Merge pull request #43 from athbaltzis/master

include electron microscopy EM structures

docs/.html/index.html

@@ -2994,7 +2994,7 @@ <h6>Template search paramaters<a class="headerlink" href="#template-search-param
 <p>To use Expresso, you have different option from an entirely automated procedure to tailored procedure, by selecting either your own structures or by defining different criteria for the template selection. You can have an exhaustive list in the <strong>T-Coffee Technical Documentation</strong> (subsection <strong>Template based T-Coffee modes</strong>) yet the most important parameters for the template selection are the following:</p>
 <blockquote>
 <div><ul class="simple">
-<li><p><strong>-pdb_type</strong>    : type of structure (“d” for diffraction/XRAY or “n” NMR structures)</p></li>
+<li><p><strong>-pdb_type</strong>    : type of structure (“d” for diffraction/XRAY or “n” NMR structures or "e" for electron microscopy/EM)</p></li>
 <li><p><strong>-pdb_min_cov</strong> : minimum coverage between query sequence and template (from 0-100%)</p></li>
 <li><p><strong>-pdb_min_sim</strong> : minimum identity between query sequence and template (from 0-100%)</p></li>
 </ul>
@@ -5063,7 +5063,7 @@ <h5>Database searches parameters<a class="headerlink" href="#database-searches-p
 <ul class="simple">
 <li><p><strong>-pdb_type</strong> (usage:<strong>-pdb_type=[d,n,m,dnm,dn]</strong>/default:<strong>-pdb_type=d</strong>)</p></li>
 </ul>
-<p>The different types are as follow: “d” stands for XRAY structures (diffraction), “n” stands for NMR structures and “m” stands for models.</p>
+<p>The different types are as follow: “d” stands for XRAY structures (diffraction), “n” stands for NMR structures, "e" stands for EM structures and “m” stands for models.</p>
 <ul class="simple">
 <li><p><strong>-pdb_min_sim</strong> (usage:<strong>-pdb_min_sim= [%identity]</strong>/default:35)</p></li>
 </ul>

docs/tcoffee_main_documentation.rst

@@ -1270,7 +1270,7 @@ Template search paramaters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 To use Expresso, you have different option from an entirely automated procedure to tailored procedure, by selecting either your own structures or by defining different criteria for the template selection. You can have an exhaustive list in the **T-Coffee Technical Documentation** (subsection **Template based T-Coffee modes**) yet the most important parameters for the template selection are the following:
 
- - **-pdb_type**    : type of structure ("d" for diffraction/XRAY or "n" NMR structures)
+ - **-pdb_type**    : type of structure ("d" for diffraction/XRAY or "n" NMR structures or "e" EM structures)
  - **-pdb_min_cov** : minimum coverage between query sequence and template (from 0-100%)
  - **-pdb_min_sim** : minimum identity between query sequence and template (from 0-100%)
 
@@ -1444,7 +1444,7 @@ By Default, RSAP-Coffee only runs sap, but you can also run other structural met
 
    $#: t_coffee <yourseq.fasta> -mode rsapcoffee -method sap_pair, mustang_pair, TMalign_pair -template_file <template file>
 
-The default procedure is meant to handle a muxture of PDB files and sequences. All possble PDB sequences pairs are aligned using strucure based methods (structural library) and all possiblée sequence pairs (including PDB sequences) sequences are then aligned using the R-Coffee mode (secondary library). In the secondary library, the PDB sequences are aligned using their experimentallyerived secondary structures, as estimated by X3DNA. Note that id you aonly have structures, you may use the folloing command lines to carry out a strict structure based sequence alignment:
+The default procedure is meant to handle a muxture of PDB files and sequences. All possble PDB sequences pairs are aligned using strucure based methods (structural library) and all possibl�e sequence pairs (including PDB sequences) sequences are then aligned using the R-Coffee mode (secondary library). In the secondary library, the PDB sequences are aligned using their experimentallyerived secondary structures, as estimated by X3DNA. Note that id you aonly have structures, you may use the folloing command lines to carry out a strict structure based sequence alignment:
 
 ::
 

docs/tcoffee_technical_documentation.rst

@@ -721,7 +721,7 @@ Minimum coverage for inclusion of a sequence in a PSI-BLAST profile.
 Database for PDB template to be selected by EXPRESSO. By default it runs on the PDB, but you can specify a version installed locally on your system,
 
 - **-pdb_type** (usage:**-pdb_type=[d,n,m,dnm,dn]**/default:**-pdb_type=d**)
-The different types are as follow: "d" stands for XRAY structures (diffraction), "n" stands for NMR structures and "m" stands for models.
+The different types are as follow: "d" stands for XRAY structures (diffraction), "n" stands for NMR structures, "e" stands for EM structures and "m" stands for models.
 
 - **-pdb_min_sim** (usage:**-pdb_min_sim= [%identity]**/default:35)
 Minimum % identity for a PDB template to be selected by Expresso.

lib/perl/lib/scripts/tc_generic_method.pl

@@ -645,6 +645,7 @@ sub type2etype
 
     if ( $type=~/n/){$etype.="NMR ";}
     if ( $type=~/d/){$etype.="diffraction ";}
+	if ( $type=~/e/){$etype.="EM ";}
     if ( $type=~/m/){$etype.="model ";}
     return $etype;
   }
@@ -672,6 +673,7 @@ sub pdb_has_right_type
 
     if ( $r eq "NMR" && $type=~/n/){return 1;}
     elsif ( $r eq "diffraction" && $type=~/d/){return 1;}
+	elsif ( $r eq "EM" && $type=~/e/){return 1;}
     elsif ( $r eq "model" && $type=~/m/){return 1;}
     else {return 0;}
   }

lib/t_coffee_lib/t_coffee.c

@@ -3039,7 +3039,7 @@ get_cl_param(\
 			    /*TYPE*/      "S"              ,\
 			    /*OPTIONAL?*/ OPTIONAL         ,\
 			    /*MAX Nval*/  1                ,\
-			    /*DOC*/       "d: diffraction, n: nmr, m:model" ,\
+			    /*DOC*/       "d: diffraction, n: nmr, e: em, m:model" ,\
 			    /*Parameter*/ &pdb_type          ,\
 			    /*Def 1*/     "d"             ,\
 			    /*Def 2*/     "d"             ,\