molar 1.3.4

Molar is a rust library for analysis of MD trajectories and molecular modeling
Documentation 
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use crate::prelude::*;
use sorted_vec::SortedSet;

/// Verifies that topology and state have matching number of atoms.
/// Coords must always match. Velocities and forces must match if non-empty.
pub(crate) fn check_topology_state_sizes(
    topology: &Topology,
    state: &State,
) -> Result<(), super::TopologyStateSizesError> {
    let n = topology.len();
    if state.coords.len() != n {
        Err(super::TopologyStateSizesError(n, state.coords.len()))?
    }
    if !state.velocities.is_empty() && state.velocities.len() != n {
        Err(super::TopologyStateSizesError(n, state.velocities.len()))?
    }
    if !state.forces.is_empty() && state.forces.len() != n {
        Err(super::TopologyStateSizesError(n, state.forces.len()))?
    }
    Ok(())
}

//------------------------------
// Operations on sorted vectors
//------------------------------

/// Computes the union of two sorted slices
/// No check is performed if they are indeed sorted!
///
/// Returns a new set containing all elements that are in either set
pub(crate) unsafe fn union_sorted<T: Ord + Clone + Copy>(lhs: &[T], rhs: &[T]) -> SortedSet<T> {
    let mut l = 0;
    let mut r = 0;

    let mut ret = vec![];

    while l < lhs.len() && r < rhs.len() {
        if lhs[l] < rhs[r] {
            ret.push(lhs[l]);
            l += 1;
        } else if lhs[l] > rhs[r] {
            ret.push(rhs[r]);
            r += 1;
        } else {
            ret.push(lhs[l]);
            l += 1;
            r += 1;
        }
    }

    if l < lhs.len() {
        ret.extend(lhs[l..].into_iter().cloned());
    } else if r < rhs.len() {
        ret.extend(rhs[r..].into_iter().cloned());
    }

    unsafe { SortedSet::from_sorted(ret) }
}

/// Computes the intersection of two sorted sets
///
/// Returns a new set containing elements that appear in both sets
pub(crate) unsafe fn intersection_sorted<T: Ord + Clone + Copy>(
    lhs: &[T],
    rhs: &[T],
) -> SortedSet<T> {
    let mut l = 0;
    let mut r = 0;

    let mut ret = vec![];

    while l < lhs.len() && r < rhs.len() {
        if lhs[l] < rhs[r] {
            while l < lhs.len() && lhs[l] < rhs[r] {
                l += 1
            }
        } else if lhs[l] > rhs[r] {
            while r < lhs.len() && lhs[l] > rhs[r] {
                r += 1
            }
        } else {
            ret.push(lhs[l]);
            l += 1;
            r += 1;
        }
    }

    unsafe { SortedSet::from_sorted(ret) }
}

/// Computes the difference between two sorted sets
///
/// Returns a new set containing elements from the first set that do not appear in the second set
pub(crate) unsafe fn difference_sorted<T: Ord + Clone + Copy>(
    lhs: &[T],
    rhs: &[T],
) -> SortedSet<T> {
    let mut l = 0;
    let mut r = 0;

    let mut ret = vec![];

    while l < lhs.len() && r < rhs.len() {
        if lhs[l] < rhs[r] {
            while l < lhs.len() && lhs[l] < rhs[r] {
                ret.push(lhs[l]);
                l += 1;
            }
        } else if lhs[l] > rhs[r] {
            while r < lhs.len() && lhs[l] > rhs[r] {
                r += 1
            }
        } else {
            l += 1;
            r += 1;
        }
    }

    if l < lhs.len() {
        ret.extend(lhs[l..].into_iter().cloned());
    }

    unsafe { SortedSet::from_sorted(ret) }
}

// Convert local selection indexes to global
pub(super) fn local_to_global(
    local: impl Iterator<Item = usize>,
    subset: &[usize],
) -> Result<SortedSet<usize>, SelectionError> {
    Ok(local
        .map(|i| {
            subset
                .get(i)
                .cloned()
                .ok_or_else(|| SelectionError::LocalToGlobal(i, subset.len() - 1))
        })
        .collect::<Result<Vec<_>, _>>()?
        .into())
}

#[cfg(test)]
mod tests {
    use super::*;
    use sorted_vec::SortedSet;

    #[test]
    fn test_union_sorted() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 3, 5, 7, 10, 12]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3, 6, 8]);
        let result = unsafe{union_sorted(&set1, &set2)};
        let expected: SortedSet<usize> =
            SortedSet::from_unsorted(vec![1, 2, 3, 5, 6, 7, 8, 10, 12]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_union_sorted_empty() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![]);
        let result = unsafe{union_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_union_sorted_disjoint() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![4, 5, 6]);
        let result = unsafe{union_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3, 4, 5, 6]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_union_sorted_subset() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3]);
        let result = unsafe{union_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_intersection_sorted() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 3, 5, 7, 10, 12]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3, 6, 7, 10]);
        let result = unsafe{intersection_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![3, 7, 10]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_intersection_sorted_empty() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![4, 5, 6]);
        let result = unsafe{intersection_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![]);
        println!("{:?}", result);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_intersection_sorted_subset() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3, 4, 5]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3]);
        let result = unsafe{intersection_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_intersection_sorted_identical() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        let result = unsafe{intersection_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_difference_sorted() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![3, 5, 7, 10, 12, 13]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3, 6, 7, 10]);
        let result = unsafe{difference_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![5, 12, 13]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_difference_sorted_empty() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![]);
        let result = unsafe{difference_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_difference_sorted_subset() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3, 4, 5]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![2, 3]);
        let result = unsafe{difference_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 4, 5]);
        assert_eq!(result, expected);
    }

    #[test]
    fn test_difference_sorted_identical() {
        let set1: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3]);
        let set2: SortedSet<usize> = SortedSet::from_unsorted(vec![1, 2, 3, 5]);
        let result = unsafe{difference_sorted(&set1, &set2)};
        let expected: SortedSet<usize> = SortedSet::from_unsorted(vec![]);
        assert_eq!(result, expected);
    }
}