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Improve Conformational Sampling of Small and Large Ring Molecules (#2999)

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* improvements for smal anr large ring conformer generation

* add documentation and reorder parameters in EmbedParam

* resolve merge conflict due to coordMap null pointer

* minor changes to address merge comments

* reorder variables in EmbedParameters

* add regression test for small ring and macrocycle torsion preferences

* not apply small ring torsions to bridged ring systems

* fix and test for bridged small rings torsion pattern exclusion

* add ETKDGv3 and srETKDGv3 option to keep compatiblity for original ETKDG

* EKTDG version 3 related minor fix

* add reference to doc string

* Java wrapper for ETKDGv3

* fix doc

* change CPCI to shared_ptr, but it seems to be much slower

* minor modifications to small bridged ring systems, and share_ptr from previous commit is fine

* rollback from shared_ptr(map) to just map

* run clang-format

Co-authored-by: Shuzhe Wang <shuwang@eu-login-10.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-14.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-17.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-45.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-05.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-15.euler.ethz.ch>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
This commit is contained in:
hjuinj
2020-03-23 21:57:46 +08:00
committed by GitHub
parent a6cafc4635
commit acdfe26dea
18 changed files with 1516 additions and 168 deletions
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20
Code/DistGeom/DistGeomUtils.cpp
View File

@@ -25,6 +25,7 @@
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h>
#include <boost/dynamic_bitset.hpp>
#include <ForceField/MMFF/Nonbonded.h>
namespace DistGeom {
const double EIGVAL_TOL = 0.001;
@@ -363,6 +364,25 @@ ForceFields::ForceField *construct3DForceField(
return field;
} // construct3DForceField
ForceFields::ForceField *construct3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails,
const std::map<std::pair<unsigned int, unsigned int>, double> &CPCI) {
auto *field = construct3DForceField(mmat, positions, etkdgDetails);
bool is1_4 = false;
// double dielConst = 1.0;
boost::uint8_t dielModel = 1;
for (const auto &charge : CPCI) {
auto *contrib = new ForceFields::MMFF::EleContrib(
field, charge.first.first, charge.first.second, charge.second,
dielModel, is1_4);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
return field;
}
ForceFields::ForceField *constructPlain3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails) {

18
Code/DistGeom/DistGeomUtils.h
View File

@@ -138,6 +138,24 @@ RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *construct3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails);
//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
// constraints, as well as atom pairwise Columbic interactions
/*!
\param mmat Distance bounds matrix
\param positions A vector of pointers to 3D Points to write out the
resulting coordinates
\param etkdgDetails Contains information about the ETKDG force field
\param CPCI Contains which atom pair(s) have what strength of
attractive/repulsive electrostatic interaction(s)
<b>NOTE:</b> the caller is responsible for deleting this force field.
*/
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *construct3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails,
const std::map<std::pair<unsigned int, unsigned int>, double> &CPCI);
//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
// constraints
/*!