ Open Babel is developed by a cast of many, including currrent maintainers .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see -<\fBhttp://openbabel.org/wiki/THANKS\fR> +\%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br