Started using auth_asym_id #95

Author: douweschulte

changelog.md

@@ -11,6 +11,9 @@ All versions are properly annotated on [github](https://github.com/douweschulte/
 * Implemented `FromIterator` for the `PDB` struct
 * Removed requirement for `atom_site.pdbx_formal_charge`, `atom_site.group_PDB`, `atom_site.occupancy`, and `atom_site.B_iso_or_equiv` for mmCIF files (thanks to #93)
 * Added support for SCALE, ORIGX, and MTRIX in mmCIF files (open and save)
+* Fixed ignoring some of the `auth_*` series of mmCIF columns, by giving them precedence over the `label_*` columns in `seq_id` and `asym_id` (thanks to #95)
+* Fixed remark-type-number 400 missing from the valid number list (thanks to #96)
+* Fixed a small bug in saving MtriX records (thanks to #96)
 
 ### v0.9.2
 * Added `open_mmcif_raw`

src/read/mmcif/parser.rs

@@ -320,21 +320,22 @@ fn parse_atoms(input: &Loop, pdb: &mut PDB) -> Option<Vec<PDBError>> {
         8,  ATOM_ANISOU_3_2, "_atom_site.aniso_U[3][2]", Optional;
         9,  ATOM_ANISOU_3_3, "_atom_site.aniso_U[3][3]", Optional;
         10, ATOM_ASYM_ID, "atom_site.label_asym_id", Required;
-        11, ATOM_B, "atom_site.B_iso_or_equiv", Optional;
-        12, ATOM_CHARGE, "atom_site.pdbx_formal_charge", Optional;
-        13, ATOM_COMP_ID, "atom_site.label_comp_id", Required;
-        14, ATOM_GROUP, "atom_site.group_PDB", Optional;
-        15, ATOM_ID, "atom_site.id", Required;
-        16, ATOM_INSERTION, "atom_site.pdbx_PDB_ins_code", Optional;
-        17, ATOM_MODEL, "atom_site.pdbx_PDB_model_num", Optional;
-        18, ATOM_NAME, "atom_site.label_atom_id", Required;
-        19, ATOM_OCCUPANCY, "atom_site.occupancy", Optional;
-        20, ATOM_SEQ_ID, "atom_site.label_seq_id", Required;
-        21, ATOM_AUTH_SEQ_ID, "atom_site.auth_seq_id", Optional;
-        22, ATOM_TYPE, "atom_site.type_symbol", Required;
-        23, ATOM_X, "atom_site.Cartn_x", Required;
-        24, ATOM_Y, "atom_site.Cartn_y", Required;
-        25, ATOM_Z, "atom_site.Cartn_z", Required;
+        11, ATOM_AUTH_ASYM_ID, "atom_site.auth_asym_id", Optional;
+        12, ATOM_B, "atom_site.B_iso_or_equiv", Optional;
+        13, ATOM_CHARGE, "atom_site.pdbx_formal_charge", Optional;
+        14, ATOM_COMP_ID, "atom_site.label_comp_id", Required;
+        15, ATOM_GROUP, "atom_site.group_PDB", Optional;
+        16, ATOM_ID, "atom_site.id", Required;
+        17, ATOM_INSERTION, "atom_site.pdbx_PDB_ins_code", Optional;
+        18, ATOM_MODEL, "atom_site.pdbx_PDB_model_num", Optional;
+        19, ATOM_NAME, "atom_site.label_atom_id", Required;
+        20, ATOM_OCCUPANCY, "atom_site.occupancy", Optional;
+        21, ATOM_SEQ_ID, "atom_site.label_seq_id", Required;
+        22, ATOM_AUTH_SEQ_ID, "atom_site.auth_seq_id", Optional;
+        23, ATOM_TYPE, "atom_site.type_symbol", Required;
+        24, ATOM_X, "atom_site.Cartn_x", Required;
+        25, ATOM_Y, "atom_site.Cartn_y", Required;
+        26, ATOM_Z, "atom_site.Cartn_z", Required;
     );
 
     let positions_: Vec<Result<Option<usize>, PDBError>> = COLUMNS
@@ -398,8 +399,9 @@ fn parse_atoms(input: &Loop, pdb: &mut PDB) -> Option<Vec<PDBError>> {
             parse_column!(get_isize, ATOM_SEQ_ID)
                 .unwrap_or_else(|| pdb.total_residue_count() as isize)
         });
-        let chain_name =
-            parse_column!(get_text, ATOM_ASYM_ID).expect("Chain name should be provided");
+        let chain_name = parse_column!(get_text, ATOM_AUTH_ASYM_ID).unwrap_or_else(|| {
+            parse_column!(get_text, ATOM_ASYM_ID).expect("Chain name should be provided")
+        });
         let pos_x = parse_column!(get_f64, ATOM_X).expect("Atom X position should be provided");
         let pos_y = parse_column!(get_f64, ATOM_Y).expect("Atom Y position should be provided");
         let pos_z = parse_column!(get_f64, ATOM_Z).expect("Atom Z position should be provided");

src/save/mmcif.rs

@@ -231,6 +231,7 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id 
 _atom_site.label_comp_id 
 _atom_site.label_asym_id 
+_atom_site.auth_asym_id 
 _atom_site.label_entity_id 
 _atom_site.label_seq_id 
 _atom_site.auth_seq_id 
@@ -276,8 +277,9 @@ _atom_site.aniso_U[3][3]"
                             atom.name().to_string(),          // Name
                             conformer.alternative_location().unwrap_or(".").to_string(), // Alternative location
                             conformer.name().to_string(), // Residue name
-                            chain.id().to_string(),       // Chain name
-                            chain_index.to_string(),      // Entity ID, using chain serial number
+                            number_to_base26(chain_index), // Label Chain name, defined to be without gaps
+                            chain.id().to_string(),        // Auth Chain name
+                            chain_index.to_string(),       // Entity ID, using chain serial number
                             (residue_index + 1).to_string(), // `label_seq_id` defined to be [1-N] where N is the index
                             residue.serial_number().to_string(), // Residue serial number
                             residue.insertion_code().unwrap_or(".").to_string(), // Insertion code

src/structs/mod.rs

@@ -21,7 +21,7 @@ pub use chain::Chain;
 pub use conformer::Conformer;
 pub use database_reference::*;
 pub use elements::{AtomicRadius, Element};
-use helper::*;
+pub(crate) use helper::*;
 pub use hierarchy::*;
 pub use model::Model;
 pub use mtrix::MtriX;