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Merge branch 'master' into modern_cxx

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# Conflicts:
#	.travis.yml
#	Code/GraphMol/FileParsers/MolFileParser.cpp
#	Code/GraphMol/FileParsers/MolFileStereochem.cpp
#	Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
#	Code/GraphMol/MolAlign/testMolAlign.cpp
#	Code/GraphMol/MolDraw2D/MolDraw2D.cpp
#	Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
#	Code/GraphMol/QueryOps.cpp
#	Code/GraphMol/ROMol.cpp
#	Code/GraphMol/SmilesParse/test.cpp
#	Code/GraphMol/Trajectory/Trajectory.cpp
#	Code/GraphMol/Wrap/Atom.cpp
#	Code/GraphMol/Wrap/Bond.cpp
#	Code/GraphMol/new_canon.cpp
#	Code/RDGeneral/testDict.cpp
#	Code/SimDivPickers/Wrap/MaxMinPicker.cpp
This commit is contained in:
Greg Landrum
2017-10-05 05:58:38 +02:00
parent a2970f1b8a b7d2cfbc8e
commit 87786c08b5
151 changed files with 8886 additions and 2715 deletions
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16
Code/DistGeom/BoundsMatrix.h
View File

@@ -34,8 +34,8 @@ class BoundsMatrix : public RDNumeric::SquareMatrix<double> {
//! Get the upper bound between points i and j
inline double getUpperBound(unsigned int i, unsigned int j) const {
URANGE_CHECK(i, d_nRows - 1);
URANGE_CHECK(j, d_nCols - 1);
URANGE_CHECK(i, d_nRows);
URANGE_CHECK(j, d_nCols);
if (i < j) {
return getVal(i, j);
@@ -46,8 +46,8 @@ class BoundsMatrix : public RDNumeric::SquareMatrix<double> {
//! Set the lower bound between points i and j
inline void setUpperBound(unsigned int i, unsigned int j, double val) {
URANGE_CHECK(i, d_nRows - 1);
URANGE_CHECK(j, d_nCols - 1);
URANGE_CHECK(i, d_nRows);
URANGE_CHECK(j, d_nCols);
CHECK_INVARIANT(val >= 0.0, "Negative upper bound");
if (i < j) {
setVal(i, j, val);
@@ -67,8 +67,8 @@ class BoundsMatrix : public RDNumeric::SquareMatrix<double> {
//! Set the lower bound between points i and j
inline void setLowerBound(unsigned int i, unsigned int j, double val) {
URANGE_CHECK(i, d_nRows - 1);
URANGE_CHECK(j, d_nCols - 1);
URANGE_CHECK(i, d_nRows);
URANGE_CHECK(j, d_nCols);
CHECK_INVARIANT(val >= 0.0, "Negative lower bound");
if (i < j) {
setVal(j, i, val);
@@ -88,8 +88,8 @@ class BoundsMatrix : public RDNumeric::SquareMatrix<double> {
//! Get the lower bound between points i and j
inline double getLowerBound(unsigned int i, unsigned int j) const {
URANGE_CHECK(i, d_nRows - 1);
URANGE_CHECK(j, d_nCols - 1);
URANGE_CHECK(i, d_nRows);
URANGE_CHECK(j, d_nCols);
if (i < j) {
return getVal(j, i);

8
Code/DistGeom/ChiralViolationContrib.cpp
View File

@@ -14,10 +14,10 @@ ChiralViolationContrib::ChiralViolationContrib(ForceFields::ForceField *owner,
PRECONDITION(owner, "bad owner");
PRECONDITION(cset, "bad chiral set")
URANGE_CHECK(cset->d_idx1, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx2, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx3, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx4, owner->positions().size() - 1);
URANGE_CHECK(cset->d_idx1, owner->positions().size());
URANGE_CHECK(cset->d_idx2, owner->positions().size());
URANGE_CHECK(cset->d_idx3, owner->positions().size());
URANGE_CHECK(cset->d_idx4, owner->positions().size());
dp_forceField = owner;

4
Code/DistGeom/DistViolationContrib.cpp
View File

@@ -20,8 +20,8 @@ DistViolationContrib::DistViolationContrib(ForceFields::ForceField *owner,
double ub, double lb,
double weight) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size() - 1);
URANGE_CHECK(idx2, owner->positions().size() - 1);
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
dp_forceField = owner;
d_end1Idx = idx1;