replace all lovoalign site references

m3g · Apr 9, 2024 · 46548a3 · 46548a3
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commit 46548a3
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Showing 19 changed files with 28 additions and 28 deletions.
diff --git a/_includes/atd-scripts/tail.html b/_includes/atd-scripts/tail.html
@@ -18,7 +18,7 @@
         <tr>
           <td>
             <a href=/packmol target="_blank">Packmol</a><br>
-            <a href=http://www.ime.unicamp.br/~martinez/lovoalign target="_blank">LovoAlign</a><br>
+            <a href=https://m3g.github.io/lovoalign target="_blank">LovoAlign</a><br>
             <a href=/main/software.html target="_blank">Author's software page</a><br>
             <a href=http://www.ime.usp.br/~egbirgin/tango target="_blank">The TANGO project</a><br>
           </td>

diff --git a/_includes/lovofit/tail.html b/_includes/lovofit/tail.html
@@ -18,9 +18,9 @@
         <tr>
           <td>
             <a href=/packmol target="_blank">Packmol</a><br>
-            <a href=http://www.ime.unicamp.br/~martinez/lovoalign target="_blank">LovoAlign</a><br>
+            <a href=https://m3g.github.io/lovoalign target="_blank">LovoAlign</a><br>
             <a href=/mdlovofit target="_blank">MDLovoFit</a><br>
-            <a href=http://m3g.github.io/ target="_blank">M3G home-page</a><br>
+            <a href=https://m3g.github.io/ target="_blank">M3G home-page</a><br>
             <a href=http://www.ime.usp.br/~egbirgin/tango target="_blank">The TANGO project</a><br>
           </td>
         </tr>

diff --git a/_includes/main/picks.html b/_includes/main/picks.html
@@ -39,12 +39,12 @@
 
     var ii = 5
     text[ii] = "Automatic identification of mobile substructures in protein MD simulations."
-    link[ii] = "http://m3g.github.io/mdlovofit"
+    link[ii] = "https://m3g.github.io/mdlovofit"
     img[ii] = "https://m3g.github.io/packmol/mdlovofit.png"
 
     var ii = 6
     text[ii] = "TopoLink: Find the shortest path at a protein surface for XL evaluation."
-    link[ii] = "http://m3g.github.io/topolink"
+    link[ii] = "https://m3g.github.io/topolink"
     img[ii] = "/main/picks/topolink_drawing.png"
 
     var rand = 1000/text.length

diff --git a/_includes/mdlovofit/tail.html b/_includes/mdlovofit/tail.html
@@ -18,7 +18,7 @@
         <tr>
           <td>
             <a href=https://m3g.github.io/packmol target="_blank">Packmol</a><br>
-            <a href=http://www.ime.unicamp.br/~martinez/lovoalign target="_blank">LovoAlign</a><br>
+            <a href=https://m3g.github.io/lovoalign target="_blank">LovoAlign</a><br>
             <a href=https://m3g.github.io/lovofit target="_blank">LovoFit</a><br>
             <a href=https://m3g.github.io/main/software.html target="_blank">Author's software page</a><br>
             <a href=http://www.ime.usp.br/~egbirgin/tango target="_blank">The TANGO project</a><br>

diff --git a/_includes/topolink/head-refresh.html b/_includes/topolink/head-refresh.html
@@ -1,6 +1,6 @@
 <head>
 <meta http-equiv="refresh" content="30; url=./index.html">
-<link rel="stylesheet" type="text/css" href="http://m3g.github.io/topolink/estilo.css">
+<link rel="stylesheet" type="text/css" href="https://m3g.github.io/topolink/estilo.css">
 <title>TOPOLINK - Institute of Chemistry - UNICAMP</title>
 {% include js/popup.js %}
 </head>

diff --git a/_includes/topolink/menu.html b/_includes/topolink/menu.html
@@ -54,7 +54,7 @@
             <a href=http://daltonlab.iqm.unicamp.br target="_blank">Dalton MS lab</a><br>
             <a href=http://patternlabforproteomics.org/sim-xl/ target="_blank">SIM-XL</a><br>
             <a href=/gscore target="_blank">G-score</a><br>
-            <a href=http://www.ime.unicamp.br/~martinez/lovoalign target="_blank">LovoAlign</a><br>
+            <a href=https://m3g.github.io/lovoalign target="_blank">LovoAlign</a><br>
             <a href=/packmol target="_blank">Packmol</a><br>
             <a href=/mdlovofit target="_blank">MDLovoFit</a><br>
             <a href=/main/software.html target="_blank">Group software page</a><br>

diff --git a/_includes/utils/tail.html b/_includes/utils/tail.html
@@ -18,7 +18,7 @@
         <tr>
           <td>
             <a href=/packmol target="_blank">Packmol</a><br>
-            <a href=http://www.ime.unicamp.br/~martinez/lovoalign target="_blank">LovoAlign</a><br>
+            <a href=https://m3g.github.io/lovoalign target="_blank">LovoAlign</a><br>
             <a href=/mdlovofit target="_blank">MDLovoFit</a><br>
             <a href=/main/software.html target="_blank">Author's software page</a><br>
             <a href=http://www.ime.usp.br/~egbirgin/tango target="_blank">The TANGO project</a><br>

diff --git a/cgi-bin/topolink/server/inputfile.inp b/cgi-bin/topolink/server/inputfile.inp
@@ -2,7 +2,7 @@
 # TOPOLINK input file example
 #
 # L. Martinez - Institute of Chemistry, University of Campinas
-# http://m3g.github.io
+# https://m3g.github.io
 #
 
 # PDB file (can be provided in the command line, overwriting this definition)

diff --git a/cgi-bin/topolink/stats/by_linker_type.tcl b/cgi-bin/topolink/stats/by_linker_type.tcl
@@ -5,7 +5,7 @@ puts ""
 
 # Start page
 
-set url "http://m3g.github.io/topolink"
+set url "https://m3g.github.io/topolink"
 set topolink_dir "../../../topolink"
 
 # html header

diff --git a/cgi-bin/topolink/stats/head_and_tail.py b/cgi-bin/topolink/stats/head_and_tail.py
@@ -1,6 +1,6 @@
 #!/usr/bin/python
 
-url="http://m3g.github.io/topolink" 
+url="https://m3g.github.io/topolink" 
 source_files="../../../topolink"
 
 def htmlTop() :

diff --git a/lovoalign/lovoresult.f b/lovoalign/lovoresult.f
@@ -17,7 +17,7 @@
 c         worst match.
 c
 c  For being used with lovoalign:
-c  http://www.ime.unicamp.br/~martinez/lovoalign
+c  https://m3g.github.io/lovoalign
 c
 c  L. Martinez, 2007
 c

diff --git a/main/bysubject.html b/main/bysubject.html
@@ -184,7 +184,7 @@ <h3><br> Protein structure modeling </h3>
 Bioinformatics, 35(17), 3005-3012, 2019.
 <a target="_blank" href=https://academic.oup.com//bioinformatics/advance-article/doi/10.1093/bioinformatics/btz013/5284907?guestAccessKey=ab5645d5-cea6-4c5d-a512-a9f4bdf69f08>[Full Text]</a>
 <a target="_blank"
-href=http://m3g.github.io/topolink/xlff.html>[XLFF site]</a>
+href=https://m3g.github.io/topolink/xlff.html>[XLFF site]</a>
 </td></tr>
 
 <tr><td width=55px valign=top align=right><b><li></b></td>
@@ -196,7 +196,7 @@ <h3><br> Protein structure modeling </h3>
 Bioinformatics, 35(17), 3169-3170, 2019.
 <a target="_blank" href=https://academic.oup.com//bioinformatics/advance-article/doi/10.1093/bioinformatics/btz014/5284905?guestAccessKey=0093e023-e666-49bc-8d6e-e711d09eba0a>[Full Text]</a>
 <a target="_blank"
-href=http://m3g.github.io/topolink>[TopoLink site]</a>
+href=https://m3g.github.io/topolink>[TopoLink site]</a>
 </td></tr>
 
 <tr><td width=55px valign=top align=right><b><li></b></td>
@@ -328,7 +328,7 @@ <h3><br> Molecular modeling methods and software </h3>
 <a href=./publications/2008_j_glob_optim.pdf>[PDF]</a>
 Software associated to this article: 
 <a target=_blank_ href=https://m3g.github.io/mdlovofit>MDLovoFit </a>,
-<a target=_blank_ href=http://www.ime.unicamp.br/~martinez/lovoalign/home.html>LovoAlign</a>,
+<a target=_blank_ href=https://m3g.github.io/lovoalign>LovoAlign</a>,
 <a target=_blank_ href=https://m3g.github.io/lovofit>LovoFit</a>
 </td></tr>
 
@@ -354,7 +354,7 @@ <h3><br> Molecular modeling methods and software </h3>
 <b> Convergent Algorithms for Protein Structural Alignment,</b>
 BMC Bioinformatics, 8, 306, 2007.
 <a href=./publications/2007_bmc_bioinf.pdf>[PDF]</a>
-Associated software: <a target="_blank" href=http://www.ime.unicamp.br/~martinez/lovoalign>[LINK]</a>
+Associated software: <a target="_blank" href=https://m3g.github.io/lovoalign>[LINK]</a>
 </td></tr>
 
 <tr><td colspan=2>

diff --git a/main/download.html b/main/download.html
@@ -50,7 +50,7 @@
 <b> Standalone executable for Windows 10 (64 bits) (for command-line use)</b>
 <br><br>
 Download the executable from here:
-<a href=http://m3g.github.io/topolink/Windows_Binaries/Windows10-64bits/topolink.exe>
+<a href=https://m3g.github.io/topolink/Windows_Binaries/Windows10-64bits/topolink.exe>
 [topolink.exe Win10-x86_64]
 </a>
 <br><br>

diff --git a/main/lovoalign.html b/main/lovoalign.html
@@ -13,7 +13,7 @@ <h2>Evaluating structural models with LovoAlign and TopoLink</h2>
 strategy to classify models).
 <br><br>
 Here we show how to use the <a
-href=http://www.ime.unicamp.br/~martinez/lovoalign>LovoAlign</a>
+href=https://m3g.github.io/lovoalign>LovoAlign</a>
 structural alignment package in combination with the
 <code>evalmodels</code> tool, to generate the data of the example plot
 below, which shows the correlation of the number of links satisfied by

diff --git a/main/publications.html b/main/publications.html
@@ -642,7 +642,7 @@
 <a href=./publications/2008_j_glob_optim.pdf>[PDF]</a>
 Software associated to this article: 
 <a target=_blank_ href=https://m3g.github.io/mdlovofit>MDLovoFit </a>,
-<a target=_blank_ href=http://www.ime.unicamp.br/~martinez/lovoalign/home.html>LovoAlign</a>,
+<a target=_blank_ href=https://m3g.github.io/lovoalign>LovoAlign</a>,
 <a target=_blank_ href=https://m3g.github.io/lovofit>LovoFit</a>
 </td></tr>
 
@@ -722,7 +722,7 @@
 <b> Convergent Algorithms for Protein Structural Alignment,</b>
 BMC Bioinformatics, 8, 306, 2007.
 <a href=./publications/2007_bmc_bioinf.pdf>[PDF]</a>
-Associated software: <a target="_blank" href=http://www.ime.unicamp.br/~martinez/lovoalign>[LINK]</a>
+Associated software: <a target="_blank" href=https://m3g.github.io/lovoalign>[LINK]</a>
 </td></tr>
 
 

diff --git a/main/software.html b/main/software.html
@@ -64,7 +64,7 @@
 <b>LovoAlign</b><br>
 Performs customizable rigid-body structural alignment using convergent
 algorithms based on Low-Order-Value-Optimization theory.
-<a target="_blank" href=http://www.ime.unicamp.br/~martinez/lovoalign>[Home-Page]</a>
+<a target="_blank" href=https://m3g.github.io/lovoalign>[Home-Page]</a>
 </td></tr>
 
 <tr><td align=left valign=top><li></td>

diff --git a/topolink/home.html b/topolink/home.html
@@ -77,19 +77,19 @@
 
           text[0] = "Combining crosslinking and coevolutionary constraints to improve protein fold prediction."
           link[0] = "https://doi.org/10.1093/bioinformatics/bty074"
-          img[0] = "http://m3g.github.io/topolink/examples/ricardo.png"
+          img[0] = "https://m3g.github.io/topolink/examples/ricardo.png"
 
           text[1] = "Coevolutinary signals and structure-based models for protein fold prediction."
           link[1] = "https://doi.org/10.1007/978-1-4939-8736-8_5"
-          img[1] = "http://m3g.github.io/topolink/examples/ricardo2.png"
+          img[1] = "https://m3g.github.io/topolink/examples/ricardo2.png"
 
           text[2] = "Statistical force-field for XL distance constraints."
           link[2] = "https://doi.org/10.1093/bioinformatics/btz013"
-          img[2] = "http://m3g.github.io/topolink/xlff/figure.png"
+          img[2] = "https://m3g.github.io/topolink/xlff/figure.png"
 
           text[2] = "On the complementarity of coevolution and XL distance constraints."
           link[2] = "https://doi.org/10.1002/prot.25843"
-          img[2] = "http://m3g.github.io/topolink/complementary.png"
+          img[2] = "https://m3g.github.io/topolink/complementary.png"
 
           var rand = 1000/text.length
           function randomhl() {

diff --git a/topolink/index.html b/topolink/index.html
@@ -5,6 +5,6 @@
   <title>M3G - Institute of Chemistry - UNICAMP</title>
   <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </head>
-<meta HTTP-EQUIV="REFRESH" content="0; url=http://m3g.github.io/topolink/home.html">
+<meta HTTP-EQUIV="REFRESH" content="0; url=https://m3g.github.io/topolink/home.html">
 Opening page...
 </html>
diff --git a/topolink/server.html b/topolink/server.html
@@ -16,7 +16,7 @@ <h2>Unfortunatelly, the server is currently unavailable. Please download the sof
 
 <br>
 
-<form action="http://m3g.github.io/cgi-bin/topolink/server/topolink.cgi" method="post" ENCTYPE="multipart/form-data">
+<form action="https://m3g.github.io/cgi-bin/topolink/server/topolink.cgi" method="post" ENCTYPE="multipart/form-data">
 
 <table align=center class="tabnoborder">
   <tr>
-Original file line number
+Diff line change
@@ Expand Up @@
     <br>
-    <form action="http://m3g.github.io/cgi-bin/topolink/server/topolink.cgi" method="post" ENCTYPE="multipart/form-data">
+    <form action="https://m3g.github.io/cgi-bin/topolink/server/topolink.cgi" method="post" ENCTYPE="multipart/form-data">
     <table align=center class="tabnoborder">
       <tr>
@@ Expand Down @@