diff --git a/src/mol-io/writer/ligand-encoder.ts b/src/mol-io/writer/ligand-encoder.ts index d47508b2f2bc42744066013f3c4359fbaadcf182..dbc3ccc732ba858c57a66930815c8e5afd9fd4b5 100644 --- a/src/mol-io/writer/ligand-encoder.ts +++ b/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, diff --git a/src/mol-io/writer/mol2/encoder.ts b/src/mol-io/writer/mol2/encoder.ts index a5c5eccf1af8adbeb1e1fd8ba85ea741f781ed05..a67e2d5bd314ecae7b4fe5cb8e4464f0a2beaea3 100644 --- a/src/mol-io/writer/mol2/encoder.ts +++ b/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'; diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts index 72604fefde902519fb4afd2e2fa3fb3fac3fc4f6..9a4503f1d831ce8b7fbc492a9c5289fe20699625 100644 --- a/src/mol-model-formats/structure/mmcif.ts +++ b/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) { diff --git a/src/mol-model-formats/structure/property/bonds/atom.ts b/src/mol-model-formats/structure/property/atoms/chem_comp.ts similarity index 100% rename from src/mol-model-formats/structure/property/bonds/atom.ts rename to src/mol-model-formats/structure/property/atoms/chem_comp.ts diff --git a/src/mol-model-formats/structure/property/bonds/comp.ts b/src/mol-model-formats/structure/property/bonds/chem_comp.ts similarity index 100% rename from src/mol-model-formats/structure/property/bonds/comp.ts rename to src/mol-model-formats/structure/property/bonds/chem_comp.ts diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts index 9b6d3aa6cc615cff2a4ae7bafcd6af301e169ac5..d591dc73ace5c18add487aff69b56410962c6980 100644 --- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts +++ b/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 { diff --git a/src/servers/model/properties/providers/wwpdb.ts b/src/servers/model/properties/providers/wwpdb.ts index 2ea4c70943276931303f08d4205938adf952fe49..acbc85ea0c08e8cbe414a35e6d5f7eae728426af 100644 --- a/src/servers/model/properties/providers/wwpdb.ts +++ b/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(); diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts index ec146160640505043fd656a645ea38c408821a3d..33527c99b1d7be3ebc5ea87af4ed1132d4bda585 100644 --- a/src/servers/model/server/query.ts +++ b/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,