[INFO] fetching crate pdbrust 0.7.0...
[INFO] fixing pdbrust-0.7.0 against try#622891a4e29178280638a6b63a8908bde2c0c854+cargoflags=-Zfix-edition=start=2015 for pr-157817-2
[INFO] extracting crate pdbrust 0.7.0 into /workspace/builds/worker-3-tc1/source
[INFO] started tweaking crates.io crate pdbrust 0.7.0
[INFO] removed 0 missing examples
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate pdbrust 0.7.0
[INFO] tweaked toml for crates.io crate pdbrust 0.7.0 written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate pdbrust 0.7.0 on toolchain 622891a4e29178280638a6b63a8908bde2c0c854
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate pdbrust 0.7.0 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3a6becf2bc8dde7f3fa57ede90e4f284e72d296796fc446bbb1e2c7cc0530151" "sleep" "infinity", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "002c5768862c3a5c91cdadf8ccccbbdabdbb26ac8598ae0294aeee874e4b23c0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "002c5768862c3a5c91cdadf8ccccbbdabdbb26ac8598ae0294aeee874e4b23c0" "/opt/rustwide/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=" "-e" "RUSTDOCFLAGS=" "-w" "/opt/rustwide/workdir" "--user" "0:0" "002c5768862c3a5c91cdadf8ccccbbdabdbb26ac8598ae0294aeee874e4b23c0" "/opt/rustwide/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "fix" "--allow-no-vcs" "--allow-dirty" "--frozen" "--all" "--all-targets" "--message-format=json" "-Zfix-edition=start=2015", kill_on_drop: false }`
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[INFO] [stdout] error[E0432]: unresolved import `pdbrust::summary`
[INFO] [stdout]    --> examples/batch_processing.rs:15:14
[INFO] [stdout]     |
[INFO] [stdout]  15 | use pdbrust::summary::{StructureSummary, batch_summarize, summaries_to_csv};
[INFO] [stdout]     |              ^^^^^^^ could not find `summary` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:308:9
[INFO] [stdout]     |
[INFO] [stdout] 307 | #[cfg(feature = "summary")]
[INFO] [stdout]     |       ------------------- the item is gated behind the `summary` feature
[INFO] [stdout] 308 | pub mod summary;
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `pdbrust::dockq`
[INFO] [stdout]    --> examples/dockq_detailed_comparison.rs:8:14
[INFO] [stdout]     |
[INFO] [stdout]   8 | use pdbrust::dockq::{ChainMappingStrategy, DockQOptions};
[INFO] [stdout]     |              ^^^^^ could not find `dockq` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:323:9
[INFO] [stdout]     |
[INFO] [stdout] 322 | #[cfg(feature = "dockq")]
[INFO] [stdout]     |       ----------------- the item is gated behind the `dockq` feature
[INFO] [stdout] 323 | pub mod dockq;
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find module or crate `rayon` in this scope
[INFO] [stdout]   --> examples/full_pdb_benchmark.rs:29:5
[INFO] [stdout]    |
[INFO] [stdout] 29 | use rayon::prelude::*;
[INFO] [stdout]    |     ^^^^^ use of unresolved module or unlinked crate `rayon`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `rayon`, use `cargo add rayon` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `pdbrust::parse_gzip_pdb_file`
[INFO] [stdout]    --> examples/full_pdb_benchmark.rs:31:39
[INFO] [stdout]     |
[INFO] [stdout]  31 | use pdbrust::{PdbError, PdbStructure, parse_gzip_pdb_file};
[INFO] [stdout]     |                                       ^^^^^^^^^^^^^^^^^^^ no `parse_gzip_pdb_file` in the root
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:342:53
[INFO] [stdout]     |
[INFO] [stdout] 340 | #[cfg(feature = "gzip")]
[INFO] [stdout]     |       ---------------- the item is gated behind the `gzip` feature
[INFO] [stdout] 341 | pub use parser::{
[INFO] [stdout] 342 |     parse_gzip_mmcif_file, parse_gzip_mmcif_reader, parse_gzip_pdb_file, parse_gzip_pdb_reader,
[INFO] [stdout]     |                                                     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] help: a similar name exists in the module
[INFO] [stdout]     |
[INFO] [stdout]  31 - use pdbrust::{PdbError, PdbStructure, parse_gzip_pdb_file};
[INFO] [stdout]  31 + use pdbrust::{PdbError, PdbStructure, parse_pdb_file};
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `pdbrust::geometry`
[INFO] [stdout]    --> examples/lddt_demo.rs:10:14
[INFO] [stdout]     |
[INFO] [stdout]  10 | use pdbrust::geometry::{AtomSelection, LddtOptions};
[INFO] [stdout]     |              ^^^^^^^^ could not find `geometry` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:314:9
[INFO] [stdout]     |
[INFO] [stdout] 313 | #[cfg(feature = "geometry")]
[INFO] [stdout]     |       -------------------- the item is gated behind the `geometry` feature
[INFO] [stdout] 314 | pub mod geometry;
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/lddt_demo.rs:37:28
[INFO] [stdout]    |
[INFO] [stdout] 37 |     let result = reference.lddt_to(&reference)?;
[INFO] [stdout]    |                            ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "batch_processing") due to 1 previous error
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stdout] error[E0599]: no method named `dockq_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_detailed_comparison.rs:23:28
[INFO] [stdout]    |
[INFO] [stdout] 23 |         let result = model.dockq_to(&native)?;
[INFO] [stdout]    |                            ^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `pdbrust::geometry`
[INFO] [stdout]    --> examples/geometry_demo.rs:11:14
[INFO] [stdout]     |
[INFO] [stdout]  11 | use pdbrust::geometry::AtomSelection;
[INFO] [stdout]     |              ^^^^^^^^ could not find `geometry` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:314:9
[INFO] [stdout]     |
[INFO] [stdout] 313 | #[cfg(feature = "geometry")]
[INFO] [stdout]     |       -------------------- the item is gated behind the `geometry` feature
[INFO] [stdout] 314 | pub mod geometry;
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `pdbrust::dockq`
[INFO] [stdout]    --> examples/dockq_validation.rs:11:14
[INFO] [stdout]     |
[INFO] [stdout]  11 | use pdbrust::dockq::{ChainMappingStrategy, DockQOptions};
[INFO] [stdout]     |              ^^^^^ could not find `dockq` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:323:9
[INFO] [stdout]     |
[INFO] [stdout] 322 | #[cfg(feature = "dockq")]
[INFO] [stdout]     |       ----------------- the item is gated behind the `dockq` feature
[INFO] [stdout] 323 | pub mod dockq;
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_detailed_comparison.rs:88:28
[INFO] [stdout]    |
[INFO] [stdout] 88 |         let result = model.dockq_to_with_options(&native, options)?;
[INFO] [stdout]    |                            ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `keep_only_chain` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:29:29
[INFO] [stdout]    |
[INFO] [stdout] 29 |     let chain_a = structure.keep_only_chain("A");
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `keep_only_ca` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:36:29
[INFO] [stdout]    |
[INFO] [stdout] 36 |     let ca_only = structure.keep_only_ca();
[INFO] [stdout]    |                             ^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `keep_only_backbone` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:40:30
[INFO] [stdout]    |
[INFO] [stdout] 40 |     let backbone = structure.keep_only_backbone();
[INFO] [stdout]    |                              ^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `get_ca_coords` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:47:31
[INFO] [stdout]    |
[INFO] [stdout] 47 |     let ca_coords = structure.get_ca_coords(None);
[INFO] [stdout]    |                               ^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `get_ca_coords` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:51:39
[INFO] [stdout]    |
[INFO] [stdout] 51 |     let chain_a_ca_coords = structure.get_ca_coords(Some("A"));
[INFO] [stdout]    |                                       ^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `remove_ligands` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:58:32
[INFO] [stdout]    |
[INFO] [stdout] 58 |     let no_ligands = structure.remove_ligands();
[INFO] [stdout]    |                                ^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `remove_hydrogens` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:66:34
[INFO] [stdout]    |
[INFO] [stdout] 66 |     let no_hydrogens = structure.remove_hydrogens();
[INFO] [stdout]    |                                  ^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `remove_ligands` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:78:10
[INFO] [stdout]    |
[INFO] [stdout] 77 |       let cleaned = structure
[INFO] [stdout]    |  ___________________-
[INFO] [stdout] 78 | |         .remove_ligands()
[INFO] [stdout]    | |         -^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout]    | |_________|
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `remove_ligands` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/filtering_demo.rs:87:29
[INFO] [stdout]    |
[INFO] [stdout] 87 |     let ca_repr = structure.remove_ligands().keep_only_ca();
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `get_centroid` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/filtering_demo.rs:100:32
[INFO] [stdout]     |
[INFO] [stdout] 100 |     let (cx, cy, cz) = mutable.get_centroid();
[INFO] [stdout]     |                                ^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `center_structure` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/filtering_demo.rs:104:13
[INFO] [stdout]     |
[INFO] [stdout] 104 |     mutable.center_structure();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `get_centroid` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/filtering_demo.rs:105:32
[INFO] [stdout]     |
[INFO] [stdout] 105 |     let (cx, cy, cz) = mutable.get_centroid();
[INFO] [stdout]     |                                ^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/lddt_demo.rs:62:29
[INFO] [stdout]    |
[INFO] [stdout] 62 |     let result = translated.lddt_to(&reference)?;
[INFO] [stdout]    |                             ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `renumber_atoms` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/filtering_demo.rs:109:13
[INFO] [stdout]     |
[INFO] [stdout] 109 |     mutable.renumber_atoms();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `normalize_chain_ids` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/filtering_demo.rs:118:17
[INFO] [stdout]     |
[INFO] [stdout] 118 |     multi_chain.normalize_chain_ids();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `get_chain_ids` with a similar name
[INFO] [stdout]     |
[INFO] [stdout] 118 -     multi_chain.normalize_chain_ids();
[INFO] [stdout] 118 +     multi_chain.get_chain_ids();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `pdbrust::dockq`
[INFO] [stdout]    --> examples/dockq_demo.rs:11:14
[INFO] [stdout]     |
[INFO] [stdout]  11 | use pdbrust::dockq::{ChainMappingStrategy, DockQOptions};
[INFO] [stdout]     |              ^^^^^ could not find `dockq` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:323:9
[INFO] [stdout]     |
[INFO] [stdout] 322 | #[cfg(feature = "dockq")]
[INFO] [stdout]     |       ----------------- the item is gated behind the `dockq` feature
[INFO] [stdout] 323 | pub mod dockq;
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `reindex_residues` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/filtering_demo.rs:123:15
[INFO] [stdout]     |
[INFO] [stdout] 123 |     reindexed.reindex_residues();
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `get_residues` with a similar name
[INFO] [stdout]     |
[INFO] [stdout] 123 -     reindexed.reindex_residues();
[INFO] [stdout] 123 +     reindexed.get_residues();
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0599`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "filtering_demo") due to 15 previous errors
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/dockq_detailed_comparison.rs:160:28
[INFO] [stdout]     |
[INFO] [stdout] 160 |         let result = model.dockq_to_with_options(&native, options)?;
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find module or crate `rayon` in this scope
[INFO] [stdout]    --> examples/full_pdb_benchmark.rs:251:27
[INFO] [stdout]     |
[INFO] [stdout] 251 |         let num_threads = rayon::current_num_threads();
[INFO] [stdout]     |                           ^^^^^ use of unresolved module or unlinked crate `rayon`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `rayon`, use `cargo add rayon` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:25:29
[INFO] [stdout]    |
[INFO] [stdout] 25 |     let chain_a = structure.select("chain A")?;
[INFO] [stdout]    |                             ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:29:30
[INFO] [stdout]    |
[INFO] [stdout] 29 |     let ca_atoms = structure.select("name CA")?;
[INFO] [stdout]    |                              ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/lddt_demo.rs:67:27
[INFO] [stdout]    |
[INFO] [stdout] 67 |     let rmsd = translated.rmsd_to(&reference)?;
[INFO] [stdout]    |                           ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:33:34
[INFO] [stdout]    |
[INFO] [stdout] 33 |     let met_residues = structure.select("resname MET")?;
[INFO] [stdout]    |                                  ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `get_ligand_names` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/ligand_quality_demo.rs:34:34
[INFO] [stdout]    |
[INFO] [stdout] 34 |     let ligand_names = structure.get_ligand_names();
[INFO] [stdout]    |                                  ^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find `dockq` in `pdbrust`
[INFO] [stdout]    --> examples/dockq_demo.rs:97:35
[INFO] [stdout]     |
[INFO] [stdout]  97 | fn print_result(result: &pdbrust::dockq::DockQResult) {
[INFO] [stdout]     |                                   ^^^^^ could not find `dockq` in `pdbrust`
[INFO] [stdout]     |
[INFO] [stdout] note: found an item that was configured out
[INFO] [stdout]    --> src/lib.rs:323:9
[INFO] [stdout]     |
[INFO] [stdout] 322 | #[cfg(feature = "dockq")]
[INFO] [stdout]     |       ----------------- the item is gated behind the `dockq` feature
[INFO] [stdout] 323 | pub mod dockq;
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:37:26
[INFO] [stdout]    |
[INFO] [stdout] 37 |     let res1 = structure.select("resid 1")?;
[INFO] [stdout]    |                          ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:41:31
[INFO] [stdout]    |
[INFO] [stdout] 41 |     let res_range = structure.select("resid 1:10")?;
[INFO] [stdout]    |                               ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `ligand_pose_quality` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/ligand_quality_demo.rs:50:41
[INFO] [stdout]    |
[INFO] [stdout] 50 |         if let Some(report) = structure.ligand_pose_quality(ligand_name) {
[INFO] [stdout]    |                                         ^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:45:31
[INFO] [stdout]    |
[INFO] [stdout] 45 |     let nitrogens = structure.select("element N")?;
[INFO] [stdout]    |                               ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:54:30
[INFO] [stdout]    |
[INFO] [stdout] 54 |     let backbone = structure.select("backbone")?;
[INFO] [stdout]    |                              ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:57:29
[INFO] [stdout]    |
[INFO] [stdout] 57 |     let protein = structure.select("protein")?;
[INFO] [stdout]    |                             ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:60:31
[INFO] [stdout]    |
[INFO] [stdout] 60 |     let all_atoms = structure.select("all")?;
[INFO] [stdout]    |                               ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:70:32
[INFO] [stdout]    |
[INFO] [stdout] 70 |     let chain_a_ca = structure.select("chain A and name CA")?;
[INFO] [stdout]    |                                ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `all_ligand_pose_quality` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/ligand_quality_demo.rs:133:29
[INFO] [stdout]     |
[INFO] [stdout] 133 |     let reports = structure.all_ligand_pose_quality();
[INFO] [stdout]     |                             ^^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:74:32
[INFO] [stdout]    |
[INFO] [stdout] 74 |     let met_or_gln = structure.select("resname MET or resname GLN")?;
[INFO] [stdout]    |                                ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:81:34
[INFO] [stdout]    |
[INFO] [stdout] 81 |     let not_hydrogen = structure.select("not hydrogen")?;
[INFO] [stdout]    |                                  ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:85:30
[INFO] [stdout]    |
[INFO] [stdout] 85 |     let complex1 = structure.select("(resid 1 or resid 2) and name CA")?;
[INFO] [stdout]    |                              ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/selection_demo.rs:97:33
[INFO] [stdout]    |
[INFO] [stdout] 97 |     let low_bfactor = structure.select("bfactor < 20.0")?;
[INFO] [stdout]    |                                 ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:100:36
[INFO] [stdout]     |
[INFO] [stdout] 100 |     let high_occupancy = structure.select("occupancy >= 0.5")?;
[INFO] [stdout]     |                                    ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:110:30
[INFO] [stdout]     |
[INFO] [stdout] 110 |     let complex2 = structure.select("chain A and backbone and bfactor < 30.0")?;
[INFO] [stdout]     |                              ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:117:29
[INFO] [stdout]     |
[INFO] [stdout] 117 |     let termini = structure.select("(resid 1:10 or resid 67:76) and name CA")?;
[INFO] [stdout]     |                             ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:124:33
[INFO] [stdout]     |
[INFO] [stdout] 124 |     let heavy_atoms = structure.select("protein and not hydrogen")?;
[INFO] [stdout]     |                                 ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:137:35
[INFO] [stdout]     |
[INFO] [stdout] 137 |     let ca_via_select = structure.select("name CA")?.get_num_atoms();
[INFO] [stdout]     |                                   ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0599`.
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `keep_only_ca` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:138:35
[INFO] [stdout]     |
[INFO] [stdout] 138 |     let ca_via_method = structure.keep_only_ca().get_num_atoms();
[INFO] [stdout]     |                                   ^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_validation.rs:39:24
[INFO] [stdout]    |
[INFO] [stdout] 39 |     let result = model.dockq_to(&native)?;
[INFO] [stdout]    |                        ^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:147:35
[INFO] [stdout]     |
[INFO] [stdout] 147 |     let bb_via_select = structure.select("backbone")?.get_num_atoms();
[INFO] [stdout]     |                                   ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `keep_only_backbone` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:148:35
[INFO] [stdout]     |
[INFO] [stdout] 148 |     let bb_via_method = structure.keep_only_backbone().get_num_atoms();
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/lddt_demo.rs:88:26
[INFO] [stdout]    |
[INFO] [stdout] 88 |     let result = rotated.lddt_to(&reference)?;
[INFO] [stdout]    |                          ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/dockq_detailed_comparison.rs:268:28
[INFO] [stdout]     |
[INFO] [stdout] 268 |         let result = model.dockq_to_with_options(&native, options)?;
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:157:38
[INFO] [stdout]     |
[INFO] [stdout] 157 |     let chain_via_select = structure.select("chain A")?.get_num_atoms();
[INFO] [stdout]     |                                      ^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `keep_only_chain` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:158:38
[INFO] [stdout]     |
[INFO] [stdout] 158 |     let chain_via_method = structure.keep_only_chain("A").get_num_atoms();
[INFO] [stdout]     |                                      ^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no associated function or constant named `validate_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:173:34
[INFO] [stdout]     |
[INFO] [stdout] 173 |     match pdbrust::PdbStructure::validate_selection("chain A and name CA") {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^^^ associated function or constant not found in `PdbStructure`
[INFO] [stdout]     |
[INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions:
[INFO] [stdout]       PdbStructure::new
[INFO] [stdout]       PdbStructure::from_file
[INFO] [stdout]    --> src/core/pdb.rs:98:5
[INFO] [stdout]     |
[INFO] [stdout]  98 |     pub fn new() -> Self {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 126 |     pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self, PdbError> {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "ligand_quality_demo") due to 3 previous errors
[INFO] [stdout] error[E0599]: no associated function or constant named `validate_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:179:34
[INFO] [stdout]     |
[INFO] [stdout] 179 |     match pdbrust::PdbStructure::validate_selection("") {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^^^ associated function or constant not found in `PdbStructure`
[INFO] [stdout]     |
[INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions:
[INFO] [stdout]       PdbStructure::new
[INFO] [stdout]       PdbStructure::from_file
[INFO] [stdout]    --> src/core/pdb.rs:98:5
[INFO] [stdout]     |
[INFO] [stdout]  98 |     pub fn new() -> Self {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 126 |     pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self, PdbError> {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:38:27
[INFO] [stdout]    |
[INFO] [stdout] 38 |     let rmsd = structure1.rmsd_to(&structure2)?;
[INFO] [stdout]    |                           ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no associated function or constant named `validate_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:185:34
[INFO] [stdout]     |
[INFO] [stdout] 185 |     match pdbrust::PdbStructure::validate_selection("(chain A and name CA") {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^^^ associated function or constant not found in `PdbStructure`
[INFO] [stdout]     |
[INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions:
[INFO] [stdout]       PdbStructure::new
[INFO] [stdout]       PdbStructure::from_file
[INFO] [stdout]    --> src/core/pdb.rs:98:5
[INFO] [stdout]     |
[INFO] [stdout]  98 |     pub fn new() -> Self {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 126 |     pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self, PdbError> {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no associated function or constant named `validate_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/selection_demo.rs:191:34
[INFO] [stdout]     |
[INFO] [stdout] 191 |     match pdbrust::PdbStructure::validate_selection("invalid_keyword") {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^^^ associated function or constant not found in `PdbStructure`
[INFO] [stdout]     |
[INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions:
[INFO] [stdout]       PdbStructure::new
[INFO] [stdout]       PdbStructure::from_file
[INFO] [stdout]    --> src/core/pdb.rs:98:5
[INFO] [stdout]     |
[INFO] [stdout]  98 |     pub fn new() -> Self {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 126 |     pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self, PdbError> {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0599`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "selection_demo") due to 28 previous errors
[INFO] [stdout] Some errors have detailed explanations: E0432, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_validation.rs:93:24
[INFO] [stdout]    |
[INFO] [stdout] 93 |     let result = model.dockq_to_with_options(&native, options)?;
[INFO] [stdout]    |                        ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to_with_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:46:30
[INFO] [stdout]    |
[INFO] [stdout] 46 |     let rmsd_ca = structure1.rmsd_to_with_selection(&structure2, AtomSelection::CaOnly)?;
[INFO] [stdout]    |                              ^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_demo.rs:29:25
[INFO] [stdout]    |
[INFO] [stdout] 29 |     let result = native.dockq_to(&native)?;
[INFO] [stdout]    |                         ^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:105:28
[INFO] [stdout]     |
[INFO] [stdout] 105 |     let result = perturbed.lddt_to(&reference)?;
[INFO] [stdout]     |                            ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "dockq_detailed_comparison") due to 5 previous errors
[INFO] [stdout] error[E0599]: no method named `par_iter` found for struct `Vec<PathBuf>` in the current scope
[INFO] [stdout]    --> examples/full_pdb_benchmark.rs:257:15
[INFO] [stdout]     |
[INFO] [stdout] 257 |         files.par_iter().for_each(|path| {
[INFO] [stdout]     |               ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rayon-1.10.0/src/iter/mod.rs:289:8
[INFO] [stdout]     |
[INFO] [stdout] 289 |     fn par_iter(&'data self) -> Self::Iter;
[INFO] [stdout]     |        -------- the method is available for `Vec<PathBuf>` here
[INFO] [stdout]     |
[INFO] [stdout]     = help: items from traits can only be used if the trait is in scope
[INFO] [stdout] help: trait `IntoParallelRefIterator` which provides `par_iter` is implemented but not in scope; perhaps you want to import it
[INFO] [stdout]     |
[INFO] [stdout]  21 + use rayon::iter::IntoParallelRefIterator;
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `iter` with a similar name
[INFO] [stdout]     |
[INFO] [stdout] 257 -         files.par_iter().for_each(|path| {
[INFO] [stdout] 257 +         files.iter().for_each(|path| {
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:128:19
[INFO] [stdout]     |
[INFO] [stdout] 128 |         perturbed.lddt_to_with_options(&reference, AtomSelection::CaOnly, strict_options)?;
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:136:19
[INFO] [stdout]     |
[INFO] [stdout] 136 |         perturbed.lddt_to_with_options(&reference, AtomSelection::CaOnly, small_radius)?;
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find module or crate `rayon` in this scope
[INFO] [stdout]    --> examples/full_pdb_benchmark.rs:653:44
[INFO] [stdout]     |
[INFO] [stdout] 653 |         writeln!(w, "Rayon Threads:   {}", rayon::current_num_threads()).unwrap();
[INFO] [stdout]     |                                            ^^^^^ use of unresolved module or unlinked crate `rayon`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `rayon`, use `cargo add rayon` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to_with_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:50:30
[INFO] [stdout]    |
[INFO] [stdout] 50 |     let rmsd_bb = structure1.rmsd_to_with_selection(&structure2, AtomSelection::Backbone)?;
[INFO] [stdout]    |                              ^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `per_residue_lddt_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:149:29
[INFO] [stdout]     |
[INFO] [stdout] 149 |     let per_res = perturbed.per_residue_lddt_to(&reference)?;
[INFO] [stdout]     |                             ^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/dockq_validation.rs:143:24
[INFO] [stdout]     |
[INFO] [stdout] 143 |     let result = model.dockq_to(&native)?;
[INFO] [stdout]     |                        ^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_demo.rs:50:28
[INFO] [stdout]    |
[INFO] [stdout] 50 |     let result = perturbed.dockq_to_with_options(&native, options)?;
[INFO] [stdout]    |                            ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:181:41
[INFO] [stdout]     |
[INFO] [stdout] 181 |     let lddt_result = heavily_perturbed.lddt_to(&reference)?;
[INFO] [stdout]     |                                         ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:182:41
[INFO] [stdout]     |
[INFO] [stdout] 182 |     let rmsd_direct = heavily_perturbed.rmsd_to(&reference)?;
[INFO] [stdout]     |                                         ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `align_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:183:49
[INFO] [stdout]     |
[INFO] [stdout] 183 |     let (_, aligned_result) = heavily_perturbed.align_to(&reference)?;
[INFO] [stdout]     |                                                 ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `into` with a similar name, but with different arguments
[INFO] [stdout]    --> /rustc/622891a4e29178280638a6b63a8908bde2c0c854/library/core/src/convert/mod.rs:456:4
[INFO] [stdout] help: some of the expressions' fields have a method of the same name
[INFO] [stdout]     |
[INFO] [stdout] 183 |     let (_, aligned_result) = heavily_perturbed.atoms.align_to(&reference)?;
[INFO] [stdout]     |                                                 ++++++
[INFO] [stdout] 183 |     let (_, aligned_result) = heavily_perturbed.connects.align_to(&reference)?;
[INFO] [stdout]     |                                                 +++++++++
[INFO] [stdout] 183 |     let (_, aligned_result) = heavily_perturbed.models.align_to(&reference)?;
[INFO] [stdout]     |                                                 +++++++
[INFO] [stdout] 183 |     let (_, aligned_result) = heavily_perturbed.remarks.align_to(&reference)?;
[INFO] [stdout]     |                                                 ++++++++
[INFO] [stdout]     = and 2 other candidates
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:196:29
[INFO] [stdout]     |
[INFO] [stdout] 196 |     let lddt_ca = reference.lddt_to_with_options(
[INFO] [stdout]     |                   ----------^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/dockq_validation.rs:211:24
[INFO] [stdout]     |
[INFO] [stdout] 211 |     let result = model.dockq_to_with_options(&native, options)?;
[INFO] [stdout]     |                        ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to_with_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:54:31
[INFO] [stdout]    |
[INFO] [stdout] 54 |     let rmsd_all = structure1.rmsd_to_with_selection(&structure2, AtomSelection::AllAtoms)?;
[INFO] [stdout]    |                               ^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `lddt_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/lddt_demo.rs:201:29
[INFO] [stdout]     |
[INFO] [stdout] 201 |     let lddt_bb = reference.lddt_to_with_options(
[INFO] [stdout]     |                   ----------^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to_with_options` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_demo.rs:71:28
[INFO] [stdout]    |
[INFO] [stdout] 71 |     let result = bad_model.dockq_to_with_options(&native, options)?;
[INFO] [stdout]    |                            ^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `dockq_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/dockq_demo.rs:89:26
[INFO] [stdout]    |
[INFO] [stdout] 89 |     let result = swapped.dockq_to(&native)?;
[INFO] [stdout]    |                          ^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "dockq_validation") due to 5 previous errors
[INFO] [stdout] error[E0599]: no method named `rmsd_to_with_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:58:34
[INFO] [stdout]    |
[INFO] [stdout] 58 |     let rmsd_custom = structure1.rmsd_to_with_selection(
[INFO] [stdout]    |                       -----------^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0433, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0433, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "full_pdb_benchmark") due to 5 previous errors
[INFO] [stderr] error: could not compile `pdbrust` (example "dockq_demo") due to 6 previous errors
[INFO] [stderr] error: could not compile `pdbrust` (example "lddt_demo") due to 14 previous errors
[INFO] [stdout] error[E0599]: no method named `align_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:69:40
[INFO] [stdout]    |
[INFO] [stdout] 69 |     let (aligned, result) = structure1.align_to(&structure2)?;
[INFO] [stdout]    |                                        ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout] help: there is a method `into` with a similar name, but with different arguments
[INFO] [stdout]   --> /rustc/622891a4e29178280638a6b63a8908bde2c0c854/library/core/src/convert/mod.rs:456:4
[INFO] [stdout] help: some of the expressions' fields have a method of the same name
[INFO] [stdout]    |
[INFO] [stdout] 69 |     let (aligned, result) = structure1.atoms.align_to(&structure2)?;
[INFO] [stdout]    |                                        ++++++
[INFO] [stdout] 69 |     let (aligned, result) = structure1.connects.align_to(&structure2)?;
[INFO] [stdout]    |                                        +++++++++
[INFO] [stdout] 69 |     let (aligned, result) = structure1.models.align_to(&structure2)?;
[INFO] [stdout]    |                                        +++++++
[INFO] [stdout] 69 |     let (aligned, result) = structure1.remarks.align_to(&structure2)?;
[INFO] [stdout]    |                                        ++++++++
[INFO] [stdout]    = and 2 other candidates
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `align_to_with_selection` found for struct `PdbStructure` in the current scope
[INFO] [stdout]   --> examples/geometry_demo.rs:79:20
[INFO] [stdout]    |
[INFO] [stdout] 79 |         structure1.align_to_with_selection(&structure2, AtomSelection::Backbone)?;
[INFO] [stdout]    |                    ^^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `per_residue_rmsd_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/geometry_demo.rs:89:30
[INFO] [stdout]     |
[INFO] [stdout]  89 |     let per_res = structure1.per_residue_rmsd_to(&structure2)?;
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `get_residues` with a similar name, but with different arguments
[INFO] [stdout]    --> src/core/pdb.rs:231:5
[INFO] [stdout]     |
[INFO] [stdout] 231 |     pub fn get_residues(&self) -> Vec<(i32, String)> {
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `rmsd_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/geometry_demo.rs:134:32
[INFO] [stdout]     |
[INFO] [stdout] 134 |     let self_rmsd = structure1.rmsd_to(&structure1)?;
[INFO] [stdout]     |                                ^^^^^^^ method not found in `PdbStructure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `align_to` found for struct `PdbStructure` in the current scope
[INFO] [stdout]    --> examples/geometry_demo.rs:137:39
[INFO] [stdout]     |
[INFO] [stdout] 137 |     let (_, self_result) = structure1.align_to(&structure1)?;
[INFO] [stdout]     |                                       ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `into` with a similar name, but with different arguments
[INFO] [stdout]    --> /rustc/622891a4e29178280638a6b63a8908bde2c0c854/library/core/src/convert/mod.rs:456:4
[INFO] [stdout] help: some of the expressions' fields have a method of the same name
[INFO] [stdout]     |
[INFO] [stdout] 137 |     let (_, self_result) = structure1.atoms.align_to(&structure1)?;
[INFO] [stdout]     |                                       ++++++
[INFO] [stdout] 137 |     let (_, self_result) = structure1.connects.align_to(&structure1)?;
[INFO] [stdout]     |                                       +++++++++
[INFO] [stdout] 137 |     let (_, self_result) = structure1.models.align_to(&structure1)?;
[INFO] [stdout]     |                                       +++++++
[INFO] [stdout] 137 |     let (_, self_result) = structure1.remarks.align_to(&structure1)?;
[INFO] [stdout]     |                                       ++++++++
[INFO] [stdout]     = and 2 other candidates
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0432, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0432`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `pdbrust` (example "geometry_demo") due to 11 previous errors
[INFO] running `Command { std: "docker" "inspect" "002c5768862c3a5c91cdadf8ccccbbdabdbb26ac8598ae0294aeee874e4b23c0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "002c5768862c3a5c91cdadf8ccccbbdabdbb26ac8598ae0294aeee874e4b23c0", kill_on_drop: false }`
[INFO] [stdout] 002c5768862c3a5c91cdadf8ccccbbdabdbb26ac8598ae0294aeee874e4b23c0
