@datagrok/sequence-translator 1.0.17 → 1.1.0

package/link-bio

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+cd ../../libraries/bio
+./cleanup && npm i && npm run build && npm link
+
+cd -
+npm link @datagrok-libraries/bio

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.0.17",
+  "version": "1.1.0",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
@@ -13,12 +13,13 @@
     "directory": "packages/SequenceTranslator"
   },
   "dependencies": {
+    "@datagrok-libraries/chem-meta": "^1.0.9",
     "@datagrok-libraries/utils": "^1.17.2",
+    "@datagrok-libraries/tutorials": "^1.3.2",
+    "cash-dom": "^8.1.0",
+    "datagrok-api": "^1.10.2",
     "@types/react": "^18.0.15",
-    "@datagrok-libraries/bio": "^5.11.1",
-    "@deck.gl/core": "8.8.12",
-    "@luma.gl/core": "8.5.17",
-    "datagrok-api": "^1.8.2",
+    "@datagrok-libraries/bio": "^5.32.1",
     "datagrok-tools": "^4.1.2",
     "npm": "^8.11.0",
     "openchemlib": "6.0.1",
@@ -27,26 +28,23 @@
     "typescript": "^4.7.4"
   },
   "devDependencies": {
-    "@types/jest": "^27.0.0",
     "@types/jquery": "^3.5.14",
-    "@typescript-eslint/eslint-plugin": "^4.29.1",
-    "@typescript-eslint/parser": "^4.29.1",
-    "cash-dom": "^8.1.0",
-    "eslint": "^7.32.0",
-    "eslint-config-google": "^0.14.0",
-    "jest": "^27.0.0",
-    "jest-html-reporter": "^3.5.0",
-    "puppeteer": "^13.7.0",
-    "ts-jest": "^27.0.0",
-    "webpack": "^5.31.0",
-    "webpack-cli": "^4.6.0",
     "@types/js-yaml": "^4.0.5",
-    "js-yaml": "^4.1.0",
     "@types/node-fetch": "^2.6.2",
-    "node-fetch": "^2.6.7"
-  },
-  "grokDependencies": {
-    "@datagrok/chem": "1.3.32"
+    "@types/react": "^18.0.15",
+    "@typescript-eslint/eslint-plugin": "latest",
+    "@typescript-eslint/parser": "parser",
+    "css-loader": "^6.7.3",
+    "datagrok-tools": "^4.7.10",
+    "eslint": "^7.32.0",
+    "eslint-config-google": "latest",
+    "style-loader": "^3.3.1",
+    "ts-loader": "^9.3.1",
+    "typescript": "^4.7.4",
+    "webpack": "^5.75.0",
+    "webpack-cli": "latest",
+    "@datagrok/chem": "1.5.7",
+    "@datagrok/bio": "^2.1.12"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",
@@ -59,13 +57,17 @@
     "release-sequencetranslator-public": "grok publish public --release",
     "debug-sequencetranslator-local": "grok publish local",
     "release-sequencetranslator-local": "grok publish local --release",
-    "test": "jest",
-    "test-dev": "set HOST=dev && jest",
-    "test-local": "set HOST=localhost && jest"
+    "lint": "eslint \"./src/**/*.ts\"",
+    "lint-fix": "eslint \"./src/**/*.ts\" --fix",
+    "test": "grok test",
+    "test-dev": "grok test --host dev",
+    "test-local": "grok test --host localhost"
   },
-  "sources": [
-    "css/style.css",
-    "vendors/openchemlib-full.js"
+  "canEdit": [
+    "Developers"
+  ],
+  "canView": [
+    "All users"
   ],
   "category": "Bioinformatics"
 }

package/scripts/build-monomer-lib.py

@@ -1,178 +1,447 @@
+# pylint: disable=no-member
+import os.path
+import sys
 from io import TextIOWrapper
+from typing import Optional
 
 from rdkit import Chem
+from rdkit.Chem.rdchem import Mol
 
 import orjson
 
 import click
 
-from click_default_group import DefaultGroup
-from rdkit.Chem.rdchem import Mol
-
-
-def molAddCollection(mol: Mol, name: str, title: str = None) -> str:
+BEGIN_ATOM_LINE = 'M  V30 BEGIN ATOM'
+END_ATOM_LINE = 'M  V30 END ATOM'
+BEGIN_BOND_LINE = 'M  V30 BEGIN BOND'
+END_BOND_LINE = 'M  V30 END BOND'
+BEGIN_COLLECTION_LINE = 'M  V30 BEGIN COLLECTION'
+END_COLLECTION_LINE = 'M  V30 END COLLECTION'
+COLLECTION_STEABS_LINE = 'M  V30 MDLV30/STEABS'
+IDX_OF_FIRST_VALUE = 7
+NUM_OF_BOND_POSITIONAL_ARGS = 4
+CFG = "CFG="
+
+
+def mol_add_collection(mol: Mol,
+                       name: str,
+                       title: Optional[str] = None,
+                       src_mol: Optional[str] = None) -> str:
     """
     Get and postprocess (atom's CFG, title, e.t.c.) molblock
-    :param mol:    Mol molecule structure / object
-    :param name:   Monomer name to add to molblock title
-    :param title:  title to replace in Chem.MolToMolBlock() string output
-    :return:       molblock string
+    :param mol:      Mol molecule structure / object
+    :param name:     Monomer name to add to molblock title string
+    :param title:    Title to replace in Chem.MolToMolBlock() string output
+    :param src_mol:  Source molblock data, to restore optional CFG
+    :return:         molblock string
     """
     res: str = Chem.MolToMolBlock(mol, forceV3000=True)  # MolToMolFile
 
-    mb_line_list: list[str] = res.split('\n')
+    molblock_line_list: list[str] = res.split('\n')
     if title:
-        mb_line_list[1] = title
+        molblock_line_list[1] = title
 
-    if name and name not in mb_line_list[1]:
-        mb_line_list[1] += '|' + name
+    if name and name not in molblock_line_list[1]:
+        molblock_line_list[1] += '|' + name
 
-    end_bond_idx: int = mb_line_list.index('M  V30 END BOND')
     chirality = [atom.GetChiralTag() for atom in mol.GetAtoms()]
-    begin_atom_idx = mb_line_list.index('M  V30 BEGIN ATOM')
-    end_atom_idx = mb_line_list.index('M  V30 END ATOM')
-    for atom_idx in range(1, end_atom_idx - begin_atom_idx):
-        line_idx = begin_atom_idx + atom_idx
-        atom_ch = chirality[atom_idx - 1]
-        if atom_ch != Chem.rdchem.CHI_UNSPECIFIED:
-            mb_line_list[line_idx] += " CFG={0}".format(int(atom_ch))
-
-    steabs: list[int] = [i + 1 for (i, ch) in enumerate(chirality) if ch != Chem.rdchem.CHI_UNSPECIFIED]
-    if len(steabs) > 0:
-        steabs_str: str = "M  V30 MDLV30/STEABS ATOMS=({count} {list})" \
-            .format(count=len(steabs), list=' '.join([str(idx) for idx in steabs]))
-
-        mb_line_list = mb_line_list[:(end_bond_idx + 1)] + \
-                       ["M  V30 BEGIN COLLECTION", steabs_str, "M  V30 END COLLECTION"] + \
-                       mb_line_list[(end_bond_idx + 1):]
-
-    return '\n'.join(mb_line_list)
 
+    # preserve chirality for bonds from src_mol
+    tgt_mol_file_map = MolFileMap.parse(res)
+    steabs = []
+    if src_mol:
+        src_mol_file_map = MolFileMap.parse(src_mol)
+        if len(tgt_mol_file_map.mol_file.atom_list) != len(src_mol_file_map.mol_file.atom_list):
+            raise ValueError(f"Atoms count of src and tgt differs for monomer '{name}'.")
+
+        # restore bond cfg values lost/transformed by rdkit
+        for (src_bond_idx0, (bond_key, src_bond)) in enumerate(src_mol_file_map.mol_file.bonds.items()):
+            if src_bond.cfg:
+                if bond_key not in tgt_mol_file_map.mol_file.bonds:
+                    raise KeyError(f"Bond key '{bond_key}' not found in tgt bonds.")
+                tgt_bond: MolFileBond = tgt_mol_file_map.mol_file.bonds[bond_key]
+                tgt_bond_cfg_str: str = ' '.join(tgt_bond.cfg)
+                src_bond_cfg_str: str = ' '.join(src_bond.cfg)
+                if tgt_bond_cfg_str != src_bond_cfg_str:
+                    molblock_line_list[tgt_mol_file_map.begin_bond_idx + tgt_bond.bond_idx] += f" {src_bond_cfg_str}"
+
+
+        # remove bond cfg values added by rdkit
+        for (tgt_bond_idx0, (bond_key, tgt_bond)) in enumerate(tgt_mol_file_map.mol_file.bonds.items()):
+            if tgt_bond.cfg:
+                if bond_key not in src_mol_file_map.mol_file.bonds:
+                    raise KeyError(f"Bond key '{bond_key}' not found in src bonds.")
+                src_bond: MolFileBond = src_mol_file_map.mol_file.bonds[bond_key]
+                src_bond_cfg_str: str = ' '.join(src_bond.cfg)
+                tgt_bond_cfg_str: str = ' '.join(tgt_bond.cfg)
+                if tgt_bond_cfg_str != src_bond_cfg_str:
+                    new_line = molblock_line_list[tgt_mol_file_map.begin_bond_idx + tgt_bond.bond_idx].replace(tgt_bond_cfg_str, "")
+                    molblock_line_list[tgt_mol_file_map.begin_bond_idx + tgt_bond.bond_idx] = new_line
+
+        for (tgt_atom_idx0, tgt_atom) in enumerate(tgt_mol_file_map.mol_file.atom_list):
+            src_atom = src_mol_file_map.mol_file.atom_list[tgt_atom_idx0]
+            atom_chirality = chirality[tgt_atom_idx0]
+            if src_atom.cfg:
+                molblock_line_list[tgt_mol_file_map.begin_atom_idx + tgt_atom_idx0 + 1] += " {0}".format(
+                    ' '.join(src_atom.cfg))
+                steabs.append(tgt_atom_idx0 + 1)
+            elif atom_chirality != Chem.rdchem.CHI_UNSPECIFIED:
+                molblock_line_list[tgt_mol_file_map.begin_atom_idx + tgt_atom_idx0 + 1] += " CFG={0}".format(int(atom_chirality))
+                steabs.append(tgt_atom_idx0 + 1)
+            elif src_atom.atom_idx in src_mol_file_map.mol_file.collection_steabs:
+                raise KeyError(f"Source STEABS atom '{src_atom}' not accounted")
+            elif tgt_atom.atom_idx in tgt_mol_file_map.mol_file.collection_steabs:
+                raise KeyError(f"Target STEABS atom '{tgt_atom}' not accounted")
 
-def molfile2molfile(src_mol: str, name: str) -> str:
-    mol: Mol = Chem.MolFromMolBlock(src_mol)
-    src_mf_lines = src_mol.split('\n')
-    title = src_mf_lines[1]
-    return molAddCollection(mol, name, title=title)
-
-
-def smiles2molfile(smiles: str, name: str) -> str:
-    mol: Mol = Chem.MolFromSmiles(smiles)
-    return molAddCollection(mol, name)
-
-
-CodesType = dict[str, dict[str, list[str]]]
+    if len(steabs) > 0:
+        steabs_str: str = COLLECTION_STEABS_LINE + " ATOMS=({count} {list})".format(
+            count=len(steabs),
+            list=' '.join([str(idx) for idx in steabs]))
+        if tgt_mol_file_map.collection_steabs_idx:
+            molblock_line_list[tgt_mol_file_map.collection_steabs_idx] = steabs_str
+        elif tgt_mol_file_map.begin_collection_idx is not None:
+            tgt_collection_steabs_idx = tgt_mol_file_map.begin_collection_idx + 1
+            molblock_line_list = molblock_line_list[:tgt_collection_steabs_idx] + \
+                           [steabs_str] + \
+                           molblock_line_list[tgt_collection_steabs_idx:]
+        else:
+            tgt_collection_idx = tgt_mol_file_map.end_bond_idx + 1
+            molblock_line_list = molblock_line_list[:tgt_collection_idx] + \
+                           [BEGIN_COLLECTION_LINE, steabs_str, END_COLLECTION_LINE] + \
+                           molblock_line_list[tgt_collection_idx:]
+
+    return '\n'.join(molblock_line_list)
+
+
+def prepare_molblock(src_molblock: str, name: str) -> str:
+    """Loads mol from src_mol str. Fixed title, adds chirality to atoms and preserves chirality for bonds."""
+    # Using sanitize=False leads to unwanted moving stereo (invalid?) CFGs to other bonds
+    mol: Mol = Chem.MolFromMolBlock(src_molblock, removeHs=False)
+    src_molblock_lines = src_molblock.split('\n')
+    title = src_molblock_lines[1]
+    return mol_add_collection(mol, name, title=title, src_mol=src_molblock)
 
 
 class Monomer:
-    def __init__(self,
-                 symbol: str, name: str, molfile: str, smiles: str,
-                 codes: CodesType):
+    def __init__(self, symbol: str, name: str, molfile: str, smiles: str,
+                 meta: dict):
         self.monomerType = 'Backbone'
         self.smiles = smiles
         self.name = name
         self.author = 'SequenceTranslator'
-        self.molfile = molfile2molfile(molfile, name) if molfile else smiles2molfile(smiles, name)
-        self.naturalAnalog = ''
-        self.rgroups = [
-            {
-                "capGroupSmiles": "O[*:1]",
-                "alternateId": "R1-OH",
-                "capGroupName": "OH",
-                "label": "R1"
-            },
-            {
-                "capGroupSmiles": "O[*:2]",
-                "alternateId": "R2-OH",
-                "capGroupName": "OH",
-                "label": "R2"
-            }]
+        self.molfile = prepare_molblock(molfile, name)
+        self.rgroups = [{
+            "capGroupSmiles": "O[*:1]",
+            "alternateId": "R1-OH",
+            "capGroupName": "OH",
+            "label": "R1"
+        }, {
+            "capGroupSmiles": "O[*:2]",
+            "alternateId": "R2-OH",
+            "capGroupName": "OH",
+            "label": "R2"
+        }]
         self.createDate = None
         self.id = 0
         self.polymerType = 'RNA'
         self.symbol = symbol
-        self.codes: CodesType = codes
+        self.meta = meta
 
     @staticmethod
     def from_json(src_json: {}):
         obj = Monomer(src_json['symbol'], src_json['name'],
                       src_json['molfile'], src_json['smiles'],
-                      src_json['codes'])
+                      src_json['meta'])
         return obj
 
     def to_json(self):
         return {
-            'monomerType': self.monomerType,
-            'smiles': self.smiles,
+            'symbol': self.symbol,
             'name': self.name,
-            'author': self.author,
             'molfile': self.molfile,
-            'naturalAnalog': self.naturalAnalog,
-            'rgroups': self.rgroups,
-            'createDate': self.createDate,
+            'author': self.author,
             'id': self.id,
+            'rgroups': self.rgroups,
+            'smiles': self.smiles,
             'polymerType': self.polymerType,
-            'symbol': self.symbol,
-            'codes': self.codes,
+            'monomerType': self.monomerType,
+            'createDate': self.createDate,
+            'meta': self.meta,
         }
 
 
-def codes2monomers(codes_json: {}) -> dict[str, Monomer]:
-    monomers_res: dict[str, Monomer] = {}
-    for (codes_src, src_dict) in codes_json.items():
-        for (codes_type, monomers_dict) in src_dict.items():
-            for (codes_code, monomer_json) in monomers_dict.items():
-                monomer_name = monomer_json['name']
-                if monomer_name not in monomers_res:
-                    symbol = monomer_json['name']
-                    name = monomer_json['name']
-                    smiles = monomer_json['SMILES']
-                    monomers_res[monomer_name] = Monomer(symbol, name, None, smiles, {})
-                codes = monomers_res[monomer_name].codes
-                if codes_src not in codes:
-                    codes[codes_src] = {}
-                if codes_type not in codes[codes_src]:
-                    codes[codes_src][codes_type] = [];
-                codes[codes_src][codes_type].append(codes_code)
-    return monomers_res
-
-
-@click.group(cls=DefaultGroup, default='main')
-def cli():
-    pass
-
-
-@cli.command()
-@click.pass_context
-@click.option('--initial', 'initial_f',
-              help='Initial monomers source file.',
-              type=click.File('r', 'utf-8'))
-@click.option('--lib', 'lib_f',
+class MolFileAtom:
+    """
+    Wrapper for data extracted from molfile atom line
+    """
+    def __init__(self, v3k_atom_line: str):
+        self._atom_line = v3k_atom_line
+        self._atom_line_splitted: [] = self.\
+            _atom_line[IDX_OF_FIRST_VALUE:].split(' ')
+        self._atom_idx = int(self._atom_line_splitted[0].strip())
+        # we cannot use positional argument for cfg for it is a kwarg
+        cfg_item = list(filter(
+            lambda x: x.startswith(CFG), self._atom_line_splitted
+            ))
+        self._cfg = cfg_item
+
+    @property
+    def atom_line_str(self) -> str:
+        return self._atom_line
+
+    @property
+    def atom_idx(self):
+        return self._atom_idx
+
+    @property
+    def atom_line_splitted(self) -> list[str]:
+        return self.atom_line_splitted
+
+    @property
+    def cfg(self) -> list[str]:
+        return self._cfg
+
+    @property
+    def cfg_int(self) -> int:
+        return self._cfg
+
+    def __str__(self):
+        return self._atom_line
+
+    def __repr__(self):
+        return str(self)
+
+
+class MolFileBond:
+    """
+    Wrapper for data extracted from molfile bond line
+    """
+    def __init__(self, v3k_bond_line: str):
+        self._bond_line = v3k_bond_line
+        self._bond_line_splitted: [] = self.\
+            _bond_line[IDX_OF_FIRST_VALUE:].split(' ')
+        self._bond_idx = int(self._bond_line_splitted[0].strip())
+        self._key = self._bond_line_splitted[0:NUM_OF_BOND_POSITIONAL_ARGS]
+        cfg_item = list(filter(
+            lambda x: x.startswith(CFG), self._bond_line_splitted
+            ))
+        self._cfg = cfg_item
+
+    @property
+    def bond_line(self) -> str:
+        return self._bond_line
+
+    @property
+    def bond_idx(self):
+        return self._bond_idx
+
+    @property
+    def bond_line_splitted(self) -> list[str]:
+        return self._bond_line_splitted
+
+    @property
+    def key(self):
+        return self._key
+
+    @property
+    def cfg(self) -> list[str]:
+        return self._cfg
+
+    def __str__(self):
+        return self._bond_line
+
+    def __repr__(self):
+        return str(self)
+
+
+class MolFileV3K:
+    """
+    Wrapper for data extracted from molfile
+    """
+    def __init__(
+            self, title: str, atom_list: list[MolFileAtom],
+            bond_list: list[MolFileBond],
+            collection_steabs: list[int] = None
+            ):
+        self._title = title
+        self._atom_list = atom_list
+        self._bond_list = bond_list
+        self.collection_steabs = [] if collection_steabs is None \
+            else collection_steabs
+
+        self._bonds: dict = {}
+        for bond in self._bond_list:
+            # list is unhashable type, but tuple is
+            bond_key = tuple((int(v) for v in bond.key))
+            self._bonds[bond_key] = bond
+
+    @property
+    def atom_list(self):
+        return self._atom_list
+
+    @property
+    def bond_list(self):
+        return self._bond_list
+
+    @property
+    def bonds(self) -> dict:
+        return self._bonds
+
+
+class MolFileMap:
+    def __init__(self, src: str, mol_file_obj: MolFileV3K,
+                 atom_block_idx_boundaries: tuple[int, int],
+                 bond_block_idx_boundaries: tuple[int, int],
+                 collection_idx_boundaries: tuple[int, int] = None,
+                 collection_steabs_idx: int = None):
+        self._src = src
+        self._mol_file = mol_file_obj
+        self.begin_atom_idx = atom_block_idx_boundaries[0]
+        self.end_atom_idx = atom_block_idx_boundaries[1]
+        self.begin_bond_idx = bond_block_idx_boundaries[0]
+        self.end_bond_idx = bond_block_idx_boundaries[1]
+        self.begin_collection_idx = None if collection_idx_boundaries is None \
+            else collection_idx_boundaries[0]
+        self.end_collection_idx = None if collection_idx_boundaries is None \
+            else collection_idx_boundaries[1]
+        self.collection_steabs_idx = collection_steabs_idx
+
+    @property
+    def src(self):
+        return self._src
+
+    @property
+    def mol_file(self):
+        return self._mol_file
+
+    @staticmethod
+    def parse(molblock_src: str):
+        molblock_line_list: list[str] = \
+            [line.rstrip() for line in molblock_src.split('\n')]
+        title: str = molblock_line_list[1]
+
+        def get_idx_boundaries(begin_str: str, end_str: str):
+            return tuple([
+                molblock_line_list.index(begin_str),
+                molblock_line_list.index(end_str)
+                ])
+
+        def get_wrapper_list(
+                begin_idx: int, end_idx: int, wrapper_constructor
+                ):
+            """
+            For the list of atom/bond wrapper objects
+            """
+            item_count = end_idx - begin_idx - 1  # for atoms or bonds
+            wrapper_list = [None] * item_count
+            for item_idx in range(1, item_count + 1):
+                line_idx = begin_idx + item_idx
+                line = molblock_line_list[line_idx]
+                item = wrapper_constructor(line)
+                wrapper_list[item_idx - 1] = item
+            return wrapper_list
+
+        atom_block_idx_boundaries = get_idx_boundaries(
+                BEGIN_ATOM_LINE, END_ATOM_LINE)
+        bond_block_idx_boundaries = get_idx_boundaries(
+                BEGIN_BOND_LINE, END_BOND_LINE)
+        atom_list = get_wrapper_list(
+                atom_block_idx_boundaries[0],
+                atom_block_idx_boundaries[1], MolFileAtom)
+        bond_list = get_wrapper_list(
+                bond_block_idx_boundaries[0],
+                bond_block_idx_boundaries[1], MolFileBond)
+
+        collection_idx_boundaries = None
+        collection_steabs_idx = None
+        collection_steabs: list[int] = []
+        if BEGIN_COLLECTION_LINE in molblock_line_list and END_COLLECTION_LINE in molblock_line_list:
+            collection_idx_boundaries = get_idx_boundaries(
+                    BEGIN_COLLECTION_LINE, END_COLLECTION_LINE)
+            collection_count: int = collection_idx_boundaries[1] - \
+                collection_idx_boundaries[0] - 1
+            for collection_idx in range(1, collection_count + 1):
+                line_idx = collection_idx_boundaries[0] + collection_idx
+                collection_line = molblock_line_list[line_idx]
+                if collection_line.startswith(COLLECTION_STEABS_LINE):
+                    steabs_str = collection_line[len(COLLECTION_STEABS_LINE + " ATOMS=("):-1]
+                    collection_steabs = [int(atom_num_str.strip()) for atom_num_str in steabs_str.split(' ')[1:]]
+                    collection_steabs_idx = line_idx
+                else:
+                    raise ValueError(f"Unexpected collection line '{collection_line}'.")
+
+        mol_file = MolFileV3K(title, atom_list, bond_list, collection_steabs)
+        return MolFileMap(
+                molblock_src, mol_file,
+                atom_block_idx_boundaries, bond_block_idx_boundaries,
+                collection_idx_boundaries, collection_steabs_idx)
+
+
+def compile_object_for_monomer(monomer_name: str):
+    """
+    Compile HELM library object for the given monomers from files
+    """
+    default = monomer_name + '/default.json'
+    meta = monomer_name + '/meta.json'
+    molfile = monomer_name + '/molfile.mol'
+    for file in [default, meta, molfile]:
+        if not os.path.isfile(file):
+            raise FileNotFoundError(file)
+
+    monomer_json = {}
+    default_json = {}
+    meta_json = {}
+
+    with open(default, 'r') as default_json_file:
+        default_json_str = default_json_file.read()
+        default_json = orjson.loads(default_json_str)
+    with open(meta, 'r') as meta_json_file:
+        meta_json_str = meta_json_file.read()
+        meta_json = orjson.loads(meta_json_str)
+
+    monomer_json = {**default_json, 'meta': meta_json}
+    with open(molfile, 'r') as monomer_mol_f:
+        monomer_mol_lines = [line.rstrip() for line in monomer_mol_f.readlines()]
+        monomer_mol_txt = '\n'.join(monomer_mol_lines)
+        monomer_json['molfile'] = monomer_mol_txt
+    # print(monomer_json)
+    return monomer_json
+
+
+@click.command()
+@click.option('--lib',
+              'output_library',
               help='Output library (HELM format) file.',
               type=click.File('wb', 'utf-8'))
-@click.option('--add', 'add_f_list', multiple=True,
-              help='Additional libraries to build.',
+@click.option('--add-list',
+              'monomer_list_file',
+              multiple=False,
+              help='File with list of monomer names',
               type=click.File('r', 'utf-8'))
-def main(ctx, initial_f: TextIOWrapper, lib_f: TextIOWrapper, add_f_list: list[TextIOWrapper]):
-    initial_json_str = initial_f.read()
-
-    initial_json = orjson.loads(initial_json_str)
+def main(output_library: TextIOWrapper,
+         monomer_list_file: TextIOWrapper):
+    name_to_monomer_dict: dict[str, Monomer] = {}
+    monomer_name_list = []
+    for monomer_name in [m for m in monomer_list_file.read().split('\n') if m]:
+        monomer_name_list.append(monomer_name)
 
-    monomers: dict[str, Monomer] = codes2monomers(initial_json)
+    print(monomer_name_list)
 
-    for add_f in add_f_list:
-        add_json_str = add_f.read()
-        add_json = orjson.loads(add_json_str)
-        for add_m in add_json:
-            m = Monomer.from_json(add_m)
-            monomers[m.name] = m
+    for monomer_name in monomer_name_list:
+        # trying to load mol data if file with .mol extension exists
+        monomer_obj = compile_object_for_monomer(monomer_name)
+        try:
+            monomer_obj = Monomer.from_json(monomer_obj)
+            name_to_monomer_dict[monomer_obj.name] = monomer_obj
+        except Exception as ex:
+            sys.stderr.write(f"Invalid monomer '{monomer_obj['name']}' error:\n{str(ex)}")
 
-    add_json = [m.to_json() for m in monomers.values()]
+    resulting_json = [obj.to_json() for obj in name_to_monomer_dict.values()]
+    resulting_json = sorted(resulting_json, key=lambda x: x['name'])
 
-    lib_json_txt = orjson.dumps(add_json, option=orjson.OPT_INDENT_2)
-    lib_f.write(lib_json_txt)
-    k = 11
+    lib_json_txt = orjson.dumps(resulting_json, option=orjson.OPT_INDENT_2)
+    output_library.write(lib_json_txt)
 
 
 if __name__ == '__main__':
-    cli()
+    main()