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// *************************************************************************
// Copyright [2016] [RCSB]
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
//
// This file is the header file for the MMTF parser for the C language.
//
// The authors of this code are: Julien Ferte (http://www.julienferte.com/),
// Anthony Bradley, Thomas Holder.
//
//
// Other contributors: Yana Valasatava, Gazal Kalyan, Alexander Rose.
//
// *************************************************************************
#ifndef MMTF_PARSER_H
#define MMTF_PARSER_H
#include <stdbool.h>
#include <stdint.h>
#include <stdlib.h>
#ifdef __cplusplus
extern "C" {
#endif
/**
* @brief MMTF spec version which this library implements
*/
#define MMTF_SPEC_VERSION_MAJOR 1
#define MMTF_SPEC_VERSION_MINOR 0
#define WITHCOUNT(name) \
name; \
size_t name##Count
/**
* @brief Group (residue) level data store
*
* https://github.com/rcsb/mmtf/blob/HEAD/spec.md#group-data
*/
typedef struct {
int32_t* formalChargeList;
char** WITHCOUNT(atomNameList);
char** WITHCOUNT(elementList);
int32_t* WITHCOUNT(bondAtomList);
int8_t* WITHCOUNT(bondOrderList);
char* groupName;
char singleLetterCode;
char* chemCompType;
} MMTF_GroupType;
/**
* @brief Entity type.
*
* https://github.com/rcsb/mmtf/blob/HEAD/spec.md#entitylist
*/
typedef struct {
int32_t* WITHCOUNT(chainIndexList);
char* description;
char* type;
char* sequence;
} MMTF_Entity;
/**
* @brief Transformation definition for a set of chains.
*
* https://github.com/rcsb/mmtf/blob/HEAD/spec.md#bioassemblylist
*/
typedef struct {
int32_t* WITHCOUNT(chainIndexList);
float matrix[16];
} MMTF_Transform;
/**
* @brief Data store for the biological assembly annotation.
*
* https://github.com/rcsb/mmtf/blob/HEAD/spec.md#bioassemblylist
*/
typedef struct {
MMTF_Transform* WITHCOUNT(transformList);
char* name;
} MMTF_BioAssembly;
/**
* @brief Top level MMTF data container.
*
* https://github.com/rcsb/mmtf/blob/HEAD/spec.md#fields
*/
typedef struct {
char* mmtfVersion;
char* mmtfProducer;
float unitCell[6];
char* spaceGroup;
char* structureId;
char* title;
char* depositionDate;
char* releaseDate;
MMTF_BioAssembly* WITHCOUNT(bioAssemblyList);
MMTF_Entity* WITHCOUNT(entityList);
char** WITHCOUNT(experimentalMethods);
float resolution;
float rFree;
float rWork;
int32_t numBonds;
int32_t numAtoms;
int32_t numGroups;
int32_t numChains;
int32_t numModels;
MMTF_GroupType* WITHCOUNT(groupList);
int32_t* WITHCOUNT(bondAtomList);
int8_t* WITHCOUNT(bondOrderList);
float* xCoordList;
float* yCoordList;
float* zCoordList;
float* bFactorList;
int32_t* atomIdList;
char* altLocList;
float* occupancyList;
int32_t* groupIdList;
int32_t* groupTypeList;
int8_t* secStructList;
char* insCodeList;
int32_t* sequenceIndexList;
char** WITHCOUNT(chainIdList);
char** WITHCOUNT(chainNameList);
int32_t* groupsPerChain;
int32_t* chainsPerModel;
// PyMOL
int32_t* pymolRepsList;
int32_t* pymolColorList;
} MMTF_container;
/*
* Macros for declaration generic initialization and destroying functions
*/
#define CODEGEN_MMTF_parser_TYPE(type) \
type* type##_new(void); \
void type##_init(type*); \
void type##_destroy(type*); \
void type##_clear(type*); \
void type##_free(type*);
/**
* @fn MMTF_container * MMTF_container_new()
* @brief Allocate and initialize a new empty MMTF container
* @return pointer which needs to be freed with ::MMTF_container_free
*
* @fn void MMTF_container_free(MMTF_container* container)
* @brief Destroy the instance and free the memory
* @param container A MMTF container which has been allocated with ::MMTF_container_new
*
* @fn void MMTF_container_init(MMTF_container * container)
* @brief Initialize an empty MMTF container
* @param container Uninitialized memory, needs to be destroyed with ::MMTF_container_destroy
*
* @fn void MMTF_container_destroy(MMTF_container* container)
* @brief Destroy the instance and leave the memory uninitialized
* @param container A MMTF container which has been initialized with ::MMTF_container_init
*/
// clang-format off
CODEGEN_MMTF_parser_TYPE(MMTF_container)
CODEGEN_MMTF_parser_TYPE(MMTF_BioAssembly)
CODEGEN_MMTF_parser_TYPE(MMTF_Transform)
CODEGEN_MMTF_parser_TYPE(MMTF_Entity)
CODEGEN_MMTF_parser_TYPE(MMTF_GroupType)
#undef CODEGEN_MMTF_parser_TYPE
/**
* @brief Decode a MMTF_container from a string
* @param[in] buffer file contents
* @param[in] size file size
* @param[out] container initialized but empty MMTF container to populate with data
* @return true on success, false if an error occured
*/
bool MMTF_unpack_from_string(const char* buffer, size_t size, MMTF_container* container);
// clang-format on
/**
* @brief Decode a MMTF_container from a file
* @param[in] filename file path of an uncompressed .mmtf file
* @param[out] container initialized but empty MMTF container to populate with data
* @return true on success, false if an error occured
*/
bool MMTF_unpack_from_file(const char* filename, MMTF_container* container);
#undef WITHCOUNT
#ifdef __cplusplus
}
#endif
#endif
// vi:sw=4:expandtab
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