The amsart document class has a very strict way in which it sets things up, specifically because it is meant for publication submissions. As such, there's not much in terms of user-interface variation available. This is a good thing. However, it requires a complete revamp of the ToC-generation and interaction in order for it to be flexible.
Here is something that seems to satisfy all your requirements without using any additional packages (except etoolbox):
\documentclass{amsart}
\usepackage[showframe,paper=a5paper]{geometry}% Just for this example
\usepackage{etoolbox}
% Modifications to amsart ToC-related macros...
\makeatletter
\let\old@tocline\@tocline
\let\section@tocline\@tocline
% Insert a dotted ToC-line for \subsection and \subsubsection only
\newcommand{\subsection@dotsep}{4.5}
\newcommand{\subsubsection@dotsep}{4.5}
\patchcmd{\@tocline}
{\hfil}
{\nobreak
\leaders\hbox{$\m@th
\mkern \subsection@dotsep mu\hbox{.}\mkern \subsection@dotsep mu$}\hfill
\nobreak}{}{}
\let\subsection@tocline\@tocline
\let\@tocline\old@tocline
\patchcmd{\@tocline}
{\hfil}
{\nobreak
\leaders\hbox{$\m@th
\mkern \subsubsection@dotsep mu\hbox{.}\mkern \subsubsection@dotsep mu$}\hfill
\nobreak}{}{}
\let\subsubsection@tocline\@tocline
\let\@tocline\old@tocline
\let\old@l@subsection\l@subsection
\let\old@l@subsubsection\l@subsubsection
\def\@tocwriteb#1#2#3{%
\begingroup
\@xp\def\csname #2@tocline\endcsname##1##2##3##4##5##6{%
\ifnum##1>\c@tocdepth
\else \sbox\z@{##5\let\indentlabel\@tochangmeasure##6}\fi}%
\csname l@#2\endcsname{#1{\csname#2name\endcsname}{\@secnumber}{}}%
\endgroup
\addcontentsline{toc}{#2}%
{\protect#1{\csname#2name\endcsname}{\@secnumber}{#3}}}%
% Handle section-specific indentation and number width of ToC-related entries
\newlength{\@tocsectionindent}
\newlength{\@tocsubsectionindent}
\newlength{\@tocsubsubsectionindent}
\newlength{\@tocsectionnumwidth}
\newlength{\@tocsubsectionnumwidth}
\newlength{\@tocsubsubsectionnumwidth}
\newcommand{\settocsectionnumwidth}[1]{\setlength{\@tocsectionnumwidth}{#1}}
\newcommand{\settocsubsectionnumwidth}[1]{\setlength{\@tocsubsectionnumwidth}{#1}}
\newcommand{\settocsubsubsectionnumwidth}[1]{\setlength{\@tocsubsubsectionnumwidth}{#1}}
\newcommand{\settocsectionindent}[1]{\setlength{\@tocsectionindent}{#1}}
\newcommand{\settocsubsectionindent}[1]{\setlength{\@tocsubsectionindent}{#1}}
\newcommand{\settocsubsubsectionindent}[1]{\setlength{\@tocsubsubsectionindent}{#1}}
% Handle section-specific formatting and vertical skip of ToC-related entries
% \@tocline{<level>}{<vspace>}{<indent>}{<numberwidth>}{<extra>}{<text>}{<pagenum>}
\renewcommand{\l@section}{\section@tocline{1}{\@tocsectionvskip}{\@tocsectionindent}{}{\@tocsectionformat}}%
\renewcommand{\l@subsection}{\subsection@tocline{2}{\@tocsubsectionvskip}{\@tocsubsectionindent}{}{\@tocsubsectionformat}}%
\renewcommand{\l@subsubsection}{\subsubsection@tocline{3}{\@tocsubsubsectionvskip}{\@tocsubsubsectionindent}{}{\@tocsubsubsectionformat}}%
\newcommand{\@tocsectionformat}{}
\newcommand{\@tocsubsectionformat}{}
\newcommand{\@tocsubsubsectionformat}{}
\expandafter\def\csname toc@1format\endcsname{\@tocsectionformat}
\expandafter\def\csname toc@2format\endcsname{\@tocsubsectionformat}
\expandafter\def\csname toc@3format\endcsname{\@tocsubsubsectionformat}
\newcommand{\settocsectionformat}[1]{\renewcommand{\@tocsectionformat}{#1}}
\newcommand{\settocsubsectionformat}[1]{\renewcommand{\@tocsubsectionformat}{#1}}
\newcommand{\settocsubsubsectionformat}[1]{\renewcommand{\@tocsubsubsectionformat}{#1}}
\newlength{\@tocsectionvskip}
\newcommand{\settocsectionvskip}[1]{\setlength{\@tocsectionvskip}{#1}}
\newlength{\@tocsubsectionvskip}
\newcommand{\settocsubsectionvskip}[1]{\setlength{\@tocsubsectionvskip}{#1}}
\newlength{\@tocsubsubsectionvskip}
\newcommand{\settocsubsubsectionvskip}[1]{\setlength{\@tocsubsubsectionvskip}{#1}}
% Adjust section-specific ToC-related macros to have a fixed-width numbering framework
\patchcmd{\tocsection}{\indentlabel}{\makebox[\@tocsectionnumwidth][l]}{}{}
\patchcmd{\tocsubsection}{\indentlabel}{\makebox[\@tocsubsectionnumwidth][l]}{}{}
\patchcmd{\tocsubsubsection}{\indentlabel}{\makebox[\@tocsubsubsectionnumwidth][l]}{}{}
% Allow for section-specific page numbering format of ToC-related entries
\newcommand{\@sectypepnumformat}{}
\renewcommand{\contentsline}[1]{%
\expandafter\let\expandafter\@sectypepnumformat\csname @toc#1pnumformat\endcsname%
\csname l@#1\endcsname}
\newcommand{\@tocsectionpnumformat}{}
\newcommand{\@tocsubsectionpnumformat}{}
\newcommand{\@tocsubsubsectionpnumformat}{}
\newcommand{\setsectionpnumformat}[1]{\renewcommand{\@tocsectionpnumformat}{#1}}
\newcommand{\setsubsectionpnumformat}[1]{\renewcommand{\@tocsubsectionpnumformat}{#1}}
\newcommand{\setsubsubsectionpnumformat}[1]{\renewcommand{\@tocsubsubsectionpnumformat}{#1}}
\renewcommand{\@tocpagenum}[1]{%
\hfill {\mdseries\@sectypepnumformat #1}}
% Small correction to Appendix, since it's still a \section which should be handled differently
\let\oldappendix\appendix
\renewcommand{\appendix}{%
\leavevmode\oldappendix%
\addtocontents{toc}{%
\protect\settowidth{\protect\@tocsectionnumwidth}{\protect\@tocsectionformat\sectionname\space}%
\protect\addtolength{\protect\@tocsectionnumwidth}{2em}}%
}
\makeatother
% #1 (default is as required)
% #2
% #3
\makeatletter
\settocsectionnumwidth{2em}
\settocsubsectionnumwidth{2.5em}
\settocsubsubsectionnumwidth{3em}
\settocsectionindent{1pc}%
\settocsubsectionindent{\dimexpr\@tocsectionindent+\@tocsectionnumwidth}%
\settocsubsubsectionindent{\dimexpr\@tocsubsectionindent+\@tocsubsectionnumwidth}%
\makeatother
% #4 & #5
\settocsectionvskip{10pt}
\settocsubsectionvskip{0pt}
\settocsubsubsectionvskip{0pt}
% #6 & #7
% See #3
% #8
\renewcommand{\contentsnamefont}{\bfseries\Large}
% #9
\settocsectionformat{\bfseries}
\settocsubsectionformat{\mdseries}
\settocsubsubsectionformat{\mdseries}
\setsectionpnumformat{\bfseries}
\setsubsectionpnumformat{\mdseries}
\setsubsubsectionpnumformat{\mdseries}
% #10
% Insert the following command inside your text where you want the ToC to have a page break
\newcommand{\tocpagebreak}{\leavevmode\addtocontents{toc}{\protect\clearpage}}
% #11
\let\oldtableofcontents\tableofcontents
\renewcommand{\tableofcontents}{%
\vspace*{-\linespacing}% Default gap to top of CONTENTS is \linespacing.
\oldtableofcontents}
\setcounter{tocdepth}{3}
\begin{document}
\tableofcontents
\section{First section}
\subsection{First subsection}
\subsection{Second subsection}
\subsubsection{First subsubsection}
\subsubsection{Second subsubsection}
\section{Second section}
\subsection{First subsection}
\tocpagebreak
\subsection{Second subsection}
\subsubsection{First subsubsection}
\subsubsection{Second subsubsection}
\appendix
\section{An appendix section}
\subsection{First appendix subsection}
\subsection{Second appendix subsection}
\subsubsection{First appendix subsubsection}
\subsubsection{Second appendix subsubsection}
\end{document}
Specific to the requirements:
This is the default setting under amsart, so there's nothing to be done in this regard.
Only the \subsection and \subsubsection ToC entries have been adjusted to include a dotted line. This was taken from latex.ltx's \@dottedtocline that uses leaders.
Adjustments to the spacing between the dots can be achieved using (for example)
\makeatletter
\renewcommand{\subsection@dotsep}{5}% Adjust subsection dot gap
\renewcommand{\subsubsection@dotsep}{5}% Adjust subsubsection dot gap
\makeatother
The default values for both are 4.5.
The indentation can be set for each of the section levels \section, \subsection and \subsubsection, in addition to the width of the numbers in the ToC. The following self-explanatory macros set the defaults:
\makeatletter
\settocsectionnumwidth{2em}
\settocsubsectionnumwidth{2.5em}
\settocsubsubsectionnumwidth{3em}
\settocsectionindent{1pc}%
\settocsubsectionindent{\dimexpr\@tocsectionindent+\@tocsectionnumwidth}%
\settocsubsubsectionindent{\dimexpr\@tocsubsectionindent+\@tocsubsectionnumwidth}%
\makeatother
The subsection and subsubsection indents are set relative to the sections and subsections, making them line up within the ToC as required.
The default \@tocline macro of amsart provides a vertical skip before every sectional unit. This has been customized and can be set with a number of user-interface macros. The defaults are:
\settocsectionvskip{10pt}
\settocsubsectionvskip{0pt}
\settocsubsubsectionvskip{0pt}
This leaves a gap of at least 10pt above a \section heading, but no gap (0pt) above a subsection or subsubsection.
See (4) above.
This can be adjusted using the number widths as refined in (3) above.
See (6).
\contentsnamefont holds the formatting of the ToC heading. A simple \renewcommand suffices to changes this. For example,
\renewcommand{\contentsnamefont}{\bfseries\Large}
Each sectional heading in the ToC can be formatted at the "number+title" and "page number" level via the following self-explanatory macros:
\settocsectionformat{\bfseries}
\settocsubsectionformat{\mdseries}
\settocsubsubsectionformat{\mdseries}
\setsectionpnumformat{\bfseries}
\setsubsectionpnumformat{\mdseries}
\setsubsubsectionpnumformat{\mdseries}
(Optional) Insert \tocpagebreak within your document at the appropriate place between sectional units where you want the equivalent location to be broken in the ToC.
(Optional) \tableofcontents can be adjusted to insert a negative \vspace where appropriate.
This adaptation is not compatible with hyperref, unfortunately. If that is required, one may be better off by recreating the ToC and sectional unit layout using packages that support this in a more consistent/uniform way, and using a different class like article.
Best Answer
revtex4-1(specifically theapsstyle) does not rely ontocdepthand prints sections, subsections and subsubsections in the table of contents independently on the counter's value.The only way to remove sections level is to redefine the relative command producing the entry in the table of contents so they do nothing. One has to keep in mind that the class has been produced to print paper for some journals, which have their styles and authors should not change them.
Of course, you're justified to look for a change if you're using the class for personal purposes. Doing the change in a paper to be submitted will only annoy the copy editors.