From 6709fc385eec7e04acf7f9207e541f5540f264c7 Mon Sep 17 00:00:00 2001
From: Zepei Xu <xuzepei19950617@gmail.com>
Date: Thu, 5 Oct 2017 18:03:16 -0700
Subject: [PATCH] Have basics, but formatting is not complete because of
unclearness. Not using computations, wait, async, promise. And small fix
---
src/reader/mol2/parser.ts | 136 +++++++++++++++++++++++++++-----------
1 file changed, 96 insertions(+), 40 deletions(-)
diff --git a/src/reader/mol2/parser.ts b/src/reader/mol2/parser.ts
index b97792a6f..b63939f64 100644
--- a/src/reader/mol2/parser.ts
+++ b/src/reader/mol2/parser.ts
@@ -3,7 +3,9 @@ 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'
+import Computation from '../../utils/computation' ////////// not using this
+
+
interface State {
tokenizer: Tokenizer,
@@ -11,6 +13,8 @@ interface State {
///////////// not including Computation.chunker /////////////
}
+
+
function createEmptyMolecule(): Schema.Molecule {
return {
mol_name: '',
@@ -26,6 +30,9 @@ function createEmptyMolecule(): Schema.Molecule {
};
}
+
+
+
function State(tokenizer: Tokenizer): State { //////////// not having ctx: Computation.Context as a parameter //////////////
return {
tokenizer,
@@ -34,9 +41,10 @@ function State(tokenizer: Tokenizer): State { //////////// not having ctx: Compu
};
}
-/**
- * title string (free format string, optional time in ps after 't=')
- */
+
+
+
+
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
@@ -63,74 +71,122 @@ function handleMolecule(state: State) {
}
-/**
- * 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);
+ // default all false
+ const hasSubst_id = false;
+ const hasSubst_name = false;
+ const hasCharge = false;
+ const hasStatus_bit = false;
+
+ /*
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(lines);
+ const undefInt = UndefinedColumn(molecule.num_atoms, ColumnType.int);
+ const undefFloat = UndefinedColumn(molecule.num_atoms, ColumnType.float);
+ const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
+ const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
- const col = FixedColumn({ data: tokenizer.data, lines, rowCount: state.numberOfAtoms });
+ /////// wanted to have const undef = UndefinedColumn(molecule.num_atoms) like col, but failed
+ /////// some unclear about the formatting, like the field sizes
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),
+ atom_id: col(0, 7, ColumnType.int),
+ atom_name: col(7, 9, ColumnType.str), ////// don't know use str or pooledStr
+ x: col(16, 10, ColumnType.float),
+ y: col(26, 10, ColumnType.float),
+ z: col(36, 10, ColumnType.float),
+ atom_type: col(46, 0, ColumnType.str), ////// don't know use str or pooledStr //////// don't know which is the atom_type
+ // optional properties
+ subst_id: hasSubst_id ? col(0, 0, ColumnType.int) : undefInt,
+ subst_name: hasSubst_name ? col(0, 0, ColumnType.str) : undefStr,///////// don't know use str or pooledStr
+ charge: hasCharge ? col(0, 0, ColumnType.float) : undefFloat, //////// don't know use int or float
+ status_bit: hasStatus_bit ? col(0, 0, ColumnType.pooledStr) : undefPooledStr, ////////// don't know use str or pooledStr
};
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 handleBonds(state: State): Schema.Bonds {
+ const { tokenizer, molecule } = state;
+
+ ////////// not using readLinesAsync /////////
+ const lines = Tokenizer.readLines(tokenizer, molecule.num_bonds);
+
+ // default all false
+ const hasStatus_bit = false;
+
+ /*
+ 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(lines);
+ const undefInt = UndefinedColumn(molecule.num_bonds, ColumnType.int);
+ const undefFloat = UndefinedColumn(molecule.num_bonds, ColumnType.float);
+ const undefStr = UndefinedColumn(molecule.num_bonds, ColumnType.str);
+ const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
+
+ /////// wanted to have const undef = UndefinedColumn(molecule.num_atoms) like col, but failed
+
+ /////// some unclear about the formatting, like the field sizes
+ const ret = {
+ count: molecule.num_bonds,
+ bond_id: col(0, 6, ColumnType.int),
+ origin_atom_id: col(6, 6, ColumnType.int),
+ target_atom_id: col(12, 6, ColumnType.int),
+ bond_type: col(18, 5, ColumnType.str), ///////// don't know use str or pooledStr
+ // optional properties
+ status_bits: hasStatus_bit ? col(0, 0, ColumnType.str) : undefStr, ///////// don't know use str or pooledStr
+ };
+
+ return ret;
}
-function parseInternal(data: string): Result<Schema.File> {
- const tokenizer = TokenizerState(data);
+
+
+
+//////// not using async here
+function parseInternal(data: string): Result<Schema.File> { /////// not having ctx as a parameter, and not returning Promise
+ const tokenizer = Tokenizer(data);
const structures: Schema.Structure[] = [];
while (tokenizer.position < data.length) {
- const state = createState(tokenizer);
+ const state = State(tokenizer);//////////different
handleMolecule(state);
const atoms = handleAtoms(state);
- handleBoxVectors(state);
- structures.push({ header: state.header, atoms });
+ const bonds = handleBonds(state);
+ structures.push({ molecule: state.molecule, atoms, bonds });
}
const result: Schema.File = { structures };
return Result.success(result);
}
+
+
+
+
+///////// diffrent than gro parser
export function parse(data: string) {
return parseInternal(data);
}
--
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