fixes doctest

src/read/general.rs

@@ -26,19 +26,19 @@ pub type ReadResult = std::result::Result<(PDB, Vec<PDBError>), Vec<PDBError>>;
 /// # Related
 /// If you want to open a file from memory see [`open_raw`]. There are also function to open a specified file type directly
 /// see [`crate::open_pdb`] and [`crate::open_mmcif`] respectively.
-pub fn open(
-    filename: impl AsRef<str>,
-    level: StrictnessLevel,
-) -> ReadResult {
-    open_with_options(filename, &ReadOptions::new().level(level))
+pub fn open(filename: impl AsRef<str>, level: StrictnessLevel) -> ReadResult {
+    open_with_options(filename, &ReadOptions::new().set_level(level))
 }
 
 /// Opens a files based on the given options.
-pub(in crate::read) fn open_with_options(filename: impl AsRef<str>, options: &ReadOptions) -> ReadResult {
+pub(in crate::read) fn open_with_options(
+    filename: impl AsRef<str>,
+    options: &ReadOptions,
+) -> ReadResult {
     if check_extension(&filename, "pdb") {
-        open_pdb(filename, level)
+        open_pdb(filename, options.level)
     } else if check_extension(&filename, "cif") {
-        open_mmcif(filename, level)
+        open_mmcif(filename, options.level)
     } else {
         Err(vec![PDBError::new(
             ErrorLevel::BreakingError,
@@ -60,10 +60,7 @@ pub(in crate::read) fn open_with_options(filename: impl AsRef<str>, options: &Re
 /// These functions are useful if you are using a non-standard compression algorithm or way of
 /// storing the data.
 #[cfg(feature = "compression")]
-pub fn open_gz(
-    filename: impl AsRef<str>,
-    level: StrictnessLevel,
-) -> ReadResult {
+pub fn open_gz(filename: impl AsRef<str>, level: StrictnessLevel) -> ReadResult {
     let filename = filename.as_ref();
 
     if check_extension(filename, "gz") {

src/read/read_options.rs

@@ -1,6 +1,6 @@
 use crate::StrictnessLevel;
 
-use super::general::{ReadResult, open_with_options};
+use super::general::{open_with_options, ReadResult};
 
 /// Used to set which format to read the file in.
 #[derive(Debug, Clone, Copy, Default)]
@@ -29,11 +29,9 @@ impl From<&str> for Format {
 ///
 /// This builder exposes the ability to configure how a [`PDB`] is loaded.
 ///
-/// Generally speaking, when using `ReaderOptions`, you'll first call
-/// [`OpenOptions::new`], then chain calls to methods to set each option, then
-/// call [`OpenOptions::open`], passing the path of the file you're trying to
-/// open. This will give you a [`io::Result`] with a [`File`] inside that you
-/// can further operate on.
+/// Generally speaking, when using `ReadOptions`, you'll first call
+/// [`ReadOptions::new`], then chain calls to methods to set each option, then
+/// call [`ReadOptions::read`].
 ///
 /// # Examples
 ///
@@ -43,32 +41,32 @@ impl From<&str> for Format {
 /// use pdbtbx::*;
 ///
 /// let pdb = ReadOptions::new()
-///     .format(Format::Pdb)
-///     .level(StrictnessLevel::Loose)
-///     .discard_hydrogens(true)
+///     .set_format(Format::Auto)
+///     .set_level(StrictnessLevel::Loose)
+///     .set_discard_hydrogens(true)
 ///     .read("1CRN.pdb");
 //
 /// ```
 #[derive(Debug, Default)]
 pub struct ReadOptions {
     /// The format to read the file in.
-    format: Format,
+    pub(crate) format: Format,
 
     /// The strictness level to use when reading the file.
-    level: StrictnessLevel,
+    pub(crate) level: StrictnessLevel,
 
     /// Controls whether to capitalise the chains in the structure.
-    capitalise_chains: bool,
+    pub(crate) capitalise_chains: bool,
 
     /// Decompress
     #[cfg(feature = "compression")]
-    decompress: bool,
+    pub(crate) decompress: bool,
 
     /// Discard hydrogens
-    discard_hydrogens: bool,
+    pub(crate) discard_hydrogens: bool,
 
     /// Only read the first model
-    only_first_model: bool,
+    pub(crate) only_first_model: bool,
 }
 
 impl ReadOptions {
@@ -78,38 +76,38 @@ impl ReadOptions {
     }
 
     /// Sets the format to read the file in.
-    pub fn format(&mut self, format: Format) -> &mut Self{
+    pub fn set_format(&mut self, format: Format) -> &mut Self {
         self.format = format;
         self
     }
 
     /// Sets the strictness level to use when reading the file.
-    pub fn level(&mut self, level: StrictnessLevel) -> &mut Self {
+    pub fn set_level(&mut self, level: StrictnessLevel) -> &mut Self {
         self.level = level;
         self
     }
 
     /// Sets whether to capitalise the chains in the structure.
-    pub fn capitalise_chains(&mut self, capitalise_chains: bool) -> &mut Self{
+    pub fn set_capitalise_chains(&mut self, capitalise_chains: bool) -> &mut Self {
         self.capitalise_chains = capitalise_chains;
         self
     }
 
     /// Sets whether to decompress the file.
     #[cfg(feature = "compression")]
-    pub fn decompress(&mut self, decompress: bool) -> &mut Self{
+    pub fn set_decompress(&mut self, decompress: bool) -> &mut Self {
         self.decompress = decompress;
         self
     }
 
     /// Sets whether to discard hydrogens.
-    pub fn discard_hydrogens(&mut self, discard_hydrogens: bool) -> &mut Self {
+    pub fn set_discard_hydrogens(&mut self, discard_hydrogens: bool) -> &mut Self {
         self.discard_hydrogens = discard_hydrogens;
         self
     }
 
     /// Sets whether to only keep the first model.
-    pub fn only_first_model(&mut self, only_first_model: bool) -> &mut Self {
+    pub fn set_only_first_model(&mut self, only_first_model: bool) -> &mut Self {
         self.only_first_model = only_first_model;
         self
     }
@@ -119,5 +117,3 @@ impl ReadOptions {
         open_with_options(path, self)
     }
 }
-
-