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Fix cmap calc for heterotypic slab #47

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Merged
gitesei merged 1 commit into from
Feb 18, 2026
Merged

Fix cmap calc for heterotypic slab #47

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8 changes: 7 additions & 1 deletion calvados/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -922,6 +922,11 @@ def calc_contact_map(path,sysname,output_path,chainid_dict={},is_slab=False,inpu
name_2 = name_1
chainid_dict[name_1] = np.arange(traj.top.n_chains)

print(name_1)
print(chainid_dict[name_1])
print(name_2)
print(chainid_dict[name_2])

N_res_1 = traj.top.chain(chainid_dict[name_1][0]).n_residues
N_res_2 = traj.top.chain(chainid_dict[name_2][0]).n_residues

Expand Down Expand Up @@ -950,7 +955,8 @@ def calc_contact_map(path,sysname,output_path,chainid_dict={},is_slab=False,inpu
chainid_dict[name_2] = chainid_dict[name_1]
cm_z = cmtraj.xyz[:,chainid_dict[name_1],2]
# per-frame central-chain indices
chainid_dict[name_1] = np.argmin(np.abs(cm_z),axis=1)
ids_central = np.argmin(np.abs(cm_z),axis=1)
chainid_dict[name_1] = np.array([chainid_dict[name_1][idx] for idx in ids_central])

cmap = np.zeros((N_res_1,N_res_2))
for chain_1 in np.unique(chainid_dict[name_1]):
Expand Down