add pdbx_structure_determination_methodology mmcif field and Model helpers

CHANGELOG.md

@@ -16,6 +16,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix polymer-gap visual coloring with cartoon theme
 - Add formal-charge color theme (#328)
 - Add more coloring options to cartoon theme
+- Add `pdbx_structure_determination_methodology` mmcif field and `Model` helpers
 
 ## [v4.5.0] - 2024-07-28
 

data/cif-field-names/mmcif-field-names.csv

@@ -263,6 +263,7 @@ software.version
 struct.entry_id
 struct.title
 struct.pdbx_descriptor
+struct.pdbx_structure_determination_methodology
 
 struct_asym.id
 struct_asym.pdbx_blank_PDB_chainid_flag

src/extensions/model-archive/quality-assessment/color/plddt.ts

@@ -8,7 +8,7 @@
 
 import { QualityAssessment, QualityAssessmentProvider } from '../prop';
 import { Location } from '../../../../mol-model/location';
-import { Bond, StructureElement, Unit } from '../../../../mol-model/structure';
+import { Bond, Model, StructureElement, Unit } from '../../../../mol-model/structure';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { Color } from '../../../../mol-util/color';
@@ -91,7 +91,7 @@ export const PLDDTConfidenceColorThemeProvider: ColorTheme.Provider<PLDDTConfide
     factory: PLDDTConfidenceColorTheme,
     getParams: getPLDDTConfidenceColorThemeParams,
     defaultValues: PD.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT') || m.atomicConformation.B_iso_or_equiv.isDefined),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT') || (m.atomicConformation.B_iso_or_equiv.isDefined && !Model.isExperimental(m))),
     ensureCustomProperties: {
         attach: async (ctx: CustomProperty.Context, data: ThemeDataContext) => {
             if (data.structure) {

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1033,6 +1033,10 @@ export const mmCIF_Schema = {
          * and to distinguish this structural result from others.
          */
         title: str,
+        /**
+         * Indicates if the structure was determined using experimental, computational, or integrative methods
+         */
+        pdbx_structure_determination_methodology: Aliased<'experimental' | 'integrative' | 'computational'>(str),
         /**
          * An automatically generated descriptor for an NDB structure or
          * the unstructured content of the PDB COMPND record.

src/mol-model/structure/model/model.ts

@@ -378,6 +378,33 @@ export namespace Model {
         return false;
     }
 
+    export function isExperimental(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const { db } = model.sourceData.data;
+        for (let i = 0; i < db.struct.pdbx_structure_determination_methodology.rowCount; i++) {
+            if (db.struct.pdbx_structure_determination_methodology.value(i).toLowerCase() === 'experimental') return true;
+        }
+        return false;
+    }
+
+    export function isIntegrative(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const { db } = model.sourceData.data;
+        for (let i = 0; i < db.struct.pdbx_structure_determination_methodology.rowCount; i++) {
+            if (db.struct.pdbx_structure_determination_methodology.value(i).toLowerCase() === 'integrative') return true;
+        }
+        return false;
+    }
+
+    export function isComputational(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const { db } = model.sourceData.data;
+        for (let i = 0; i < db.struct.pdbx_structure_determination_methodology.rowCount; i++) {
+            if (db.struct.pdbx_structure_determination_methodology.value(i).toLowerCase() === 'computational') return true;
+        }
+        return false;
+    }
+
     export function hasXrayMap(model: Model): boolean {
         if (!MmcifFormat.is(model.sourceData)) return false;
         // Check exprimental method to exclude models solved with