128 lines
3.8 KiB
C
128 lines
3.8 KiB
C
#include "debug.h"
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#include <ctype.h>
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#include <stdbool.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#define MAX_ATOMS 1000
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#define MAX_LINE_LENGTH 256
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#define MAX_NEIGHBOURS 4
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typedef struct Atom {
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float x, y, z;
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char atom_type[3];
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int idx;
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int num_neighbours;
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int bond_orders[MAX_NEIGHBOURS];
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struct Atom *neighbours[MAX_NEIGHBOURS];
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bool bonds_drawn;
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} Atom;
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typedef struct Molecule {
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Atom atoms[MAX_ATOMS];
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int num_atoms;
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} Molecule;
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void addBond(Atom *atom1, Atom *atom2, int bond_order);
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Molecule parseSDF(const char *filename) {
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FILE *file = fopen(filename, "r");
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if (!file) {
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fprintf(stderr, "Error opening file %s\n", filename);
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exit(1);
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}
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Molecule mol;
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mol.num_atoms = 0;
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char line[MAX_LINE_LENGTH];
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while (fgets(line, MAX_LINE_LENGTH, file) != NULL) {
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// break if you reach M END
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if (strncmp(line, "M END", 6) == 0) {
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D printf("Reached END\n");
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break;
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}
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// continue of line contains V2000 or V3000
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if (strstr(line, "V2000") || strstr(line, "V3000"))
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continue;
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// Parse the atoms and their coordinates
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if (isdigit(line[4]) && isdigit(line[6]) && isalpha(line[31])) {
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sscanf(line, "\t%f\t%f\t%f\t%s", &mol.atoms[mol.num_atoms].x,
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&mol.atoms[mol.num_atoms].y, &mol.atoms[mol.num_atoms].z,
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mol.atoms[mol.num_atoms].atom_type);
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mol.atoms[mol.num_atoms].idx = mol.num_atoms + 1;
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mol.atoms[mol.num_atoms].bonds_drawn = false;
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++mol.num_atoms;
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}
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// Parse the connectivity info block, atom count in SDF starts at 1
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if (isdigit(line[2]) && isdigit(line[20])) {
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int atom_idx, neighbour_idx, bond_order;
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sscanf(line, "%d %d %d", &atom_idx, &neighbour_idx, &bond_order);
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D printf("idx %d, buurman %d, multipliciteit %d\n", atom_idx,
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neighbour_idx, bond_order);
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addBond(&mol.atoms[atom_idx - 1], &mol.atoms[neighbour_idx - 1],
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bond_order);
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}
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}
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if (fclose(file)) {
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fprintf(stderr, "Error CLOSING file %s for some reason!\n", filename);
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exit(1);
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};
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return mol;
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}
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void addBond(Atom *atom1, Atom *atom2, int bond_order) {
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if (atom1->num_neighbours < MAX_NEIGHBOURS &&
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atom2->num_neighbours < MAX_NEIGHBOURS) {
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atom1->neighbours[atom1->num_neighbours] = atom2;
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atom1->bond_orders[atom1->num_neighbours] = bond_order;
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atom1->num_neighbours++;
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atom2->neighbours[atom2->num_neighbours] = atom1;
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atom2->bond_orders[atom2->num_neighbours] = bond_order;
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atom2->num_neighbours++;
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} else {
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D printf("ERROR: MAX_NEIGHBOURS exceeded!\n");
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}
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}
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void normalizeCoordinates(Molecule *mol, int width, int height) {
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float min_x = mol->atoms[0].x, max_x = mol->atoms[0].x;
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float min_y = mol->atoms[0].y, max_y = mol->atoms[0].y;
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float min_z = mol->atoms[0].z, max_z = mol->atoms[0].z;
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// Find min and max coords
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for (int i = 1; i < mol->num_atoms; i++) {
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if (mol->atoms[i].x < min_x)
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min_x = mol->atoms[i].x;
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if (mol->atoms[i].x > max_x)
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max_x = mol->atoms[i].x;
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if (mol->atoms[i].y < min_y)
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min_y = mol->atoms[i].y;
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if (mol->atoms[i].y > max_y)
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max_y = mol->atoms[i].y;
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if (mol->atoms[i].z < min_z)
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min_z = mol->atoms[i].z;
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if (mol->atoms[i].z > max_z)
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max_z = mol->atoms[i].z;
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}
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// Scaling factors
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float scale_x = (float)width / (max_x - min_x) / 100;
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float scale_y = (float)height / (max_y - min_y) / 100;
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// Yeah well there is no depth to a screen lol
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float scale_z = (float)height / (max_z - min_z) / 100;
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// Normalize coordinates, lets hope we never need the original coords lmao
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for (int i = 0; i < mol->num_atoms; i++) {
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mol->atoms[i].x = (mol->atoms[i].x - min_x) * scale_x;
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mol->atoms[i].y = (mol->atoms[i].y - min_y) * scale_y;
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mol->atoms[i].z = (mol->atoms[i].z - min_z) * scale_z;
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}
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}
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