minor imrpovements

Author: Nantia Leonidou

.gitignore

@@ -135,7 +135,9 @@ dmypy.json
 
 # other
 SBOannotator_main_RothiaModel.py
+old_functions.py
 testSQL.py
+MANIFEST.in
 .DS_Store
 ~$*
 /create_dbs

README.md

@@ -1,5 +1,5 @@
 # SBOannotator
-<img align="right" src="SBOannotator_logo.png" alt="drawing" width="200"/>
+<img align="right" src="SBOannotator_logo.png" alt="drawing" width="250"/>
 
 **SBOannotator: a Python tool for the automated assignment of Systems Biology Ontology terms**
 
@@ -54,7 +54,6 @@ Packages:
 + `doc`: an SBML document
 + `model_libsbml`: SBML model of interest
 + `modelType`: type of modelling framework (see below)
-+ `modelAnnotated`: True, if model already includes annotations with EC numbers
 + `database_name`: name of imported database, without extension
 + `new_filename`: file name for output model
 

main.py

@@ -29605,7 +29605,7 @@
           <fbc:geneProductRef fbc:geneProduct="G_PP_0399"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="R_ASPTRS" sboTerm="SBO:0000182" id="R_ASPTRS" name="Aspartyl-tRNA synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="R_ASPTRS" sboTerm="SBO:0000695" id="R_ASPTRS" name="Aspartyl-tRNA synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
             <rdf:Description rdf:about="#R_ASPTRS">
@@ -32818,7 +32818,7 @@
           <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="R_CYSTRS" sboTerm="SBO:0000182" id="R_CYSTRS" name="Cysteinyl-tRNA synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="R_CYSTRS" sboTerm="SBO:0000695" id="R_CYSTRS" name="Cysteinyl-tRNA synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
             <rdf:Description rdf:about="#R_CYSTRS">
@@ -35361,7 +35361,7 @@
           <fbc:geneProductRef fbc:geneProduct="G_PP_1893"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="R_DHFS" sboTerm="SBO:0000182" id="R_DHFS" name="Dihydrofolate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="R_DHFS" sboTerm="SBO:0000695" id="R_DHFS" name="Dihydrofolate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
             <rdf:Description rdf:about="#R_DHFS">
@@ -42390,7 +42390,7 @@
           <speciesReference species="M_ni2_e" stoichiometry="1" constant="true"/>
         </listOfReactants>
       </reaction>
-      <reaction metaid="R_GLUTRS" sboTerm="SBO:0000182" id="R_GLUTRS" name="Glutamyl-tRNA synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="R_GLUTRS" sboTerm="SBO:0000695" id="R_GLUTRS" name="Glutamyl-tRNA synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
             <rdf:Description rdf:about="#R_GLUTRS">
@@ -54171,7 +54171,7 @@
           <fbc:geneProductRef fbc:geneProduct="G_PP_5056"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="R_FERULCOAS" sboTerm="SBO:0000182" id="R_FERULCOAS" name="Feruloyl coenzyme A synthetase  AMP forming " reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="R_FERULCOAS" sboTerm="SBO:0000695" id="R_FERULCOAS" name="Feruloyl coenzyme A synthetase  AMP forming " reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
             <rdf:Description rdf:about="#R_FERULCOAS">