diff --git a/avogadro/qtplugins/templatetool/ligands/1-carbonyl.png b/avogadro/qtplugins/templatetool/ligands/1-carbonyl.png index 992f918e3c..5a71380bf9 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/1-carbonyl.png and b/avogadro/qtplugins/templatetool/ligands/1-carbonyl.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/1-cyano.png b/avogadro/qtplugins/templatetool/ligands/1-cyano.png index d4de2fa700..8c3459ef9a 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/1-cyano.png and b/avogadro/qtplugins/templatetool/ligands/1-cyano.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/1-ethyl.png b/avogadro/qtplugins/templatetool/ligands/1-ethyl.png index 85c0bd0a2f..d78fa09049 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/1-ethyl.png and b/avogadro/qtplugins/templatetool/ligands/1-ethyl.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/1-isopropyl.png b/avogadro/qtplugins/templatetool/ligands/1-isopropyl.png 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--git a/avogadro/qtplugins/templatetool/ligands/2-ethylenediamine.png b/avogadro/qtplugins/templatetool/ligands/2-ethylenediamine.png index ce0f4fec9b..5ed0f7942c 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/2-ethylenediamine.png and b/avogadro/qtplugins/templatetool/ligands/2-ethylenediamine.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/3-terpyridine.png b/avogadro/qtplugins/templatetool/ligands/3-terpyridine.png index 845698d5b6..cbd0d94252 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/3-terpyridine.png and b/avogadro/qtplugins/templatetool/ligands/3-terpyridine.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/4-phthalocyanine.png b/avogadro/qtplugins/templatetool/ligands/4-phthalocyanine.png index f8352ececb..17f179d40d 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/4-phthalocyanine.png and b/avogadro/qtplugins/templatetool/ligands/4-phthalocyanine.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/4-porphin.png b/avogadro/qtplugins/templatetool/ligands/4-porphin.png index 4b63b40852..789cb451fd 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/4-porphin.png and b/avogadro/qtplugins/templatetool/ligands/4-porphin.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/4-salen.png b/avogadro/qtplugins/templatetool/ligands/4-salen.png index 53488c9906..8133d33dec 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/4-salen.png and b/avogadro/qtplugins/templatetool/ligands/4-salen.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/6-edta.png b/avogadro/qtplugins/templatetool/ligands/6-edta.png index c5f6a32501..0f1b68d5c9 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/6-edta.png and b/avogadro/qtplugins/templatetool/ligands/6-edta.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/amide.png b/avogadro/qtplugins/templatetool/ligands/amide.png index 1481ed7473..a95ff206bc 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/amide.png and b/avogadro/qtplugins/templatetool/ligands/amide.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/carboxylate.png b/avogadro/qtplugins/templatetool/ligands/carboxylate.png index 18fcf9c4b7..cbc8e9c84e 100644 Binary files a/avogadro/qtplugins/templatetool/ligands/carboxylate.png and b/avogadro/qtplugins/templatetool/ligands/carboxylate.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/ethylene.cjson b/avogadro/qtplugins/templatetool/ligands/ethylene.cjson new file mode 100644 index 0000000000..f0b87d013b --- /dev/null +++ b/avogadro/qtplugins/templatetool/ligands/ethylene.cjson @@ -0,0 +1,84 @@ +{ + "chemicalJson": 1, + "atoms": { + "coords": { + "3d": [ + -1.5534, + 0.0749, + 0.2664, + -1.1883, + 0.1873, + 1.3083, + -0.6202, + 1.3071, + 1.4603, + -1.4535, + -0.6764, + 1.7673, + -0.1841, + 1.6185, + 2.4293, + -0.5234, + 2.0418, + 0.6403 + ] + }, + "elements": { + "number": [ + 0, + 6, + 6, + 1, + 1, + 1 + ] + }, + "formalCharges": [ + 0, + 0, + 0, + 0, + 0, + 0 + ] + }, + "partialCharges": { + "Gasteiger": [ + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0 + ] + }, + "bonds": { + "connections": { + "index": [ + 0, + 1, + 1, + 2, + 1, + 3, + 2, + 4, + 2, + 5 + ] + }, + "order": [ + 1, + 2, + 1, + 1, + 1 + ] + }, + "properties": { + "name": "", + "totalCharge": 0, + "totalSpinMultiplicity": 2, + "totalEnergy": 0.0 + } +} diff --git a/avogadro/qtplugins/templatetool/ligands/ethylene.png b/avogadro/qtplugins/templatetool/ligands/ethylene.png new file mode 100644 index 0000000000..2b02c86b82 Binary files /dev/null and b/avogadro/qtplugins/templatetool/ligands/ethylene.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/ethyne.cjson b/avogadro/qtplugins/templatetool/ligands/ethyne.cjson new file mode 100644 index 0000000000..3ca2a4be22 --- /dev/null +++ b/avogadro/qtplugins/templatetool/ligands/ethyne.cjson @@ -0,0 +1,66 @@ +{ + "chemicalJson": 1, + "atoms": { + "coords": { + "3d": [ + -2.6584, + -0.0146, + -0.0614, + -2.3373, + -0.3508, + 0.7114, + -1.9233, + -0.7914, + 1.7521, + -1.5732, + -1.1666, + 2.6719 + ] + }, + "elements": { + "number": [ + 0, + 6, + 6, + 1 + ] + }, + "formalCharges": [ + 0, + 0, + 0, + 0 + ] + }, + "partialCharges": { + "Gasteiger": [ + 0.0, + 0.0, + 0.0, + 0.0 + ] + }, + "bonds": { + "connections": { + "index": [ + 0, + 1, + 1, + 2, + 2, + 3 + ] + }, + "order": [ + 1, + 3, + 1 + ] + }, + "properties": { + "name": "", + "totalCharge": 0, + "totalSpinMultiplicity": 2, + "totalEnergy": 0.0 + } +} diff --git a/avogadro/qtplugins/templatetool/ligands/ethyne.png b/avogadro/qtplugins/templatetool/ligands/ethyne.png new file mode 100644 index 0000000000..4be9930e4f Binary files /dev/null and b/avogadro/qtplugins/templatetool/ligands/ethyne.png differ diff --git a/avogadro/qtplugins/templatetool/ligands/phosphate.cjson b/avogadro/qtplugins/templatetool/ligands/phosphate.cjson new file mode 100644 index 0000000000..7bad9e4ab8 --- /dev/null +++ b/avogadro/qtplugins/templatetool/ligands/phosphate.cjson @@ -0,0 +1,101 @@ +{ + "chemicalJson": 1, + "atoms": { + "coords": { + "3d": [ + -1.0432, + -3.0021, + -1.018, + -0.6229, + -2.4983, + -0.3244, + 0.0053, + -1.1643, + -0.9673, + 0.1276, + -1.2157, + -2.4175, + 1.3655, + -0.9921, + -0.1479, + -0.8777, + 0.0094, + -0.3854, + 2.0864, + -1.3719, + -0.6453, + -0.8116, + 0.0459, + 0.5684 + ] + }, + "elements": { + "number": [ + 0, + 8, + 15, + 8, + 8, + 8, + 1, + 1 + ] + }, + "formalCharges": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ] + }, + "partialCharges": { + "Gasteiger": [ + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0 + ] + }, + "bonds": { + "connections": { + "index": [ + 0, + 1, + 1, + 2, + 2, + 3, + 2, + 4, + 2, + 5, + 4, + 6, + 5, + 7 + ] + }, + "order": [ + 1, + 1, + 2, + 1, + 1, + 1, + 1 + ] + }, + "properties": { + "name": "", + "totalCharge": 0, + "totalSpinMultiplicity": 2 + } +} diff --git a/avogadro/qtplugins/templatetool/ligands/phosphate.png b/avogadro/qtplugins/templatetool/ligands/phosphate.png new file mode 100644 index 0000000000..9af6404389 Binary files /dev/null and b/avogadro/qtplugins/templatetool/ligands/phosphate.png differ diff --git a/avogadro/qtplugins/templatetool/template.qrc b/avogadro/qtplugins/templatetool/template.qrc index a18d502b2c..9293fe07a7 100644 --- a/avogadro/qtplugins/templatetool/template.qrc +++ b/avogadro/qtplugins/templatetool/template.qrc @@ -33,9 +33,12 @@ ligands/6-edta.png ligands/amide.png ligands/carboxylate.png + ligands/ethylene.png + ligands/ethyne.png ligands/ester.png ligands/nitro.png ligands/phenyl.png + ligands/phosphate.png ligands/sulfonate.png ligands/eta2-ethylene.png ligands/eta5-cyclopentyl.png @@ -78,8 +81,11 @@ ligands/amide.cjson ligands/carboxylate.cjson ligands/ester.cjson + ligands/ethylene.cjson + ligands/ethyne.cjson ligands/nitro.cjson ligands/phenyl.cjson + ligands/phosphate.cjson ligands/sulfonate.cjson ligands/eta2-ethylene.cjson ligands/eta5-cyclopentyl.cjson diff --git a/avogadro/qtplugins/templatetool/templatetool.cpp b/avogadro/qtplugins/templatetool/templatetool.cpp index 6124a1728b..1f5bb20158 100644 --- a/avogadro/qtplugins/templatetool/templatetool.cpp +++ b/avogadro/qtplugins/templatetool/templatetool.cpp @@ -377,8 +377,6 @@ void TemplateTool::atomLeftClick(QMouseEvent*) // - otherwise use the template Molecule templateMolecule; - qDebug() << "ligandString: " << m_toolWidget->ligandString(); - if (m_toolWidget->ligandString() == "Clipboard") { const QMimeData* mimeData(QApplication::clipboard()->mimeData()); diff --git a/avogadro/qtplugins/templatetool/templatetoolwidget.ui b/avogadro/qtplugins/templatetool/templatetoolwidget.ui index 2dc432b357..fb1dbf0b5d 100644 --- a/avogadro/qtplugins/templatetool/templatetoolwidget.ui +++ b/avogadro/qtplugins/templatetool/templatetoolwidget.ui @@ -481,6 +481,16 @@ ester + + + ethylene + + + + + ethyne + + nitro @@ -491,6 +501,11 @@ phenyl + + + phosphate + + sulfonate