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c5de9f8843
* added *S-S* and bounds overwriting tests * fixed *S-S* * added bounds overwriting test * searching for the bug * added test case * improved tests + fixed bug 9166 * updated ref mols * regenerated refs * clean up * changed ref data * removed print statements * Update Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Typo Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Incooperated suggestions * applied remaining suggestions * restored imports --------- Co-authored-by: Katharina Buchthal <katharina.buchthal@phys.chem.ethz.ch> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
80 lines
3.3 KiB
C++
80 lines
3.3 KiB
C++
//
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// Copyright (C) 2004-2019 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef RD_BOUNDS_MATRIX_BUILDER_H
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#define RD_BOUNDS_MATRIX_BUILDER_H
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#include <DistGeom/BoundsMatrix.h>
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namespace RDKit {
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class ROMol;
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namespace DGeomHelpers {
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//! Set default upper and lower distance bounds in a distance matrix
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/*!
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\param mmat pointer to the bounds matrix to be altered
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\param defaultMin default value for the lower distance bounds
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\param defaultMax default value for the upper distance bounds
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*/
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RDKIT_DISTGEOMHELPERS_EXPORT void initBoundsMat(DistGeom::BoundsMatrix *mmat,
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double defaultMin = 0.0,
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double defaultMax = 1000.0);
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/*! \overload
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*/
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RDKIT_DISTGEOMHELPERS_EXPORT void initBoundsMat(DistGeom::BoundsMatPtr mmat,
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double defaultMin = 0.0,
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double defaultMax = 1000.0);
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//! Set upper and lower distance bounds between atoms in a molecule based on
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/// topology
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/*!
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This consists of setting 1-2, 1-3 and 1-4 distance based on bond lengths,
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bond angles and torsion angle ranges. Optionally 1-5 bounds can also be set,
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in particular, for path that contain rigid 1-4 paths.
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The final step involves setting lower bound to the sum of the vdW radii for
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the remaining atom pairs.
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\param mol The molecule of interest
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\param mmat Bounds matrix to the bounds are written
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\param set15bounds If true try to set 1-5 bounds also based on topology
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\param scaleVDW If true scale the sum of the vdW radii while setting lower
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bounds
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so that a smaller value (0.7*(vdw1 + vdw2) ) is used for
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paths
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that are less five bonds apart.
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\param useMacrocycle14config If 1-4 distances bound heuristics for
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macrocycles is used <b>Note</b> For some strained systems the bounds matrix
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resulting from setting 1-5 bounds may fail triangle smoothing. In these cases
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it is recommended to back out and recompute the bounds matrix with no 1-5
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bounds and with vdW scaling.
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*/
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RDKIT_DISTGEOMHELPERS_EXPORT void setTopolBounds(
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const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds = true,
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bool scaleVDW = false, bool useMacrocycle14config = false,
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bool forceTransAmides = true, bool set14bounds = true,
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bool set13bounds = true);
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/*! \overload for experimental torsion angle preferences
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*/
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RDKIT_DISTGEOMHELPERS_EXPORT void setTopolBounds(
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const ROMol &mol, DistGeom::BoundsMatPtr mmat,
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std::vector<std::pair<int, int>> &bonds,
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std::vector<std::vector<int>> &angles, bool set15bounds = true,
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bool scaleVDW = false, bool useMacrocycle14config = false,
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bool forceTransAmides = true, bool set14bounds = true,
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bool set13bounds = true);
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//! generate the vectors of bonds and angles used by (ET)KDG
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RDKIT_DISTGEOMHELPERS_EXPORT void collectBondsAndAngles(
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const ROMol &mol, std::vector<std::pair<int, int>> &bonds,
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std::vector<std::vector<int>> &angles);
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} // namespace DGeomHelpers
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} // namespace RDKit
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#endif
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