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Commit 10b13860 authored by Zepei Xu's avatar Zepei Xu
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have basics, but formatting is not complete because of unclearness. not using... 

have basics, but formatting is not complete because of unclearness. not using computations, wait, async, promise.
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examples/adrenalin.mol2 0 → 100644
+ 60
− 0
View file @ 10b13860
@<TRIPOS>MOLECULE
5816
26 26 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 1.7394 -2.1169 -1.0894 O.3 1 LIG1 -0.3859
2 O -2.2941 1.0781 -1.7979 O.3 1 LIG1 -0.5033
3 O -3.6584 0.5842 0.5722 O.3 1 LIG1 -0.5033
4 N 2.6359 1.0243 0.7030 N.3 1 LIG1 -0.3162
5 C 1.6787 -1.1447 -0.0373 C.3 1 LIG1 0.0927
6 C 0.2684 -0.6866 0.1208 C.ar 1 LIG1 -0.0143
7 C 2.6376 0.0193 -0.3576 C.3 1 LIG1 0.0258
8 C -0.3658 -0.0099 -0.9212 C.ar 1 LIG1 -0.0109
9 C -0.4164 -0.9343 1.3105 C.ar 1 LIG1 -0.0524
10 C -1.6849 0.4191 -0.7732 C.ar 1 LIG1 0.1586
11 C -1.7353 -0.5053 1.4585 C.ar 1 LIG1 -0.0162
12 C -2.3696 0.1713 0.4166 C.ar 1 LIG1 0.1582
13 C 3.5645 2.1013 0.3950 C.3 1 LIG1 -0.0157
14 H 2.0210 -1.6511 0.8741 H 1 LIG1 0.0656
15 H 2.3808 0.4742 -1.3225 H 1 LIG1 0.0453
16 H 3.6478 -0.3931 -0.4831 H 1 LIG1 0.0453
17 H 0.1501 0.1801 -1.8589 H 1 LIG1 0.0659
18 H 0.0640 -1.4598 2.1315 H 1 LIG1 0.0622
19 H 2.9013 0.5888 1.5858 H 1 LIG1 0.1217
20 H -2.2571 -0.7050 2.3907 H 1 LIG1 0.0655
21 H 2.6646 -2.4067 -1.1652 H 1 LIG1 0.2103
22 H 3.2862 2.6124 -0.5325 H 1 LIG1 0.0388
23 H 4.5925 1.7346 0.3078 H 1 LIG1 0.0388
24 H 3.5401 2.8441 1.1985 H 1 LIG1 0.0388
25 H -3.2008 1.2997 -1.5231 H 1 LIG1 0.2923
26 H -3.9690 0.3259 1.4570 H 1 LIG1 0.2923
@<TRIPOS>BOND
1 1 5 1
2 1 21 1
3 2 10 1
4 2 25 1
5 3 12 1
6 3 26 1
7 4 7 1
8 4 13 1
9 4 19 1
10 5 6 1
11 5 7 1
12 5 14 1
13 6 8 ar
14 6 9 ar
15 7 15 1
16 7 16 1
17 8 10 ar
18 8 17 1
19 9 11 ar
20 9 18 1
21 10 12 ar
22 11 12 ar
23 11 20 1
24 13 22 1
25 13 23 1
26 13 24 1
\ No newline at end of file
examples/sp-after.mol2 0 → 100644
+ 71
− 0
View file @ 10b13860
@<TRIPOS>MOLECULE
ZINC12921206_1_1
30 33 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 10.8630 31.3859 32.2468 1 CAN 0.0000
2 C2 11.5701 31.4080 33.4817 1 CAN 0.0000
3 C3 17.5821 22.4473 38.5639 1 CAN 0.0000
4 C4 17.9273 24.7114 37.0200 1 CAN 0.0000
5 C5 10.5243 30.1190 31.8528 1 CAN 0.0000
6 C6 12.3942 31.2627 36.0033 1 CAN 0.0000
7 C7 12.3703 30.0954 35.2910 1 CAN 0.0000
8 C8 12.7652 28.9134 36.0072 1 CAN 0.0000
9 C9 16.4753 23.1064 38.0609 1 CAN 0.0000
10 C10 16.6480 24.2419 37.2829 1 CAN 0.0000
11 C11 18.8581 22.9199 38.3189 1 CAN 0.0000
12 C12 19.0369 24.0561 37.5370 1 CAN 0.0000
13 C13 11.8010 30.1533 33.9700 1 CAN 0.0000
14 C14 12.9774 29.2537 37.3208 1 CAN 0.0000
15 C15 13.3581 27.0671 37.7950 1 CAN 0.0000
16 C16 13.0045 27.5630 35.4958 1 CAN 0.0000
17 C17 14.5101 24.5014 36.0984 1 CAN 0.0000
18 C18 15.0909 22.6148 38.4220 1 CAN 0.0000
19 C19 19.6116 21.0974 39.7116 1 CAN 0.0000
20 C20 21.4990 23.9541 37.7136 1 CAN 0.0000
21 C21 13.2073 25.2763 36.0792 1 CAN 0.0000
22 N1 13.3019 28.3134 38.2813 1 CAN 0.0000
23 N2 13.2604 26.6887 36.4706 1 CAN 0.0000
24 N3 15.5062 24.9862 36.8657 1 CAN 0.0000
25 O1 13.0317 27.1909 34.3441 1 CAN 0.0000
26 O2 14.6486 23.4801 35.4573 1 CAN 0.0000
27 O3 19.9073 22.2497 38.8981 1 CAN 0.0000
28 O4 20.2810 24.5742 37.2617 1 CAN 0.0000
29 S1 11.0122 28.9270 33.0152 1 CAN 0.0000
30 S2 12.7971 30.9513 37.6624 1 CAN 0.0000
@<TRIPOS>BOND
1 1 2 0
2 1 5 0
3 2 13 0
4 3 11 0
5 3 9 0
6 4 12 0
7 4 10 0
8 5 29 0
9 6 7 0
10 6 30 0
11 7 8 0
12 7 13 0
13 8 14 0
14 8 16 0
15 9 10 0
16 9 18 0
17 10 24 0
18 11 27 0
19 11 12 0
20 12 28 0
21 13 29 0
22 14 22 0
23 14 30 0
24 15 22 0
25 15 23 0
26 16 23 0
27 16 25 0
28 17 21 0
29 17 24 0
30 17 26 0
31 19 27 0
32 20 28 0
33 21 23 0
examples/sp-ido40.mol2 0 → 100644
+ 109
− 0
View file @ 10b13860
@<TRIPOS>MOLECULE
ZINC12921206_1
49 52 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C1 0.6216 -0.2760 -6.8683 C.ar 1 <1> -0.0541
2 C2 0.3683 -0.8994 -5.6124 C.ar 1 <1> -0.0469
3 C3 -0.4563 -9.3380 -7.8499 C.ar 1 <1> -0.0116
4 C4 -1.3323 -7.7730 -5.7131 C.ar 1 <1> 0.0052
5 C5 1.6788 0.6049 -6.8049 C.ar 1 <1> -0.0237
6 C6 1.0293 -0.0678 -2.1894 C.ar 1 <1> -0.0133
7 C7 1.2229 -0.9407 -3.2374 C.ar 1 <1> 0.0102
8 C8 1.3908 -2.2806 -2.7857 C.ar 1 <1> 0.0803
9 C9 0.4711 -8.6946 -7.0304 C.ar 1 <1> -0.0256
10 C10 0.0332 -7.9122 -5.9620 C.ar 1 <1> 0.0401
11 C11 -1.8217 -9.1987 -7.6011 C.ar 1 <1> 0.1619
12 C12 -2.2597 -8.4163 -6.5327 C.ar 1 <1> 0.1633
13 C13 1.2418 -0.4712 -4.6368 C.ar 1 <1> 0.0206
14 C14 1.3196 -2.3849 -1.4088 C.ar 1 <1> 0.1157
15 C15 1.6389 -4.5865 -1.3837 C.ar 1 <1> 0.1003
16 C16 1.6164 -3.4830 -3.5741 C.ar 1 <1> 0.2632
17 C17 0.6789 -6.4424 -4.0211 C.2 1 <1> 0.2371
18 C18 1.9274 -8.8602 -7.3213 C.3 1 <1> -0.0378
19 C19 -2.1874 -10.6131 -9.4777 C.3 1 <1> 0.0790
20 C20 -3.9546 -7.4559 -5.1686 C.3 1 <1> 0.0790
21 C21 1.9636 -5.9327 -3.3970 C.3 1 <1> 0.1040
22 N1 1.4391 -3.5205 -0.6696 N.ar 1 <1> -0.2298
23 N2 1.7329 -4.6371 -2.7763 N.ar 1 <1> -0.2898
24 N3 0.9585 -7.2517 -5.1191 N.am 1 <1> -0.2837
25 O1 1.6923 -3.4619 -4.7990 O.2 1 <1> -0.2669
26 O2 -0.4256 -6.1563 -3.5700 O.2 1 <1> -0.2735
27 O3 -2.7176 -9.8330 -8.4079 O.3 1 <1> -0.4914
28 O4 -3.5906 -8.2727 -6.2796 O.3 1 <1> -0.4914
29 S1 2.3612 0.6778 -5.2360 S.2 1 <1> -0.0966
30 S2 1.0512 -0.8647 -0.6747 S.2 1 <1> -0.0763
31 H1 0.0574 -0.4648 -7.7724 H 1 <1> 0.0623
32 H2 -0.4177 -1.6249 -5.4418 H 1 <1> 0.0629
33 H3 -0.1187 -9.9489 -8.6838 H 1 <1> 0.0658
34 H4 -1.6794 -7.1646 -4.8809 H 1 <1> 0.0674
35 H5 2.0837 1.2088 -7.6047 H 1 <1> 0.0693
36 H6 0.8746 1.0019 -2.2311 H 1 <1> 0.0700
37 H7 1.7520 -5.5673 -0.8940 H 1 <1> 0.1030
38 H8 2.2679 -8.0781 -8.0093 H 1 <1> 0.0278
39 H9 2.5235 -8.8023 -6.4025 H 1 <1> 0.0278
40 H10 2.1317 -9.8382 -7.7740 H 1 <1> 0.0278
41 H11 -3.0074 -11.0637 -10.0422 H 1 <1> 0.0660
42 H12 -1.5373 -11.3932 -9.0735 H 1 <1> 0.0660
43 H13 -1.6073 -9.9638 -10.1376 H 1 <1> 0.0660
44 H14 -5.0433 -7.4258 -5.0787 H 1 <1> 0.0660
45 H15 -3.5623 -6.4462 -5.3135 H 1 <1> 0.0660
46 H16 -3.5278 -7.8834 -4.2582 H 1 <1> 0.0660
47 H17 2.7361 -5.8372 -4.1665 H 1 <1> 0.0589
48 H18 2.3025 -6.6506 -2.6435 H 1 <1> 0.0589
49 H19 1.9385 -7.3938 -5.3543 H 1 <1> 0.1549
@<TRIPOS>BOND
1 1 2 ar
2 1 5 ar
3 2 13 ar
4 3 9 ar
5 3 11 ar
6 4 10 ar
7 4 12 ar
8 5 29 ar
9 6 7 ar
10 6 30 ar
11 7 8 ar
12 7 13 1
13 8 14 ar
14 8 16 ar
15 9 10 ar
16 9 18 1
17 10 24 1
18 11 12 ar
19 11 27 1
20 12 28 1
21 13 29 ar
22 14 22 ar
23 14 30 ar
24 15 22 ar
25 15 23 ar
26 16 23 ar
27 16 25 2
28 17 21 1
29 17 24 am
30 17 26 2
31 19 27 1
32 20 28 1
33 21 23 1
34 1 31 1
35 2 32 1
36 3 33 1
37 4 34 1
38 5 35 1
39 6 36 1
40 15 37 1
41 18 38 1
42 18 39 1
43 18 40 1
44 19 41 1
45 19 42 1
46 19 43 1
47 20 44 1
48 20 45 1
49 20 46 1
50 21 47 1
51 21 48 1
52 24 49 1
src/reader/mol2/parser.ts 0 → 100644
+ 138
− 0
View file @ 10b13860
import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
import { ColumnType, UndefinedColumn } from '../common/column'
import * as Schema from './schema'
import Result from '../result'
//import Computation from '../../utils/computation'
interface State {
tokenizer: Tokenizer,
molecule: Schema.Molecule,
///////////// not including Computation.chunker /////////////
}
function createEmptyMolecule(): Schema.Molecule {
return {
mol_name: '',
num_atoms: 0,
num_bonds: 0,
num_subst: 0,
num_feat: 0,
num_sets: 0,
mol_type: '',
charge_type: '',
status_bits:'',
mol_comment: ''
};
}
function State(tokenizer: Tokenizer): State { //////////// not having ctx: Computation.Context as a parameter //////////////
return {
tokenizer,
molecule: createEmptyMolecule(),
//////////// not having chunker: Computation.chunker(ctx, 100000) ///////////
};
}
/**
* title string (free format string, optional time in ps after 't=')
*/
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
Tokenizer.markLine(tokenizer);
let name = Tokenizer.getTokenString(tokenizer);
molecule.mol_name = name;
Tokenizer.markLine(tokenizer);
const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
molecule.num_atoms = parseInt(values[0]);
molecule.num_bonds = parseInt(values[1]);
molecule.num_subst = parseInt(values[2]);
molecule.num_feat = parseInt(values[3]);
molecule.num_sets = parseInt(values[4]);
Tokenizer.markLine(tokenizer);
molecule.mol_type = Tokenizer.getTokenString(tokenizer);
Tokenizer.markLine(tokenizer);
molecule.charge_type = Tokenizer.getTokenString(tokenizer);
// skip the empty line
Tokenizer.markLine(tokenizer)
}
/**
* This format is fixed, ie. all columns are in a fixed position.
* Optionally (for now only yet with trjconv) you can write gro files
* with any number of decimal places, the format will then be n+5
* positions with n decimal places (n+1 for velocities) in stead
* of 8 with 3 (with 4 for velocities). Upon reading, the precision
* will be inferred from the distance between the decimal points
* (which will be n+5). Columns contain the following information
* (from left to right):
* residue number (5 positions, integer)
* residue name (5 characters)
* atom name (5 characters)
* atom number (5 positions, integer)
* position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places)
* velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places)
*/
function handleAtoms(state: State): Schema.Atoms {
const { tokenizer, molecule } = state;
////////// not using readLinesAsync /////////
const lines = Tokenizer.readLines(tokenizer, molecule.num_atoms);
const pO = 20;
const pW = state.header.precision.position + 5;
const vO = pO + 3 * pW;
const vW = state.header.precision.velocity + 4;
const col = FixedColumn({ data: tokenizer.data, lines, rowCount: state.numberOfAtoms });
const ret = {
count: molecule.num_atoms,
atom_id: col(0, 0, ColumnType.int),
atom_name: col(0, 0, ColumnType.str),
x: col(0, 0, ColumnType.float),
};
return ret;
}
/**
* box vectors (free format, space separated reals), values:
* v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y),
* the last 6 values may be omitted (they will be set to zero).
* Gromacs only supports boxes with v1(y)=v1(z)=v2(z)=0.
*/
function handleBoxVectors(state: State) {
const { tokenizer } = state;
markLine(tokenizer);
const values = getTokenString(tokenizer).trim().split(/\s+/g);
state.header.box = [+values[0], +values[1], +values[2]];
}
function parseInternal(data: string): Result<Schema.File> {
const tokenizer = TokenizerState(data);
const structures: Schema.Structure[] = [];
while (tokenizer.position < data.length) {
const state = createState(tokenizer);
handleMolecule(state);
const atoms = handleAtoms(state);
handleBoxVectors(state);
structures.push({ header: state.header, atoms });
}
const result: Schema.File = { structures };
return Result.success(result);
}
export function parse(data: string) {
return parseInternal(data);
}
export default parse;
\ No newline at end of file
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