STM32 Port configuration via structures

 How Does STM32CubeIDE

  /*Configure GPIO pin : Pd3 */
  GPIO_InitStruct.Pin = GPIO_PIN_3;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(GPIOd, &GPIO_InitStruct);

 Now what is GPIOD and GPIO_InitStruct

GPIOD the definition is deep inside CMSIS "Drivers\CMSIS\Device\ST\STM32F4xx\Include\stm32f411xe.h"

#define GPIOD               ((GPIO_TypeDef *) GPIOD_BASE)

and  GPIOD_BASE declared in same file

#define GPIOD_BASE            (AHB1PERIPH_BASE + 0x0C00UL)

Now GPIO_InitStruct is comes from  the line GPIO_InitTypeDef GPIO_InitStruct = {0};  so the structure GPIO_InitTypeDef is as follows as defined in 

typedef struct
{
  uint32_t Pin; /*!< Specifies the GPIO pins to be configured.
     This parameter can be any value of @ref GPIO_pins_define */
  uint32_t Mode;   /*!< Specifies the operating mode for the selected pins.
    This parameter can be a value of @ref GPIO_mode_define */
  uint32_t Pull;   /*!< Specifies the Pull-up or Pull-Down activation for the selected pins.
   This parameter can be a value of @ref GPIO_pull_define */
  uint32_t Speed; /*!< Specifies the speed for the selected pins.
  This parameter can be a value of @ref GPIO_speed_define */
  uint32_t Alternate;  /*!< Peripheral to be connected to the selected pins. 
   This parameter can be a value of @ref GPIO_Alternate_function_selection */
}GPIO_InitTypeDef;

Next is stm32f4xx_hal_gpio.c where the HAL_GPIO_init() is defined

void HAL_GPIO_Init(GPIO_TypeDef  *GPIOx, GPIO_InitTypeDef *GPIO_Init)
{
  uint32_t position;
  uint32_t ioposition = 0x00U;
  uint32_t iocurrent = 0x00U;
  uint32_t temp = 0x00U;

  /* Check the parameters */
  assert_param(IS_GPIO_ALL_INSTANCE(GPIOx));
  assert_param(IS_GPIO_PIN(GPIO_Init->Pin));
  assert_param(IS_GPIO_MODE(GPIO_Init->Mode));
  assert_param(IS_GPIO_PULL(GPIO_Init->Pull));

  /* Configure the port pins */
  for(position = 0U; position < GPIO_NUMBER; position++)
  {
    /* Get the IO position */
    ioposition = 0x01U << position;
    /* Get the current IO position */
    iocurrent = (uint32_t)(GPIO_Init->Pin) & ioposition;

    if(iocurrent == ioposition)
    {
      /*--------------------- GPIO Mode Configuration ------------------------*/
      /* In case of Output or Alternate function mode selection */
      if((GPIO_Init->Mode == GPIO_MODE_OUTPUT_PP) || (GPIO_Init->Mode == GPIO_MODE_AF_PP) ||
         (GPIO_Init->Mode == GPIO_MODE_OUTPUT_OD) || (GPIO_Init->Mode == GPIO_MODE_AF_OD))
      {
        /* Check the Speed parameter */
        assert_param(IS_GPIO_SPEED(GPIO_Init->Speed));
        /* Configure the IO Speed */
        temp = GPIOx->OSPEEDR; 
        temp &= ~(GPIO_OSPEEDER_OSPEEDR0 << (position * 2U));
        temp |= (GPIO_Init->Speed << (position * 2U));
        GPIOx->OSPEEDR = temp;

        /* Configure the IO Output Type */
        temp = GPIOx->OTYPER;
        temp &= ~(GPIO_OTYPER_OT_0 << position) ;
        temp |= (((GPIO_Init->Mode & GPIO_OUTPUT_TYPE) >> 4U) << position);
        GPIOx->OTYPER = temp;
       }

      /* Activate the Pull-up or Pull down resistor for the current IO */
      temp = GPIOx->PUPDR;
      temp &= ~(GPIO_PUPDR_PUPDR0 << (position * 2U));
      temp |= ((GPIO_Init->Pull) << (position * 2U));
      GPIOx->PUPDR = temp;

      /* In case of Alternate function mode selection */
      if((GPIO_Init->Mode == GPIO_MODE_AF_PP) || (GPIO_Init->Mode == GPIO_MODE_AF_OD))
      {
        /* Check the Alternate function parameter */
        assert_param(IS_GPIO_AF(GPIO_Init->Alternate));
        /* Configure Alternate function mapped with the current IO */
        temp = GPIOx->AFR[position >> 3U];
        temp &= ~(0xFU << ((uint32_t)(position & 0x07U) * 4U)) ;
        temp |= ((uint32_t)(GPIO_Init->Alternate) << (((uint32_t)position & 0x07U) * 4U));
        GPIOx->AFR[position >> 3U] = temp;
      }

      /* Configure IO Direction mode (Input, Output, Alternate or Analog) */
      temp = GPIOx->MODER;
      temp &= ~(GPIO_MODER_MODER0 << (position * 2U));
      temp |= ((GPIO_Init->Mode & GPIO_MODE) << (position * 2U));
      GPIOx->MODER = temp;

      /*--------------------- EXTI Mode Configuration ------------------------*/
      /* Configure the External Interrupt or event for the current IO */
      if((GPIO_Init->Mode & EXTI_MODE) == EXTI_MODE)
      {
        /* Enable SYSCFG Clock */
        __HAL_RCC_SYSCFG_CLK_ENABLE();

        temp = SYSCFG->EXTICR[position >> 2U];
        temp &= ~(0x0FU << (4U * (position & 0x03U)));
        temp |= ((uint32_t)(GPIO_GET_INDEX(GPIOx)) << (4U * (position & 0x03U)));
        SYSCFG->EXTICR[position >> 2U] = temp;

        /* Clear EXTI line configuration */
        temp = EXTI->IMR;
        temp &= ~((uint32_t)iocurrent);
        if((GPIO_Init->Mode & GPIO_MODE_IT) == GPIO_MODE_IT)
        {
          temp |= iocurrent;
        }
        EXTI->IMR = temp;

        temp = EXTI->EMR;
        temp &= ~((uint32_t)iocurrent);
        if((GPIO_Init->Mode & GPIO_MODE_EVT) == GPIO_MODE_EVT)
        {
          temp |= iocurrent;
        }
        EXTI->EMR = temp;

        /* Clear Rising Falling edge configuration */
        temp = EXTI->RTSR;
        temp &= ~((uint32_t)iocurrent);
        if((GPIO_Init->Mode & RISING_EDGE) == RISING_EDGE)
        {
          temp |= iocurrent;
        }
        EXTI->RTSR = temp;

        temp = EXTI->FTSR;
        temp &= ~((uint32_t)iocurrent);
        if((GPIO_Init->Mode & FALLING_EDGE) == FALLING_EDGE)
        {
          temp |= iocurrent;
        }
        EXTI->FTSR = temp;
      }
    }
  }
}