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Remove C models #214

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777f64e
Use more accurate mass values
RalfG Feb 9, 2024
1d713a8
Replace remaining C model files with .xgboost models
RalfG Feb 9, 2024
062db9d
Format C and Cython code
RalfG Feb 9, 2024
994cd68
Fix calculating correlations if some peptides could not be processed …
RalfG Feb 9, 2024
00e96d6
Avoid type conversions
RalfG Feb 9, 2024
41198c9
Clean up setup.py
RalfG Feb 9, 2024
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253 changes: 137 additions & 116 deletions ms2pip/_cython_modules/ms2pip_features_c.c
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Original file line number Diff line number Diff line change
@@ -1,128 +1,149 @@
// Compute feature vectors from peptide
unsigned int* get_v_ms2pip(int peplen, unsigned short* peptide, unsigned short* modpeptide, int charge)
{
int i,j,k;
unsigned int *get_v_ms2pip(int peplen, unsigned short *peptide, unsigned short *modpeptide, int charge)
{
int i, j, k;

int fnum = 1; //first value in v is its length
int fnum = 1; // first value in v is its length

for (i=0; i < 19; i++) {
count_n[i] = 0;
count_c[i] = 0;
}
for (i = 0; i < 19; i++)
{
count_n[i] = 0;
count_c[i] = 0;
}

//I need this for Omega
//important for sptms!!
peptide_buf[0] = peptide[0];
for (i=0; i < peplen; i++) {
if (peptide[i+1] > 18) {
peptide_buf[i+1] = sptm_mapper[peptide[i+1]];
}
else {
peptide_buf[i+1] = peptide[i+1];
}
count_c[peptide_buf[i+1]]++;
}
// I need this for Omega
// important for sptms!!
peptide_buf[0] = peptide[0];
for (i = 0; i < peplen; i++)
{
if (peptide[i + 1] > 18)
{
peptide_buf[i + 1] = sptm_mapper[peptide[i + 1]];
}
else
{
peptide_buf[i + 1] = peptide[i + 1];
}
count_c[peptide_buf[i + 1]]++;
}

int num_shared = 0;
int num_shared = 0;

shared_features[num_shared++] = peplen;
shared_features[num_shared++] = charge;
shared_features[num_shared++] = peplen;
shared_features[num_shared++] = charge;

shared_features[num_shared] = 0;
if (charge == 1) {
shared_features[num_shared] = 1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 2) {
shared_features[num_shared] =1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 3) {
shared_features[num_shared] =1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 4) {
shared_features[num_shared] =1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge >= 5) {
shared_features[num_shared] =1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 1)
{
shared_features[num_shared] = 1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 2)
{
shared_features[num_shared] = 1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 3)
{
shared_features[num_shared] = 1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge == 4)
{
shared_features[num_shared] = 1;
}
num_shared++;
shared_features[num_shared] = 0;
if (charge >= 5)
{
shared_features[num_shared] = 1;
}
num_shared++;

for (j=0; j < num_props; j++) {
for (i=0; i < peplen; i++) {
props_buffer[i] = props[j][peptide_buf[i+1]];
}
qsort(props_buffer,peplen,sizeof(unsigned int),cmpfunc);
shared_features[num_shared++] = props_buffer[0];
shared_features[num_shared++] = props_buffer[(int)(0.25*(peplen-1))];
shared_features[num_shared++] = props_buffer[(int)(0.5*(peplen-1))];
shared_features[num_shared++] = props_buffer[(int)(0.75*(peplen-1))];
shared_features[num_shared++] = props_buffer[peplen-1];
}
for (j = 0; j < num_props; j++)
{
for (i = 0; i < peplen; i++)
{
props_buffer[i] = props[j][peptide_buf[i + 1]];
}
qsort(props_buffer, peplen, sizeof(unsigned int), cmpfunc);
shared_features[num_shared++] = props_buffer[0];
shared_features[num_shared++] = props_buffer[(int)(0.25 * (peplen - 1))];
shared_features[num_shared++] = props_buffer[(int)(0.5 * (peplen - 1))];
shared_features[num_shared++] = props_buffer[(int)(0.75 * (peplen - 1))];
shared_features[num_shared++] = props_buffer[peplen - 1];
}

for (i=0; i < peplen-1; i++) {
for (j=0; j<num_shared; j++) {
v[fnum++] = shared_features[j];
}
v[fnum++] = i+1; // length of N-term ion
v[fnum++] = peplen-i; // length of C-term ion
count_n[peptide_buf[i+1]]++;
count_c[peptide_buf[peplen-i]]--;
for (i = 0; i < peplen - 1; i++)
{
for (j = 0; j < num_shared; j++)
{
v[fnum++] = shared_features[j];
}
v[fnum++] = i + 1; // length of N-term ion
v[fnum++] = peplen - i; // length of C-term ion
count_n[peptide_buf[i + 1]]++;
count_c[peptide_buf[peplen - i]]--;

for (j=0; j < 19; j++) {
v[fnum++] = count_n[j]; // amino acid count in N-term ion
v[fnum++] = count_c[j]; // amino acid count in C-term ion
}
for (j = 0; j < 19; j++)
{
v[fnum++] = count_n[j]; // amino acid count in N-term ion
v[fnum++] = count_c[j]; // amino acid count in C-term ion
}

for (j=0; j < num_props; j++) {
v[fnum++] = props[j][peptide_buf[1]];
v[fnum++] = props[j][peptide_buf[peplen]];
if (i==0) {
v[fnum++] = 0;
}
else {
v[fnum++] = props[j][peptide_buf[i-1]];
}
v[fnum++] = props[j][peptide_buf[i]];
v[fnum++] = props[j][peptide_buf[i+1]];
if (i==(peplen-1)) {
v[fnum++] = 0;
}
else {
v[fnum++] = props[j][peptide_buf[i+2]];
}
unsigned int s = 0;
for (k=0; k <= i; k++) {
props_buffer[k] = props[j][peptide_buf[k+1]];
s+= props_buffer[k];
}
v[fnum++] = s;
qsort(props_buffer,i+1,sizeof(unsigned int),cmpfunc);
v[fnum++] = props_buffer[0];
v[fnum++] = props_buffer[(int)(0.25*i)];
v[fnum++] = props_buffer[(int)(0.5*i)];
v[fnum++] = props_buffer[(int)(0.75*i)];
v[fnum++] = props_buffer[i];
s = 0;
for (k=i+1; k < peplen; k++) {
props_buffer[k-i-1] = props[j][peptide_buf[k+1]];
s+= props_buffer[k-i-1];
}
v[fnum++] = s;
qsort(props_buffer,peplen-i-1,sizeof(unsigned int),cmpfunc);
v[fnum++] = props_buffer[0];
v[fnum++] = props_buffer[(int)(0.25*(peplen-i-1))];
v[fnum++] = props_buffer[(int)(0.5*(peplen-i-1))];
v[fnum++] = props_buffer[(int)(0.75*(peplen-i-1))];
v[fnum++] = props_buffer[peplen-i-2];
}
}
v[0] = fnum-1;
return v;
for (j = 0; j < num_props; j++)
{
v[fnum++] = props[j][peptide_buf[1]];
v[fnum++] = props[j][peptide_buf[peplen]];
if (i == 0)
{
v[fnum++] = 0;
}
else
{
v[fnum++] = props[j][peptide_buf[i - 1]];
}
v[fnum++] = props[j][peptide_buf[i]];
v[fnum++] = props[j][peptide_buf[i + 1]];
if (i == (peplen - 1))
{
v[fnum++] = 0;
}
else
{
v[fnum++] = props[j][peptide_buf[i + 2]];
}
unsigned int s = 0;
for (k = 0; k <= i; k++)
{
props_buffer[k] = props[j][peptide_buf[k + 1]];
s += props_buffer[k];
}
v[fnum++] = s;
qsort(props_buffer, i + 1, sizeof(unsigned int), cmpfunc);
v[fnum++] = props_buffer[0];
v[fnum++] = props_buffer[(int)(0.25 * i)];
v[fnum++] = props_buffer[(int)(0.5 * i)];
v[fnum++] = props_buffer[(int)(0.75 * i)];
v[fnum++] = props_buffer[i];
s = 0;
for (k = i + 1; k < peplen; k++)
{
props_buffer[k - i - 1] = props[j][peptide_buf[k + 1]];
s += props_buffer[k - i - 1];
}
v[fnum++] = s;
qsort(props_buffer, peplen - i - 1, sizeof(unsigned int), cmpfunc);
v[fnum++] = props_buffer[0];
v[fnum++] = props_buffer[(int)(0.25 * (peplen - i - 1))];
v[fnum++] = props_buffer[(int)(0.5 * (peplen - i - 1))];
v[fnum++] = props_buffer[(int)(0.75 * (peplen - i - 1))];
v[fnum++] = props_buffer[peplen - i - 2];
}
}
v[0] = fnum - 1;
return v;
}
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