c language
Assignment 1 – C Molecule Manipulation Library Version 1.01 (last update: Jan. 11, 20:00) Changes highlighted in yellow Due date: Tue, Jan 31, 9:00 AM Summary and Purpose For this assignment, you will be writing a small C library that implements a number of functions to represent and manipulate molecules. Deliverables You will be submitting: 1) A file called mol.h that contains your typedefs, structure definitions and function prototypes (see below). 2) A file called mol.c that contains your function code. 3) A makefile that contains the instructions for the following targets: a. mol.o – a position independent (-fpic) object code file created from mol.c. b. libmol.so – a shared library (-shared) created from mol.o. c. clean – this target should delete all .o, .so and executable files. All compilation must be done with the -std=c99 -Wall -pedantic options and produce no warnings or errors. The makefile must correctly identify all relevant dependencies and include them as prerequisites in its rules. You will submit all of your work via git to the School’s gitlab server. (As per instructions in the labs.) Under no condition will an assignment be accepted by any other means. This is an individual assignment. Any evidence of code sharing will be investigated and, if appropriate, adjudicated using the University’s Academic Integrity rules. Setting up your work environment and using git: Decide on your development environment. You can work on your own machine, the SoCS VM, no machine, or the SoCS ssh servers. However, you must test your code on the SoCS servers or SoCS VM as this is where it will be evaluated. If your code does not work properly on the SoCS systems, then it does not work. git clone https://gitlab.socs.uoguelph.ca/2750W23/skremer/A1 But, use your own login ID instead of skremer. Then, cd A1, to move to the assignment directory. Work in the A1 directory. Use the command: git add filename For each file that you create as part of your code (one .c file, one .h file, and the makefile). Every so often (especially if you get something working), use the command: git commit -a to commit your changes. Use the command: git tag -a Jan10a -m ’implemented the first two functions’ You will need to use a tag like “Jan10a” to request help with your code via the course help page. And then make sure to use: git push –-all –-follow-tags to push everything to the server with the tag included. If you want to make sure you know exactly what’s on the server you can rename the A1 directory to A1.day1 and then use git clone https://gitlab.socs.uoguelph.ca/2750W23/skremer/A1 to get a copy of exactly what is currently in the repo. You can use the same command to retrieve your code on a different machine or architecture. E.g. to move your code from your laptop development to the SoCS server for testing. Structures and typedefs used for your assignment (include these in your .h file) typedef struct atom { char element[3]; double x, y, z; } atom; atom defines a structure that describes an atom and its position in 3-dimensional space. element is a null-terminated string representing the element name of the atom (e.g. Na for sodium). x, y, and z are double precision floating point numbers describing the position in Angstroms (Å) of the atom relative to a common origin for a molecule. typedef struct bond { atom *a1, *a2; unsigned char epairs; } bond; bond defines a structure that represents a co-valent bond between two atoms. a1 and a2 are pointers to the two atoms in the co-valent bond. epairs is the number of electron pairs in the bond (i.e. epairs=2 represents a double bond). The atoms pointed to by a1 and a2 will be allocated and stored elsewhere, so it will never be necessary to free a1 or a2. typedef struct molecule { unsigned short atom_max, atom_no; atom *atoms, **atom_ptrs; unsigned short bond_max, bond_no; bond *bonds, **bond_ptrs; } molecule; molecule represents a molecule which consists of zero or more atoms, and zero or more bonds. atom_max is a non-negative integer that records the dimensionality of an array pointed to by atoms. atom_no is the number of atoms currently stored in the array atoms. Note atom_no must never be larger than atom_max. You will be responsible for allocating enough memory to the atoms pointer. bond_max is a non-negative integer that records the dimensionality of an array pointed to by bonds. bond_no is the number of bonds currently stored in the array bonds. Note bond_no must never be larger than bond_max. You will be responsible for allocating enough memory to the bonds pointer. atom_ptrs and bond_ptrs are arrays of pointers. Their dimensionalities will correspond to the atoms and bonds arrays, respectively. These pointers in these pointer arrays will be initialized to point to their corresponding structures. E.g. atom_ptrs[0] will point to atoms[0]. Later we will sort the order of the pointers to allow for an alternate traversal (ordering) of the atoms/bonds. typedef double xform_matrix[3][3]; xform_matrix reprents a 3-d affine transformation matrix (an extension of the 2-d affine transformation you saw in the first lab). Function prototypes and descriptions for your assignment void atomset( atom *atom, char element[3], double *x, double *y, double *z ); This function should copy the values pointed to by element, x, y, and z into the atom stored at atom. You may assume that sufficient memory has been allocated at all pointer addresses. Note that using pointers for the function “inputs”, x, y, and z, is done here to match the function arguments of atomget. void atomget( atom *atom, char element[3], double *x, double *y, double *z ); This function should copy the values in the atom stored at atom to the locations pointed to by element, x, y, and z. You may assume that sufficient memory has been allocated at all pointer addresses. Note that using pointers for the function “input”, atom, is done here to match the function arguments of atomset. void bondset( bond *bond, atom *a1, atom *a2, unsigned char epairs ); This function should copy the values a1, a2 and epairs into the corresponding structure attributes in bond. You may assume that sufficient memory has been allocated at all pointer addresses. Note you are not copying atom structures, only the addresses of the atom structures. void bondget( bond *bond, atom *a1, atom *a2, unsigned char epairs ); void bondget( bond *bond, atom **a1, atom **a2, unsigned char *epairs ); This function should copy the structure attributes in bond to their corresponding arguments: a1, a2 and epairs. You may assume that sufficient memory has been allocated at all pointer addresses. Note you are not copying atom structures, only the addresses of the atom structures. molecule *molmalloc( unsigned short atom_max, unsigned short bond_max ); This function should return the address of a malloced area of memory, large enough to hold a molecule. The value of atom_max should be copied into the structure; the value of atom_no in the structure should be set to zero; and, the arrays atoms and atom_ptrs should be malloced to have enough memory to hold atom_max atoms and pointers (respectively). The value of bond_max should be copied into the structure; the value of bond_no in the structure should be set to zero; and, the arrays bonds and bond_ptrs should be malloced to have enough memory to hold bond_max bonds and pointers (respectively). molecule *molcopy( molecule *src ); This function should return the address of a malloced area of memory, large enough to hold a molecule. Additionally, the values of atom_max, atom_no, bond_max, bond_no should be copied from src into the new structure. Finally, the arrays atoms, atom_ptrs, bonds and bond_ptrs must be allocated to match the size of the ones in src. You should re-use (i.e. call) the molmalloc function in this function. void molfree( molecule *ptr ); This function should free the memory associated with the molecule pointed to by ptr. This includes the arrays atoms, atom_ptrs, bonds, bond_ptrs. void molappend_atom( molecule *molecule, atom *atom ); This function should copy the data pointed to by atom to the first “empty” atom in atoms in the molecule pointed to by molecule, and set the first “empty” pointer in atom_ptrs to the same atom in the atoms array incrementing the value of atom_no. If atom_no equals atom_max, then atom_max must be incremented, and the capacity of the atoms, and atom_ptrs arrays increased accordingly. If atom_max was 0, it should be incremented to 1, otherwise it should be doubled. Increasing the capacity of atoms, and atom_ptrs should be done using realloc so that a larger amount of memory is allocated and the existing data is copied to the new location. void molappend_bond( molecule *molecule, bond *bond ); This function should operate like that molappend_atom function, except for bonds. void molsort( molecule *molecule ); This function should sort the atom_ptrs array in place in order of increasing z value. I.e. atom_ptrs[0] should point to the atom that contains the lowest z value and atom_ptrs[atom_no-1] should contain the highest z value. It should also sort the bond_ptrs array in place in order of increasing “z value”. Since bonds don’t have a z attribute, their z value is assumed to be the average z value of their two atoms. I.e. bond_ptrs[0] should point to the bond that has the lowest z value and bond_ptrs[atom_no-1] should contain the highest z value.Hint: use qsort. void xrotation( xform_matrix xform_matrix, unsigned short deg ); This function will allocate, compute, and return an affine transformation matrix corresponding to a rotation of deg degrees around the x-axis. This matrix must be freed by the user when no- longer needed. void yrotation( xform_matrix xform_matrix, unsigned short deg ); This function will allocate, compute, and return an affine transformation matrix corresponding to a rotation of deg degrees around the y-axis. This matrix must be freed by the user when no- longer needed. void zrotation( xform_matrix xform_matrix, unsigned short deg ); This function will allocate, compute, and return an affine transformation matrix corresponding to a rotation of deg degrees around the z-axis. This matrix must be freed by the user when no- longer needed. void mol_xform( molecule *molecule, xform_matrix matrix ); This function will apply the transformation matrix to all the atoms of the molecule by performing a vector matrix multiplication on the x, y, z coordinates. Your code should malloc only as much memory as required in the function descriptions. All malloc return values must be checked before accessing memory. If malloc returns a NULL value, the return value of the calling function should also be NULL. You can write additional helper functions as necessary to make sure your code is modular, readable, and easy to modify. Testing You are responsible for testing your code to make sure that it works as required. The CourseLink web-site will be updated with some test programs to get you started. However, we will use a different set of test programs to grade your code, so you need to make sure that your code performs according to the instructions above by writing more test code. Your assignment will be tested on the SoCS servers. If you are developing in a different environment, you will need to allow