Added support for MtriX in mmCIF #64

douweschulte · Jul 20, 2022 · a1ac5cb · a1ac5cb
1 parent bdf2b5a
commit a1ac5cb
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Showing 3 changed files with 99 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -32,7 +32,7 @@ As the main goal of this library is to allow access to the atomical data many me
 |        ANISOU | ✔️  |  ✔️  | atom_site                   |
 |         SCALE | ✔️  |  ✔️  | _atom_sites.Cartn_transf    |
 |         ORIGX | ✔️  |  ✔️  | _database_PDB_matrix.origx  |
-|        MATRIX | ✔️  |  ❌  | ?                           |
+|        MATRIX | ✔️  |  ✔️  | struct_ncs_oper             |
 |       CRYSTAL | ✔️  |  ✔️  | cell + symmetry             |
 |         MODEL | ✔️  |  ✔️  | atom_site                   |
 |        MASTER | 〰️  |  ❌  | _pdbx_database_PDB_master   |

diff --git a/src/read/mmcif/parser.rs b/src/read/mmcif/parser.rs
@@ -60,6 +60,7 @@ fn parse_mmcif(
     let mut pdb = PDB::default();
     let mut errors: Vec<PDBError> = Vec::new();
     let mut unit_cell = UnitCell::default();
+    let mut mtrix_id = None;
 
     pdb.identifier = Some(input.name.clone());
 
@@ -140,6 +141,59 @@ fn parse_mmcif(
                             #[allow(clippy::unwrap_used)]
                             parse_matrix(s, get_f64(&single.content, &context),pdb.origx.as_mut().unwrap(), &context)
                         }
+                        s if s.starts_with("structs_ncs_oper.") => {
+                            if s.ends_with("id") {
+                                match get_usize(&single.content, &context) {
+                                    Err(e) => Some(e),
+                                    Ok(Some(id)) => {
+                                        mtrix_id = Some(id);
+                                        pdb.add_mtrix(MtriX::new(id, TransformationMatrix::identity(), true));
+                                        None
+                                    }
+                                    Ok(None) => Some(PDBError::new(
+                                        ErrorLevel::InvalidatingError,
+                                        "MtriX with missing ID",
+                                        "If a MtriX id is given it should be a number not a missing value.",
+                                        context.clone(),
+                                    ))
+                                }
+                            } else {
+                                #[allow(clippy::unwrap_used)]
+                                match mtrix_id {
+                                    Some(id) => { 
+                                        let mut mtrix = pdb.mtrix_mut().find(|m| m.serial_number == id).unwrap();
+                                        if s.ends_with("code") {
+                                            match get_text(&single.content, &context) {
+                                                Ok(Some(t)) if t == "given" => {mtrix.contained = true; None},
+                                                Ok(Some(t)) if t == "generate" => {mtrix.contained = false; None},
+                                                Ok(Some(_)) => Some(PDBError::new(
+                                                    ErrorLevel::InvalidatingError,
+                                                    "MtriX code invalid",
+                                                    "Only the values 'generate' and 'given' are valid for `_struct_ncs_oper.code`.",
+                                                    context.clone(),
+                                                )),
+                                                _ => Some(PDBError::new(
+                                                    ErrorLevel::InvalidatingError,
+                                                    "MtriX code invalid",
+                                                    "The value for `_struct_ncs_oper.code` should be a textual value.",
+                                                    context.clone(),
+                                                )),
+                                            }
+                                        } else if s.ends_with("details") {
+                                            None // Ignore the details, it will not be saved somewhere
+                                        } else {
+                                            parse_matrix(s, get_f64(&single.content, &context),&mut mtrix.transformation, &context)
+                                        }
+                                    },
+                                    None => Some(PDBError::new(
+                                        ErrorLevel::InvalidatingError,
+                                        "MtriX matrix given without ID",
+                                        "The MtriX ID (`_struct_ncs_oper.id`) should be given before any matrix information is given.",
+                                        context.clone(),
+                                    ))
+                                }
+                            }
+                        }
                         _ => None,
                     }
                     .map(|e| vec![e])

diff --git a/src/save/mmcif.rs b/src/save/mmcif.rs
@@ -104,7 +104,8 @@ _cell.Z_PDB              {}",
     if let Some(scale) = &pdb.scale {
         let ma = scale.matrix();
         write!(
-            "_atom_sites.entry_id                   '{}'
+            "# Scale definition
+            _atom_sites.entry_id                   '{}'
 _atom_sites.Cartn_transf_matrix[1][1]  {}
 _atom_sites.Cartn_transf_matrix[1][2]  {}
 _atom_sites.Cartn_transf_matrix[1][3]  {}
@@ -137,7 +138,8 @@ _atom_sites.Cartn_transf_vector[3]     {}",
     if let Some(origx) = &pdb.origx {
         let ma = origx.matrix();
         write!(
-            "_database_PDB_matrix.entry_id                   '{}'
+            "# OrigX definition
+_database_PDB_matrix.entry_id                   '{}'
 _database_PDB_matrix.origx[1][1]  {}
 _database_PDB_matrix.origx[1][2]  {}
 _database_PDB_matrix.origx[1][3]  {}
@@ -166,6 +168,46 @@ _database_PDB_matrix.origx_vector[3]     {}",
         );
     }
 
+    // MtriX
+    for mtrix in pdb.mtrix() {
+        let ma = mtrix.transformation.matrix();
+        write!(
+            r#"# OrigX definition
+_struct_ncs_oper.id            '{}'
+_struct_ncs_oper.code          {}
+_struct_ncs_oper.matrix[1][1]  {}
+_struct_ncs_oper.matrix[1][2]  {}
+_struct_ncs_oper.matrix[1][3]  {}
+_struct_ncs_oper.matrix[2][1]  {}
+_struct_ncs_oper.matrix[2][2]  {}
+_struct_ncs_oper.matrix[2][3]  {}
+_struct_ncs_oper.matrix[3][1]  {}
+_struct_ncs_oper.matrix[3][2]  {}
+_struct_ncs_oper.matrix[3][3]  {}
+_struct_ncs_oper.vector[1]     {}
+_struct_ncs_oper.vector[2]     {}
+_struct_ncs_oper.vector[3]     {}"#,
+            mtrix.serial_number,
+            if mtrix.contained {
+                "given"
+            } else {
+                "generated"
+            },
+            ma[0][0],
+            ma[0][1],
+            ma[0][2],
+            ma[1][0],
+            ma[1][1],
+            ma[1][2],
+            ma[2][0],
+            ma[2][1],
+            ma[2][2],
+            ma[0][3],
+            ma[1][3],
+            ma[2][3],
+        );
+    }
+
     if let Some(symmetry) = &pdb.symmetry {
         write!(
             "# Space group definition