Rename pages/User Guide.py to pages/1_User Guide.py

pages/{User Guide.py → 1_User Guide.py}

@@ -5,7 +5,7 @@ def indented_markdown(text, indentation=40, font_size=25):
     st.markdown(indented_text, unsafe_allow_html=True)
 
 
-original_title = '<p style="font-family:Trebuchet MS; color:#FD7456; font-size: 35px; font-weight:bold">ASCARIS:  Positional Feature Annotation and Protein Structure-Based Representation of Single Amino Acid Variations</p>'
+original_title = '<p style="font-family:Trebuchet MS; color:#FD7456; font-size: 35px; font-weight:bold">ASCARIS User Guide</p>'
 st.markdown(original_title, unsafe_allow_html=True)
 
 
@@ -23,7 +23,7 @@ text = '<p style="font-family:Trebuchet MS;  font-size: 20x">Run ASCARIS for onl
 st.markdown(text, unsafe_allow_html=True)
 
 
-text = 'Type your variation of interest in the form of the example:'
+text = 'Type your SAV data point in the following format:'
 indented_markdown(text, indentation=40, font_size=16)
 
 text = 'P13637-T-613-M'
@@ -33,11 +33,11 @@ st.text('')
 st.text('')
 
 
-text = '<p style="font-family:Trebuchet MS;  font-size: 25">Run ASCARIS for more than one datapoints:</p>'
+text = '<p style="font-family:Trebuchet MS;  font-size: 25">Run ASCARIS for more than one datapoint:</p>'
 st.markdown(text, unsafe_allow_html=True)
 
 
-text = 'Type your variation of interest in the form of the example:'
+text = 'Type your SAV data point in the following format:'
 indented_markdown(text, indentation=40, font_size=16)
 text = 'P13637-T-613-M, Q9Y4W6-N-432-T, Q9Y4W6-N-432-T'
 indented_markdown(text, indentation=40, font_size=16)
@@ -45,10 +45,10 @@ indented_markdown(text, indentation=40, font_size=16)
 st.text('')
 st.text('')
 
-body = '<p style="font-family:Trebuchet MS;  font-size: 25px; font-weight:bold">Structure Selection</p>'
+body = '<p style="font-family:Trebuchet MS;  font-size: 25px; font-weight:bold">Selection of the Structure Resource</p>'
 st.markdown(body, unsafe_allow_html=True)
 
-body = '<p style="font-family:Trebuchet MS;  font-size: 20x">Users may select where to retrieve their structures to map annotations. If the selection is PDB-ModBase-SwissModel, please select option 1; if the selection is AlphaFold, please select 2 from the dropdown menu.</p>'
+body = '<p style="font-family:Trebuchet MS;  font-size: 20x">Users should select their preferred protein structure resource for the annotation mapping step. If you wish to use PDB-ModBase-SwissModel, please select option 1(ModBase-SwissModel is only used when PDB models are not available for the given SAV); if you wish to use AlphaFold, please select 2 from the dropdown menu.</p>'
 st.markdown(body, unsafe_allow_html=True)
 
 st.text('')
@@ -57,9 +57,5 @@ st.text('')
 body = '<p style="font-family:Trebuchet MS;  font-size: 25px; font-weight:bold">Imputation</p>'
 st.markdown(body, unsafe_allow_html=True)
 
-body = '<p style="font-family:Trebuchet MS;  font-size: 20x">ASCARIS calculates distance information for annotations and domains, as well as SASA values whenever a structure is available, or variation is found on the selected structure. Otherwise, such values are reported as NaN. ASCARIS feature vector can be created either by imputing NaN values in the dataset, or by viewing them as NaNs. Imputation is done by taking the median value of corresponding column feature. Users can select where they want their output to be imputed or not imputed from the dropdown menu.</p>'
-st.markdown(body, unsafe_allow_html=True)
-
-
-
-
+body = '<p style="font-family:Trebuchet MS;  font-size: 20x">ASCARIS calculates spatial distance-based features for annotations and domains, as well as SASA values, wherever structural information is available. Otherwise, such values are reported as NaN. ASCARIS feature vectors can be created either by imputing those NaN values in the dataset, or by leaving them as they are. Imputation is done by taking the median value of the corresponding column (feature). Users can choose whether or not to use imputation from the drop-down menu.</p>'
+st.markdown(body, unsafe_allow_html=True)