rename to atoms/chem_comp and bonds/chem_comp

src/mol-io/writer/ligand-encoder.ts

@@ -7,8 +7,8 @@
 import { StringBuilder } from '../../mol-util';
 import Writer from './writer';
 import { Encoder, Category, Field } from './cif/encoder';
-import { ComponentAtom } from '../../mol-model-formats/structure/property/bonds/atom';
-import { ComponentBond } from '../../mol-model-formats/structure/property/bonds/comp';
+import { ComponentAtom } from '../../mol-model-formats/structure/property/atoms/chem_comp';
+import { ComponentBond } from '../../mol-model-formats/structure/property/bonds/chem_comp';
 
 interface Atom {
     Cartn_x: number,

src/mol-io/writer/mol2/encoder.ts

@@ -9,7 +9,7 @@ import { LigandEncoder } from '../ligand-encoder';
 import { StringBuilder } from '../../../mol-util';
 import { getCategoryInstanceData } from '../cif/encoder/util';
 import { BondType } from '../../../mol-model/structure/model/types';
-import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/comp';
+import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/chem_comp';
 
 // type MOL_TYPE = 'SMALL' | 'BIOPOLYMER' | 'PROTEIN' | 'NUCLEIC_ACID' | 'SACCHARIDE';
 // type CHARGE_TYPE = 'NO_CHARGES' | 'DEL_RE' | 'GASTEIGER' | 'GAST_HUCK' | 'HUCKEL' | 'PULLMAN' | 'GAUSS80_CHARGES' | 'AMPAC_CHARGES' | 'MULLIKEN_CHARGES' | 'DICT_ CHARGES' | 'MMFF94_CHARGES' | 'USER_CHARGES';

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

@@ -15,7 +15,7 @@ import { ModelSymmetry } from './property/symmetry';
 import { ModelSecondaryStructure } from './property/secondary-structure';
 import { Table } from '../../mol-data/db';
 import { AtomSiteAnisotrop } from './property/anisotropic';
-import { ComponentBond } from './property/bonds/comp';
+import { ComponentBond } from './property/bonds/chem_comp';
 import { StructConn } from './property/bonds/struct_conn';
 
 function modelSymmetryFromMmcif(model: Model) {

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -14,7 +14,7 @@ import { SortedArray } from '../../../../../mol-data/int';
 import { getIntraBondOrderFromTable } from '../../../model/properties/atomic/bonds';
 import StructureElement from '../../element';
 import { IndexPairBonds } from '../../../../../mol-model-formats/structure/property/bonds/index-pair';
-import { ComponentBond } from '../../../../../mol-model-formats/structure/property/bonds/comp';
+import { ComponentBond } from '../../../../../mol-model-formats/structure/property/bonds/chem_comp';
 import { StructConn } from '../../../../../mol-model-formats/structure/property/bonds/struct_conn';
 
 function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.UnitIndex[], _order: number[], _flags: number[], atomCount: number): IntraUnitBonds {

src/servers/model/properties/providers/wwpdb.ts

@@ -10,8 +10,8 @@ import { AttachModelProperty } from '../../property-provider';
 import { CIF } from '../../../../mol-io/reader/cif';
 import { getParam } from '../../../common/util';
 import { mmCIF_Database, mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
-import { ComponentBond } from '../../../../mol-model-formats/structure/property/bonds/comp';
-import { ComponentAtom } from '../../../../mol-model-formats/structure/property/bonds/atom';
+import { ComponentBond } from '../../../../mol-model-formats/structure/property/bonds/chem_comp';
+import { ComponentAtom } from '../../../../mol-model-formats/structure/property/atoms/chem_comp';
 import { CCD_Database, CCD_Schema } from '../../../../mol-io/reader/cif/schema/ccd';
 
 require('util.promisify').shim();

src/servers/model/server/query.ts

@@ -22,13 +22,13 @@ import CifField = CifWriter.Field
 import { splitCamelCase } from '../../../mol-util/string';
 import { Encoder } from '../../../mol-io/writer/cif/encoder';
 import { Encoding } from './api';
-import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/comp';
+import { ComponentBond } from '../../../mol-model-formats/structure/property/bonds/chem_comp';
 import { SdfWriter } from '../../../mol-io/writer/sdf';
 import { MolWriter } from '../../../mol-io/writer/mol';
 import { Mol2Writer } from '../../../mol-io/writer/mol2';
 import { MolEncoder } from '../../../mol-io/writer/mol/encoder';
 import { Mol2Encoder } from '../../../mol-io/writer/mol2/encoder';
-import { ComponentAtom } from '../../../mol-model-formats/structure/property/bonds/atom';
+import { ComponentAtom } from '../../../mol-model-formats/structure/property/atoms/chem_comp';
 
 export interface Stats {
     structure: StructureWrapper,