added some code docs

src/mol-model/structure/model/properties/atomic/conformation.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column } from 'mol-data/db'
@@ -13,14 +14,36 @@ export interface AtomicConformation {
     // ID is part of conformation because mmCIF is a leaky abstraction
     // that assigns different atom ids to corresponding atoms in different models
     // ... go figure.
+
+    /**
+     * Uniquely identifies an atom, i.e. even accross models in a mmCIF file.
+     */
     atomId: Column<number>,
 
+    /**
+     * The fraction of the atom type present at this site. The sum of the occupancies of all the atom types
+     * at this site may not significantly exceed 1.0 unless it is a dummy site.
+     */
     occupancy: Column<number>,
+    /**
+     * Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter,
+     * B~eq~, calculated from the anisotropic displacement parameters.
+     */
     B_iso_or_equiv: Column<number>
 
     // Coordinates. Generally, not to be accessed directly because the coordinate might be
     // transformed by an operator. Use Unit.getPosition instead.
+
+    /**
+     * The x coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     x: ArrayLike<number>,
+    /**
+     * The y coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     y: ArrayLike<number>,
+    /**
+     * The z coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     z: ArrayLike<number>
 }

src/mol-model/structure/model/properties/atomic/hierarchy.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column, Table } from 'mol-data/db'
@@ -12,10 +13,31 @@ import { ChainIndex, EntityIndex, ResidueIndex, ElementIndex } from '../../index
 import SortedRanges from 'mol-data/int/sorted-ranges';
 
 export const AtomsSchema = {
+    /**
+     * The chemical element of this atom site.
+     * For mmCIF files, this points to atom_type.symbol in the ATOM_TYPE category.
+     */
     type_symbol: Column.Schema.Aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
+    /**
+     * A component of the identifier for this atom site.
+     * This is a standardized name for the atom within its residue.
+     * For mmCIF files, this points to chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
+     */
     label_atom_id: mmCIF.atom_site.label_atom_id,
+    /**
+     * An alternative identifier for label_atom_id that may be provided by an author
+     * in order to match the identification used in the publication that describes the structure.
+     */
     auth_atom_id: mmCIF.atom_site.auth_atom_id,
+    /**
+     * A component of the identifier for this atom site.
+     * Identifies an alternative conformation for this atom site.
+     */
     label_alt_id: mmCIF.atom_site.label_alt_id,
+    /**
+     * The net integer charge assigned to this atom.
+     * This is the formal charge assignment normally found in chemical diagrams.
+     */
     pdbx_formal_charge: mmCIF.atom_site.pdbx_formal_charge
     // id, occupancy and B_iso_or_equiv are part of conformation
 };
@@ -24,19 +46,52 @@ export type AtomsSchema = typeof AtomsSchema
 export interface Atoms extends Table<AtomsSchema> { }
 
 export const ResiduesSchema = {
+    /**
+     * The group of atoms to which the atom site belongs. This data item is provided for
+     * compatibility with the original Protein Data Bank format, and only for that purpose.
+     */
     group_PDB: mmCIF.atom_site.group_PDB,
+    /**
+     * A component of the identifier for this atom site.
+     * For mmCIF files, this points to chem_comp.id in the CHEM_COMP category.
+     */
     label_comp_id: mmCIF.atom_site.label_comp_id,
+    /**
+     * An alternative identifier for atom_site.label_comp_id that may be provided by an author
+     * in order to match the identification used in the publication that describes the structure.
+     */
     auth_comp_id: mmCIF.atom_site.auth_comp_id,
+    /**
+     * For mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+     */
     label_seq_id: mmCIF.atom_site.label_seq_id,
+    /**
+     * An alternative identifier for atom_site.label_seq_id that may be provided by an author
+     * in order to match the identification used in the publication that describes the structure.
+     */
     auth_seq_id: mmCIF.atom_site.auth_seq_id,
+    /**
+     * PDB insertion code.
+     */
     pdbx_PDB_ins_code: mmCIF.atom_site.pdbx_PDB_ins_code,
 };
 export type ResiduesSchema = typeof ResiduesSchema
 export interface Residues extends Table<ResiduesSchema> { }
 
 export const ChainsSchema = {
+    /**
+     * A component of the identifier for this atom site.
+     * For mmCIF files, this points to struct_asym.id in the STRUCT_ASYM category.
+     */
     label_asym_id: mmCIF.atom_site.label_asym_id,
+    /**
+     * An alternative identifier for atomsite.label_asym_id that may be provided by an author
+     * in order to match the identification used in the publication that describes the structure.
+     */
     auth_asym_id: mmCIF.atom_site.auth_asym_id,
+    /**
+     * For mmCIF files, this points to _entity.id in the ENTITY category.
+     */
     label_entity_id: mmCIF.atom_site.label_entity_id
 }
 export type ChainsSchema = typeof ChainsSchema

src/mol-model/structure/model/properties/coarse/conformation.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import UUID from 'mol-util/uuid'
@@ -14,17 +15,47 @@ export interface CoarseConformation {
 }
 
 export interface CoarseSphereConformation {
+    /**
+     * The x coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     x: ArrayLike<number>,
+    /**
+     * The y coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     y: ArrayLike<number>,
+    /**
+     * The z coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     z: ArrayLike<number>,
+    /**
+     * The radius associated with the primitive sphere object at this position.
+     */
     radius: ArrayLike<number>,
+    /**
+     * The Root Mean Square Fluctuation (RMSF) observed in the primitive sphere object at this position.
+     */
     rmsf: ArrayLike<number>
 }
 
 export interface CoarseGaussianConformation {
+    /**
+     * The x coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     x: ArrayLike<number>,
+    /**
+     * The y coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     y: ArrayLike<number>,
+    /**
+     * The z coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
+     */
     z: ArrayLike<number>,
+    /**
+     * The weight of the gaussian object.
+     */
     weight: ArrayLike<number>,
+    /**
+     * Data item of the covariance matrix representing the Gaussian object.
+     */
     covariance_matrix: ArrayLike<Mat3>
 }

src/mol-model/structure/model/properties/coarse/hierarchy.ts

@@ -23,9 +23,25 @@ export interface CoarsedElementKeys {
 
 export interface CoarseElementData {
     count: number,
+    /**
+     * The entity identifier corresponding to this coarse object.
+     * In mmCIF files, this points to entity_poly_seq.entity_id in the ENTITY_POLY category.
+     */
     entity_id: Column<string>,
+    /**
+     * An asym/strand identifier corresponding to this coarse object.
+     * In mmCIF files, this points to struct_asym.id in the STRUCT_ASYM category
+     */
     asym_id: Column<string>,
+    /**
+     * The leading sequence index corresponding to this coarse object.
+     * In mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY category.
+     */
     seq_id_begin: Column<number>,
+    /**
+     * The trailing sequence index corresponding to this coarse object.
+     * In mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY category.
+     */
     seq_id_end: Column<number>,
 
     chainElementSegments: Segmentation<ElementIndex, ChainIndex>,