From 58e0ba016e91e74c15df6750ba2daeff0c4fd057 Mon Sep 17 00:00:00 2001
From: JonStargaryen <sebastian.bittrich@rcsb.org>
Date: Tue, 28 Jul 2020 11:20:01 -0700
Subject: [PATCH] rename to atoms/chem_comp and bonds/chem_comp
---
src/mol-io/writer/ligand-encoder.ts | 4 ++--
src/mol-io/writer/mol2/encoder.ts | 2 +-
src/mol-model-formats/structure/mmcif.ts | 2 +-
.../structure/property/{bonds/atom.ts => atoms/chem_comp.ts} | 0
.../structure/property/bonds/{comp.ts => chem_comp.ts} | 0
src/mol-model/structure/structure/unit/bonds/intra-compute.ts | 2 +-
src/servers/model/properties/providers/wwpdb.ts | 4 ++--
src/servers/model/server/query.ts | 4 ++--
8 files changed, 9 insertions(+), 9 deletions(-)
rename src/mol-model-formats/structure/property/{bonds/atom.ts => atoms/chem_comp.ts} (100%)
rename src/mol-model-formats/structure/property/bonds/{comp.ts => chem_comp.ts} (100%)
diff --git a/src/mol-io/writer/ligand-encoder.ts b/src/mol-io/writer/ligand-encoder.ts
index d47508b2f..dbc3ccc73 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 a5c5eccf1..a67e2d5bd 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 72604fefd..9a4503f1d 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 9b6d3aa6c..d591dc73a 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 2ea4c7094..acbc85ea0 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 ec1461606..33527c99b 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,
--
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