Fixed #96 and small other bug

Author: douweschulte

example-pdbs/2btv.pdb

@@ -55,6 +55,11 @@ impl PDBError {
         &self.short_description
     }
 
+    /// Gives the long description for this error
+    pub fn long_description(&self) -> &str {
+        &self.long_description
+    }
+
     /// Gives the context for this error
     pub const fn context(&self) -> &Context {
         &self.context

src/error/pdberror.rs

@@ -102,7 +102,9 @@ where
             errors.extend(line_errors);
             match result {
                 LexItem::Header(_, _, identifier) => pdb.identifier = Some(identifier),
-                LexItem::Remark(num, text) => pdb.add_remark(num, text.to_string()),
+                LexItem::Remark(num, text) => {
+                    let _ = pdb.add_remark(num, text.to_string()); // Better error messages are created downstream
+                }
                 LexItem::Atom(
                     hetero,
                     serial_number,

src/read/pdb/parser.rs

@@ -64,10 +64,10 @@ pub fn valid_remark_type_number(number: usize) -> bool {
 }
 
 /// The valid remark type numbers as of PDB v3.30
-const REMARK_TYPES: [usize; 41] = [
+const REMARK_TYPES: [usize; 42] = [
     0, 1, 2, 3, 4, 5, 100, 200, 205, 210, 215, 217, 230, 240, 245, 247, 250, 265, 280, 285, 290,
-    300, 350, 375, 450, 465, 470, 475, 480, 500, 525, 600, 610, 615, 620, 630, 650, 700, 800, 900,
-    999,
+    300, 350, 375, 400, 450, 465, 470, 475, 480, 500, 525, 600, 610, 615, 620, 630, 650, 700, 800,
+    900, 999,
 ];
 
 /// All amino acids. Includes Amber-specific naming conventions for (de-)protonated versions, CYS involved in

src/reference_tables.rs

@@ -416,6 +416,7 @@ pub fn save_pdb_raw<T: Write>(pdb: &PDB, mut sink: BufWriter<T>, level: Strictne
         let m = mtrix.transformation.matrix();
         print_line(vec![
             (0, "MTRIX1"),
+            (0, " "),
             (3, mtrix.serial_number.to_string().as_str()),
             (10, &format!("{:10.6}", m[0][0])),
             (10, &format!("{:10.6}", m[0][1])),
@@ -427,6 +428,7 @@ pub fn save_pdb_raw<T: Write>(pdb: &PDB, mut sink: BufWriter<T>, level: Strictne
         ]);
         print_line(vec![
             (0, "MTRIX2"),
+            (0, " "),
             (3, mtrix.serial_number.to_string().as_str()),
             (10, &format!("{:10.6}", m[1][0])),
             (10, &format!("{:10.6}", m[1][1])),
@@ -438,6 +440,7 @@ pub fn save_pdb_raw<T: Write>(pdb: &PDB, mut sink: BufWriter<T>, level: Strictne
         ]);
         print_line(vec![
             (0, "MTRIX3"),
+            (0, " "),
             (3, mtrix.serial_number.to_string().as_str()),
             (10, &format!("{:10.6}", m[2][0])),
             (10, &format!("{:10.6}", m[2][1])),

src/save/pdb.rs

@@ -1,8 +1,8 @@
 #![allow(dead_code)]
-use crate::reference_tables;
 use crate::structs::hierarchy::*;
-use crate::structs::*;
 use crate::transformation::TransformationMatrix;
+use crate::{reference_tables, PDBError};
+use crate::{structs::*, Context};
 use doc_cfg::doc_cfg;
 #[cfg(feature = "rayon")]
 use rayon::prelude::*;
@@ -108,20 +108,39 @@ impl PDB {
     /// * `remark_type` - the remark-type-number
     /// * `remark_text` - the free line of text, containing the actual remark
     ///
-    /// ## Panics
-    /// It panics if the text if too long, the text contains invalid characters or the remark-type-number is not valid (wwPDB v3.30).
-    pub fn add_remark(&mut self, remark_type: usize, remark_text: String) {
-        assert!(reference_tables::valid_remark_type_number(remark_type), "The given remark-type-number is not valid, see wwPDB v3.30 for valid remark-type-numbers");
-        assert!(
-            valid_text(&remark_text),
-            "The given remark text contains invalid characters."
-        );
-        // As the text can only contain ASCII len() on strings is fine (it returns the length in bytes)
-        if remark_text.len() > 70 {
-            println!("WARNING: The given remark text is too long, the maximal length is 68 characters, the given string is {} characters.", remark_text.len());
+    /// ## Fails
+    /// It fails if the text if too long, the text contains invalid characters or the remark-type-number is not valid (wwPDB v3.30).
+    pub fn add_remark(&mut self, remark_type: usize, remark_text: String) -> Result<(), PDBError> {
+        let context = Context::show(format!("REMARK {:3} {}", remark_type, remark_text));
+        if !reference_tables::valid_remark_type_number(remark_type) {
+            return Err(PDBError::new(
+                crate::ErrorLevel::InvalidatingError,
+                "Remark-type-number invalid", 
+                "The given remark-type-number is not valid, see wwPDB v3.30 for valid remark-type-numbers", 
+                context));
         }
+        if !valid_text(&remark_text) {
+            return Err(PDBError::new(
+                crate::ErrorLevel::InvalidatingError,
+                "Remark text invalid",
+                "The given remark text contains invalid characters.",
+                context,
+            ));
+        }
+
+        // As the text can only contain ASCII len() on strings is fine (it returns the length in bytes)
+        let res = if remark_text.len() > 70 {
+            Err(PDBError::new(
+                crate::ErrorLevel::LooseWarning,
+                "Remark text too long", 
+                format!("The given remark text is too long, the maximal length is 68 characters, the given string is {} characters.", remark_text.len()), 
+                context))
+        } else {
+            Ok(())
+        };
 
         self.remarks.push((remark_type, remark_text));
+        res
     }
 
     /// Delete the remarks matching the given predicate.