diff --git a/Cargo.lock b/Cargo.lock index 3295346..70092d2 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -104,6 +104,21 @@ dependencies = [ "chrono", ] +[[package]] +name = "bit-set" +version = "0.5.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1" +dependencies = [ + "bit-vec", +] + +[[package]] +name = "bit-vec" +version = "0.6.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb" + [[package]] name = "bitflags" version = "1.3.2" @@ -123,7 +138,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4c2f7349907b712260e64b0afe2f84692af14a454be26187d9df565c7f69266a" dependencies = [ "memchr", - "regex-automata", + "regex-automata 0.3.9", "serde", ] @@ -271,6 +286,17 @@ dependencies = [ "libc", ] +[[package]] +name = "fancy-regex" +version = "0.13.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "531e46835a22af56d1e3b66f04844bed63158bc094a628bec1d321d9b4c44bf2" +dependencies = [ + "bit-set", + "regex-automata 0.4.3", + "regex-syntax 0.8.2", +] + [[package]] name = "fastrand" version = "2.0.0" @@ -283,9 +309,18 @@ version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "31a7a908b8f32538a2143e59a6e4e2508988832d5d4d6f7c156b3cbc762643a5" +[[package]] +name = "float-cmp" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "98de4bbd547a563b716d8dfa9aad1cb19bfab00f4fa09a6a4ed21dbcf44ce9c4" +dependencies = [ + "num-traits", +] + [[package]] name = "gcenter" -version = "1.1.1" +version = "1.2.0" dependencies = [ "assert_cmd", "backitup", @@ -306,22 +341,26 @@ checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b" [[package]] name = "groan_rs" -version = "0.4.1" +version = "0.6.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6a1fa86d0c89e3f90a982e2a8fc905cc5e56c2457f09bc2e5819160f9b241834" +checksum = "680ab034b12662c808d3fe8313369e21dfd1265b52e559656471561af694261c" dependencies = [ "cc", "colored", + "fancy-regex", + "float-cmp", "indexmap", "regex", + "serde", + "serde_yaml", "thiserror", ] [[package]] name = "hashbrown" -version = "0.14.0" +version = "0.14.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c6201b9ff9fd90a5a3bac2e56a830d0caa509576f0e503818ee82c181b3437a" +checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604" [[package]] name = "heck" @@ -360,12 +399,13 @@ dependencies = [ [[package]] name = "indexmap" -version = "2.0.0" +version = "2.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d5477fe2230a79769d8dc68e0eabf5437907c0457a5614a9e8dddb67f65eb65d" +checksum = "d530e1a18b1cb4c484e6e34556a0d948706958449fca0cab753d649f2bce3d1f" dependencies = [ "equivalent", "hashbrown", + "serde", ] [[package]] @@ -388,6 +428,12 @@ dependencies = [ "either", ] +[[package]] +name = "itoa" +version = "1.0.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c" + [[package]] name = "jobserver" version = "0.1.26" @@ -514,8 +560,8 @@ checksum = "ebee201405406dbf528b8b672104ae6d6d63e6d118cb10e4d51abbc7b58044ff" dependencies = [ "aho-corasick", "memchr", - "regex-automata", - "regex-syntax", + "regex-automata 0.3.9", + "regex-syntax 0.7.5", ] [[package]] @@ -526,7 +572,18 @@ checksum = "59b23e92ee4318893fa3fe3e6fb365258efbfe6ac6ab30f090cdcbb7aa37efa9" dependencies = [ "aho-corasick", "memchr", - "regex-syntax", + "regex-syntax 0.7.5", +] + +[[package]] +name = "regex-automata" +version = "0.4.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5f804c7828047e88b2d32e2d7fe5a105da8ee3264f01902f796c8e067dc2483f" +dependencies = [ + "aho-corasick", + "memchr", + "regex-syntax 0.8.2", ] [[package]] @@ -535,6 +592,12 @@ version = "0.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da" +[[package]] +name = "regex-syntax" +version = "0.8.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f" + [[package]] name = "rustix" version = "0.38.14" @@ -548,26 +611,45 @@ dependencies = [ "windows-sys", ] +[[package]] +name = "ryu" +version = "1.0.16" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f98d2aa92eebf49b69786be48e4477826b256916e84a57ff2a4f21923b48eb4c" + [[package]] name = "serde" -version = "1.0.188" +version = "1.0.193" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cf9e0fcba69a370eed61bcf2b728575f726b50b55cba78064753d708ddc7549e" +checksum = "25dd9975e68d0cb5aa1120c288333fc98731bd1dd12f561e468ea4728c042b89" dependencies = [ "serde_derive", ] [[package]] name = "serde_derive" -version = "1.0.188" +version = "1.0.193" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4eca7ac642d82aa35b60049a6eccb4be6be75e599bd2e9adb5f875a737654af2" +checksum = "43576ca501357b9b071ac53cdc7da8ef0cbd9493d8df094cd821777ea6e894d3" dependencies = [ "proc-macro2", "quote", "syn", ] +[[package]] +name = "serde_yaml" +version = "0.9.29" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a15e0ef66bf939a7c890a0bf6d5a733c70202225f9888a89ed5c62298b019129" +dependencies = [ + "indexmap", + "itoa", + "ryu", + "serde", + "unsafe-libyaml", +] + [[package]] name = "strsim" version = "0.10.0" @@ -630,6 +712,12 @@ version = "1.0.12" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b" +[[package]] +name = "unsafe-libyaml" +version = "0.2.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ab4c90930b95a82d00dc9e9ac071b4991924390d46cbd0dfe566148667605e4b" + [[package]] name = "utf8parse" version = "0.2.1" diff --git a/Cargo.toml b/Cargo.toml index 708e537..631819c 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -2,7 +2,7 @@ name = "gcenter" authors = ["Ladislav Bartos "] description = "Center Any Group in a Gromacs Trajectory" -version = "1.1.1" +version = "1.2.0" license = "MIT" edition = "2021" repository = "https://github.com/Ladme/gcenter" @@ -16,7 +16,7 @@ exclude = ["/tests"] backitup = "0.1.1" clap = { version = "4.4.3", features = ["derive"] } colored = "2.0.4" -groan_rs = "0.4.1" +groan_rs = "0.6.1" thiserror = "1.0.48" [dev-dependencies] diff --git a/src/argparse.rs b/src/argparse.rs index 657e489..8c03662 100644 --- a/src/argparse.rs +++ b/src/argparse.rs @@ -1,5 +1,5 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos //! Implementation of a command line argument parser. @@ -66,7 +66,8 @@ If the simulation steps coincide, only the first of these frames is centered and long = "reference", help = "Group to center", default_value = "Protein", - long_help = "Specify the group to be centered. Use VMD-like 'groan selection language' to define the group. This language also supports ndx group names." + long_help = "Specify the group to be centered. Use VMD-like 'groan selection language' to define the group. This language also supports ndx group names.", + value_parser = validate_reference )] pub reference: String, @@ -125,6 +126,15 @@ If the simulation steps coincide, only the first of these frames is centered and )] pub zdimension: bool, + #[arg( + long = "com", + action, + help = "Center frames using center of mass", + default_value_t = false, + long_help = "Use center of mass instead of center of geometry when centering the reference group. This requires information about atom masses. If not explicitely provided, the masses are guessed." + )] + pub com: bool, + #[arg( long = "silent", action, @@ -161,6 +171,15 @@ fn validate_trajectory_type(s: &str) -> Result { } } +/// Validate that the GSL query does not contain any unsupported keywords. +fn validate_reference(s: &str) -> Result { + if s.contains("molecule with") || s.contains("mol with") { + Err(String::from("gcenter does not employ connectivity and therefore does not support GSL keyword `molecule with`")) + } else { + Ok(s.to_owned()) + } +} + /// Perform various sanity checks: /// a) Check that the input and output files are not identical. /// This protects the user from accidentaly overwriting their data. @@ -214,7 +233,7 @@ fn sanity_check_inputs(args: &Args) -> Result<(), RunError> { } } -pub fn parse() -> Result> { +pub fn parse() -> Result> { let args = Args::parse(); sanity_check_inputs(&args)?; diff --git a/src/center.rs b/src/center.rs index 6c65e1d..c4846d6 100644 --- a/src/center.rs +++ b/src/center.rs @@ -1,121 +1,48 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos //! Implementation of the centering procedure. -use colored::{ColoredString, Colorize}; +use colored::Colorize; use groan_rs::errors::ReadTrajError; use groan_rs::files::FileType; use groan_rs::prelude::*; -use std::io::{self, Write}; use std::path::Path; use crate::argparse::Args; -#[derive(Debug, Clone, Copy, PartialEq)] -enum ProgressStatus { - Running, - Completed, - Failed, -} - -/// Structure containing formatting for the printing of the centering progress. -#[derive(Debug, PartialEq)] -struct ProgressPrinter { - status: ProgressStatus, - print_freq: u64, - silent: bool, - step_fmt: ColoredString, - time_fmt: ColoredString, - running_fmt: ColoredString, - completed_fmt: ColoredString, - failed_fmt: ColoredString, -} - -impl ProgressPrinter { - /// Create default instance of the `ProgressPrinter`. - fn new(silent: bool) -> Self { - ProgressPrinter { - silent, - print_freq: 500000, - status: ProgressStatus::Running, - step_fmt: "Step:".cyan(), - time_fmt: "Time:".bright_purple(), - running_fmt: "CENTERING".yellow(), - completed_fmt: "COMPLETED".green(), - failed_fmt: " FAILED! ".red(), - } - } - - /// Print progress info with formatting from `ProgressPrinter`. - fn print(&self, sim_step: u64, sim_time: u64) { - if !self.silent - && (self.status != ProgressStatus::Running || sim_step % self.print_freq == 0) - { - match self.status { - ProgressStatus::Running => print!("[{: ^9}] ", self.running_fmt), - ProgressStatus::Completed => print!("[{: ^9}] ", self.completed_fmt), - ProgressStatus::Failed => print!("[{: ^9}] ", self.failed_fmt), - } - - print!( - "{} {:12} | {} {:12} ps\r", - self.step_fmt, sim_step, self.time_fmt, sim_time - ); - - io::stdout().flush().unwrap(); - } - } - - fn set_status(&mut self, status: ProgressStatus) { - self.status = status; - } -} - /// Center the reference group and write an output gro or pdb file. fn center_structure_file( system: &mut System, output: &str, output_type: FileType, dimension: Dimension, -) -> Result<(), Box> { - system.atoms_center("Reference", dimension)?; + com: bool, +) -> Result<(), Box> { + if com { + system.atoms_center_mass("Reference", dimension)? + } else { + system.atoms_center("Reference", dimension)?; + } match output_type { FileType::GRO => system.write_gro(output, system.has_velocities())?, - FileType::PDB => system.write_pdb(output)?, + FileType::PDB => system.write_pdb(output, system.has_bonds())?, _ => panic!("Gcenter error. Output file has unsupported file extension but this should have been handled before."), } Ok(()) } -/// Center a single simulation frame. -fn center_frame( - frame: &mut System, - dimension: Dimension, - writer: &mut impl TrajWrite, - printer: &ProgressPrinter, -) -> Result<(), Box> { - printer.print( - frame.get_simulation_step(), - frame.get_simulation_time() as u64, - ); - frame.atoms_center("Reference", dimension)?; - writer.write_frame()?; - - Ok(()) -} - /// Check for duplicate frames at trajectory boundaries and center the frame. fn handle_frame( frame: Result<&mut System, ReadTrajError>, dimension: Dimension, writer: &mut impl TrajWrite, - printer: &ProgressPrinter, last_step: Option, is_first_frame: &mut bool, -) -> Result<(), Box> { + com: bool, +) -> Result<(), Box> { let frame = frame?; if *is_first_frame { @@ -129,7 +56,15 @@ fn handle_frame( *is_first_frame = false; } - center_frame(frame, dimension, writer, printer) + if com { + frame.atoms_center_mass("Reference", dimension)?; + } else { + frame.atoms_center("Reference", dimension)?; + } + + writer.write_frame()?; + + Ok(()) } /// Center any trajectory file. @@ -137,19 +72,22 @@ fn center_traj_file<'a, Reader>( system: &'a mut System, trajectory: impl AsRef, writer: &mut impl TrajWrite, - start_time: Option, - end_time: Option, - step: usize, + args: &Args, dimension: Dimension, - printer: &ProgressPrinter, last_step: Option, is_last_file: bool, -) -> Result<(), Box> +) -> Result<(), Box> where Reader: TrajRead<'a> + TrajRangeRead<'a> + TrajStepRead<'a> + 'a, Reader::FrameData: FrameDataTime, { let mut reader = system.traj_iter::(&trajectory)?; + if !args.silent { + reader = + reader.print_progress(ProgressPrinter::new() + .with_running_msg("CENTERING".yellow()) + .with_newline_at_end(false)); + } let mut is_first_frame = true; @@ -158,20 +96,20 @@ where frame, dimension, writer, - printer, last_step, &mut is_first_frame, + args.com, ) }; - match (start_time, end_time, step) { - (Some(s), _, 1) => match reader.with_range(s, end_time.unwrap_or(f32::MAX)) { + match (args.start_time, args.end_time, args.step) { + (Some(s), _, 1) => match reader.with_range(s, args.end_time.unwrap_or(f32::MAX)) { Ok(mut r) => r.try_for_each(process_frame)?, Err(ReadTrajError::StartNotFound(_)) if !is_last_file => (), Err(e) => return Err(Box::new(e)), }, - (_, Some(e), 1) => match reader.with_range(start_time.unwrap_or(0.0), e) { + (_, Some(e), 1) => match reader.with_range(args.start_time.unwrap_or(0.0), e) { Ok(mut r) => r.try_for_each(process_frame)?, Err(ReadTrajError::StartNotFound(_)) if !is_last_file => (), Err(e) => return Err(Box::new(e)), @@ -179,13 +117,13 @@ where (None, None, 1) => reader.try_for_each(process_frame)?, - (Some(s), _, step) => match reader.with_range(s, end_time.unwrap_or(f32::MAX)) { + (Some(s), _, step) => match reader.with_range(s, args.end_time.unwrap_or(f32::MAX)) { Ok(r) => r.with_step(step)?.try_for_each(process_frame)?, Err(ReadTrajError::StartNotFound(_)) if !is_last_file => (), Err(e) => return Err(Box::new(e)), }, - (_, Some(e), step) => match reader.with_range(start_time.unwrap_or(0.0), e) { + (_, Some(e), step) => match reader.with_range(args.start_time.unwrap_or(0.0), e) { Ok(r) => r.with_step(step)?.try_for_each(process_frame)?, Err(ReadTrajError::StartNotFound(_)) if !is_last_file => (), Err(e) => return Err(Box::new(e)), @@ -203,8 +141,7 @@ fn center_trajectories( args: &Args, writer: &mut impl TrajWrite, dimension: Dimension, - printer: &ProgressPrinter, -) -> Result<(), Box> { +) -> Result<(), Box> { for (t, traj) in args.trajectories.iter().enumerate() { let input_type = FileType::from_name(traj); @@ -216,16 +153,24 @@ fn center_trajectories( // check whether this is a last file let is_last_file = t == args.trajectories.len() - 1; + // check whether we have already reached the requested end time + // skip the rest of the files, if this is the case + // NOTE: this will only work if there is a time in the trajectory that exactly matches `args.end_time` + // in all other cases, we will have to loop through the rest of the files, but that's not really an issue + // since we just check the first trajectory frame for each of them + if let Some(end) = args.end_time { + if system.get_simulation_time() >= end { + return Ok(()); + } + } + match input_type { FileType::XTC => center_traj_file::( system, traj, writer, - args.start_time, - args.end_time, - args.step, + args, dimension, - printer, last_step, is_last_file, )?, @@ -234,11 +179,8 @@ fn center_trajectories( system, traj, writer, - args.start_time, - args.end_time, - args.step, + args, dimension, - printer, last_step, is_last_file, )?, @@ -255,54 +197,30 @@ pub fn center( system: &mut System, args: &Args, dimension: Dimension, -) -> Result<(), Box> { +) -> Result<(), Box> { // determine type of the output file let output_type = FileType::from_name(&args.output); if args.trajectories.is_empty() { // trajectory file not provided, center the structure file - center_structure_file(system, &args.output, output_type, dimension)?; + center_structure_file(system, &args.output, output_type, dimension, args.com)?; } else { - let mut printer = ProgressPrinter::new(args.silent); - - let return_type = match output_type { + match output_type { FileType::XTC => { let mut writer = XtcWriter::new(system, &args.output)?; - center_trajectories(system, args, &mut writer, dimension, &printer) + center_trajectories(system, args, &mut writer, dimension)? } FileType::TRR => { let mut writer = TrrWriter::new(system, &args.output)?; - center_trajectories(system, args, &mut writer, dimension, &printer) + center_trajectories(system, args, &mut writer, dimension)? } _ => panic!("Gcenter error. Output file has unsupported file extension but this should have been handled before."), }; - match return_type { - Ok(_) => { - printer.set_status(ProgressStatus::Completed); - printer.print( - system.get_simulation_step(), - system.get_simulation_time() as u64, - ); - - if !args.silent { - println!("\n") - } - } - Err(e) => { - printer.set_status(ProgressStatus::Failed); - printer.print( - system.get_simulation_step(), - system.get_simulation_time() as u64, - ); - - if !args.silent { - println!("\n") - } - - return Err(e); - } + if !args.silent { + println!("\n"); } + } Ok(()) diff --git a/src/errors.rs b/src/errors.rs index 77e7522..84adec7 100644 --- a/src/errors.rs +++ b/src/errors.rs @@ -1,5 +1,5 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos //! Implementation of errors originating from the `gcenter` program. @@ -29,25 +29,6 @@ pub enum RunError { BoxNotOrthogonal, #[error("{} simulation box is not a valid simulation box; some required dimensions are not positive\n", "error:".red().bold())] BoxNotValid, + #[error("{} simulation box is not defined\n", "error:".red().bold())] + BoxNotDefined, } - -/* // [DEV] print all RunErrors -pub fn print_all_errors() { - let errors = vec![ - RunError::IOMatch(String::from("N/A")), - RunError::OutputUnsupported(String::from("N/A")), - RunError::IdenticalInputFiles(String::from("N/A"), String::from("N/A")), - RunError::StepJoinUnsupported(3), - RunError::InputStructureNotFound(String::from("N/A")), - RunError::InputTrajectoryNotFound(String::from("N/A")), - RunError::EmptyReference(String::from("N/A")), - RunError::AutodetectionFailed, - RunError::BoxNotOrthogonal, - RunError::BoxNotValid, - ]; - - for e in errors { - println!("{}", e); - } -} -*/ diff --git a/src/lib.rs b/src/lib.rs index 87baa31..ef6541a 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,5 +1,5 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos mod argparse; mod center; @@ -7,6 +7,7 @@ mod errors; mod reference; use colored::Colorize; +use groan_rs::errors::ElementError; use groan_rs::prelude::*; use std::path::Path; @@ -66,11 +67,27 @@ fn print_options(args: &Args, system: &System, dim: &Dimension) { println!("[STEP] {}", &args.step.to_string().bright_blue()); } + if args.com { + println!("[METHOD] {}", "center of mass".bright_blue()); + } + println!(); } +/// Guess elements for target system printing warnings and returning errors. +fn guess_elements(system: &mut System) -> Result<(), Box> { + match system.guess_elements(Elements::default()) { + Ok(_) => Ok(()), + Err(ElementError::ElementGuessWarning(e)) => { + eprintln!("{}", ElementError::ElementGuessWarning(e)); + Ok(()) + } + Err(e) => Err(Box::from(e)), + } +} + /// Perform the centering. -pub fn run() -> Result<(), Box> { +pub fn run() -> Result<(), Box> { let args = argparse::parse()?; if !args.silent { @@ -78,9 +95,6 @@ pub fn run() -> Result<(), Box> { println!("{}", version.bold()); } - // [DEV] print all errors - // errors::print_all_errors(); - // construct a dimension; if no dimension has been chosen, use all of them let dim: Dimension = match [args.xdimension, args.ydimension, args.zdimension].into() { Dimension::None => Dimension::XYZ, @@ -90,15 +104,19 @@ pub fn run() -> Result<(), Box> { // read structure file let mut system = System::from_file(&args.structure)?; - // check that box has positive dimensions - if !system.get_box_as_ref().is_valid() { - return Err(Box::from(RunError::BoxNotValid)); - } + // check the simulation is valid (defined, non-zero and orthogonal) + match system.get_box_as_ref() { + None => return Err(Box::from(RunError::BoxNotDefined)), + Some(x) => { + if x.is_zero() { + return Err(Box::from(RunError::BoxNotValid)); + } - // check that the simulation box is orthogonal - if !system.get_box_as_ref().is_orthogonal() { - return Err(Box::from(RunError::BoxNotOrthogonal)); - } + if !x.is_orthogonal() { + return Err(Box::from(RunError::BoxNotOrthogonal)); + } + } + }; // read ndx file system.read_ndx_with_default(&args.index, "index.ndx")?; @@ -130,6 +148,21 @@ pub fn run() -> Result<(), Box> { } } + // guess elements and assign masses, if needed + if args.com { + if !args.silent { + println!("{} center of mass calculation requested; will guess elements and assign masses...\n", "note:".purple().bold()); + } + + guess_elements(&mut system)?; + } else if args.reference.contains("element") { + if !args.silent { + println!("{} element keyword detected in query; will guess elements...\n", "note:".purple().bold()); + } + + guess_elements(&mut system)?; + } + // select reference atoms reference::create_reference(&mut system, &args)?; diff --git a/src/main.rs b/src/main.rs index 031a2af..2aade98 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,5 +1,5 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos use std::process; diff --git a/src/reference.rs b/src/reference.rs index 5f41520..cbf5156 100644 --- a/src/reference.rs +++ b/src/reference.rs @@ -1,5 +1,5 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos //! Implementation of reference atoms selection. @@ -14,23 +14,27 @@ use crate::errors::RunError; pub fn create_reference( system: &mut System, args: &Args, -) -> Result<(), Box> { +) -> Result<(), Box> { let autodetect = match system.group_create("Reference", &args.reference) { // ignore group overwrite Ok(_) | Err(GroupError::AlreadyExistsWarning(_)) => false, // if the reference group is 'Protein' and such group does not exist, try autodetecting the protein atoms Err(GroupError::InvalidQuery(_)) if &args.reference == "Protein" => { - if !args.silent { - println!( - "{} group '{}' not found. Autodetecting protein atoms...\n", - "warning:".yellow().bold(), - "Protein".yellow() - ); - } - match system.group_create("Reference", "@protein") { - Ok(_) | Err(GroupError::AlreadyExistsWarning(_)) => true, - Err(_) => panic!("gcenter: Fatal Error. Autodetection failed."), + Ok(_) | Err(GroupError::AlreadyExistsWarning(_)) => { + if !args.silent { + println!( + "{} group '{}' not found. Autodetected {} protein atoms.\n", + "warning:".yellow().bold(), + "Protein".yellow(), + format!("{}", system.group_get_n_atoms("Reference").unwrap()) + .bright_blue() + ); + } + + true + } + Err(_) => panic!("\ngcenter: Fatal Error. Autodetection failed."), } } // propagate all the other errors diff --git a/tests/main.rs b/tests/main.rs index a749b71..c431c9e 100644 --- a/tests/main.rs +++ b/tests/main.rs @@ -1,5 +1,5 @@ // Released under MIT License. -// Copyright (c) 2023 Ladislav Bartos +// Copyright (c) 2023-2024 Ladislav Bartos #[cfg(test)] mod pass_tests { @@ -25,6 +25,49 @@ mod pass_tests { )); } + #[test] + fn xyz_gro_com() { + let output = Builder::new().suffix(".gro").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "--com", + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_xyz_com.gro", + output.path().to_str().unwrap() + )); + } + + #[test] + fn z_gro_com() { + let output = Builder::new().suffix(".gro").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "--com", + "-z", + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_z_com.gro", + output.path().to_str().unwrap() + )); + } + #[test] fn xyz_gro_to_pdb() { let output = Builder::new().suffix(".pdb").tempfile().unwrap(); @@ -42,6 +85,28 @@ mod pass_tests { )); } + #[test] + fn xy_gro_to_pdb_com() { + let output = Builder::new().suffix(".pdb").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "--com", + "-xy", + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_xy_com.pdb", + output.path().to_str().unwrap() + )); + } + #[test] fn xyz_pdb_to_gro() { let output = Builder::new().suffix(".gro").tempfile().unwrap(); @@ -278,6 +343,28 @@ mod pass_tests { )); } + #[test] + fn xyz_xtc_com() { + let output = Builder::new().suffix(".xtc").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "-ftests/test_files/input_aa_peptide.xtc", + "--com", + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_xyz_com.xtc", + output.path().to_str().unwrap() + )); + } + #[test] fn xyz_xtc_explicit() { let output = Builder::new().suffix(".xtc").tempfile().unwrap(); @@ -342,6 +429,28 @@ mod pass_tests { )); } + #[test] + fn xyz_trr_to_trr_com() { + let output = Builder::new().suffix(".trr").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "-ftests/test_files/input_aa_peptide.trr", + "--com", + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_xyz_com.trr", + output.path().to_str().unwrap() + )); + } + #[test] fn xyz_trr_to_xtc() { let output = Builder::new().suffix(".xtc").tempfile().unwrap(); @@ -518,6 +627,58 @@ mod pass_tests { )); } + #[test] + fn yz_xtc_com_begin_end_step() { + let output = Builder::new().suffix(".xtc").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "-ftests/test_files/input_aa_peptide.xtc", + "--com", + "-yz", + "-b10", + "-e80", + "-s3" + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_yz_com_begin_end_step.xtc", + output.path().to_str().unwrap() + )); + } + + #[test] + fn x_trr_com_begin_end_step() { + let output = Builder::new().suffix(".trr").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "-ftests/test_files/input_aa_peptide.trr", + "--com", + "-x", + "-b10", + "-e80", + "-s2" + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_x_com_begin_end_step.trr", + output.path().to_str().unwrap() + )); + } + #[test] fn complicated_group() { let output = Builder::new().suffix(".xtc").tempfile().unwrap(); @@ -818,6 +979,30 @@ mod pass_tests { )); } + #[test] + fn xyz_xtc_multiple_inputs_end_early() { + let output = Builder::new().suffix(".xtc").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input.gro", + &output_arg, + "-ftests/test_files/input_part1.xtc", + "-ftests/test_files/input_part2.xtc", + "-ftests/test_files/input_part3.xtc", + "-e100", + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_xyz_end_early.xtc", + output.path().to_str().unwrap() + )); + } + #[test] fn xyz_trr_begin_end() { let output = Builder::new().suffix(".trr").tempfile().unwrap(); @@ -1134,6 +1319,27 @@ mod pass_tests { output.path().to_str().unwrap() )); } + + #[test] + fn xyz_gro_element_query() { + let output = Builder::new().suffix(".gro").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input_aa_peptide.gro", + &output_arg, + "-relement name carbon nitrogen hydrogen oxygen" + ]) + .assert() + .success(); + + assert!(file_diff::diff( + "tests/test_files/output_xyz_aa_peptide.gro", + output.path().to_str().unwrap() + )); + } } #[cfg(test)] @@ -1334,6 +1540,18 @@ mod fail_tests { .failure(); } + #[test] + fn undefined_box() { + let output = Builder::new().suffix(".gro").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args(["-ctests/test_files/input_tiny_nobox.pdb", &output_arg]) + .assert() + .failure(); + } + #[test] fn no_extension() { let output = Builder::new().tempfile().unwrap(); @@ -1445,4 +1663,34 @@ mod fail_tests { .assert() .failure(); } + + #[test] + fn unknown_mass() { + let output = Builder::new().suffix(".gro").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args([ + "-ctests/test_files/input.gro", + "--com", + "-r@membrane", + &output_arg, + ]) + .assert() + .failure(); + } + + #[test] + fn molwith_unsupported() { + let output = Builder::new().suffix(".gro").tempfile().unwrap(); + let output_arg = format!("-o{}", output.path().display()); + + Command::cargo_bin("gcenter") + .unwrap() + .args(["-ctests/test_files/input.gro", "-rmolecule with serial 17", &output_arg]) + .assert() + .failure(); + } + } diff --git a/tests/test_files/input_aa_peptide.gro b/tests/test_files/input_aa_peptide.gro new file mode 100644 index 0000000..d8f3aa9 --- /dev/null +++ b/tests/test_files/input_aa_peptide.gro @@ -0,0 +1,366 @@ +AA peptide in a large box +363 + 1SER N 1 4.322 3.899 4.993 0.0617 0.5184 0.2735 + 1SER H1 2 4.240 3.880 5.049 -0.6908 -0.7011 -1.1721 + 1SER H2 3 4.338 3.807 4.955 -0.7154 0.4550 0.0906 + 1SER H3 4 4.400 3.927 5.051 -0.6465 3.3158 0.0179 + 1SER CA 5 4.281 3.993 4.887 0.2322 -0.3472 -0.5670 + 1SER HA 6 4.177 3.977 4.858 -0.1864 -0.2599 0.8480 + 1SER CB 7 4.284 4.130 4.953 -0.0923 -1.0250 0.9005 + 1SER HB1 8 4.218 4.133 5.039 -2.7751 -0.1527 -1.0690 + 1SER HB2 9 4.246 4.214 4.894 1.5703 -0.7739 0.1075 + 1SER OG 10 4.414 4.183 4.972 -0.4378 0.3508 -0.3267 + 1SER HG 11 4.407 4.251 5.039 0.3306 -1.3589 1.6057 + 1SER C 12 4.362 3.986 4.758 0.6932 1.5894 -0.4126 + 1SER O 13 4.310 3.996 4.647 -0.0444 0.1061 -0.2316 + 2LEU N 14 4.491 3.953 4.767 0.4717 0.8344 0.1005 + 2LEU H 15 4.536 3.932 4.855 0.9891 -1.7354 -0.6644 + 2LEU CA 16 4.587 3.959 4.658 0.1872 0.2027 -0.1921 + 2LEU HA 17 4.580 4.052 4.603 1.9183 -0.1149 -1.0180 + 2LEU CB 18 4.724 3.955 4.726 0.2173 0.1824 -0.2539 + 2LEU HB1 19 4.741 3.860 4.777 -0.2350 0.1491 -0.1608 + 2LEU HB2 20 4.720 4.033 4.802 0.5116 0.7942 -0.8612 + 2LEU CG 21 4.846 3.977 4.637 0.2286 -0.1291 -0.3171 + 2LEU HG 22 4.819 4.042 4.554 0.4774 0.0519 -0.2555 + 2LEU CD1 23 4.895 3.848 4.570 -0.7002 -0.4755 -0.3435 + 2LEU HD11 24 4.908 3.772 4.647 -2.3897 -1.9478 -1.4461 + 2LEU HD12 25 4.827 3.817 4.491 0.3965 -0.9949 -1.1056 + 2LEU HD13 26 4.986 3.867 4.514 -0.5886 0.5598 0.1580 + 2LEU CD2 27 4.962 4.033 4.719 0.0075 -0.3078 0.1237 + 2LEU HD21 28 5.046 4.053 4.653 0.4064 1.5135 1.1292 + 2LEU HD22 29 4.933 4.120 4.778 2.1811 0.8041 -0.3642 + 2LEU HD23 30 4.973 3.966 4.804 -1.5710 2.2168 2.5088 + 2LEU C 31 4.568 3.842 4.562 0.1926 -0.1437 0.2257 + 2LEU O 32 4.557 3.873 4.444 0.6914 -0.6509 0.0437 + 3LEU N 33 4.554 3.718 4.609 -0.0598 -0.1234 0.2087 + 3LEU H 34 4.561 3.704 4.709 -1.1286 -2.5043 0.0058 + 3LEU CA 35 4.521 3.600 4.532 0.1131 0.1042 -0.2165 + 3LEU HA 36 4.601 3.584 4.461 0.1195 -1.5046 0.1271 + 3LEU CB 37 4.517 3.476 4.620 -0.3645 0.0332 -0.3350 + 3LEU HB1 38 4.423 3.487 4.676 -1.5416 -1.3895 -1.9134 + 3LEU HB2 39 4.610 3.472 4.677 -1.5130 -2.2084 1.5745 + 3LEU CG 40 4.495 3.340 4.555 -0.1143 -0.0085 -0.3302 + 3LEU HG 41 4.416 3.341 4.480 -0.5812 -0.9032 0.1414 + 3LEU CD1 42 4.450 3.226 4.646 -0.5550 0.1246 -0.3821 + 3LEU HD11 43 4.358 3.249 4.701 0.7874 0.7891 1.7162 + 3LEU HD12 44 4.430 3.140 4.583 0.1413 -1.2966 1.2589 + 3LEU HD13 45 4.532 3.202 4.714 -0.6877 0.1249 -0.2190 + 3LEU CD2 46 4.616 3.300 4.471 0.5973 0.2069 0.5705 + 3LEU HD21 47 4.598 3.231 4.388 0.2751 0.7716 0.1663 + 3LEU HD22 48 4.669 3.387 4.431 -1.9361 0.9472 -1.4460 + 3LEU HD23 49 4.686 3.273 4.550 0.7486 1.7881 1.0072 + 3LEU C 50 4.389 3.616 4.457 -0.0309 -0.6280 -0.1259 + 3LEU O 51 4.381 3.575 4.341 0.1980 -0.5278 -0.1774 + 4SER N 52 4.281 3.674 4.511 0.4017 -0.0395 0.1212 + 4SER H 53 4.279 3.716 4.603 0.8422 -1.4944 0.8299 + 4SER CA 54 4.166 3.696 4.426 0.1524 0.0527 0.4799 + 4SER HA 55 4.142 3.609 4.365 0.0037 0.0918 0.4816 + 4SER CB 56 4.047 3.717 4.518 0.0044 -0.6389 0.4523 + 4SER HB1 57 4.043 3.629 4.581 1.5008 -0.9020 0.2147 + 4SER HB2 58 3.959 3.736 4.455 0.9191 -0.3783 -0.7825 + 4SER OG 59 4.063 3.827 4.605 0.9511 -0.3333 -0.0938 + 4SER HG 60 4.086 3.789 4.690 -1.0470 -1.6639 -0.0713 + 4SER C 61 4.181 3.817 4.335 0.8569 -0.2434 0.1918 + 4SER O 62 4.120 3.814 4.228 0.3176 0.4118 0.4677 + 5SER N 63 4.256 3.923 4.366 0.0634 0.4019 -0.0379 + 5SER H 64 4.303 3.922 4.456 0.1924 -0.9278 -0.0965 + 5SER CA 65 4.292 4.032 4.278 0.4241 0.5711 0.3145 + 5SER HA 66 4.206 4.073 4.226 0.5336 -0.8307 -1.0416 + 5SER CB 67 4.360 4.142 4.358 0.6430 0.1559 0.7035 + 5SER HB1 68 4.404 4.214 4.289 -0.2487 2.8655 2.7652 + 5SER HB2 69 4.445 4.100 4.412 -0.1944 -0.4083 1.6110 + 5SER OG 70 4.284 4.211 4.455 -0.3287 -0.1325 0.1546 + 5SER HG 71 4.266 4.154 4.530 4.0386 -0.1720 1.4383 + 5SER C 72 4.374 3.978 4.161 0.0833 0.0925 0.2929 + 5SER O 73 4.356 4.020 4.047 -0.5133 -0.4097 0.1955 + 6LEU N 74 4.463 3.879 4.175 0.0916 0.0705 0.0880 + 6LEU H 75 4.475 3.842 4.269 0.5975 0.4991 0.1921 + 6LEU CA 76 4.531 3.816 4.064 -0.0585 -0.0814 0.0824 + 6LEU HA 77 4.574 3.887 3.994 0.4126 -1.1192 -0.7092 + 6LEU CB 78 4.639 3.731 4.129 0.2714 0.3381 0.0862 + 6LEU HB1 79 4.587 3.670 4.203 -0.4523 2.2449 1.2222 + 6LEU HB2 80 4.704 3.793 4.191 -0.2779 1.2216 -0.2248 + 6LEU CG 81 4.728 3.648 4.036 -0.2104 0.1053 -0.1702 + 6LEU HG 82 4.671 3.570 3.986 0.8224 0.2341 -1.6186 + 6LEU CD1 83 4.843 3.586 4.114 -0.2686 -0.2632 -0.3790 + 6LEU HD11 84 4.920 3.543 4.049 0.5983 -2.7465 2.1019 + 6LEU HD12 85 4.895 3.658 4.176 -0.3928 0.6432 -1.3095 + 6LEU HD13 86 4.805 3.511 4.183 1.3919 -1.3839 -0.6050 + 6LEU CD2 87 4.801 3.730 3.930 0.5350 -0.3733 -0.0313 + 6LEU HD21 88 4.875 3.675 3.872 1.1155 -0.9264 1.1849 + 6LEU HD22 89 4.723 3.773 3.868 0.6686 -1.4125 -0.9368 + 6LEU HD23 90 4.856 3.811 3.979 -1.2848 -0.3201 2.0800 + 6LEU C 91 4.430 3.734 3.985 -0.1118 -0.0290 0.0952 + 6LEU O 92 4.441 3.722 3.863 0.2247 -0.2103 0.1405 + 7LEU N 93 4.331 3.666 4.044 -0.2431 -0.1275 -0.2364 + 7LEU H 94 4.328 3.664 4.145 -1.9043 -2.1052 -0.2649 + 7LEU CA 95 4.241 3.577 3.974 0.0985 -0.5307 -0.1673 + 7LEU HA 96 4.295 3.536 3.889 -1.4727 0.3066 -1.6328 + 7LEU CB 97 4.180 3.478 4.073 -0.3314 -0.4031 -0.3007 + 7LEU HB1 98 4.085 3.439 4.038 -0.0125 -1.0143 -0.4977 + 7LEU HB2 99 4.162 3.529 4.168 -1.6866 1.3660 -1.4402 + 7LEU CG 100 4.280 3.368 4.109 -0.1483 0.0438 0.5813 + 7LEU HG 101 4.378 3.397 4.148 1.6712 -2.7912 -1.5128 + 7LEU CD1 102 4.296 3.282 3.984 -0.8374 0.1095 0.4454 + 7LEU HD11 103 4.357 3.193 3.998 2.1323 1.7705 -0.8729 + 7LEU HD12 104 4.200 3.252 3.942 -0.3958 -0.4434 -0.1703 + 7LEU HD13 105 4.347 3.338 3.905 0.3857 -1.6065 -0.0271 + 7LEU CD2 106 4.222 3.272 4.213 0.3904 -0.2376 0.6273 + 7LEU HD21 107 4.205 3.329 4.305 4.0207 -0.4446 1.5744 + 7LEU HD22 108 4.126 3.234 4.178 1.0539 -1.3100 -0.0846 + 7LEU HD23 109 4.291 3.196 4.250 1.8278 0.8442 0.2528 + 7LEU C 110 4.138 3.662 3.900 0.3083 0.0007 0.1448 + 7LEU O 111 4.091 3.627 3.792 0.0818 0.4306 0.1076 + 8SER N 112 4.109 3.783 3.946 0.0960 -0.1399 0.3818 + 8SER H 113 4.151 3.817 4.032 2.8065 0.6207 -1.1216 + 8SER CA 114 4.028 3.882 3.877 0.1467 -0.2812 0.1213 + 8SER HA 115 3.934 3.836 3.847 -0.8717 1.5545 0.3711 + 8SER CB 116 4.005 3.997 3.974 -0.2288 -0.0258 -0.2682 + 8SER HB1 117 3.959 4.080 3.920 0.5591 0.3801 -0.3377 + 8SER HB2 118 4.108 4.026 3.996 0.2798 1.9681 -4.2463 + 8SER OG 119 3.929 3.958 4.086 0.1181 -0.0621 -0.0433 + 8SER HG 120 3.990 3.920 4.149 0.8212 0.5786 -0.3232 + 8SER C 121 4.109 3.933 3.758 0.3725 -0.6970 0.0925 + 8SER O 122 4.052 3.942 3.650 -0.2962 -0.0529 0.4873 + 9SER N 123 4.237 3.970 3.767 0.2654 -0.3520 0.2206 + 9SER H 124 4.269 3.972 3.863 -1.7614 -0.7124 0.9612 + 9SER CA 125 4.323 4.005 3.657 -0.0696 -0.1121 0.0326 + 9SER HA 126 4.285 4.091 3.602 0.7801 0.0947 -0.2537 + 9SER CB 127 4.464 4.033 3.708 -0.0717 0.1767 -0.1165 + 9SER HB1 128 4.517 4.077 3.623 0.9121 -0.8221 -0.0440 + 9SER HB2 129 4.498 3.933 3.736 -1.6706 -0.4751 -0.4322 + 9SER OG 130 4.466 4.133 3.808 0.2398 0.5250 -0.4671 + 9SER HG 131 4.433 4.110 3.895 0.7610 -1.8520 -0.8245 + 9SER C 132 4.325 3.897 3.550 0.0351 0.1942 -0.2775 + 9SER O 133 4.317 3.927 3.431 0.4348 -0.1011 -0.3803 + 10LEU N 134 4.336 3.772 3.594 -0.3937 0.2311 -0.0571 + 10LEU H 135 4.352 3.757 3.693 3.0040 2.2036 -0.1435 + 10LEU CA 136 4.332 3.657 3.507 -0.0815 -0.2346 0.5289 + 10LEU HA 137 4.403 3.685 3.430 -1.6045 3.7513 0.3398 + 10LEU CB 138 4.386 3.533 3.578 0.1346 -0.2100 0.4081 + 10LEU HB1 139 4.306 3.495 3.641 -0.1559 0.4170 0.4332 + 10LEU HB2 140 4.471 3.568 3.637 0.1368 1.2863 -0.4355 + 10LEU CG 141 4.434 3.428 3.478 -0.6381 0.1849 -0.3902 + 10LEU HG 142 4.354 3.384 3.418 -1.1804 -0.8232 1.0097 + 10LEU CD1 143 4.490 3.322 3.573 -0.4136 0.1963 -0.5113 + 10LEU HD11 144 4.553 3.256 3.514 -0.9941 1.5623 -2.8165 + 10LEU HD12 145 4.564 3.367 3.638 0.0794 -1.1049 -0.1387 + 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-1.1539 -0.1651 -0.3802 + 20SER CB 307 4.009 3.872 2.096 -0.3811 0.1913 0.3225 + 20SER HB1 308 4.050 3.886 1.996 -1.1680 2.5766 0.2800 + 20SER HB2 309 4.036 3.771 2.128 -0.5541 -0.2431 -0.8409 + 20SER OG 310 4.063 3.964 2.189 0.0775 0.3806 -0.1271 + 20SER HG 311 4.021 3.966 2.275 -2.5896 -1.4886 -1.2486 + 20SER C 312 3.798 3.786 1.988 0.5912 -0.4515 -0.1110 + 20SER O 313 3.770 3.815 1.872 0.5495 -0.0412 -0.0000 + 21LEU N 314 3.767 3.668 2.042 0.0574 -0.2729 -0.0130 + 21LEU H 315 3.788 3.649 2.139 -0.5189 1.4578 0.4882 + 21LEU CA 316 3.698 3.559 1.975 -0.0433 0.0777 -0.4867 + 21LEU HA 317 3.756 3.535 1.886 2.4214 0.6731 0.8698 + 21LEU CB 318 3.712 3.439 2.068 0.2419 0.1589 -0.4233 + 21LEU HB1 319 3.662 3.457 2.164 0.0254 0.5099 -0.6000 + 21LEU HB2 320 3.814 3.429 2.106 -0.4950 -3.0636 1.0028 + 21LEU CG 321 3.668 3.305 2.010 0.1333 0.1422 -0.3032 + 21LEU HG 322 3.561 3.310 1.987 -0.1080 -0.5917 0.5964 + 21LEU CD1 323 3.679 3.200 2.120 -0.2963 0.2542 -0.1479 + 21LEU HD11 324 3.640 3.103 2.089 -1.1384 0.8727 -1.0605 + 21LEU HD12 325 3.782 3.193 2.157 0.6733 -0.6542 -2.7969 + 21LEU HD13 326 3.620 3.244 2.200 1.7397 3.1218 -0.0586 + 21LEU CD2 327 3.742 3.241 1.894 0.8173 -0.3527 0.3963 + 21LEU HD21 328 3.834 3.191 1.924 -0.3224 -2.4064 0.6971 + 21LEU HD22 329 3.685 3.158 1.851 1.0498 0.9935 -2.8166 + 21LEU HD23 330 3.741 3.310 1.810 -2.0183 0.8630 1.3335 + 21LEU C 331 3.558 3.601 1.933 0.0800 0.3070 -0.6737 + 21LEU O 332 3.511 3.575 1.822 -0.7245 -0.2617 -0.2123 + 22LEU N 333 3.483 3.658 2.027 0.1458 -0.2383 -0.2869 + 22LEU H 334 3.524 3.681 2.117 -0.3290 1.6898 -0.5139 + 22LEU CA 335 3.339 3.677 2.022 0.2074 0.4765 0.3681 + 22LEU HA 336 3.303 3.595 1.960 1.4409 -0.6364 1.0582 + 22LEU CB 337 3.277 3.650 2.159 0.0828 0.5894 0.3338 + 22LEU HB1 338 3.170 3.664 2.141 0.0124 0.8657 0.9529 + 22LEU HB2 339 3.318 3.733 2.216 3.0361 -1.7332 1.8365 + 22LEU CG 340 3.298 3.517 2.231 -0.5147 0.2565 -0.0982 + 22LEU HG 341 3.405 3.498 2.238 -1.0390 -2.7746 0.9192 + 22LEU CD1 342 3.242 3.392 2.163 0.0198 -0.0197 -0.0332 + 22LEU HD11 343 3.140 3.410 2.129 1.0874 2.1636 -2.4627 + 22LEU HD12 344 3.293 3.372 2.069 -0.8838 2.0850 -1.0382 + 22LEU HD13 345 3.249 3.302 2.224 -0.6512 -0.9604 -1.3023 + 22LEU CD2 346 3.226 3.529 2.365 0.1656 0.0296 0.2910 + 22LEU HD21 347 3.119 3.539 2.349 0.3070 2.0610 0.3561 + 22LEU HD22 348 3.241 3.452 2.441 -1.7651 1.7983 2.6160 + 22LEU HD23 349 3.265 3.616 2.416 -1.1196 0.3242 0.8001 + 22LEU C 350 3.307 3.813 1.962 -0.5297 0.1672 0.0456 + 22LEU O 351 3.200 3.871 1.982 -0.3082 0.7718 -0.4988 + 23SER N 352 3.397 3.878 1.888 -0.1656 -0.1847 0.1748 + 23SER H 353 3.491 3.842 1.882 1.0432 2.5477 0.9680 + 23SER CA 354 3.374 3.998 1.811 -0.0332 -0.2547 0.0252 + 23SER HA 355 3.288 4.049 1.855 0.1756 -0.4733 0.6990 + 23SER CB 356 3.495 4.090 1.825 -0.2286 -0.0240 0.2073 + 23SER HB1 357 3.491 4.178 1.760 -0.6917 1.6212 2.3527 + 23SER HB2 358 3.584 4.034 1.798 -0.1411 -0.2623 0.9591 + 23SER OG 359 3.502 4.123 1.962 0.2482 -0.0754 0.1980 + 23SER HG 360 3.537 4.046 2.007 -1.4741 -0.5602 0.8199 + 23SER C 361 3.339 3.975 1.664 0.6378 -0.1065 -0.1614 + 23SER OC1 362 3.347 3.856 1.627 0.4397 -0.3374 0.5243 + 23SER OC2 363 3.325 4.069 1.583 -0.3367 -0.1819 -0.0864 + 8.36432 8.68132 10.41583 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/tests/test_files/input_aa_peptide.trr b/tests/test_files/input_aa_peptide.trr new file mode 100644 index 0000000..871bf04 Binary files /dev/null and b/tests/test_files/input_aa_peptide.trr differ diff --git a/tests/test_files/input_aa_peptide.xtc b/tests/test_files/input_aa_peptide.xtc new file mode 100644 index 0000000..12ac595 Binary files /dev/null and b/tests/test_files/input_aa_peptide.xtc differ diff --git a/tests/test_files/input_tiny_nobox.pdb b/tests/test_files/input_tiny_nobox.pdb new file mode 100644 index 0000000..2a1c181 --- /dev/null +++ b/tests/test_files/input_tiny_nobox.pdb @@ -0,0 +1,7 @@ +TITLE Membrane +MODEL 1 +ATOM 1 BB ASN 1 59.870 21.370 67.470 1.00 0.00 +ATOM 2 SC1 ASN 1 60.870 20.730 70.950 1.00 0.00 +ATOM 3 BB LEU 2 58.660 19.300 65.500 1.00 0.00 +TER +ENDMDL diff --git a/tests/test_files/output_x_com_begin_end_step.trr b/tests/test_files/output_x_com_begin_end_step.trr new file mode 100644 index 0000000..336141f Binary files /dev/null and b/tests/test_files/output_x_com_begin_end_step.trr differ diff --git a/tests/test_files/output_xy_com.pdb b/tests/test_files/output_xy_com.pdb new file mode 100644 index 0000000..9978299 --- /dev/null +++ b/tests/test_files/output_xy_com.pdb @@ -0,0 +1,370 @@ +TITLE AA peptide in a large box +REMARK THIS IS A SIMULATION BOX +CRYST1 83.643 86.813 104.158 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 N SER 1 44.569 44.752 49.930 1.00 0.00 +ATOM 2 H1 SER 1 43.749 44.562 50.490 1.00 0.00 +ATOM 3 H2 SER 1 44.729 43.832 49.550 1.00 0.00 +ATOM 4 H3 SER 1 45.349 45.032 50.510 1.00 0.00 +ATOM 5 CA SER 1 44.159 45.692 48.870 1.00 0.00 +ATOM 6 HA SER 1 43.119 45.532 48.580 1.00 0.00 +ATOM 7 CB SER 1 44.189 47.062 49.530 1.00 0.00 +ATOM 8 HB1 SER 1 43.529 47.092 50.390 1.00 0.00 +ATOM 9 HB2 SER 1 43.809 47.902 48.940 1.00 0.00 +ATOM 10 OG SER 1 45.489 47.592 49.720 1.00 0.00 +ATOM 11 HG SER 1 45.419 48.272 50.390 1.00 0.00 +ATOM 12 C SER 1 44.969 45.622 47.580 1.00 0.00 +ATOM 13 O SER 1 44.449 45.722 46.470 1.00 0.00 +ATOM 14 N LEU 2 46.259 45.292 47.670 1.00 0.00 +ATOM 15 H LEU 2 46.709 45.082 48.550 1.00 0.00 +ATOM 16 CA LEU 2 47.219 45.352 46.580 1.00 0.00 +ATOM 17 HA LEU 2 47.149 46.282 46.030 1.00 0.00 +ATOM 18 CB LEU 2 48.589 45.312 47.260 1.00 0.00 +ATOM 19 HB1 LEU 2 48.759 44.362 47.770 1.00 0.00 +ATOM 20 HB2 LEU 2 48.549 46.092 48.020 1.00 0.00 +ATOM 21 CG LEU 2 49.809 45.532 46.370 1.00 0.00 +ATOM 22 HG LEU 2 49.539 46.182 45.540 1.00 0.00 +ATOM 23 CD1 LEU 2 50.299 44.242 45.700 1.00 0.00 +ATOM 24 HD11 LEU 2 50.429 43.482 46.470 1.00 0.00 +ATOM 25 HD12 LEU 2 49.619 43.932 44.910 1.00 0.00 +ATOM 26 HD13 LEU 2 51.209 44.432 45.140 1.00 0.00 +ATOM 27 CD2 LEU 2 50.969 46.092 47.190 1.00 0.00 +ATOM 28 HD21 LEU 2 51.809 46.292 46.530 1.00 0.00 +ATOM 29 HD22 LEU 2 50.679 46.962 47.780 1.00 0.00 +ATOM 30 HD23 LEU 2 51.079 45.422 48.040 1.00 0.00 +ATOM 31 C LEU 2 47.029 44.182 45.620 1.00 0.00 +ATOM 32 O LEU 2 46.919 44.492 44.440 1.00 0.00 +ATOM 33 N LEU 3 46.889 42.942 46.090 1.00 0.00 +ATOM 34 H LEU 3 46.959 42.802 47.090 1.00 0.00 +ATOM 35 CA LEU 3 46.559 41.762 45.320 1.00 0.00 +ATOM 36 HA LEU 3 47.359 41.602 44.610 1.00 0.00 +ATOM 37 CB LEU 3 46.519 40.522 46.200 1.00 0.00 +ATOM 38 HB1 LEU 3 45.579 40.632 46.760 1.00 0.00 +ATOM 39 HB2 LEU 3 47.449 40.482 46.770 1.00 0.00 +ATOM 40 CG LEU 3 46.299 39.162 45.550 1.00 0.00 +ATOM 41 HG LEU 3 45.509 39.172 44.800 1.00 0.00 +ATOM 42 CD1 LEU 3 45.849 38.022 46.460 1.00 0.00 +ATOM 43 HD11 LEU 3 44.929 38.252 47.010 1.00 0.00 +ATOM 44 HD12 LEU 3 45.649 37.162 45.830 1.00 0.00 +ATOM 45 HD13 LEU 3 46.669 37.782 47.140 1.00 0.00 +ATOM 46 CD2 LEU 3 47.509 38.762 44.710 1.00 0.00 +ATOM 47 HD21 LEU 3 47.329 38.072 43.880 1.00 0.00 +ATOM 48 HD22 LEU 3 48.039 39.632 44.310 1.00 0.00 +ATOM 49 HD23 LEU 3 48.209 38.492 45.500 1.00 0.00 +ATOM 50 C LEU 3 45.239 41.922 44.570 1.00 0.00 +ATOM 51 O LEU 3 45.159 41.512 43.410 1.00 0.00 +ATOM 52 N SER 4 44.159 42.502 45.110 1.00 0.00 +ATOM 53 H SER 4 44.139 42.922 46.030 1.00 0.00 +ATOM 54 CA SER 4 43.009 42.722 44.260 1.00 0.00 +ATOM 55 HA SER 4 42.769 41.852 43.650 1.00 0.00 +ATOM 56 CB SER 4 41.819 42.932 45.180 1.00 0.00 +ATOM 57 HB1 SER 4 41.779 42.052 45.810 1.00 0.00 +ATOM 58 HB2 SER 4 40.939 43.122 44.550 1.00 0.00 +ATOM 59 OG SER 4 41.979 44.032 46.050 1.00 0.00 +ATOM 60 HG SER 4 42.209 43.652 46.900 1.00 0.00 +ATOM 61 C SER 4 43.159 43.932 43.350 1.00 0.00 +ATOM 62 O SER 4 42.549 43.902 42.280 1.00 0.00 +ATOM 63 N SER 5 43.909 44.992 43.660 1.00 0.00 +ATOM 64 H SER 5 44.379 44.982 44.560 1.00 0.00 +ATOM 65 CA SER 5 44.269 46.082 42.780 1.00 0.00 +ATOM 66 HA SER 5 43.409 46.492 42.260 1.00 0.00 +ATOM 67 CB SER 5 44.949 47.182 43.580 1.00 0.00 +ATOM 68 HB1 SER 5 45.389 47.902 42.890 1.00 0.00 +ATOM 69 HB2 SER 5 45.799 46.762 44.120 1.00 0.00 +ATOM 70 OG SER 5 44.189 47.872 44.550 1.00 0.00 +ATOM 71 HG SER 5 44.009 47.302 45.300 1.00 0.00 +ATOM 72 C SER 5 45.089 45.542 41.610 1.00 0.00 +ATOM 73 O SER 5 44.909 45.962 40.470 1.00 0.00 +ATOM 74 N LEU 6 45.979 44.552 41.750 1.00 0.00 +ATOM 75 H LEU 6 46.099 44.182 42.690 1.00 0.00 +ATOM 76 CA LEU 6 46.659 43.922 40.640 1.00 0.00 +ATOM 77 HA LEU 6 47.089 44.632 39.940 1.00 0.00 +ATOM 78 CB LEU 6 47.739 43.072 41.290 1.00 0.00 +ATOM 79 HB1 LEU 6 47.219 42.462 42.030 1.00 0.00 +ATOM 80 HB2 LEU 6 48.389 43.692 41.910 1.00 0.00 +ATOM 81 CG LEU 6 48.629 42.242 40.360 1.00 0.00 +ATOM 82 HG LEU 6 48.059 41.462 39.860 1.00 0.00 +ATOM 83 CD1 LEU 6 49.779 41.622 41.140 1.00 0.00 +ATOM 84 HD11 LEU 6 50.549 41.192 40.490 1.00 0.00 +ATOM 85 HD12 LEU 6 50.299 42.342 41.760 1.00 0.00 +ATOM 86 HD13 LEU 6 49.399 40.872 41.830 1.00 0.00 +ATOM 87 CD2 LEU 6 49.359 43.062 39.300 1.00 0.00 +ATOM 88 HD21 LEU 6 50.099 42.512 38.720 1.00 0.00 +ATOM 89 HD22 LEU 6 48.579 43.492 38.680 1.00 0.00 +ATOM 90 HD23 LEU 6 49.909 43.872 39.790 1.00 0.00 +ATOM 91 C LEU 6 45.649 43.102 39.850 1.00 0.00 +ATOM 92 O LEU 6 45.759 42.982 38.630 1.00 0.00 +ATOM 93 N LEU 7 44.659 42.422 40.440 1.00 0.00 +ATOM 94 H LEU 7 44.629 42.402 41.450 1.00 0.00 +ATOM 95 CA LEU 7 43.759 41.532 39.740 1.00 0.00 +ATOM 96 HA LEU 7 44.299 41.122 38.890 1.00 0.00 +ATOM 97 CB LEU 7 43.149 40.542 40.730 1.00 0.00 +ATOM 98 HB1 LEU 7 42.199 40.152 40.380 1.00 0.00 +ATOM 99 HB2 LEU 7 42.969 41.052 41.680 1.00 0.00 +ATOM 100 CG LEU 7 44.149 39.442 41.090 1.00 0.00 +ATOM 101 HG LEU 7 45.129 39.732 41.480 1.00 0.00 +ATOM 102 CD1 LEU 7 44.309 38.582 39.840 1.00 0.00 +ATOM 103 HD11 LEU 7 44.919 37.692 39.980 1.00 0.00 +ATOM 104 HD12 LEU 7 43.349 38.282 39.420 1.00 0.00 +ATOM 105 HD13 LEU 7 44.819 39.142 39.050 1.00 0.00 +ATOM 106 CD2 LEU 7 43.569 38.482 42.130 1.00 0.00 +ATOM 107 HD21 LEU 7 43.399 39.052 43.050 1.00 0.00 +ATOM 108 HD22 LEU 7 42.609 38.102 41.780 1.00 0.00 +ATOM 109 HD23 LEU 7 44.259 37.722 42.500 1.00 0.00 +ATOM 110 C LEU 7 42.729 42.382 39.000 1.00 0.00 +ATOM 111 O LEU 7 42.259 42.032 37.920 1.00 0.00 +ATOM 112 N SER 8 42.439 43.592 39.460 1.00 0.00 +ATOM 113 H SER 8 42.859 43.932 40.320 1.00 0.00 +ATOM 114 CA SER 8 41.629 44.582 38.770 1.00 0.00 +ATOM 115 HA SER 8 40.689 44.122 38.470 1.00 0.00 +ATOM 116 CB SER 8 41.399 45.732 39.740 1.00 0.00 +ATOM 117 HB1 SER 8 40.939 46.562 39.200 1.00 0.00 +ATOM 118 HB2 SER 8 42.429 46.022 39.960 1.00 0.00 +ATOM 119 OG SER 8 40.639 45.342 40.860 1.00 0.00 +ATOM 120 HG SER 8 41.249 44.962 41.490 1.00 0.00 +ATOM 121 C SER 8 42.439 45.092 37.580 1.00 0.00 +ATOM 122 O SER 8 41.869 45.182 36.500 1.00 0.00 +ATOM 123 N SER 9 43.719 45.462 37.670 1.00 0.00 +ATOM 124 H SER 9 44.039 45.482 38.630 1.00 0.00 +ATOM 125 CA SER 9 44.579 45.812 36.570 1.00 0.00 +ATOM 126 HA SER 9 44.199 46.672 36.020 1.00 0.00 +ATOM 127 CB SER 9 45.989 46.092 37.080 1.00 0.00 +ATOM 128 HB1 SER 9 46.519 46.532 36.230 1.00 0.00 +ATOM 129 HB2 SER 9 46.329 45.092 37.360 1.00 0.00 +ATOM 130 OG SER 9 46.009 47.092 38.080 1.00 0.00 +ATOM 131 HG SER 9 45.679 46.862 38.950 1.00 0.00 +ATOM 132 C SER 9 44.599 44.732 35.500 1.00 0.00 +ATOM 133 O SER 9 44.519 45.032 34.310 1.00 0.00 +ATOM 134 N LEU 10 44.709 43.482 35.940 1.00 0.00 +ATOM 135 H LEU 10 44.869 43.332 36.930 1.00 0.00 +ATOM 136 CA LEU 10 44.669 42.332 35.070 1.00 0.00 +ATOM 137 HA LEU 10 45.379 42.612 34.300 1.00 0.00 +ATOM 138 CB LEU 10 45.209 41.092 35.780 1.00 0.00 +ATOM 139 HB1 LEU 10 44.409 40.712 36.410 1.00 0.00 +ATOM 140 HB2 LEU 10 46.059 41.442 36.370 1.00 0.00 +ATOM 141 CG LEU 10 45.689 40.042 34.780 1.00 0.00 +ATOM 142 HG LEU 10 44.889 39.602 34.180 1.00 0.00 +ATOM 143 CD1 LEU 10 46.249 38.982 35.730 1.00 0.00 +ATOM 144 HD11 LEU 10 46.879 38.322 35.140 1.00 0.00 +ATOM 145 HD12 LEU 10 46.989 39.432 36.380 1.00 0.00 +ATOM 146 HD13 LEU 10 45.509 38.402 36.270 1.00 0.00 +ATOM 147 CD2 LEU 10 46.789 40.512 33.840 1.00 0.00 +ATOM 148 HD21 LEU 10 47.259 39.622 33.420 1.00 0.00 +ATOM 149 HD22 LEU 10 46.349 41.132 33.060 1.00 0.00 +ATOM 150 HD23 LEU 10 47.589 40.952 34.440 1.00 0.00 +ATOM 151 C LEU 10 43.339 42.042 34.380 1.00 0.00 +ATOM 152 O LEU 10 43.299 41.702 33.200 1.00 0.00 +ATOM 153 N LEU 11 42.219 42.062 35.120 1.00 0.00 +ATOM 154 H LEU 11 42.299 42.022 36.130 1.00 0.00 +ATOM 155 CA LEU 11 40.909 42.122 34.510 1.00 0.00 +ATOM 156 HA LEU 11 40.719 41.152 34.060 1.00 0.00 +ATOM 157 CB LEU 11 39.909 42.212 35.670 1.00 0.00 +ATOM 158 HB1 LEU 11 40.049 43.092 36.290 1.00 0.00 +ATOM 159 HB2 LEU 11 40.059 41.362 36.330 1.00 0.00 +ATOM 160 CG LEU 11 38.439 42.352 35.300 1.00 0.00 +ATOM 161 HG LEU 11 38.269 42.992 34.440 1.00 0.00 +ATOM 162 CD1 LEU 11 37.619 42.992 36.430 1.00 0.00 +ATOM 163 HD11 LEU 11 36.539 42.852 36.340 1.00 0.00 +ATOM 164 HD12 LEU 11 37.929 42.612 37.400 1.00 0.00 +ATOM 165 HD13 LEU 11 37.859 44.052 36.390 1.00 0.00 +ATOM 166 CD2 LEU 11 37.779 41.012 35.000 1.00 0.00 +ATOM 167 HD21 LEU 11 38.219 40.432 34.190 1.00 0.00 +ATOM 168 HD22 LEU 11 37.599 40.342 35.840 1.00 0.00 +ATOM 169 HD23 LEU 11 36.779 41.192 34.600 1.00 0.00 +ATOM 170 C LEU 11 40.649 43.272 33.550 1.00 0.00 +ATOM 171 O LEU 11 39.979 43.162 32.520 1.00 0.00 +ATOM 172 N LYS 12 41.189 44.432 33.930 1.00 0.00 +ATOM 173 H LYS 12 41.699 44.492 34.790 1.00 0.00 +ATOM 174 CA LYS 12 41.199 45.592 33.050 1.00 0.00 +ATOM 175 HA LYS 12 40.129 45.752 32.890 1.00 0.00 +ATOM 176 CB LYS 12 41.609 46.832 33.820 1.00 0.00 +ATOM 177 HB1 LYS 12 42.669 46.742 34.060 1.00 0.00 +ATOM 178 HB2 LYS 12 40.979 46.882 34.710 1.00 0.00 +ATOM 179 CG LYS 12 41.569 48.162 33.070 1.00 0.00 +ATOM 180 HG1 LYS 12 42.249 48.082 32.220 1.00 0.00 +ATOM 181 HG2 LYS 12 41.959 48.822 33.840 1.00 0.00 +ATOM 182 CD LYS 12 40.279 48.802 32.570 1.00 0.00 +ATOM 183 HD1 LYS 12 40.689 49.742 32.200 1.00 0.00 +ATOM 184 HD2 LYS 12 39.619 48.952 33.420 1.00 0.00 +ATOM 185 CE LYS 12 39.629 48.132 31.360 1.00 0.00 +ATOM 186 HE1 LYS 12 39.349 47.082 31.490 1.00 0.00 +ATOM 187 HE2 LYS 12 40.469 48.092 30.660 1.00 0.00 +ATOM 188 NZ LYS 12 38.479 48.802 30.750 1.00 0.00 +ATOM 189 HZ1 LYS 12 38.719 49.742 30.480 1.00 0.00 +ATOM 190 HZ2 LYS 12 38.189 48.322 29.910 1.00 0.00 +ATOM 191 HZ3 LYS 12 37.689 48.872 31.370 1.00 0.00 +ATOM 192 C LYS 12 41.909 45.382 31.720 1.00 0.00 +ATOM 193 O LYS 12 41.319 45.532 30.660 1.00 0.00 +ATOM 194 N LEU 13 43.109 44.792 31.720 1.00 0.00 +ATOM 195 H LEU 13 43.639 44.612 32.560 1.00 0.00 +ATOM 196 CA LEU 13 43.849 44.312 30.570 1.00 0.00 +ATOM 197 HA LEU 13 44.039 45.162 29.920 1.00 0.00 +ATOM 198 CB LEU 13 45.269 43.862 30.860 1.00 0.00 +ATOM 199 HB1 LEU 13 45.199 43.102 31.640 1.00 0.00 +ATOM 200 HB2 LEU 13 45.829 44.642 31.370 1.00 0.00 +ATOM 201 CG LEU 13 46.189 43.332 29.750 1.00 0.00 +ATOM 202 HG LEU 13 45.599 42.582 29.230 1.00 0.00 +ATOM 203 CD1 LEU 13 47.449 42.652 30.260 1.00 0.00 +ATOM 204 HD11 LEU 13 47.289 41.592 30.440 1.00 0.00 +ATOM 205 HD12 LEU 13 48.139 42.712 29.420 1.00 0.00 +ATOM 206 HD13 LEU 13 47.809 43.122 31.180 1.00 0.00 +ATOM 207 CD2 LEU 13 46.489 44.522 28.850 1.00 0.00 +ATOM 208 HD21 LEU 13 45.609 44.972 28.380 1.00 0.00 +ATOM 209 HD22 LEU 13 47.099 45.212 29.430 1.00 0.00 +ATOM 210 HD23 LEU 13 47.189 44.382 28.020 1.00 0.00 +ATOM 211 C LEU 13 43.079 43.212 29.840 1.00 0.00 +ATOM 212 O LEU 13 42.849 43.452 28.650 1.00 0.00 +ATOM 213 N LEU 14 42.459 42.302 30.590 1.00 0.00 +ATOM 214 H LEU 14 42.639 42.242 31.580 1.00 0.00 +ATOM 215 CA LEU 14 41.719 41.232 29.950 1.00 0.00 +ATOM 216 HA LEU 14 42.409 40.762 29.260 1.00 0.00 +ATOM 217 CB LEU 14 41.169 40.232 30.960 1.00 0.00 +ATOM 218 HB1 LEU 14 40.429 40.582 31.680 1.00 0.00 +ATOM 219 HB2 LEU 14 42.009 39.892 31.580 1.00 0.00 +ATOM 220 CG LEU 14 40.509 39.012 30.320 1.00 0.00 +ATOM 221 HG LEU 14 39.559 39.362 29.930 1.00 0.00 +ATOM 222 CD1 LEU 14 40.079 38.062 31.440 1.00 0.00 +ATOM 223 HD11 LEU 14 39.459 37.252 31.060 1.00 0.00 +ATOM 224 HD12 LEU 14 40.989 37.722 31.930 1.00 0.00 +ATOM 225 HD13 LEU 14 39.419 38.472 32.210 1.00 0.00 +ATOM 226 CD2 LEU 14 41.399 38.342 29.280 1.00 0.00 +ATOM 227 HD21 LEU 14 41.809 38.932 28.460 1.00 0.00 +ATOM 228 HD22 LEU 14 42.269 37.892 29.770 1.00 0.00 +ATOM 229 HD23 LEU 14 40.799 37.492 28.970 1.00 0.00 +ATOM 230 C LEU 14 40.579 41.872 29.170 1.00 0.00 +ATOM 231 O LEU 14 40.279 41.482 28.040 1.00 0.00 +ATOM 232 N SER 15 39.879 42.912 29.650 1.00 0.00 +ATOM 233 H SER 15 40.139 43.242 30.570 1.00 0.00 +ATOM 234 CA SER 15 38.679 43.532 29.130 1.00 0.00 +ATOM 235 HA SER 15 38.089 42.832 28.550 1.00 0.00 +ATOM 236 CB SER 15 37.819 44.132 30.240 1.00 0.00 +ATOM 237 HB1 SER 15 36.849 44.442 29.850 1.00 0.00 +ATOM 238 HB2 SER 15 38.389 44.922 30.720 1.00 0.00 +ATOM 239 OG SER 15 37.629 43.172 31.260 1.00 0.00 +ATOM 240 HG SER 15 38.469 43.162 31.730 1.00 0.00 +ATOM 241 C SER 15 39.049 44.502 28.020 1.00 0.00 +ATOM 242 O SER 15 38.219 44.792 27.160 1.00 0.00 +ATOM 243 N SER 16 40.289 44.992 27.970 1.00 0.00 +ATOM 244 H SER 16 40.999 44.592 28.580 1.00 0.00 +ATOM 245 CA SER 16 40.649 45.822 26.840 1.00 0.00 +ATOM 246 HA SER 16 39.899 46.482 26.410 1.00 0.00 +ATOM 247 CB SER 16 41.759 46.752 27.330 1.00 0.00 +ATOM 248 HB1 SER 16 42.099 47.322 26.470 1.00 0.00 +ATOM 249 HB2 SER 16 42.589 46.162 27.730 1.00 0.00 +ATOM 250 OG SER 16 41.399 47.612 28.390 1.00 0.00 +ATOM 251 HG SER 16 40.569 48.032 28.140 1.00 0.00 +ATOM 252 C SER 16 41.119 45.002 25.650 1.00 0.00 +ATOM 253 O SER 16 40.799 45.302 24.500 1.00 0.00 +ATOM 254 N LEU 17 41.739 43.862 25.950 1.00 0.00 +ATOM 255 H LEU 17 41.949 43.622 26.910 1.00 0.00 +ATOM 256 CA LEU 17 42.169 42.862 25.000 1.00 0.00 +ATOM 257 HA LEU 17 42.629 43.372 24.150 1.00 0.00 +ATOM 258 CB LEU 17 43.059 41.842 25.710 1.00 0.00 +ATOM 259 HB1 LEU 17 42.989 40.932 25.120 1.00 0.00 +ATOM 260 HB2 LEU 17 42.619 41.632 26.680 1.00 0.00 +ATOM 261 CG LEU 17 44.539 42.132 25.940 1.00 0.00 +ATOM 262 HG LEU 17 44.579 42.802 26.800 1.00 0.00 +ATOM 263 CD1 LEU 17 45.179 42.722 24.680 1.00 0.00 +ATOM 264 HD11 LEU 17 44.859 42.222 23.770 1.00 0.00 +ATOM 265 HD12 LEU 17 45.049 43.802 24.550 1.00 0.00 +ATOM 266 HD13 LEU 17 46.259 42.562 24.690 1.00 0.00 +ATOM 267 CD2 LEU 17 45.299 40.872 26.340 1.00 0.00 +ATOM 268 HD21 LEU 17 44.859 40.392 27.210 1.00 0.00 +ATOM 269 HD22 LEU 17 45.159 40.182 25.510 1.00 0.00 +ATOM 270 HD23 LEU 17 46.379 41.032 26.410 1.00 0.00 +ATOM 271 C LEU 17 40.929 42.202 24.410 1.00 0.00 +ATOM 272 O LEU 17 40.949 41.932 23.220 1.00 0.00 +ATOM 273 N LEU 18 39.919 41.922 25.240 1.00 0.00 +ATOM 274 H LEU 18 39.999 42.192 26.210 1.00 0.00 +ATOM 275 CA LEU 18 38.639 41.452 24.740 1.00 0.00 +ATOM 276 HA LEU 18 38.819 40.712 23.970 1.00 0.00 +ATOM 277 CB LEU 18 37.999 40.862 26.000 1.00 0.00 +ATOM 278 HB1 LEU 18 37.889 41.712 26.670 1.00 0.00 +ATOM 279 HB2 LEU 18 38.739 40.202 26.440 1.00 0.00 +ATOM 280 CG LEU 18 36.659 40.162 25.790 1.00 0.00 +ATOM 281 HG LEU 18 35.939 40.782 25.250 1.00 0.00 +ATOM 282 CD1 LEU 18 36.119 39.832 27.180 1.00 0.00 +ATOM 283 HD11 LEU 18 36.049 40.882 27.450 1.00 0.00 +ATOM 284 HD12 LEU 18 35.069 39.542 27.100 1.00 0.00 +ATOM 285 HD13 LEU 18 36.779 39.172 27.750 1.00 0.00 +ATOM 286 CD2 LEU 18 36.879 38.882 24.980 1.00 0.00 +ATOM 287 HD21 LEU 18 35.969 38.272 24.950 1.00 0.00 +ATOM 288 HD22 LEU 18 37.239 39.232 24.020 1.00 0.00 +ATOM 289 HD23 LEU 18 37.539 38.262 25.580 1.00 0.00 +ATOM 290 C LEU 18 37.849 42.562 24.060 1.00 0.00 +ATOM 291 O LEU 18 37.189 42.222 23.090 1.00 0.00 +ATOM 292 N SER 19 38.029 43.832 24.440 1.00 0.00 +ATOM 293 H SER 19 38.579 44.092 25.240 1.00 0.00 +ATOM 294 CA SER 19 37.479 44.952 23.710 1.00 0.00 +ATOM 295 HA SER 19 36.429 44.702 23.580 1.00 0.00 +ATOM 296 CB SER 19 37.379 46.232 24.530 1.00 0.00 +ATOM 297 HB1 SER 19 38.339 46.532 24.930 1.00 0.00 +ATOM 298 HB2 SER 19 36.659 46.022 25.320 1.00 0.00 +ATOM 299 OG SER 19 36.929 47.352 23.790 1.00 0.00 +ATOM 300 HG SER 19 36.729 47.992 24.470 1.00 0.00 +ATOM 301 C SER 19 38.129 45.112 22.340 1.00 0.00 +ATOM 302 O SER 19 37.439 45.522 21.410 1.00 0.00 +ATOM 303 N SER 20 39.349 44.592 22.150 1.00 0.00 +ATOM 304 H SER 20 39.909 44.292 22.930 1.00 0.00 +ATOM 305 CA SER 20 39.929 44.652 20.830 1.00 0.00 +ATOM 306 HA SER 20 39.729 45.632 20.390 1.00 0.00 +ATOM 307 CB SER 20 41.439 44.482 20.960 1.00 0.00 +ATOM 308 HB1 SER 20 41.849 44.622 19.960 1.00 0.00 +ATOM 309 HB2 SER 20 41.709 43.472 21.280 1.00 0.00 +ATOM 310 OG SER 20 41.979 45.402 21.890 1.00 0.00 +ATOM 311 HG SER 20 41.559 45.422 22.750 1.00 0.00 +ATOM 312 C SER 20 39.329 43.622 19.880 1.00 0.00 +ATOM 313 O SER 20 39.049 43.912 18.720 1.00 0.00 +ATOM 314 N LEU 21 39.019 42.442 20.420 1.00 0.00 +ATOM 315 H LEU 21 39.229 42.252 21.390 1.00 0.00 +ATOM 316 CA LEU 21 38.329 41.352 19.750 1.00 0.00 +ATOM 317 HA LEU 21 38.909 41.112 18.860 1.00 0.00 +ATOM 318 CB LEU 21 38.469 40.152 20.680 1.00 0.00 +ATOM 319 HB1 LEU 21 37.969 40.332 21.640 1.00 0.00 +ATOM 320 HB2 LEU 21 39.489 40.052 21.060 1.00 0.00 +ATOM 321 CG LEU 21 38.029 38.812 20.100 1.00 0.00 +ATOM 322 HG LEU 21 36.959 38.862 19.870 1.00 0.00 +ATOM 323 CD1 LEU 21 38.139 37.762 21.200 1.00 0.00 +ATOM 324 HD11 LEU 21 37.749 36.792 20.890 1.00 0.00 +ATOM 325 HD12 LEU 21 39.169 37.692 21.570 1.00 0.00 +ATOM 326 HD13 LEU 21 37.549 38.202 22.000 1.00 0.00 +ATOM 327 CD2 LEU 21 38.769 38.172 18.940 1.00 0.00 +ATOM 328 HD21 LEU 21 39.689 37.672 19.240 1.00 0.00 +ATOM 329 HD22 LEU 21 38.199 37.342 18.510 1.00 0.00 +ATOM 330 HD23 LEU 21 38.759 38.862 18.100 1.00 0.00 +ATOM 331 C LEU 21 36.929 41.772 19.330 1.00 0.00 +ATOM 332 O LEU 21 36.459 41.512 18.220 1.00 0.00 +ATOM 333 N LEU 22 36.179 42.342 20.270 1.00 0.00 +ATOM 334 H LEU 22 36.589 42.572 21.170 1.00 0.00 +ATOM 335 CA LEU 22 34.739 42.532 20.220 1.00 0.00 +ATOM 336 HA LEU 22 34.379 41.712 19.600 1.00 0.00 +ATOM 337 CB LEU 22 34.119 42.262 21.590 1.00 0.00 +ATOM 338 HB1 LEU 22 33.049 42.402 21.410 1.00 0.00 +ATOM 339 HB2 LEU 22 34.529 43.092 22.160 1.00 0.00 +ATOM 340 CG LEU 22 34.329 40.932 22.310 1.00 0.00 +ATOM 341 HG LEU 22 35.399 40.742 22.380 1.00 0.00 +ATOM 342 CD1 LEU 22 33.769 39.682 21.630 1.00 0.00 +ATOM 343 HD11 LEU 22 32.749 39.862 21.290 1.00 0.00 +ATOM 344 HD12 LEU 22 34.279 39.482 20.690 1.00 0.00 +ATOM 345 HD13 LEU 22 33.839 38.782 22.240 1.00 0.00 +ATOM 346 CD2 LEU 22 33.609 41.052 23.650 1.00 0.00 +ATOM 347 HD21 LEU 22 32.539 41.152 23.490 1.00 0.00 +ATOM 348 HD22 LEU 22 33.759 40.282 24.410 1.00 0.00 +ATOM 349 HD23 LEU 22 33.999 41.922 24.160 1.00 0.00 +ATOM 350 C LEU 22 34.419 43.892 19.620 1.00 0.00 +ATOM 351 O LEU 22 33.349 44.472 19.820 1.00 0.00 +ATOM 352 N SER 23 35.319 44.542 18.880 1.00 0.00 +ATOM 353 H SER 23 36.259 44.182 18.820 1.00 0.00 +ATOM 354 CA SER 23 35.089 45.742 18.110 1.00 0.00 +ATOM 355 HA SER 23 34.229 46.252 18.550 1.00 0.00 +ATOM 356 CB SER 23 36.299 46.662 18.250 1.00 0.00 +ATOM 357 HB1 SER 23 36.259 47.542 17.600 1.00 0.00 +ATOM 358 HB2 SER 23 37.189 46.102 17.980 1.00 0.00 +ATOM 359 OG SER 23 36.369 46.992 19.620 1.00 0.00 +ATOM 360 HG SER 23 36.719 46.222 20.070 1.00 0.00 +ATOM 361 C SER 23 34.739 45.512 16.640 1.00 0.00 +ATOM 362 OC1 SER 23 34.819 44.322 16.270 1.00 0.00 +ATOM 363 OC2 SER 23 34.599 46.452 15.830 1.00 0.00 +TER +ENDMDL +END diff --git a/tests/test_files/output_xyz.pdb b/tests/test_files/output_xyz.pdb index 4386241..d52244f 100644 --- a/tests/test_files/output_xyz.pdb +++ b/tests/test_files/output_xyz.pdb @@ -8331,3 +8331,4 @@ ATOM 8326 CL- ION 5489 80.152 55.023 33.847 1.00 0.00 ATOM 8327 CL- ION 5490 9.003 58.273 11.057 1.00 0.00 TER ENDMDL +END diff --git a/tests/test_files/output_xyz_aa_peptide.gro b/tests/test_files/output_xyz_aa_peptide.gro new file mode 100644 index 0000000..ce8d88e --- /dev/null +++ b/tests/test_files/output_xyz_aa_peptide.gro @@ -0,0 +1,366 @@ +AA peptide in a large box + 363 + 1SER N 1 4.429 4.511 6.889 0.0617 0.5184 0.2735 + 1SER H1 2 4.347 4.492 6.945 -0.6908 -0.7011 -1.1721 + 1SER H2 3 4.445 4.419 6.851 -0.7154 0.4550 0.0906 + 1SER H3 4 4.507 4.539 6.947 -0.6465 3.3158 0.0179 + 1SER CA 5 4.388 4.605 6.783 0.2322 -0.3472 -0.5670 + 1SER HA 6 4.284 4.589 6.754 -0.1864 -0.2599 0.8480 + 1SER CB 7 4.391 4.742 6.849 -0.0923 -1.0250 0.9005 + 1SER HB1 8 4.325 4.745 6.935 -2.7751 -0.1527 -1.0690 + 1SER HB2 9 4.353 4.826 6.790 1.5703 -0.7739 0.1075 + 1SER OG 10 4.521 4.795 6.868 -0.4378 0.3508 -0.3267 + 1SER HG 11 4.514 4.863 6.935 0.3306 -1.3589 1.6057 + 1SER C 12 4.469 4.598 6.654 0.6932 1.5894 -0.4126 + 1SER O 13 4.417 4.608 6.543 -0.0444 0.1061 -0.2316 + 2LEU N 14 4.598 4.565 6.663 0.4717 0.8344 0.1005 + 2LEU H 15 4.643 4.544 6.751 0.9891 -1.7354 -0.6644 + 2LEU CA 16 4.694 4.571 6.554 0.1872 0.2027 -0.1921 + 2LEU HA 17 4.687 4.664 6.499 1.9183 -0.1149 -1.0180 + 2LEU CB 18 4.831 4.567 6.622 0.2173 0.1824 -0.2539 + 2LEU HB1 19 4.848 4.472 6.673 -0.2350 0.1491 -0.1608 + 2LEU HB2 20 4.827 4.645 6.698 0.5116 0.7942 -0.8612 + 2LEU CG 21 4.953 4.589 6.533 0.2286 -0.1291 -0.3171 + 2LEU HG 22 4.926 4.654 6.450 0.4774 0.0519 -0.2555 + 2LEU CD1 23 5.002 4.460 6.466 -0.7002 -0.4755 -0.3435 + 2LEU HD11 24 5.015 4.384 6.543 -2.3897 -1.9478 -1.4461 + 2LEU HD12 25 4.934 4.429 6.387 0.3965 -0.9949 -1.1056 + 2LEU HD13 26 5.093 4.479 6.410 -0.5886 0.5598 0.1580 + 2LEU CD2 27 5.069 4.645 6.615 0.0075 -0.3078 0.1237 + 2LEU HD21 28 5.153 4.665 6.549 0.4064 1.5135 1.1292 + 2LEU HD22 29 5.040 4.732 6.674 2.1811 0.8041 -0.3642 + 2LEU HD23 30 5.080 4.578 6.700 -1.5710 2.2168 2.5088 + 2LEU C 31 4.675 4.454 6.458 0.1926 -0.1437 0.2257 + 2LEU O 32 4.664 4.485 6.340 0.6914 -0.6509 0.0437 + 3LEU N 33 4.661 4.330 6.505 -0.0598 -0.1234 0.2087 + 3LEU H 34 4.668 4.316 6.605 -1.1286 -2.5043 0.0058 + 3LEU CA 35 4.628 4.212 6.428 0.1131 0.1042 -0.2165 + 3LEU HA 36 4.708 4.196 6.357 0.1195 -1.5046 0.1271 + 3LEU CB 37 4.624 4.088 6.516 -0.3645 0.0332 -0.3350 + 3LEU HB1 38 4.530 4.099 6.572 -1.5416 -1.3895 -1.9134 + 3LEU HB2 39 4.717 4.084 6.573 -1.5130 -2.2084 1.5745 + 3LEU CG 40 4.602 3.952 6.451 -0.1143 -0.0085 -0.3302 + 3LEU HG 41 4.523 3.953 6.376 -0.5812 -0.9032 0.1414 + 3LEU CD1 42 4.557 3.838 6.542 -0.5550 0.1246 -0.3821 + 3LEU HD11 43 4.465 3.861 6.597 0.7874 0.7891 1.7162 + 3LEU HD12 44 4.537 3.752 6.479 0.1413 -1.2966 1.2589 + 3LEU HD13 45 4.639 3.814 6.610 -0.6877 0.1249 -0.2190 + 3LEU CD2 46 4.723 3.912 6.367 0.5973 0.2069 0.5705 + 3LEU HD21 47 4.705 3.843 6.284 0.2751 0.7716 0.1663 + 3LEU HD22 48 4.776 3.999 6.327 -1.9361 0.9472 -1.4460 + 3LEU HD23 49 4.793 3.885 6.446 0.7486 1.7881 1.0072 + 3LEU C 50 4.496 4.228 6.353 -0.0309 -0.6280 -0.1259 + 3LEU O 51 4.488 4.187 6.237 0.1980 -0.5278 -0.1774 + 4SER N 52 4.388 4.286 6.407 0.4017 -0.0395 0.1212 + 4SER H 53 4.386 4.328 6.499 0.8422 -1.4944 0.8299 + 4SER CA 54 4.273 4.308 6.322 0.1524 0.0527 0.4799 + 4SER HA 55 4.249 4.221 6.261 0.0037 0.0918 0.4816 + 4SER CB 56 4.154 4.329 6.414 0.0044 -0.6389 0.4523 + 4SER HB1 57 4.150 4.241 6.477 1.5008 -0.9020 0.2147 + 4SER HB2 58 4.066 4.348 6.351 0.9191 -0.3783 -0.7825 + 4SER OG 59 4.170 4.439 6.501 0.9511 -0.3333 -0.0938 + 4SER HG 60 4.193 4.401 6.586 -1.0470 -1.6639 -0.0713 + 4SER C 61 4.288 4.429 6.231 0.8569 -0.2434 0.1918 + 4SER O 62 4.227 4.426 6.124 0.3176 0.4118 0.4677 + 5SER N 63 4.363 4.535 6.262 0.0634 0.4019 -0.0379 + 5SER H 64 4.410 4.534 6.352 0.1924 -0.9278 -0.0965 + 5SER CA 65 4.399 4.644 6.174 0.4241 0.5711 0.3145 + 5SER HA 66 4.313 4.685 6.122 0.5336 -0.8307 -1.0416 + 5SER CB 67 4.467 4.754 6.254 0.6430 0.1559 0.7035 + 5SER HB1 68 4.511 4.826 6.185 -0.2487 2.8655 2.7652 + 5SER HB2 69 4.552 4.712 6.308 -0.1944 -0.4083 1.6110 + 5SER OG 70 4.391 4.823 6.351 -0.3287 -0.1325 0.1546 + 5SER HG 71 4.373 4.766 6.426 4.0386 -0.1720 1.4383 + 5SER C 72 4.481 4.590 6.057 0.0833 0.0925 0.2929 + 5SER O 73 4.463 4.632 5.943 -0.5133 -0.4097 0.1955 + 6LEU N 74 4.570 4.491 6.071 0.0916 0.0705 0.0880 + 6LEU H 75 4.582 4.454 6.165 0.5975 0.4991 0.1921 + 6LEU CA 76 4.638 4.428 5.960 -0.0585 -0.0814 0.0824 + 6LEU HA 77 4.681 4.499 5.890 0.4126 -1.1192 -0.7092 + 6LEU CB 78 4.746 4.343 6.025 0.2714 0.3381 0.0862 + 6LEU HB1 79 4.694 4.282 6.099 -0.4523 2.2449 1.2222 + 6LEU HB2 80 4.811 4.405 6.087 -0.2779 1.2216 -0.2248 + 6LEU CG 81 4.835 4.260 5.932 -0.2104 0.1053 -0.1702 + 6LEU HG 82 4.778 4.182 5.882 0.8224 0.2341 -1.6186 + 6LEU CD1 83 4.950 4.198 6.010 -0.2686 -0.2632 -0.3790 + 6LEU HD11 84 5.027 4.155 5.945 0.5983 -2.7465 2.1019 + 6LEU HD12 85 5.002 4.270 6.072 -0.3928 0.6432 -1.3095 + 6LEU HD13 86 4.912 4.123 6.079 1.3919 -1.3839 -0.6050 + 6LEU CD2 87 4.908 4.342 5.826 0.5350 -0.3733 -0.0313 + 6LEU HD21 88 4.982 4.287 5.768 1.1155 -0.9264 1.1849 + 6LEU HD22 89 4.830 4.385 5.764 0.6686 -1.4125 -0.9368 + 6LEU HD23 90 4.963 4.423 5.875 -1.2848 -0.3201 2.0800 + 6LEU C 91 4.537 4.346 5.881 -0.1118 -0.0290 0.0952 + 6LEU O 92 4.548 4.334 5.759 0.2247 -0.2103 0.1405 + 7LEU N 93 4.438 4.278 5.940 -0.2431 -0.1275 -0.2364 + 7LEU H 94 4.435 4.276 6.041 -1.9043 -2.1052 -0.2649 + 7LEU CA 95 4.348 4.189 5.870 0.0985 -0.5307 -0.1673 + 7LEU HA 96 4.402 4.148 5.785 -1.4727 0.3066 -1.6328 + 7LEU CB 97 4.287 4.090 5.969 -0.3314 -0.4031 -0.3007 + 7LEU HB1 98 4.192 4.051 5.934 -0.0125 -1.0143 -0.4977 + 7LEU HB2 99 4.269 4.141 6.064 -1.6866 1.3660 -1.4402 + 7LEU CG 100 4.387 3.980 6.005 -0.1483 0.0438 0.5813 + 7LEU HG 101 4.485 4.009 6.044 1.6712 -2.7912 -1.5128 + 7LEU CD1 102 4.403 3.894 5.880 -0.8374 0.1095 0.4454 + 7LEU HD11 103 4.464 3.805 5.894 2.1323 1.7705 -0.8729 + 7LEU HD12 104 4.307 3.864 5.838 -0.3958 -0.4434 -0.1703 + 7LEU HD13 105 4.454 3.950 5.801 0.3857 -1.6065 -0.0271 + 7LEU CD2 106 4.329 3.884 6.109 0.3904 -0.2376 0.6273 + 7LEU HD21 107 4.312 3.941 6.201 4.0207 -0.4446 1.5744 + 7LEU HD22 108 4.233 3.846 6.074 1.0539 -1.3100 -0.0846 + 7LEU HD23 109 4.398 3.808 6.146 1.8278 0.8442 0.2528 + 7LEU C 110 4.245 4.274 5.796 0.3083 0.0007 0.1448 + 7LEU O 111 4.198 4.239 5.688 0.0818 0.4306 0.1076 + 8SER N 112 4.216 4.395 5.842 0.0960 -0.1399 0.3818 + 8SER H 113 4.258 4.429 5.928 2.8065 0.6207 -1.1216 + 8SER CA 114 4.135 4.494 5.773 0.1467 -0.2812 0.1213 + 8SER HA 115 4.041 4.448 5.743 -0.8717 1.5545 0.3711 + 8SER CB 116 4.112 4.609 5.870 -0.2288 -0.0258 -0.2682 + 8SER HB1 117 4.066 4.692 5.816 0.5591 0.3801 -0.3377 + 8SER HB2 118 4.215 4.638 5.892 0.2798 1.9681 -4.2463 + 8SER OG 119 4.036 4.570 5.982 0.1181 -0.0621 -0.0433 + 8SER HG 120 4.097 4.532 6.045 0.8212 0.5786 -0.3232 + 8SER C 121 4.216 4.545 5.654 0.3725 -0.6970 0.0925 + 8SER O 122 4.159 4.554 5.546 -0.2962 -0.0529 0.4873 + 9SER N 123 4.344 4.582 5.663 0.2654 -0.3520 0.2206 + 9SER H 124 4.376 4.584 5.759 -1.7614 -0.7124 0.9612 + 9SER CA 125 4.430 4.617 5.553 -0.0696 -0.1121 0.0326 + 9SER HA 126 4.392 4.703 5.498 0.7801 0.0947 -0.2537 + 9SER CB 127 4.571 4.645 5.604 -0.0717 0.1767 -0.1165 + 9SER HB1 128 4.624 4.689 5.519 0.9121 -0.8221 -0.0440 + 9SER HB2 129 4.605 4.545 5.632 -1.6706 -0.4751 -0.4322 + 9SER OG 130 4.573 4.745 5.704 0.2398 0.5250 -0.4671 + 9SER HG 131 4.540 4.722 5.791 0.7610 -1.8520 -0.8245 + 9SER C 132 4.432 4.509 5.446 0.0351 0.1942 -0.2775 + 9SER O 133 4.424 4.539 5.327 0.4348 -0.1011 -0.3803 + 10LEU N 134 4.443 4.384 5.490 -0.3937 0.2311 -0.0571 + 10LEU H 135 4.459 4.369 5.589 3.0040 2.2036 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file mode 100644 index 0000000..a2648ec Binary files /dev/null and b/tests/test_files/output_xyz_com.xtc differ diff --git a/tests/test_files/output_xyz_end_early.xtc b/tests/test_files/output_xyz_end_early.xtc new file mode 100644 index 0000000..dcc7cb2 Binary files /dev/null and b/tests/test_files/output_xyz_end_early.xtc differ diff --git a/tests/test_files/output_xyz_from_trr.trr b/tests/test_files/output_xyz_from_trr.trr index 4e0fe05..9a5e6f9 100644 Binary files a/tests/test_files/output_xyz_from_trr.trr and b/tests/test_files/output_xyz_from_trr.trr differ diff --git a/tests/test_files/output_xyz_from_xtc.trr b/tests/test_files/output_xyz_from_xtc.trr index 101b0c6..9a5e6f9 100644 Binary files a/tests/test_files/output_xyz_from_xtc.trr and b/tests/test_files/output_xyz_from_xtc.trr differ diff --git a/tests/test_files/output_yz_com_begin_end_step.xtc b/tests/test_files/output_yz_com_begin_end_step.xtc new file mode 100644 index 0000000..36e8d13 Binary files /dev/null and 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HD21 268 4.351 3.463 4.661 -0.5770 -2.4830 -1.6181 + 17LEU HD22 269 4.381 3.442 4.491 -2.0420 2.3553 -1.5753 + 17LEU HD23 270 4.503 3.527 4.581 0.5807 -1.9413 0.5743 + 17LEU C 271 3.958 3.644 4.381 -0.4965 0.2544 -0.3704 + 17LEU O 272 3.960 3.617 4.262 -0.2345 -0.0428 -0.2993 + 18LEU N 273 3.857 3.616 4.464 -0.2907 0.3971 -0.0679 + 18LEU H 274 3.865 3.643 4.561 -0.7002 0.2796 0.0008 + 18LEU CA 275 3.729 3.569 4.414 0.1337 -0.2903 -0.5282 + 18LEU HA 276 3.747 3.495 4.337 0.0251 -0.5873 -0.2728 + 18LEU CB 277 3.665 3.510 4.540 -0.0434 0.0688 -0.4508 + 18LEU HB1 278 3.654 3.595 4.607 1.8534 -0.1312 0.1554 + 18LEU HB2 279 3.739 3.444 4.584 -2.1588 -0.8393 2.0212 + 18LEU CG 280 3.531 3.440 4.519 0.0226 -0.0285 -0.5482 + 18LEU HG 281 3.459 3.502 4.465 -2.2394 -1.1166 1.0735 + 18LEU CD1 282 3.477 3.407 4.658 0.2022 0.7340 -0.2896 + 18LEU HD11 283 3.470 3.512 4.685 -0.9641 0.7439 -0.5915 + 18LEU HD12 284 3.372 3.378 4.650 0.8735 -2.5939 1.0557 + 18LEU HD13 285 3.543 3.341 4.715 0.5795 0.5354 -0.9403 + 18LEU CD2 286 3.553 3.312 4.438 -0.2710 -0.4375 0.0154 + 18LEU HD21 287 3.462 3.251 4.435 -0.5732 0.0429 -1.0666 + 18LEU HD22 288 3.589 3.347 4.342 -1.8715 1.7742 0.1220 + 18LEU HD23 289 3.619 3.250 4.498 1.4703 -1.0639 -2.4471 + 18LEU C 290 3.650 3.680 4.346 0.3314 0.2909 0.1779 + 18LEU O 291 3.584 3.646 4.249 0.2002 -0.4256 0.5047 + 19SER N 292 3.668 3.807 4.384 -0.0899 0.4185 -0.0545 + 19SER H 293 3.723 3.833 4.464 -1.1873 1.3718 0.4283 + 19SER CA 294 3.613 3.919 4.311 0.3174 0.4014 -0.3865 + 19SER HA 295 3.508 3.894 4.298 0.2067 0.2937 0.6723 + 19SER CB 296 3.603 4.047 4.393 0.3932 -0.1391 0.4823 + 19SER HB1 297 3.699 4.077 4.433 1.5789 -0.0174 -2.2079 + 19SER HB2 298 3.531 4.026 4.472 0.6109 -2.3221 0.1392 + 19SER OG 299 3.558 4.159 4.319 0.1590 -0.6392 -0.1421 + 19SER HG 300 3.538 4.223 4.387 0.0424 -0.2422 -0.5428 + 19SER C 301 3.678 3.935 4.174 0.3714 0.2654 -0.3759 + 19SER O 302 3.609 3.976 4.081 0.5208 0.1261 -0.5494 + 20SER N 303 3.800 3.883 4.155 0.3182 -0.0691 0.1842 + 20SER H 304 3.856 3.853 4.233 2.5090 1.0809 -0.8665 + 20SER CA 305 3.858 3.889 4.023 -0.3538 0.1097 -0.1081 + 20SER HA 306 3.838 3.987 3.979 -1.1539 -0.1651 -0.3802 + 20SER CB 307 4.009 3.872 4.036 -0.3811 0.1913 0.3225 + 20SER HB1 308 4.050 3.886 3.936 -1.1680 2.5766 0.2800 + 20SER HB2 309 4.036 3.771 4.068 -0.5541 -0.2431 -0.8409 + 20SER OG 310 4.063 3.964 4.129 0.0775 0.3806 -0.1271 + 20SER HG 311 4.021 3.966 4.215 -2.5896 -1.4886 -1.2486 + 20SER C 312 3.798 3.786 3.928 0.5912 -0.4515 -0.1110 + 20SER O 313 3.770 3.815 3.812 0.5495 -0.0412 -0.0000 + 21LEU N 314 3.767 3.668 3.982 0.0574 -0.2729 -0.0130 + 21LEU H 315 3.788 3.649 4.079 -0.5189 1.4578 0.4882 + 21LEU CA 316 3.698 3.559 3.915 -0.0433 0.0777 -0.4867 + 21LEU HA 317 3.756 3.535 3.826 2.4214 0.6731 0.8698 + 21LEU CB 318 3.712 3.439 4.008 0.2419 0.1589 -0.4233 + 21LEU HB1 319 3.662 3.457 4.104 0.0254 0.5099 -0.6000 + 21LEU HB2 320 3.814 3.429 4.046 -0.4950 -3.0636 1.0028 + 21LEU CG 321 3.668 3.305 3.950 0.1333 0.1422 -0.3032 + 21LEU HG 322 3.561 3.310 3.927 -0.1080 -0.5917 0.5964 + 21LEU CD1 323 3.679 3.200 4.060 -0.2963 0.2542 -0.1479 + 21LEU HD11 324 3.640 3.103 4.029 -1.1384 0.8727 -1.0605 + 21LEU HD12 325 3.782 3.193 4.097 0.6733 -0.6542 -2.7969 + 21LEU HD13 326 3.620 3.244 4.140 1.7397 3.1218 -0.0586 + 21LEU CD2 327 3.742 3.241 3.834 0.8173 -0.3527 0.3963 + 21LEU HD21 328 3.834 3.191 3.864 -0.3224 -2.4064 0.6971 + 21LEU HD22 329 3.685 3.158 3.791 1.0498 0.9935 -2.8166 + 21LEU HD23 330 3.741 3.310 3.750 -2.0183 0.8630 1.3335 + 21LEU C 331 3.558 3.601 3.873 0.0800 0.3070 -0.6737 + 21LEU O 332 3.511 3.575 3.762 -0.7245 -0.2617 -0.2123 + 22LEU N 333 3.483 3.658 3.967 0.1458 -0.2383 -0.2869 + 22LEU H 334 3.524 3.681 4.057 -0.3290 1.6898 -0.5139 + 22LEU CA 335 3.339 3.677 3.962 0.2074 0.4765 0.3681 + 22LEU HA 336 3.303 3.595 3.900 1.4409 -0.6364 1.0582 + 22LEU CB 337 3.277 3.650 4.099 0.0828 0.5894 0.3338 + 22LEU HB1 338 3.170 3.664 4.081 0.0124 0.8657 0.9529 + 22LEU HB2 339 3.318 3.733 4.156 3.0361 -1.7332 1.8365 + 22LEU CG 340 3.298 3.517 4.171 -0.5147 0.2565 -0.0982 + 22LEU HG 341 3.405 3.498 4.178 -1.0390 -2.7746 0.9192 + 22LEU CD1 342 3.242 3.392 4.103 0.0198 -0.0197 -0.0332 + 22LEU HD11 343 3.140 3.410 4.069 1.0874 2.1636 -2.4627 + 22LEU HD12 344 3.293 3.372 4.009 -0.8838 2.0850 -1.0382 + 22LEU HD13 345 3.249 3.302 4.164 -0.6512 -0.9604 -1.3023 + 22LEU CD2 346 3.226 3.529 4.305 0.1656 0.0296 0.2910 + 22LEU HD21 347 3.119 3.539 4.289 0.3070 2.0610 0.3561 + 22LEU HD22 348 3.241 3.452 4.381 -1.7651 1.7983 2.6160 + 22LEU HD23 349 3.265 3.616 4.356 -1.1196 0.3242 0.8001 + 22LEU C 350 3.307 3.813 3.902 -0.5297 0.1672 0.0456 + 22LEU O 351 3.200 3.871 3.922 -0.3082 0.7718 -0.4988 + 23SER N 352 3.397 3.878 3.828 -0.1656 -0.1847 0.1748 + 23SER H 353 3.491 3.842 3.822 1.0432 2.5477 0.9680 + 23SER CA 354 3.374 3.998 3.751 -0.0332 -0.2547 0.0252 + 23SER HA 355 3.288 4.049 3.795 0.1756 -0.4733 0.6990 + 23SER CB 356 3.495 4.090 3.765 -0.2286 -0.0240 0.2073 + 23SER HB1 357 3.491 4.178 3.700 -0.6917 1.6212 2.3527 + 23SER HB2 358 3.584 4.034 3.738 -0.1411 -0.2623 0.9591 + 23SER OG 359 3.502 4.123 3.902 0.2482 -0.0754 0.1980 + 23SER HG 360 3.537 4.046 3.947 -1.4741 -0.5602 0.8199 + 23SER C 361 3.339 3.975 3.604 0.6378 -0.1065 -0.1614 + 23SER OC1 362 3.347 3.856 3.567 0.4397 -0.3374 0.5243 + 23SER OC2 363 3.325 4.069 3.523 -0.3367 -0.1819 -0.0864 + 8.36432 8.68132 10.41583