Fix carboxylate atom radii in GB-Neck2 implicit solvent (#3505)

* Access atom element field

* Update GB-Neck2 force regression test

wrappers/python/openmm/app/internal/customgbforces.py

@@ -218,7 +218,7 @@ def _get_bonded_atom_list(topology):
 
 
 def _is_carboxylateO(atom, all_bonds):
-    if atom is not E.oxygen: return False
+    if atom.element is not E.oxygen: return False
     bondeds = all_bonds[atom]
     if len(bondeds) != 1:
         return False

wrappers/python/tests/systems/ala-ala-ala-implicit-forces/GBn2_NoCutoff.xml

@@ -6,38 +6,38 @@
 		<C x="0" y="0" z="2"/>
 	</PeriodicBoxVectors>
 	<Forces>
-		<Force x="183.12361104909448" y="155.26784211796442" z="34.691159962151325"/>
-		<Force x="58.02808994091839" y="161.1479771333285" z="-6.905719184803445"/>
-		<Force x="53.116947200286404" y="-197.39924721297302" z="-191.13127107770634"/>
-		<Force x="46.218727097648014" y="-212.66428112142592" z="171.32495750170045"/>
-		<Force x="-143.51220792224802" y="-77.6749878542526" z="106.54286260678916"/>
-		<Force x="-122.2580981087889" y="-56.69313081273846" z="155.02475224419112"/>
-		<Force x="256.861210924291" y="4.991885101995734" z="56.89967589615151"/>
-		<Force x="-50.134423267799164" y="26.69582029770774" z="-148.0309316306637"/>
-		<Force x="93.82349928954996" y="-98.75344995978912" z="-30.84769608742689"/>
-		<Force x="-41.91077517758289" y="59.289304779748626" z="-110.90263298668452"/>
-		<Force x="-402.5528947784169" y="-502.5128785408756" z="146.8525667854756"/>
-		<Force x="140.35927800593402" y="706.2615945572692" z="-116.71709633774552"/>
-		<Force x="336.6168876754595" y="357.247339062576" z="-34.749492380483105"/>
-		<Force x="-415.7108187560625" y="-212.13687180023163" z="100.590812009496"/>
-		<Force x="-2064.878698363039" y="-1169.1702011127431" z="-141.28708209576615"/>
-		<Force x="-194.9400953435316" y="-24.670932939610708" z="11.635635952592624"/>
-		<Force x="-733.9608254321217" y="-237.08948410189265" z="-552.6426811401486"/>
-		<Force x="-1060.8507100087338" y="-17.22971806538561" z="-834.9535646446606"/>
-		<Force x="-11.966996404264762" y="-67.77194077117352" z="-66.3175636555273"/>
-		<Force x="-5.938422468557391" y="-.8846999866901797" z="-79.25483041064173"/>
-		<Force x="-535049.450575994" y="-759418.9456168906" z="-62586.54371173267"/>
-		<Force x="-811.1877273151022" y="-752.1488295390167" z="-559.2811902937815"/>
-		<Force x="-59122.721636109374" y="-11224.366289486006" z="4161.654215282473"/>
-		<Force x="8491.852921433589" y="-4987.486057146457" z="198.97782166846662"/>
-		<Force x="-92073.12391443842" y="-81863.60475973453" z="-3121.980801468735"/>
-		<Force x="629672.3177092219" y="832975.8356195987" z="70299.92572789358"/>
-		<Force x="137697.00593367853" y="-29842.060582353926" z="13288.173983467228"/>
-		<Force x="-16855.75815442956" y="-20321.644238398876" z="-2810.1468347196355"/>
-		<Force x="-35343.17474223994" y="19898.531265412435" z="9385.986414694597"/>
-		<Force x="-6566690.1522480175" y="1625423.158741199" z="-3339704.996853593"/>
-		<Force x="8959691.989050966" y="469395.856032878" z="202260.29458456024"/>
-		<Force x="-1344238.7618171684" y="1727648.777500562" z="3128189.6150764455"/>
-		<Force x="-1081288.5392807235" y="-3765528.083662639" z="-17472.013005055705"/>
+		<Force x="183.1243567112956" y="155.2662219287179" z="34.69206255681505"/>
+		<Force x="58.04771033669036" y="161.17016956970303" z="-6.903114147106626"/>
+		<Force x="53.150224785752904" y="-197.40061720235155" z="-191.13601083876597"/>
+		<Force x="46.26045082036918" y="-212.65019759708085" z="171.34445230522093"/>
+		<Force x="-143.77170011048602" y="-77.74160762913571" z="106.49481211218608"/>
+		<Force x="-122.27179169431452" y="-56.68587562896124" z="155.0009873855261"/>
+		<Force x="257.16239953214205" y="5.1853904695510495" z="56.88645768817427"/>
+		<Force x="-50.13302313653312" y="26.596778802608352" z="-148.04286218238366"/>
+		<Force x="93.79978556512309" y="-98.76091017108594" z="-30.809758400829992"/>
+		<Force x="-41.92933302761911" y="59.26976843547845" z="-110.90864336601263"/>
+		<Force x="-403.9033823672388" y="-502.68659835826304" z="146.49748797062006"/>
+		<Force x="140.60935911080162" y="706.1506353781041" z="-116.65684921092459"/>
+		<Force x="339.39296323414993" y="357.9778809243149" z="-33.365173007121875"/>
+		<Force x="-417.13538415736576" y="-213.45331144242368" z="99.71334254488885"/>
+		<Force x="-2067.3972355896217" y="-1169.268833895684" z="-142.2029378489919"/>
+		<Force x="-195.55930360625328" y="-24.5387791070391" z="12.175743651113098"/>
+		<Force x="-733.2182385238124" y="-237.53069104719296" z="-551.8091874935819"/>
+		<Force x="-1061.388392236174" y="-16.703214831520803" z="-835.4484605535395"/>
+		<Force x="-12.246301250114703" y="-67.86335448691992" z="-66.6953992887791"/>
+		<Force x="-6.208188396856295" y="-0.8657921664232366" z="-79.37080995462853"/>
+		<Force x="-535069.4500308718" y="-759418.9842597096" z="-62601.54429542783"/>
+		<Force x="-798.2050097631871" y="-747.7468496170957" z="-547.5574273515672"/>
+		<Force x="-59124.38353013836" y="-11240.605208399234" z="4178.184795626811"/>
+		<Force x="8489.290186271537" y="-4978.448052554144" z="194.96058241696926"/>
+		<Force x="-92070.3696789206" y="-81859.12770642585" z="-3123.9825619200374"/>
+		<Force x="629667.2763482621" y="832977.9169909301" z="70294.62011757874"/>
+		<Force x="137700.3943484268" y="-29843.94360087238" z="13293.769265442545"/>
+		<Force x="-16855.00817610922" y="-20312.117577380035" z="-2830.8719885576293"/>
+		<Force x="-35340.64041633757" y="19903.114012246115" z="9372.393681317402"/>
+		<Force x="-6566669.378637129" y="1625443.5021145195" z="-3339719.0639452995"/>
+		<Force x="8959742.726797285" y="469406.86938459316" z="202246.10001240278"/>
+		<Force x="-1344263.9912707494" y="1727600.4629095322" z="3128188.5982689834"/>
+		<Force x="-1081324.64590622" y="-3765526.3592188056" z="-17415.06264513555"/>
 	</Forces>
 </State>