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added some code docs

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Alexander Rose
2018-08-16 15:37:52 -07:00
parent 27d26fa478
commit fa1a71fc22
4 changed files with 127 additions and 2 deletions
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25
src/mol-model/structure/model/properties/atomic/conformation.ts
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@@ -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>
}

57
src/mol-model/structure/model/properties/atomic/hierarchy.ts
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@@ -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

31
src/mol-model/structure/model/properties/coarse/conformation.ts
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@@ -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>
}

16
src/mol-model/structure/model/properties/coarse/hierarchy.ts
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@@ -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>,