We are concerned with numerical simulations of quantum optical circuits under certain realistic conditions, specifically that photon quantum states are not perfectly indistinguishable. The partial photon distinguishability presents a serious limitation in implementation of optical quantum information processing. In order to properly assess its effect on quantum information protocols, accurate numerical simulations, which closely emulate quantum circuit operations, are essential. Our specific objective is to provide a computer implementation of the partial photon distinguishability which is in principle applicable to existing simulation techniques used for ideal quantum circuits and which avoids a need for their significant modification. Our approach is based on the Gram-Schmidt orthonormalization process, which is well suited for our purpose. Photonic quantum states are represented by wavepackets which contain information on their time and frequency distributions. In order to account for the partial photon distinguishability, we expand the number of degrees of freedom associated with the circuit operation extending the definition of the photon channels to incorporate wavepacket degrees of freedom. This strategy allows to define delay operations in the same footing as the linear optical elements.