File: FunctionalGroups.py

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#
#  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
#  All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
#     * Redistributions of source code must retain the above copyright
#       notice, this list of conditions and the following disclaimer.
#     * Redistributions in binary form must reproduce the above
#       copyright notice, this list of conditions and the following
#       disclaimer in the documentation and/or other materials provided
#       with the distribution.
#     * Neither the name of Novartis Institutes for BioMedical Research Inc.
#       nor the names of its contributors may be used to endorse or promote
#       products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Created by Greg Landrum, October 2006
#
import os
import re
import weakref

from rdkit import Chem
from rdkit import RDConfig
from io import StringIO


class FGHierarchyNode(object):
    children = None
    name = ""
    label = ""
    pattern = None
    smarts = ""
    rxnSmarts = ""
    parent = None
    removalReaction = None

    def __init__(self, name, patt, smarts="", label="", rxnSmarts="", parent=None):
        self.name = name
        self.pattern = patt
        if parent:
            self.parent = weakref.ref(parent)
        self.label = label
        self.smarts = smarts
        self.children = []
        self.rxnSmarts = rxnSmarts

    def __len__(self):
        res = 1
        for child in self.children:
            res += len(child)
        return res


class FuncGroupFileParseError(ValueError):
    pass


groupDefns = {}
hierarchy = None
lastData = None
lastFilename = None


def BuildFuncGroupHierarchy(fileNm=None, data=None, force=False):
    global groupDefns, hierarchy, lastData, lastFilename
    if (not force and hierarchy and (not data or data == lastData)
            and (not fileNm or fileNm == lastFilename)):
        return hierarchy[:]
    lastData = data
    splitter = re.compile('\t+')

    if not fileNm and not data:
        fileNm = os.path.join(RDConfig.RDDataDir, 'Functional_Group_Hierarchy.txt')

    if fileNm:
        inF = open(fileNm, 'r')
        lastFilename = fileNm
    elif data:
        inF = StringIO(data)
    else:
        raise ValueError("need data or filename")

    groupDefns = {}
    res = []
    for lineNo, line in enumerate(inF.readlines(), 1):
        line = line.strip()
        line = line.split('//')[0]
        if not line:
            continue
        splitL = splitter.split(line)
        if len(splitL) < 3:
            raise FuncGroupFileParseError(
                "Input line %d (%s) is not long enough." % (lineNo, repr(line)))
        label = splitL[0].strip()
        if label in groupDefns:
            raise FuncGroupFileParseError("Duplicate label on line %d." % lineNo)
        labelHierarchy = label.split('.')
        if len(labelHierarchy) > 1:
            for i in range(len(labelHierarchy) - 1):
                tmp = '.'.join(labelHierarchy[:i + 1])
                if tmp not in groupDefns:
                    raise FuncGroupFileParseError(
                        "Hierarchy member %s (line %d) not found." % (tmp, lineNo))
            parent = groupDefns['.'.join(labelHierarchy[:-1])]
        else:
            parent = None
        smarts = splitL[1]
        patt = Chem.MolFromSmarts(smarts)
        if not patt:
            raise FuncGroupFileParseError(
                'Smarts "%s" (line %d) could not be parsed.' % (smarts, lineNo))

        name = splitL[2].strip()

        rxnSmarts = ''
        if len(splitL) > 3:
            rxnSmarts = splitL[3]

        node = FGHierarchyNode(name, patt, smarts=smarts, label=label, parent=parent,
                               rxnSmarts=rxnSmarts)
        if parent:
            parent.children.append(node)
        else:
            res.append(node)
        groupDefns[label] = node
    hierarchy = res[:]
    return res


def _SetNodeBits(mol, node, res, idx):
    ms = mol.GetSubstructMatches(node.pattern)
    count = 0
    seen = {}
    for m in ms:
        if m[0] not in seen:
            count += 1
            seen[m[0]] = 1
    if count:
        res[idx] = count
        idx += 1
        for child in node.children:
            idx = _SetNodeBits(mol, child, res, idx)
    else:
        idx += len(node)
    return idx


def CreateMolFingerprint(mol, hierarchy):
    totL = 0
    for entry in hierarchy:
        totL += len(entry)
    res = [0] * totL
    idx = 0
    for entry in hierarchy:
        idx = _SetNodeBits(mol, entry, res, idx)
    return res