From 1de5501d5db210456db74178860262757279dbea Mon Sep 17 00:00:00 2001 From: Eisuke Kawashima Date: Mon, 21 Oct 2019 09:12:47 +0900 Subject: [PATCH] Update DOI resolver [ci skip] --- Code/GraphMol/Descriptors/PMI.h | 14 ++++++------ .../Descriptors/Wrap/rdMolDescriptors.cpp | 2 +- .../Fingerprints/MorganFingerprints.h | 4 ++-- .../ForceFieldHelpers/MMFF/AtomTyper.cpp | 4 ++-- Contrib/LEF/README.txt | 8 +++---- Contrib/mmpa/README.txt | 4 ++-- Docs/Book/GettingStartedInPython.rst | 22 +++++++++---------- ...etting_Started_with_RDKit_in_Python_jp.rst | 22 +++++++++---------- rdkit/Chem/Descriptors3D.py | 14 ++++++------ 9 files changed, 47 insertions(+), 47 deletions(-) diff --git a/Code/GraphMol/Descriptors/PMI.h b/Code/GraphMol/Descriptors/PMI.h index 59c568dbf..dd58e3834 100644 --- a/Code/GraphMol/Descriptors/PMI.h +++ b/Code/GraphMol/Descriptors/PMI.h @@ -18,14 +18,14 @@ class ROMol; namespace Descriptors { //! Normalized principal moments ratio 1 (=I1/I3) //! from Sauer and Schwarz JCIM 43:987-1003 (2003) -//! https://dx.doi.org/10.1021/ci025599w +//! https://doi.org/10.1021/ci025599w RDKIT_DESCRIPTORS_EXPORT double NPR1(const ROMol&, int confId = -1, bool useAtomicMasses = true, bool force = false); const std::string NPR1Version = "1.0.0"; //! Normalized principal moments ratio 2 (=I2/I3) //! from Sauer and Schwarz JCIM 43:987-1003 (2003) -//! https://dx.doi.org/10.1021/ci025599w +//! https://doi.org/10.1021/ci025599w RDKIT_DESCRIPTORS_EXPORT double NPR2(const ROMol&, int confId = -1, bool useAtomicMasses = true, bool force = false); @@ -51,7 +51,7 @@ const std::string PMI3Version = "1.0.0"; Radius of gyration from G. A. Arteca "Molecular Shape Descriptors" Reviews in Computational Chemistry vol 9 - http://dx.doi.org/10.1002/9780470125861.ch5 + https://doi.org/10.1002/9780470125861.ch5 Definition (eq: A4): sqrt(t_1 + t_2 + t_3) where t_i is the ith moment from the gyration matrix @@ -64,7 +64,7 @@ const std::string radiusOfGyrationVersion = "1.0.0"; Inertial shape factor from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: pm2 / (pm1*pm3) @@ -78,7 +78,7 @@ const std::string inertialShapeFactorVersion = "1.0.0"; Molecular eccentricity from G. A. Arteca "Molecular Shape Descriptors" Reviews in Computational Chemistry vol 9 - http://dx.doi.org/10.1002/9780470125861.ch5 + https://doi.org/10.1002/9780470125861.ch5 Definition (eq 4): sqrt(pm_3**2 -pm_1**2) / pm_3**2 where pm_i is the ith moment of inertia @@ -91,7 +91,7 @@ const std::string eccentricityVersion = "1.0.0"; molecular asphericity from A. Baumgaertner, "Shapes of flexible vesicles" J. Chem. Phys. 98:7496 (1993) - http://dx.doi.org/10.1063/1.464689 + https://doi.org/10.1063/1.464689 Definition (eq 11): 0.5 * ((t_3-t_2)**2 + (t_3-t_1)**2 + (t_2-t_1)**2)/(t_1+t_2+t_3)**2 @@ -113,7 +113,7 @@ const std::string asphericityVersion = "1.0.0"; Spherocity index from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: 3 * t_1 / (t_1+t_2+t_3) diff --git a/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp b/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp index 58d51a2bf..bf8a37076 100644 --- a/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp +++ b/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp @@ -1576,7 +1576,7 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) { python::scope().attr("_CalcPBF_version") = RDKit::Descriptors::PBFVersion; docString = "Returns the PBF (plane of best fit) descriptor " - "(http://dx.doi.org/10.1021/ci300293f)"; + "(https://doi.org/10.1021/ci300293f)"; python::def("CalcPBF", RDKit::Descriptors::PBF, (python::arg("mol"), python::arg("confId") = -1), docString.c_str()); diff --git a/Code/GraphMol/Fingerprints/MorganFingerprints.h b/Code/GraphMol/Fingerprints/MorganFingerprints.h index 9ff21ca15..05baf6b31 100644 --- a/Code/GraphMol/Fingerprints/MorganFingerprints.h +++ b/Code/GraphMol/Fingerprints/MorganFingerprints.h @@ -65,7 +65,7 @@ const std::string morganFingerprintVersion = "1.0.0"; The algorithm used is described in the paper Rogers, D. & Hahn, M. Extended-Connectivity Fingerprints. JCIM 50:742-54 (2010) - http://dx.doi.org/10.1021/ci100050t + https://doi.org/10.1021/ci100050t The original implementation was done using this paper: D. Rogers, R.D. Brown, M. Hahn J. Biomol. Screen. 10:682-6 (2005) @@ -115,7 +115,7 @@ RDKIT_FINGERPRINTS_EXPORT SparseIntVect *getFingerprint( The algorithm used is described in the paper Rogers, D. & Hahn, M. Extended-Connectivity Fingerprints. JCIM 50:742-54 (2010) - http://dx.doi.org/10.1021/ci100050t + https://doi.org/10.1021/ci100050t The original implementation was done using this paper: D. Rogers, R.D. Brown, M. Hahn J. Biomol. Screen. 10:682-6 (2005) diff --git a/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp b/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp index 3f7727de1..f145c46bb 100644 --- a/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +++ b/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp @@ -2869,7 +2869,7 @@ MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams(const ROMol &mol, } else { // MMFF.V, page 627 // Herschbach-Laurie version of Badger's rule - // J. Chem. Phys. 35, 458 (1961); http://dx.doi.org/10.1063/1.1731952 + // J. Chem. Phys. 35, 458 (1961); https://doi.org/10.1063/1.1731952 // equation (8), page 5 mmffHerschbachLaurieParams = (*mmffHerschbachLaurie)( getPeriodicTableRowHL(atomicNum1), getPeriodicTableRowHL(atomicNum2)); @@ -3575,7 +3575,7 @@ void MMFFMolProperties::computeMMFFCharges(const ROMol &mol) { } // now we compute partial charges // See Halgren, T. MMFF.V, J. Comput. Chem. 1996, 17, 616-641 - // http://dx.doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X + // https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X for (idx = 0; idx < mol.getNumAtoms(); ++idx) { const Atom *atom = mol.getAtomWithIdx(idx); atomType = this->getMMFFAtomType(idx); diff --git a/Contrib/LEF/README.txt b/Contrib/LEF/README.txt index 2ee9768be..e9221f7ec 100644 --- a/Contrib/LEF/README.txt +++ b/Contrib/LEF/README.txt @@ -1,10 +1,10 @@ This directory contains scripts for carrying out the calculations and analyis from the publications: 1) A. Vulpetti, U. Hommel, G. Landrum, R. Lewis and C. Dalvit, "Design and NMR-based screening of LEF, -a library of chemical fragments with different Local Environment of Fluorine" J. Am. Chem. Soc. 131 (2009) 12949-12959. http://dx.doi.org/10.1021/ja905207t +a library of chemical fragments with different Local Environment of Fluorine" J. Am. Chem. Soc. 131 (2009) 12949-12959. https://doi.org/10.1021/ja905207t 2) A. Vulpetti, G. Landrum, S. Ruedisser, P. Erbel and C. Dalvit, "19F NMR Chemical Shift Prediction with -Fluorine Fingerprint Descriptor" J. of Fluorine Chemistry (2010). http://dx.doi.org/10.1016/j.jfluchem.2009.12.024 +Fluorine Fingerprint Descriptor" J. of Fluorine Chemistry (2010). https://doi.org/10.1016/j.jfluchem.2009.12.024 The scripts require that the RDKit (www.rdkit.org) be installed and properly configured. @@ -34,8 +34,8 @@ Commands to run: In the event you use the scripts for publication please reference the original publications: 1) A. Vulpetti, U. Hommel, G. Landrum, R. Lewis and C. Dalvit, "Design and NMR-based screening of LEF, -a library of chemical fragments with different Local Environment of Fluorine" J. Am. Chem. Soc. 131 (2009) 12949-12959. http://dx.doi.org/10.1021/ja905207t +a library of chemical fragments with different Local Environment of Fluorine" J. Am. Chem. Soc. 131 (2009) 12949-12959. https://doi.org/10.1021/ja905207t 2) A. Vulpetti, G. Landrum, S. Ruedisser, P. Erbel and C. Dalvit, "19F NMR Chemical Shift Prediction with -Fluorine Fingerprint Descriptor" J. of Fluorine Chemistry (2010). http://dx.doi.org/10.1016/j.jfluchem.2009.12.024 +Fluorine Fingerprint Descriptor" J. of Fluorine Chemistry (2010). https://doi.org/10.1016/j.jfluchem.2009.12.024 diff --git a/Contrib/mmpa/README.txt b/Contrib/mmpa/README.txt index 7efb1db46..39e9ae0da 100644 --- a/Contrib/mmpa/README.txt +++ b/Contrib/mmpa/README.txt @@ -3,7 +3,7 @@ The fragment indexing algorithm used in the scripts is described in the followin Hussain, J., & Rea, C. (2010). "Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets." Journal of chemical information and modeling, 50(3), 339-348. -http://dx.doi.org/10.1021/ci900450m +https://doi.org/10.1021/ci900450m Wagener, M., & Lommerse, J. P. (2006). "The quest for bioisosteric replacements." Journal of chemical information and modeling, 46(2), 677-685. @@ -300,4 +300,4 @@ In the event you use the scripts for publication please reference the original p Hussain, J., & Rea, C. (2010). "Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets." Journal of chemical information and modeling, 50(3), 339-348. -http://dx.doi.org/10.1021/ci900450m +https://doi.org/10.1021/ci900450m diff --git a/Docs/Book/GettingStartedInPython.rst b/Docs/Book/GettingStartedInPython.rst index ed2159136..8db91dc98 100644 --- a/Docs/Book/GettingStartedInPython.rst +++ b/Docs/Book/GettingStartedInPython.rst @@ -2763,7 +2763,7 @@ List of Available Descriptors +-----------------------------------------------------+------------------------------------------------------------+----------+ |Autocorr2D |New in 2017.09 release. Todeschini and Consoni "Descriptors | C++ | | |from Molecular Geometry" Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | +-----------------------------------------------------+------------------------------------------------------------+----------+ @@ -2786,40 +2786,40 @@ These all require the molecule to have a 3D conformer. +-----------------------------------------------------+-------------------------------------------------------------+----------+ |Radius of gyration |G. A. Arteca "Molecular Shape Descriptors" | C++ | | |Reviews in Computational Chemistry vol 9 | | -| |http://dx.doi.org/10.1002/9780470125861.ch5 | | +| |https://doi.org/10.1002/9780470125861.ch5 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |Inertial shape factor |Todeschini and Consoni "Descriptors from Molecular Geometry" | C++ | | |Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |Eccentricity |G. A. Arteca "Molecular Shape Descriptors" | C++ | | |Reviews in Computational Chemistry vol 9 | | -| |http://dx.doi.org/10.1002/9780470125861.ch5 | | +| |https://doi.org/10.1002/9780470125861.ch5 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |Asphericity |A. Baumgaertner, "Shapes of flexible vesicles" | C++ | | |J. Chem. Phys. 98:7496 | | | |(1993) | | -| |http://dx.doi.org/10.1063/1.464689 | | +| |https://doi.org/10.1063/1.464689 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |Spherocity Index |Todeschini and Consoni "Descriptors from Molecular Geometry" | C++ | | |Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |Autocorr3D |New in 2017.09 release. Todeschini and Consoni "Descriptors | C++ | | |from Molecular Geometry" Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |RDF |New in 2017.09 release. Todeschini and Consoni "Descriptors | C++ | | |from Molecular Geometry" Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |MORSE |New in 2017.09 release. Todeschini and Consoni "Descriptors | C++ | | |from Molecular Geometry" Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | +-----------------------------------------------------+-------------------------------------------------------------+----------+ |WHIM |New in 2017.09 release. Todeschini and Consoni "Descriptors | C++ | | |from Molecular Geometry" Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | | | | | | |**Note** insufficient information is available to exactly | | | |reproduce values from DRAGON for these descriptors. We | | @@ -2827,7 +2827,7 @@ These all require the molecule to have a 3D conformer. +-----------------------------------------------------+-------------------------------------------------------------+----------+ |GETAWAY |New in 2017.09 release. Todeschini and Consoni "Descriptors | C++ | | |from Molecular Geometry" Handbook of Chemoinformatics | | -| |http://dx.doi.org/10.1002/9783527618279.ch37 | | +| |https://doi.org/10.1002/9783527618279.ch37 | | | | | | | |**Note** insufficient information is available to exactly | | | |reproduce values from DRAGON for these descriptors. We | | diff --git a/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst b/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst index e887c01b0..a7fbf1d6a 100644 --- a/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst +++ b/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst @@ -2644,7 +2644,7 @@ SSSR問題 | Autocorr2D | | 2017.09リリースで新しく導入 | C++ | | | | Todeschini and Consoni | | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | +-------------------------------------------------------+----------------------------------------------------------------------+--------+ @@ -2667,44 +2667,44 @@ SSSR問題 +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | Radius of gyration | | G. A. Arteca “Molecular Shape Descriptors” | C++ | | | | Reviews in Computational Chemistry vol 9 | | -| | | http://dx.doi.org/10.1002/9780470125861.ch5 | | +| | | https://doi.org/10.1002/9780470125861.ch5 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | Inertial shape factor | | Todeschini and Consoni | C++ | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | Eccentricity | | G. A. Arteca “Molecular Shape Descriptors” | C++ | | | | Reviews in Computational Chemistry vol 9 | | -| | | http://dx.doi.org/10.1002/9780470125861.ch5 | | +| | | https://doi.org/10.1002/9780470125861.ch5 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | Asphericity | | A. Baumgaertner, “Shapes of flexible vesicles” | C++ | | | | *J. Chem. Phys.* **98**:7496 (1993) | | -| | | http://dx.doi.org/10.1063/1.464689 | | +| | | https://doi.org/10.1063/1.464689 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | Spherocity Index | | Todeschini and Consoni | C++ | | | | “Descriptors from Molecular Geometry” | | | | | Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | Autocorr3D | | 2017.09リリースで新しく導入。 | C++ | | | | Todeschini and Consoni | | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | RDF | | 2017.09リリースで新しく導入。 | C++ | | | | Todeschini and Consoni | | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | MORSE | | 2017.09リリースで新しく導入。 | C++ | | | | Todeschini and Consoni | | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | +---------------------------+-------------------------------------------------------------------------------------------------------+------+ | WHIM | | 2017.09リリースで新しく導入。 | C++ | | | | Todeschini and Consoni | | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | | | | | | | | | **注意** DRAGONを使って求めたこれらの記述子の値を正確に再現するには十分な情報が手にはいりません。　 | | | | | 我々はこれが近い実装と信じています。 | | @@ -2712,7 +2712,7 @@ SSSR問題 | GETAWAY | | 2017.09リリースで新しく導入。 | C++ | | | | Todeschini and Consoni | | | | | “Descriptors from Molecular Geometry” Handbook of Chemoinformatics | | -| | | http://dx.doi.org/10.1002/9783527618279.ch37 | | +| | | https://doi.org/10.1002/9783527618279.ch37 | | | | | | | | | | **注意** DRAGONを使って求めたこれらの記述子の値を正確に再現するには十分な情報が手にはいりません。 | | | | | 我々はこれが近い実装と信じています。 | | diff --git a/rdkit/Chem/Descriptors3D.py b/rdkit/Chem/Descriptors3D.py index d1f7bfb41..ef1ee448a 100644 --- a/rdkit/Chem/Descriptors3D.py +++ b/rdkit/Chem/Descriptors3D.py @@ -63,7 +63,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): NPR1.__doc__ = """ Normalized principal moments ratio 1 (=I1/I3) from Sauer and Schwarz JCIM 43:987-1003 (2003) - https://dx.doi.org/10.1021/ci025599w + https://doi.org/10.1021/ci025599w **Arguments** @@ -81,7 +81,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): NPR2.__doc__ = """ Normalized principal moments ratio 2 (=I2/I3) from Sauer and Schwarz JCIM 43:987-1003 (2003) - https://dx.doi.org/10.1021/ci025599w + https://doi.org/10.1021/ci025599w **Arguments** @@ -100,7 +100,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: for planar molecules: sqrt( sqrt(pm3*pm2)/MW ) @@ -122,7 +122,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: pm2 / (pm1*pm3) @@ -143,7 +143,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: sqrt(pm3**2 -pm1**2) / pm3**2 @@ -164,7 +164,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: 0.5 * ((pm3-pm2)**2 + (pm3-pm1)**2 + (pm2-pm1)**2)/(pm1**2+pm2**2+pm3**2) @@ -185,7 +185,7 @@ if hasattr(rdMolDescriptors, 'CalcPMI1'): from Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of Chemoinformatics - http://dx.doi.org/10.1002/9783527618279.ch37 + https://doi.org/10.1002/9783527618279.ch37 Definition: 3 * pm1 / (pm1+pm2+pm3) where the moments are calculated without weights