So I've been taking doxycycline hyclate 100mg for chlamydia for a week Thursday to Thursday twice a day. Question is how long to wait to have sex?

The most sure way. Is to repeat the urine PCR test that will confirm you are cleared. Then you won't have to worry abaout incomplete treatment but in general once you are finished with the antibiotics course you are most likely cured. However, there can be treatment failures so if you want to know for sure, get a repeat test to document clearance.