texstyles 0.0.1

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Files changed (130) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +50 -0
  3. data/.travis.yml +4 -0
  4. data/Gemfile +4 -0
  5. data/LICENSE.txt +21 -0
  6. data/README.md +34 -0
  7. data/Rakefile +10 -0
  8. data/lib/texstyles.rb +26 -0
  9. data/lib/texstyles/style.rb +38 -0
  10. data/styles/a0poster-landscape.tex.erb +84 -0
  11. data/styles/a0poster-portrait.tex.erb +84 -0
  12. data/styles/aa.tex.erb +46 -0
  13. data/styles/aa_onecolumn.tex.erb +45 -0
  14. data/styles/aa_twocolumn.tex.erb +47 -0
  15. data/styles/aaai.tex.erb +29 -0
  16. data/styles/abnt.tex.erb +141 -0
  17. data/styles/acl.tex.erb +46 -0
  18. data/styles/acm.tex.erb +77 -0
  19. data/styles/acm_large.tex.erb +82 -0
  20. data/styles/acm_sig_alternate.tex.erb +116 -0
  21. data/styles/acm_sig_strict.tex.erb +90 -0
  22. data/styles/acs.tex.erb +76 -0
  23. data/styles/agu.tex.erb +211 -0
  24. data/styles/aiaa.tex.erb +84 -0
  25. data/styles/aip_preprint.tex.erb +65 -0
  26. data/styles/aip_reprint.tex.erb +67 -0
  27. data/styles/aisb2008.tex.erb +31 -0
  28. data/styles/aj_manuscript.tex.erb +76 -0
  29. data/styles/aj_preprint.tex.erb +78 -0
  30. data/styles/ajps.tex.erb +69 -0
  31. data/styles/alma.tex.erb +53 -0
  32. data/styles/ams_one.tex.erb +115 -0
  33. data/styles/ams_two.tex.erb +119 -0
  34. data/styles/apa_doc.tex.erb +21 -0
  35. data/styles/apj_emulate.tex.erb +104 -0
  36. data/styles/apj_manuscript.tex.erb +76 -0
  37. data/styles/aps.tex.erb +79 -0
  38. data/styles/aps_preprint.tex.erb +79 -0
  39. data/styles/article.tex.erb +28 -0
  40. data/styles/asp.tex.erb +26 -0
  41. data/styles/authorea-double-numbered.tex.erb +65 -0
  42. data/styles/authorea-double.tex.erb +62 -0
  43. data/styles/authorea-numbered.tex.erb +62 -0
  44. data/styles/authorea.tex.erb +59 -0
  45. data/styles/biogeosciences.tex.erb +71 -0
  46. data/styles/bioinformatics.tex.erb +34 -0
  47. data/styles/bmc.tex.erb +212 -0
  48. data/styles/book.tex.erb +22 -0
  49. data/styles/cernatsnote.tex.erb +28 -0
  50. data/styles/cernyrep.tex.erb +28 -0
  51. data/styles/chandra.tex.erb +182 -0
  52. data/styles/cogsci.tex.erb +43 -0
  53. data/styles/cornell.tex.erb +75 -0
  54. data/styles/cv.tex.erb +30 -0
  55. data/styles/development.tex.erb +55 -0
  56. data/styles/dfgproposal.tex.erb +103 -0
  57. data/styles/dod.tex.erb +221 -0
  58. data/styles/doe.tex.erb +62 -0
  59. data/styles/econf.tex.erb +174 -0
  60. data/styles/egu.tex.erb +73 -0
  61. data/styles/elsevier.tex.erb +138 -0
  62. data/styles/elsevier_review.tex.erb +140 -0
  63. data/styles/elsevier_softwarex.tex.erb +132 -0
  64. data/styles/elsevier_twocolumn.tex.erb +148 -0
  65. data/styles/empty.tex.erb +29 -0
  66. data/styles/epjc.tex.erb +78 -0
  67. data/styles/f1000.tex.erb +38 -0
  68. data/styles/frontiersENG.tex.erb +66 -0
  69. data/styles/frontiersFPHY.tex.erb +67 -0
  70. data/styles/frontiersMED.tex.erb +66 -0
  71. data/styles/frontiersSCNS.tex.erb +66 -0
  72. data/styles/g3.tex.erb +57 -0
  73. data/styles/geophysics.tex.erb +38 -0
  74. data/styles/gji.tex.erb +51 -0
  75. data/styles/hess.tex.erb +71 -0
  76. data/styles/hst.tex.erb +37 -0
  77. data/styles/iclr.tex.erb +35 -0
  78. data/styles/ieee_bare_conf.tex.erb +316 -0
  79. data/styles/ieee_bare_jrnl.tex.erb +459 -0
  80. data/styles/ieee_bare_jrnl_compsoc.tex.erb +530 -0
  81. data/styles/ifac.tex.erb +36 -0
  82. data/styles/ijcai.tex.erb +60 -0
  83. data/styles/imsart_aas.tex.erb +82 -0
  84. data/styles/imsart_as.tex.erb +82 -0
  85. data/styles/iop.tex.erb +93 -0
  86. data/styles/iram_proposal.tex.erb +93 -0
  87. data/styles/jacow.tex.erb +77 -0
  88. data/styles/jfm.tex.erb +43 -0
  89. data/styles/jhep.tex.erb +57 -0
  90. data/styles/jinst.tex.erb +46 -0
  91. data/styles/jrss.tex.erb +32 -0
  92. data/styles/jxb.tex.erb +56 -0
  93. data/styles/lncs.tex.erb +75 -0
  94. data/styles/mdpi.tex.erb +122 -0
  95. data/styles/mit.tex.erb +186 -0
  96. data/styles/mnras.tex.erb +41 -0
  97. data/styles/nasa.tex.erb +111 -0
  98. data/styles/nature.tex.erb +34 -0
  99. data/styles/nature_scirep.tex.erb +36 -0
  100. data/styles/nih.tex.erb +223 -0
  101. data/styles/nime.tex.erb +82 -0
  102. data/styles/nips.tex.erb +26 -0
  103. data/styles/nsf.tex.erb +66 -0
  104. data/styles/osaexpress.tex.erb +73 -0
  105. data/styles/osaletters.tex.erb +54 -0
  106. data/styles/peerj.tex.erb +45 -0
  107. data/styles/plos.tex.erb +69 -0
  108. data/styles/plos2015.tex.erb +237 -0
  109. data/styles/pnas.tex.erb +118 -0
  110. data/styles/report.tex.erb +17 -0
  111. data/styles/rsc.tex.erb +99 -0
  112. data/styles/sciadvances.tex.erb +120 -0
  113. data/styles/science.tex.erb +127 -0
  114. data/styles/sigchi.tex.erb +91 -0
  115. data/styles/sigplan.tex.erb +94 -0
  116. data/styles/spie.tex.erb +68 -0
  117. data/styles/spieman.tex.erb +75 -0
  118. data/styles/springer.tex.erb +92 -0
  119. data/styles/springer_twocolumn.tex.erb +92 -0
  120. data/styles/svmono.tex.erb +63 -0
  121. data/styles/trb.tex.erb +150 -0
  122. data/styles/tufte-handout.tex.erb +60 -0
  123. data/styles/uchicago.tex.erb +53 -0
  124. data/styles/ucriverside.tex.erb +79 -0
  125. data/styles/uiowa.tex.erb +78 -0
  126. data/styles/umich.tex.erb +68 -0
  127. data/styles/uvic.tex.erb +196 -0
  128. data/styles/uwollongong.tex.erb +149 -0
  129. data/texstyles.gemspec +25 -0
  130. metadata +258 -0
@@ -0,0 +1,186 @@
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+ % -*- Mode:TeX -*-
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+
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+ %% IMPORTANT: The official thesis specifications are available at:
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+ %% http://libraries.mit.edu/archives/thesis-specs/
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+ %%
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+ %% Please verify your thesis' formatting and copyright
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+ %% assignment before submission. If you notice any
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+ %% discrepancies between these templates and the
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+ %% MIT Libraries' specs, please let us know
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+ %% by e-mailing thesis@mit.edu
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+
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+ %% The documentclass options along with the pagestyle can be used to generate
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+ %% a technical report, a draft copy, or a regular thesis. You may need to
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+ %% re-specify the pagestyle after you \include cover.tex. For more
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+ %% information, see the first few lines of mitthesis.cls.
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+
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+ %\documentclass[12pt,vi,twoside]{mitthesis}
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+ %%
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+ %% If you want your thesis copyright to you instead of MIT, use the
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+ %% ``vi'' option, as above.
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+ %%
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+ %\documentclass[12pt,twoside,leftblank]{mitthesis}
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+ %%
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+ %% If you want blank pages before new chapters to be labelled ``This
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+ %% Page Intentionally Left Blank'', use the ``leftblank'' option, as
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+ %% above.
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+
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+ \documentclass[12pt,twoside]{mitthesis}
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+ \usepackage{lgrind}
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+ %% These have been added at the request of the MIT Libraries, because
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+ %% some PDF conversions mess up the ligatures. -LB, 1/22/2014
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+ \usepackage{cmap}
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+ %\usepackage[T1]{fontenc}
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+ \pagestyle{plain}
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+
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+ %% This bit allows you to either specify only the files which you wish to
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+ %% process, or `all' to process all files which you \include.
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+ %% Krishna Sethuraman (1990).
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+
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+ <%=@default_packages%>
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+
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+ <%=@header%>
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+
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+ \begin{document}
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+
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+
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+ % -*-latex-*-
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+ %
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+ % For questions, comments, concerns or complaints:
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+ % thesis@mit.edu
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+ %
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+ %
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+ % $Log: cover.tex,v $
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+ % Revision 1.8 2008/05/13 15:02:15 jdreed
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+ % Degree month is June, not May. Added note about prevdegrees.
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+ % Arthur Smith's title updated
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+ %
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+ % Revision 1.7 2001/02/08 18:53:16 boojum
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+ % changed some \newpages to \cleardoublepages
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+ %
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+ % Revision 1.6 1999/10/21 14:49:31 boojum
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+ % changed comment referring to documentstyle
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+ %
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+ % Revision 1.5 1999/10/21 14:39:04 boojum
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+ % *** empty log message ***
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+ %
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+ % Revision 1.4 1997/04/18 17:54:10 othomas
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+ % added page numbers on abstract and cover, and made 1 abstract
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+ % page the default rather than 2. (anne hunter tells me this
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+ % is the new institute standard.)
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+ %
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+ % Revision 1.4 1997/04/18 17:54:10 othomas
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+ % added page numbers on abstract and cover, and made 1 abstract
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+ % page the default rather than 2. (anne hunter tells me this
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+ % is the new institute standard.)
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+ %
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+ % Revision 1.3 93/05/17 17:06:29 starflt
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+ % Added acknowledgements section (suggested by tompalka)
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+ %
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+ % Revision 1.2 92/04/22 13:13:13 epeisach
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+ % Fixes for 1991 course 6 requirements
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+ % Phrase "and to grant others the right to do so" has been added to
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+ % permission clause
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+ % Second copy of abstract is not counted as separate pages so numbering works
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+ % out
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+ %
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+ % Revision 1.1 92/04/22 13:08:20 epeisach
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+
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+ % NOTE:
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+ % These templates make an effort to conform to the MIT Thesis specifications,
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+ % however the specifications can change. We recommend that you verify the
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+ % layout of your title page with your thesis advisor and/or the MIT
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+ % Libraries before printing your final copy.
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+ \title{<%=@long_title%>}
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+ <% if !@alternative_author_string.to_s.empty? %>
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+ <%= @alternative_author_string %>
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+ <% else %>
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+ \author{<%=@first_author%>}
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+ % If you wish to list your previous degrees on the cover page, use the
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+ % previous degrees command:
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+ % \prevdegrees{A.A., Harvard University (1985)}
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+ % You can use the \\ command to list multiple previous degrees
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+ % \prevdegrees{B.S., University of California (1978) \\
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+ % S.M., Massachusetts Institute of Technology (1981)}
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+ \department{Department}
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+ <% end %>
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+ % If the thesis is for two degrees simultaneously, list them both
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+ % separated by \and like this:
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+ % \degree{Doctor of Philosophy \and Master of Science}
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+ \degree{Bachelor Degree}
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+
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+ % As of the 2007-08 academic year, valid degree months are September,
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+ % February, or June. The default is June.
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+ \degreemonth{June}
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+ \degreeyear{1990}
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+ \thesisdate{May 18, 1990}
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+
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+ %% By default, the thesis will be copyrighted to MIT. If you need to copyright
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+ %% the thesis to yourself, just specify the `vi' documentclass option. If for
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+ %% some reason you want to exactly specify the copyright notice text, you can
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+ %% use the \copyrightnoticetext command.
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+ %\copyrightnoticetext{\copyright IBM, 1990. Do not open till Xmas.}
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+
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+ % If there is more than one supervisor, use the \supervisor command
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+ % once for each.
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+ \supervisor{Supervison}
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+
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+ % This is the department committee chairman, not the thesis committee
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+ % chairman. You should replace this with your Department's Committee
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+ % Chairman.
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+ %\chairman{Arthur C. Smith}{Chairman, Department Committee on Graduate Theses}
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+
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+ % Make the titlepage based on the above information. If you need
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+ % something special and can't use the standard form, you can specify
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+ % the exact text of the titlepage yourself. Put it in a titlepage
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+ % environment and leave blank lines where you want vertical space.
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+ % The spaces will be adjusted to fill the entire page. The dotted
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+ % lines for the signatures are made with the \signature command.
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+ \maketitle
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+
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+ % The abstractpage environment sets up everything on the page except
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+ % the text itself. The title and other header material are put at the
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+ % top of the page, and the supervisors are listed at the bottom. A
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+ % new page is begun both before and after. Of course, an abstract may
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+ % be more than one page itself. If you need more control over the
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+ % format of the page, you can use the abstract environment, which puts
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+ % the word "Abstract" at the beginning and single spaces its text.
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+
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+ %% You can either \input (*not* \include) your abstract file, or you can put
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+ %% the text of the abstract directly between the \begin{abstractpage} and
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+ %% \end{abstractpage} commands.
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+
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+ % First copy: start a new page, and save the page number.
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+ \cleardoublepage
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+ % Uncomment the next line if you do NOT want a page number on your
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+ % abstract and acknowledgments pages.
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+ % \pagestyle{empty}
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+ \setcounter{savepage}{\thepage}
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+ \begin{abstractpage}
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+ <%=@abstract%>
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+ \end{abstractpage}
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+
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+ % Additional copy: start a new page, and reset the page number. This way,
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+ % the second copy of the abstract is not counted as separate pages.
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+ % Uncomment the next 6 lines if you need two copies of the abstract
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+ % page.
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+ % \setcounter{page}{\thesavepage}
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+ % \begin{abstractpage}
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+ % \input{abstract}
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+ % \end{abstractpage}
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+
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+ \cleardoublepage
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+
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+ \section*{Acknowledgments}
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+
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+ This is the acknowledgements section. You should replace this with your
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+ own acknowledgements.
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+
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+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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+ % -*-latex-*-
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+
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+ \pagestyle{plain}
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+
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+
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+
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+
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+ %\documentclass[referee,usenatbib]{mn2e}
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+ \documentclass[usenatbib]{mn2e}
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+
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+ <%=@default_packages%>
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+
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+ %\usepackage{natbib}
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+
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+ <%=@header%>
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+
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+ \title[<%=@long_title%>]{<%=@long_title%>}
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+
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+ <% if !@alternative_author_string.to_s.empty? %>
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+ <%= @alternative_author_string %>
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+ <% else %>
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+ \author[<%=@first_author%>]{<%=@first_author%>$^{1}$<% if !@coauthor_list.to_a.empty? %><% for i in (0..@coauthor_list.length-1) %>, <%=@coauthor_list[i]%>$^{<%=i+2%>}$<% end %><% end %>\\
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+ $^{1}$<%=@first_affiliation%>
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+ <% if !@coauthor_affiliations.to_a.empty? %><% for i in (0..@coauthor_affiliations.length-1) %>\\
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+ $^{<%=i+2%>}$<%=@coauthor_affiliations[i]%><% end %><% end %>}
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+ <% end %>
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+
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+ \begin{document}
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+
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+ %\date{Accepted 1988 December 15. Received 1988 December 14; in original form 1988 October 11}
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+
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+ %\pagerange{\pageref{firstpage}--\pageref{lastpage}} \pubyear{2002}
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+
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+ \maketitle
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+
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+ \label{firstpage}
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+
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+ <%= @abstract_begin_end %>
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+
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+
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+ %\begin{keywords}
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+ %circumstellar matter -- infrared: stars.
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+ %\end{keywords}
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+
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+
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+
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+
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+
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+ \documentclass[letterpaper,12pt]{article}
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+ %\documentclass{article}
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+
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+ %% ----------------------- Header ----------------------------------
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+ %% *****************************************************************
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+ %% ""
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+ %% *****************************************************************
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+ %% -----------------------------------------------------------------
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+ %% -----------------------------------------------------------------
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+
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+ %% **************************************************************************
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+ %% Packages
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+ %% **************************************************************************
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+
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+ % \usepackage{epsfig}
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+ % \usepackage{colortbl}
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+ %\usepackage{aas_short}
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+ \usepackage{color}
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+ \usepackage{deluxetable}
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+
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+ \usepackage[sort&compress,numbers]{natbib}
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+ \usepackage{verbatim}
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+ \usepackage{caption}
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+ \captionsetup[figure]{
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+ font=footnotesize,
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+ % labelformat=empty,
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+ labelsep=none,
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+ % labelfont=bf,
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+ justification=RaggedRight
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+ }
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+
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+ <%=@default_packages %>
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+ %%***************************************************************************
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+ %% hyper-ref
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+ %%***************************************************************************
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+ \hypersetup{colorlinks=true}
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+
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+ %%***************************************************************************
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+ %% Biblio options
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+ %%***************************************************************************
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+
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+ % \bibfont{\footnotesize}
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+ \setlength{\bibsep}{0.125cm}
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+ \setlength{\bibhang}{0.25cm}
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+ \renewcommand\bibsection% force references to be a numbered section.
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+ {%
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+ \section{\refname}%
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+ }
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+ \bibpreamble{}
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+
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+ %%***************************************************************************
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+ %% Layout options
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+ %%***************************************************************************
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+
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+ \textwidth=6.5in
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+ \textheight=8.5in
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+ \topmargin=-0.25in
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+ \oddsidemargin=0.0in
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+ \evensidemargin=0.0in
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+ \setlength{\parskip}{1ex plus0.3ex minus0.2ex}
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+
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+ %\pagenumbering{arabic}
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+
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+ \usepackage{fancyhdr}
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+ \pagestyle{fancy}
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+ \fancyhf{} % delete current header and footer
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+ \lhead{\bfseries <%=@short_title%>}
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+ \rhead{\bfseries \thepage}
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+ %\rhead{\bfseries \rightmark}
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+ %\rfoot{\thepage}
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+ \renewcommand{\headrulewidth}{0.5pt}
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+ \renewcommand{\footrulewidth}{0pt}
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+ \addtolength{\headheight}{0.5pt} % space for the rule
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+ \fancypagestyle{plain}{%
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+ \fancyhead{} % get rid of headers on plain pages
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+ \renewcommand{\headrulewidth}{0pt} % and the line
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+ }
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+ \fancypagestyle{toc}{%
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+ \fancyhead{} % get rid of headers on plain pages
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+ \lhead{}
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+ \rhead{}
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+ \chead{\bfseries <%=@short_title%>}
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+ \renewcommand{\headrulewidth}{0.0pt} % and the line
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+ }
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+ \title{<%=@long_title%>}
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+ <% if !@alternative_author_string.to_s.empty? %>
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+ <%= @alternative_author_string %>
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+ <% else %>
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+ \author{<%=@first_author%><% if !@coauthor_list.to_a.empty? %><% for author in @coauthor_list %>, <%=author%><% end %><% end %>}
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+ <% end %>
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+ %% **************************************************************************
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+ %% Miscellaneous commands
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+ %% **************************************************************************
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+
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+ \hyphenation{}
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+ %
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+
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+ <%=@header%>
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+
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+
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+ %% **************************************************************************
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+ %% Begin document
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+ %% **************************************************************************s
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+
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+ \begin{document}
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+
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+ \thispagestyle{toc}
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+ \tableofcontents
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+ \newpage
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+ \setcounter{page}{1}
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+
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+ %% Template for a preprint Letter or Article for submission
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+ %% to the journal Nature.
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+ %% Written by Peter Czoschke, 26 February 2004
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+ %%
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+
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+ \documentclass{nature}
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+
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+ %% make sure you have the nature.cls and naturemag.bst files where
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+ %% LaTeX can find them
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+
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+ <%=@default_packages%>
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+
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+ <%=@header%>
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+
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+ \title{<%=@long_title%>}
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+
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+ %% Notice placement of commas and superscripts and use of &
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+ %% in the author list
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+ <% if !@alternative_author_string.to_s.empty? %>
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+ <%= @alternative_author_string %>
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+ <% else %>
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+ \author{<%=@first_author%>$^{1}$<% if !@coauthor_list.to_a.empty? %><% for i in (0..@coauthor_list.length-1) %>, <%=@coauthor_list[i]%>$^{<%=i+2%>}$<% end %><% end %>}
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+ <% end %>
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+ \begin{document}
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+
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+ \maketitle
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+
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+ \begin{affiliations}
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+ \item <%=@first_affiliation%>
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+ <% if !@coauthor_affiliations.to_a.empty? %><% for i in (0..@coauthor_affiliations.length-1) %>
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+ \item <%=@coauthor_affiliations[i]%><% end %><% end %>
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+ \end{affiliations}
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+
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+ <%= @abstract_begin_end %>
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+ % Template from WL: * <john.hammersley@gmail.com> 2015-02-09T12:07:31.197Z:
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+
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+ \documentclass[fleqn,10pt]{wlscirep}
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+
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+ <%=@default_packages%>
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+
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+ <%=@header%>
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+
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+ \title{<%=@long_title%>}
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+
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+ <% if !@alternative_author_string.to_s.empty? %>
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+ <%= @alternative_author_string %>
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+ <% else %>
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+ \author[1]{<%=@first_author%>}
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+ <% if !@coauthor_list.to_a.empty? %>
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+ <% for i in (0..@coauthor_list.length-1) %>
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+ \author[<%=i+2%>]{<%=@coauthor_list[i]%>}
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+ <% end %><% end %>
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+
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+ \affil[1]{<%=@first_affiliation%>}
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+ <% if !@coauthor_list.to_a.empty? %>
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+ <% for i in (0..@coauthor_list.length-1) %>
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+ \affil[<%=i+2%>]{<%=@coauthor_affiliations[i]%>}
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+ <% end %><% end %>
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+ <% end %>
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+
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+ <%= @abstract_begin_end %>
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+
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+ \begin{document}
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+
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+
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+ \flushbottom
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+ \maketitle
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+
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+ \thispagestyle{empty}
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+
@@ -0,0 +1,223 @@
1
+ % This example file for NIH submissions was originally written
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+ % by Bruce Donald (http://www.cs.duke.edu/brd/).
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+ %
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+ % You may freely use, modify and/or distribute this file.
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+ %
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+ \documentclass[11pt]{nih-blank}
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+ %\documentclass{article}
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+ %\documentclass[12pt]{article}%
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+ % last revision:
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+ \def\mydate{2005-06-09 13:58:03 brd}
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+
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+
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+ %%%%%%% Two column control
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+ \newif\ifdotwocol
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+ \dotwocoltrue % two col
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+ %\dotwocolfalse % one col
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+ \long\def\twocol#1#2{\ifdotwocol{#1}\else{#2}\fi}
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+ %%%%%%%
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+
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+ \def\mybeforeequation{\footnotesize}
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+ %\def\mybeforeequation{\small}
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+ %\def\mybeforeequation{}
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+
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+ \def\myafterequation{\renewcommand\baselinestretch{1.1}}
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+ %\def\myafterequation{}
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+
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+ %%%%%%%%%%%%%%%%
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+ %%%%%%%%%%%%%%%%
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+
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+ \def\citeusmark{$^{\textstyle \star}$}
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+ \def\citeus#1#2{\cite{#1}}
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+
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+ \def\crow#1#2{#2}
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+
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+ %\usepackage{denselists}
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+ %\usepackage{scaledfullpage}
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+ \usepackage[dvips]{graphicx}
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+ \usepackage{color}
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+ \usepackage{boxedminipage}
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+ \usepackage{amsfonts}
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+ \usepackage{amsmath}
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+ \usepackage{url}
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+ %\usepackage{times}
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+ %\usepackage{nih} % PHS 398 Forms
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+ %\usepackage{nihblank} % For printing on Blank PHS 398 Forms
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+ %\usepackage{confidential}
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+
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+ \def\Paper{grant application}
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+ \def\paper{application}
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+ \def\refappendix{Sec.}
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+
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+ \def\poster{(Poster)}
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+
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+ %Note from brd
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+ \long\def\todo#1{{\bf{To do:}} #1}
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+ %\long\def\todo#1{}
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+ \def\ICRA{IEEE International Conference on Robotics and Automation (ICRA)}
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+
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+ \long\def\squeezable#1{#1}
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+
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+ %\def\a5{$\alpha_{_5}$
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+
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+ \def\a5{5}
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+
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+ %\def\mycaptionsize{\normalsize}
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+ %\def\mycaptionsize{\small}
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+ %\def\mycaptionsize{\small}
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+ \def\mycaptionsize{\footnotesize}
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+ \def\mycodesize{\footnotesize}
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+ \def\myeqnsize{\small}
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+
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+ \def\sheading#1{{\bf #1:}\ }
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+ \def\sheading#1{\subsubsection{#1}}
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+ %\def\sheading#1{\bigskip {\bf #1.}}
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+
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+ \def\ssheading#1{\noindent {\bf #1.}\ }
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+
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+ \newtheorem{hypothesis}{Hypothesis}
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+ \long\def\hyp#1{\begin{hypothesis} #1 \end{hypothesis}}
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+
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+ \def\cbk#1{[{\em #1}]}
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+
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+ \def\R{\mathbb{R}}
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+ \def\midv{\mathop{\,|\,}}
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+ \def\Fscr{\mathcal{F}}
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+ \def\Gscr{\mathcal{G}}
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+ \def\Sscr{\mathcal{S}}
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+ \def\set#1{{\{#1\}}}
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+ \def\edge{\!\rightarrow\!}
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+ \def\dedge{\!\leftrightarrow\!}
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+ \newcommand{\EOP}{\nolinebreak[1]~~~\hspace*{\fill} $\Box$\vspace*{\parskip}\vspace*{1ex}}
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+ %my way of doing starred references
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+ \newcommand{\mybibitem}[1]{\bibitem{#1}
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+ \label{mybiblabel:#1}}
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+ \newcommand{\BC}{[}
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+ \newcommand{\EC}{]}
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+ \newcommand{\mycite}[1]{\ref{mybiblabel:#1}\nocite{#1}}
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+ \newcommand{\starcite}[1]{\ref{mybiblabel:#1}\citeusmark\nocite{#1}}
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+
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+
101
+ \def\degree{$^\circ$}
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+ \def\R{\mathbb{R}}
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+ \def\Fscr{\mathcal{F}}
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+ \def\set#1{{\{#1\}}}
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+ \def\edge{\!\rightarrow\!}
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+ \def\dedge{\!\leftrightarrow\!}
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+
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+ \long\def\gobble#1{}
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+ \def\Jigsaw{{\sc Jigsaw}}
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+ \def\ahelix{\ensuremath{\alpha}-helix}
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+ \def\ahelices{\ensuremath{\alpha}-helices}
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+ \def\ahelical{$\alpha$-helical}
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+ \def\bstrand{\ensuremath{\beta}-strand}
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+ \def\bstrands{\ensuremath{\beta}-strands}
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+ \def\bsheet{\ensuremath{\beta}-sheet}
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+ \def\bsheets{\ensuremath{\beta}-sheets}
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+ \def\hone{{\ensuremath{^1}\rm{H}}}
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+ \def\htwo{{$^{2}$H}}
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+ \def\cthir{{\ensuremath{^{13}}\rm{C}}}
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+ \def\nfif{{\ensuremath{^{15}}\rm{N}}}
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+ \def\hn{{\rm{H}\ensuremath{^\mathrm{N}}}}
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+ \def\hnone{{\textup{H}\ensuremath{^1_\mathrm{N}}}}
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+ \def\ca{{\rm{C}\ensuremath{^\alpha}}}
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+ \def\catwel{{\ensuremath{^{12}}\rm{C}\ensuremath{^\alpha}}}
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+ \def\ha{{\rm{H}\ensuremath{^\alpha}}}
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+ \def\cb{{\rm{C}\ensuremath{^\beta}}}
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+ \def\hb{{\rm{H}\ensuremath{^\beta}}}
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+ \def\hg{{\rm{H}\ensuremath{^\gamma}}}
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+ \def\dnn{{\ensuremath{d_{\mathrm{NN}}}}}
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+ \def\dan{{\ensuremath{d_{\alpha \mathrm{N}}}}}
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+ \def\jconst{{\ensuremath{^{3}\mathrm{J}_{\mathrm{H}^{\mathrm{N}}\mathrm{H}^{\alpha}}}} }
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+ \def\cbfb{{CBF-$\beta$}}
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+
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+ \newtheorem{defn}{Definition}
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+ \newtheorem{claim}{Claim}
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+
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+ \gobble{
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+ \psfrag{CO}[][]{\colorbox{white}{C}}
139
+ \psfrag{OO}[][]{\colorbox{white}{O}}
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+ \psfrag{CA}[][]{\colorbox{white}{\ca}}
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+ \psfrag{HA}[][]{\colorbox{white}{\ha}}
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+ \psfrag{CB}[][]{\colorbox{white}{\cb}}
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+ \psfrag{HB}[][]{\colorbox{white}{\hb}}
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+ \psfrag{HN}[][]{\colorbox{white}{\hn}}
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+ \psfrag{N15}[][]{\colorbox{white}{\nfif}}
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+ \psfrag{dnn}[][]{\dnn}
147
+ \psfrag{dan}[][]{\dan}
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+ \psfrag{phi}[][]{$\phi$}
149
+ }
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+
151
+ \newenvironment{closeenumerate}{\begin{list}{\arabic{enumi}.}{\topsep=0in\itemsep=0in\parsep=0in\usecounter{enumi}}}{\end{list}}
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+ \def\CR{\hspace{0pt}} % ``invisible'' space for line break
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+
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+
155
+
156
+ \newif\ifdbspacing
157
+ %\dbspacingtrue % For double spacing
158
+ \dbspacingfalse % For normal spacing
159
+
160
+ \ifdbspacing
161
+ \doublespacing
162
+ \newcommand{\capspacing}{\doublespace\mycaptionsize}
163
+ \else
164
+ \newcommand{\capspacing}{\mycaptionsize}
165
+ \fi
166
+
167
+ \def\rulefigure{\smallskip\hrule}
168
+
169
+ % \def\codesize{\normalsize}
170
+ \def\codesize{\small}
171
+
172
+ % Can use macros \be, \ee, \en as shortcuts
173
+ % for \begin{enumerate}, \end{enumerate}, \item
174
+ % respectively.
175
+
176
+ \usepackage[american]{babel}
177
+ <%=@header%>
178
+
179
+ \def\be{\begin{enumerate}} % Begin Enumerate
180
+ \def\ee{\end{enumerate}} % End Enumerate
181
+ \def\en{\item} % ENtry (item)
182
+ \def\bi{\begin{itemize}} % Begin Itemize
183
+ \def\ei{\end{itemize}} % End Itemize
184
+ \def\bv{\begin{verbatim}} % Begin Verbatim
185
+ \def\ev{\end{verbatim}} % End Verbatim
186
+
187
+ \def\matlab{{\sc matlab} }
188
+ \def\amber{{\sc amber} }
189
+ \def\KS{{$K^*$}}
190
+ \def\KSM{{K^*}} % K-Star Math
191
+ \def\KSTM{{\tilde{K}^*}} % K-Star Tilde Math (appx K*)
192
+ \def\KOP{{$K^{\dagger}_{o}$}} % K-Star Optimal partial
193
+ \def\KOPM{{K^{\dagger}_{o}}} % K-Star Optimal partial Math
194
+ \def\KP{{$K^{\dagger}$}} % K-Star partial
195
+ \def\KPM{{K^{\dagger}}} % K-Star partial Math
196
+ \def\KTPM{{\tilde{K}^{\dagger}}} % K-Star Tilde partial Math
197
+ \def\KD{{$K_{_D}$}}
198
+ \def\KA{{$K_{_A}$}}
199
+ \def\qpM{{q_{_P}}}
200
+ \def\qlM{{q_{_L}}}
201
+ \def\qplM{{q_{_{PL}}}}
202
+ \def\qSplM{{q^*_{_{PL}}}}
203
+ \def\KSO{{$K^*_{o}$}} % K-Star Optimal
204
+ \def\KSOM{{K^*_{o}}} % K-Star Optimal Math
205
+ \def\CBFB{{CBF-$\beta$}} % Core binding factor beta
206
+ \def\argmin{\mathop{\mathrm{argmin}}}
207
+ \def\rhl#1{{\em \underline{RYAN}: *\{{#1}\}*}}
208
+ \def\set#1{{\left\{ #1 \right\}}}
209
+ \def\Escr{{\mathcal{E}}}
210
+ \def\Jscr{{\mathcal{J}}}
211
+ \def\Kscr{{\mathcal{K}}}
212
+ \def\th{{$^{{\mathrm{th}}}$}}
213
+
214
+ \newtheorem{proposition}{Proposition}
215
+ \newtheorem{lemma}{Lemma}
216
+
217
+ \begin{document}
218
+
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+
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+
221
+
222
+
223
+