TORONTO — From the time the Nets began their rebuilding project by cleaning out the front office last February and hiring new general manager Sean Marks, the extant theory has been that the shortest path to respectability would be to trade the team’s leading asset, 7-foot center Brook Lopez, for future first-round draft picks.

With Lopez resting as prescribed by the organization’s performance team, the Nets suffered a 116-104 loss to the Raptors Tuesday night at Air Canada Centre that only served to underline how difficult it would be to part with their franchise center. The Nets’ starting lineup managed only 45 points without the club’s leading scorer and sorely lacked the rim protection Lopez provides as the Raptors outscored them in the paint, 60-44.

The Nets kept it close into the middle of the second quarter, cutting their deficit to 47-43 on a three-pointer by point guard Jeremy Lin, who made his first start in four appearances since returning from a nearly six-week absence to recover from a hamstring injury. But that’s where everything came unraveled as the Raptors finished the half on a 17-3 run for a 64-46 lead.

Coach Kenny Atkinson blamed an old bugaboo — poor transition defense. “I was upset at halftime,” Atkinson said. “I told the team our inability to get back on defense just wasn’t good enough. They had 24 points off our [17] turnovers.”

The Nets shot 29.2 percent in the second quarter and made only 1 of 9 field-goal attempts and committed three turnovers during the Raptors’ run. On one of those turnovers, Lin got back to cut off DeMar DeRozan, but none of his teammates joined him, allowing DeRozan to make an easy pass to Kyle Lowry for a gimme layup.

“That’s not what our program is going to be about,” Atkinson said. “I told the guys. I just thought we didn’t compete the way we needed to compete in the first half. That’s just a fact. I thought the second half guys took account and did a much, much better job.”

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Rondae Hollis-Jefferson led the Nets (7-20) with 19 points off the bench, Spencer Dinwiddie added 14, and Lin had 12 points and four assists in 25 minutes. The Nets shot only 39.6 percent overall and just 28.6 percent from three-point range. Lowry topped the Raptors (20-8) with 23 points, Norman Powell added 21, and DeRozan was held to 15, which is 13 below his average.

Like his coach, Lin was disappointed by the Nets’ effort. “They did whatever they wanted,” Lin said. “They killed us in transition, they got to the free-throw line, they got offensive rebounds. We just didn’t play with heart tonight.”

Atkinson said the Raptors’ “length at the rim bothered us,” and he acknowledged the Nets generally had to play small without Lopez in the middle, often moving Hollis-Jefferson from the wing to power forward.

Lin offered an emotional response when asked how much the Nets missed Lopez’s presence.

“We missed a lot of things besides just rim protection,” Lin said. “Brook is dynamic in a lot of different ways. I want Brook to play every single game, and I hope I play every game with him. I love that guy.

“But if he’s not here, everyone else has to step up, and we just didn’t play hard enough. So, everyone, including me, has to go home and figure out what can we do to play harder next game.”

The Nets must play much harder in the next two games against last season’s NBA finalists. They face Golden State at home tomorrow night before traveling to Cleveland on Friday to meet the champs. At least, Lopez will return to give them a better chance.