Merge pull request #9 from Ladme/0.11

0.11

Author: Ladme

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "groan_rs"
 description = "Gromacs Analysis Library for Rust"
-version = "0.10.0"
+version = "0.11.0"
 license = "MIT"
 edition = "2021"
 authors = ["Ladislav Bartos"]
@@ -28,14 +28,14 @@ regex = "1.11.1"
 thiserror = "2.0.12"
 serde = { version = "1.0.218", features = ["derive"] }
 serde_yaml = "0.9"
-fancy-regex = "0.14.0"
-nalgebra = "0.33.2"
+fancy-regex = "0.16.1"
+nalgebra = "0.34.0"
 minitpr = "0.2.3"
 ndarray = "0.16.1"
 hashbrown = "0.15.2"
 getset = "0.1.5"
 parking_lot = { version = "0.12.3", optional = true }
-molly = { version = "0.3.3", optional = true }
+molly = { version = "0.4.0", optional = true }
 chemfiles = { version = "0.10.41", optional = true }
 itertools = "0.14.0"
 dyn-clone = "1.0.19"

changelog.md

@@ -1,6 +1,17 @@
 
 ## Changelog for the `groan_rs` library
 
+### Version 0.11.0
+
+#### Groan Selection Language v0.11
+- Updated the `@membrane` macro, which should now match a wider variety of lipid molecules.
+- GSL queries with empty quoted blocks no longer panic.
+
+#### Bug fixes
+- GRO, PDB, and PQR files with NaN positions (or velocities) are no longer parsed and instead raise an error.
+
+***
+
 ### Version 0.10.0
 
 #### New XTC Parser

src/errors.rs

@@ -69,6 +69,9 @@ pub enum ParseGroError {
     /// Used when the "box line" in the gro file could be parsed but the simulation box is not supported by Gromacs.
     #[error("{} simulation box on line '{}' is not supported (4th, 5th, and 7th element must be zero)", "error:".red().bold(), .0.yellow())]
     UnsupportedBox(String),
+    /// Used when a gro line contains an invalid floating point number (nan, inf...).
+    #[error("{} could not parse line '{}' because it contains an invalid floating point number", "error:".red().bold(), .0.yellow())]
+    InvalidFloat(String),
 }
 
 /// Errors that can occur when reading and parsing pdb file.
@@ -94,6 +97,9 @@ pub enum ParsePdbError {
     /// Used when a "TITLE" line in the pdb file could not be parsed.
     #[error("{} could not parse line '{}' as title", "error:".red().bold(), .0.yellow())]
     ParseTitleLineErr(String),
+    /// Used when a pdb line contains an invalid floating point number (nan, inf...).
+    #[error("{} could not parse line '{}' because it contains an invalid floating point number", "error:".red().bold(), .0.yellow())]
+    InvalidFloat(String),
 }
 
 /// Errors that can occur when reading the connectivity section of a PDB file.
@@ -186,6 +192,9 @@ pub enum ParsePqrError {
     /// Used when a "TITLE" line in the pqr file could not be parsed.
     #[error("{} could not parse line '{}' as title", "error:".red().bold(), .0.yellow())]
     ParseTitleLineErr(String),
+    /// Used when a pqr line contains an invalid floating point number (nan, inf...).
+    #[error("{} could not parse line '{}' because it contains an invalid floating point number", "error:".red().bold(), .0.yellow())]
+    InvalidFloat(String),
 }
 
 /// Errors that can occur when writing a pqr file.
@@ -406,6 +415,9 @@ pub enum ReadTrajError {
     /// Used when an unknown error occurs.
     #[error("{} an unknown error occured when reading a trajectory: '{}'", "error:".red().bold(), .0.yellow())]
     UnknownError(String),
+    /// Used when an error specific to GRO files has been encountered.
+    #[error("{}", .0)]
+    GroSpecificError(ParseGroError),
 }
 
 /// Errors that can occur when writing a trajectory file.

src/io/gro_io/structure.rs

@@ -200,6 +200,10 @@ fn line_as_atom(line: &str) -> Result<Atom, ParseGroError> {
             .trim()
             .parse::<f32>()
             .map_err(|_| ParseGroError::ParseAtomLineErr(line.to_string()))?;
+
+        if !item.is_finite() {
+            return Err(ParseGroError::InvalidFloat(line.to_string()));
+        }
     }
 
     let atom = Atom::new(resid, &resname, atomid, &atomname).with_position(position.into());
@@ -214,6 +218,10 @@ fn line_as_atom(line: &str) -> Result<Atom, ParseGroError> {
                 .trim()
                 .parse::<f32>()
                 .map_err(|_| ParseGroError::ParseAtomLineErr(line.to_string()))?;
+
+            if !item.is_finite() {
+                return Err(ParseGroError::InvalidFloat(line.to_string()));
+            }
         }
 
         Ok(atom.with_velocity(velocity.into()))
@@ -555,6 +563,20 @@ mod tests_read {
             panic!("Parsing should have failed, but it succeeded.")
         }
     }
+
+    read_gro_fails!(
+        read_nan_position,
+        "test_files/nan_error.gro",
+        ParseGroError::InvalidFloat,
+        "   19ALA    SC1   39     nan   2.496   5.027  0.0733 -0.2227 -0.2563"
+    );
+
+    read_gro_fails!(
+        read_nan_velocity,
+        "test_files/nan_error_velocity.gro",
+        ParseGroError::InvalidFloat,
+        "    6VAL     BB   12   9.947   2.258   6.831 -0.2096     NaN  0.0665"
+    );
 }
 
 #[cfg(test)]

src/io/gro_io/trajectory.rs

@@ -12,7 +12,7 @@ use std::{fs::File, io::BufReader};
 use regex::Regex;
 
 use crate::auxiliary::{GRO_MAX_COORDINATE, GRO_MIN_COORDINATE};
-use crate::errors::WriteTrajError;
+use crate::errors::{ParseGroError, WriteTrajError};
 use crate::io::check_coordinate_sizes;
 use crate::io::traj_write::{PrivateTrajWrite, TrajWrite};
 use crate::prelude::{
@@ -97,6 +97,12 @@ fn read_position_velocity(
             .trim()
             .parse::<f32>()
             .map_err(|_| ReadTrajError::FrameNotFound)?;
+
+        if !item.is_finite() {
+            return Err(ReadTrajError::GroSpecificError(
+                ParseGroError::InvalidFloat(line.to_string()),
+            ));
+        }
     }
 
     let velocity = if line.trim_end().len() >= 68 {
@@ -108,6 +114,12 @@ fn read_position_velocity(
                 .trim()
                 .parse::<f32>()
                 .map_err(|_| ReadTrajError::FrameNotFound)?;
+
+            if !item.is_finite() {
+                return Err(ReadTrajError::GroSpecificError(
+                    ParseGroError::InvalidFloat(line.to_string()),
+                ));
+            }
         }
 
         Some(velocity)
@@ -430,7 +442,7 @@ impl System {
     pub fn gro_iter(
         &mut self,
         filename: impl AsRef<Path>,
-    ) -> Result<TrajReader<GroReader>, ReadTrajError> {
+    ) -> Result<TrajReader<'_, GroReader<'_>>, ReadTrajError> {
         Ok(TrajReader::wrap_traj(GroReader::new(self, filename)?))
     }
 }
@@ -939,6 +951,27 @@ mod tests_read {
             None => panic!("Iterator is empty."),
         }
     }
+
+    #[test]
+    fn gro_iter_nan_position() {
+        let mut system = System::from_file("test_files/protein.gro").unwrap();
+
+        match system
+            .gro_iter("test_files/nan_trajectory.gro")
+            .unwrap()
+            .nth(3)
+        {
+            Some(Ok(_)) => panic!("Function should have failed."),
+            Some(Err(ReadTrajError::GroSpecificError(ParseGroError::InvalidFloat(x)))) => {
+                assert_eq!(
+                    x,
+                    String::from("   23ALA    SC1   47   6.290     NaN   4.190\n")
+                )
+            }
+            Some(Err(e)) => panic!("Unexpected error type `{}` returned.", e),
+            None => panic!("Iterator is empty."),
+        }
+    }
 }
 
 #[cfg(test)]

src/io/pdb_io.rs

@@ -388,6 +388,10 @@ fn line_as_atom(line: &str) -> Result<Atom, ParsePdbError> {
             .map(|x| x / 10.0)
             .map_err(|_| ParsePdbError::ParseAtomLineErr(line.to_string()))?;
 
+        if !pos.is_finite() {
+            return Err(ParsePdbError::InvalidFloat(line.to_string()));
+        }
+
         curr += 8;
     }
 
@@ -1092,6 +1096,13 @@ mod tests_read {
         "ATOM      30  SC1 ARG A  14      32.540  35.200  34.040  1.00  0.00            "
     );
 
+    read_pdb_fails!(
+        read_nan_position,
+        "test_files/nan_error.pdb",
+        ParsePdbError::InvalidFloat,
+        "ATOM      4  SC2 LYS     2      98.640  26.920    NaN   1.00  0.00            "
+    );
+
     macro_rules! read_bonds_fails {
         ($name:ident, $file_struct:expr, $file_bonds:expr, $variant:path, $expected:expr) => {
             #[test]

src/io/pqr_io.rs

@@ -258,6 +258,10 @@ fn line_as_atom(line: &str) -> Result<Atom, ParsePqrError> {
     let y = parse_float(line, split[7 - convert])? / 10.0;
     let z = parse_float(line, split[8 - convert])? / 10.0;
 
+    if !x.is_finite() || !y.is_finite() || !z.is_finite() {
+        return Err(ParsePqrError::InvalidFloat(line.to_string()));
+    }
+
     let charge = parse_float(line, split[9 - convert])?;
     let vdw = parse_float(line, split[10 - convert])? / 10.0;
 
@@ -552,6 +556,13 @@ mod tests_read {
         ParsePqrError::ParseBoxLineErr,
         "CRYST1   60.861   60.861.3 60.861  90.00  90.00  90.00 P 1           1"
     );
+
+    read_pqr_fails!(
+        read_nan_position,
+        "test_files/nan_error.pqr",
+        ParsePqrError::InvalidFloat,
+        "ATOM     32  BB  VAL C  15      35.650  33.730  NaN     0.0000 0.0000"
+    );
 }
 
 #[cfg(test)]

src/io/trr_io.rs

@@ -374,7 +374,7 @@ impl System {
     pub fn trr_iter(
         &mut self,
         filename: impl AsRef<Path>,
-    ) -> Result<TrajReader<TrrReader>, ReadTrajError> {
+    ) -> Result<TrajReader<'_, TrrReader<'_>>, ReadTrajError> {
         Ok(TrajReader::wrap_traj(TrrReader::new(self, filename)?))
     }
 

src/io/xtc_io/mod.rs

@@ -172,7 +172,7 @@ impl System {
     pub fn xtc_iter(
         &mut self,
         filename: impl AsRef<Path>,
-    ) -> Result<TrajReader<XtcReader>, ReadTrajError> {
+    ) -> Result<TrajReader<'_, XtcReader<'_>>, ReadTrajError> {
         Ok(TrajReader::wrap_traj(XtcReader::new(self, filename)?))
     }
 

src/io/xtc_io/molly_xtc.rs

@@ -635,7 +635,7 @@ impl System {
         &mut self,
         filename: impl AsRef<Path>,
         group: &str,
-    ) -> Result<TrajReader<GroupXtcReader>, ReadTrajError> {
+    ) -> Result<TrajReader<'_, GroupXtcReader<'_>>, ReadTrajError> {
         Ok(TrajReader::wrap_traj(GroupXtcReader::new(
             self, filename, group,
         )?))